title: MDA-MB-231/4175 TfR-1(#4)

city: Shanghai

first: Qing

last: Zhao

state: None Selected

address: 555 Zuchongzhi Rd., Zhangjiang Hi-Tech Park, Shanghai, 201203, China

institute: shanghai institute of materia medica

description: Library name: Sample 8

data_processing:
Raw sequencing reads were first processed using Trimmomatic to remove adapter sequences and low-quality reads, generating high-quality clean reads. The clean reads were then aligned to the human reference genome (GRCh38/hg38) using the STAR aligner. Gene expression levels were quantified with featureCounts and expressed as counts per million (CPM) and fragments per kilobase of transcript per million mapped reads (FPKM). Finally, differential expression analysis was performed using DESeq2 to identify genes with significant expression changes between the Mock and TfR-1 overexpression groups.
Assembly: GRCh38/hg38
Supplementary files format and content: The gene expression matrix is provided as a tab-delimited text file containing read counts and FPKM values for each gene across all samples. Differential expression results are supplied in a CSV file, listing genes along with their adjusted p-values and log2 fold changes between treatment groups. In addition, alignment BAM files are included, which store the mapped sequencing reads for each individual sample.
Supplementary files format and content: The processed data include a gene-level expression matrix generated by featureCounts, provided as a tab-delimited text file. Rows represent genes and columns represent individual samples. Raw read counts are reported for each gene across all samples.

growth_protocol: MDA-MB-231/4175 breast cancer lung metastatic cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted from cells using the TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was verified by agarose gel electrophoresis.
Poly(A)-containing mRNA was purified from total RNA using oligo(dT) magnetic beads. The mRNA was then fragmented and reverse-transcribed into cDNA. Double-stranded cDNA was synthesized, end-repaired, and ligated to Illumina sequencing adapters. After size selection and PCR amplification, the final cDNA libraries were quantified using a Qubit Fluorometer and validated for quality using an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were divided into two groups:Mock control group: Transfected with empty vector plasmid using Lipofectamine 2000 reagent, following the manufacturer's instructions.TfR-1 overexpression group: Transfected with TfR-1 overexpression plasmid using Lipofectamine 2000 reagent.

value: Overexpression of TfR-1

value: batch 4


title: Optic nerve_MB-injected_S2

status: Public on Jul 22 2026

type: SRA

city: Boston

first: Milica

last: Margeta

state: MA

address: 20 Staniford Street

department: Ophthalmology

country: USA

institute: Mass Eye and Ear

description:
Library name: AMf34
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Optic Nerve

extract_protocol:
CD45+ cells from retina and optic nerve were collected by FACS sorting.
Library was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ v3.1(Dual Index), 10x Genomics).

tag: tissue

value: Optic Nerve

tag: cell type

value: CD45+ cells

tag: genotype

tag: treatment

value: MB-injected


title: Subject 7 BAL

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description: Library name: Subject 7 BAL

library_source: transcriptomic

data_processing:
PBMC RNA-seq: Reads were adapter-trimmed and quality-controlled, then aligned to the human genome using STAR. Transcript abundance was quantified with Salmon and summarized to gene-level counts using tximeta.  BAL AmpliSeq: Ion Torrent AmpliSeq RNA plugin was used to generate count tables.
Assembly: GRCh38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.

organism: Homo sapiens

source_name: BAL

extract_protocol:
Aspirated alveolar fluid and blood were collected in parallel from patients in cell preparation tubes (CPT) and immediately processed. Cells were cryopreserved and later thawed for RNA isolation. Total RNA was extracted from BAL cells and PBMCs using standard column-based RNA extraction methods according to manufacturer instructions.
BAL (AmpliSeq): Targeted RNA libraries were prepared using the Ion AmpliSeq Human Transcriptome Panel. Sixteen nanograms of total RNA was reverse transcribed, amplified, barcoded, purified with magnetic beads, and PCR-amplified per manufacturer protocol. Libraries were quantified, pooled, templated on an Ion Chef Instrument, and sequenced on an Ion Torrent S5 Prime.  PBMC (RNA-seq): Libraries were prepared using the KAPA mRNA HyperPrep kit. Poly(A)+ mRNA was isolated from 50 ng total RNA, fragmented, converted to cDNA, adapter-ligated with dual indices, PCR amplified, pooled, and sequenced on an Illumina NovaSeq 6000 (paired-end).

value: BAL

tag: gender

value: Male

tag: age


title: MDA-MB-231/4175 TfR-1(#3)

country: China

description: Library name: Sample 7

tag: cell line

tag: batch

value: batch 3


title: Grass carp, Plasma exosomes, 1st group of large fish

city: Qingdao

first: Tengfei

last: Zhu

state: Shandong

address: Nanjing Road 106, Qingdao 266071, China

institute: Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences

description: Library name: L1

data_processing:
Small RNA sequencing data were processed using the in-house small-RNA analysis pipeline (v2.5.5) with UMI support.
Raw FASTQ reads were adapter-trimmed, filtered for low-quality reads and reads containing >10% ambiguous bases, and retained only if within the configured small-RNA length range.
A 12-nt UMI was extracted from each retained read. Reads sharing the same insert sequence and UMI were collapsed to remove PCR duplicates; unique read counts were carried forward for quantification.
Clean reads were aligned with Bowtie (zero mismatches) to tRNA, SILVA rRNA, Rfam, and Repbase databases for annotation and filtering, then aligned to the HZGC01 reference genome. Known and novel miRNAs were identified using miRBase references and miRDeep2.
Per-miRNA UMI-deduplicated counts were summarized for each sample and normalized to transcripts per million (TPM) for the processed expression matrices.
Assembly: GCF_019924925.1_HZGC01
Supplementary files format and content: xlsx list file includes miRNA sequence and TPM for each Sample

organism: Ctenopharyngodon idella

source_name: Plasma

extract_protocol:
RNA was harvested using Exosome RNA Purification Kit (Simgen). 3ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit following manufacturer's protocols

value: Plasma


title: Subject 6 BAL

description: Library name: Subject 6 BAL

value: Female


title: Retina_Sham-injected_S2

description:
Library name: AMf31
10x Genomics

source_name: Retina

value: Retina

value: Sham-injected


title: MDA-MB-231/4175 TfR-1(#2)

description: Library name: Sample 6

value: batch 2


title: Retina_MB-injected_S2

description:
Library name: AMf30
10x Genomics


title: Subject 5 BAL

description: Library name: Subject 5 BAL


title: MDA-MB-231/4175 TfR-1(#1)

description: Library name: Sample 5

value: batch 1


title: Retina_MB-injected_S1

description:
Library name: AMf25
10x Genomics


title: Grass carp, Plasma exosomes, 2nd group of large fish

description: Library name: L2


title: Grass carp, Plasma exosomes, 3rd group of large fish

description: Library name: L3


title: Subject 4 BAL

description: Library name: Subject 4 BAL


title: Retina_Sham-injected_S1

description:
Library name: AMf24
10x Genomics


title: MDA-MB-231/4175 Mock(#4)

description: Library name: Sample 4

value: Mock


title: Subject 3 BAL

description: Library name: Subject 3 BAL


title: Grass carp, Plasma exosomes, 1st group of small fish

description: Library name: S1


title: MDA-MB-231/4175 Mock(#3)

description: Library name: Sample 3


title: Optic nerve_MB-injected_S1

description:
Library name: AMf21
10x Genomics


title: Grass carp, Plasma exosomes, 3rd group of small fish

description: Library name: S3


title: MDA-MB-231/4175 Mock(#2)

description: Library name: Sample 2


title: Subject 2 BAL

description: Library name: Subject 2 BAL


title: Grass carp, Plasma exosomes, 2nd group of small fish

description: Library name: S2


title: Subject 1 BAL

description: Library name: Subject 1 BAL


title: NPS_8780_CD_7

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description:
Library name: NPS_8780_CD_7
RNA-Seq of CHIM NPS

data_processing:
Paired-end reads that passed Illumina quality filters were further screened to remove sequences aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The remaining reads were aligned to the GRCh38 human reference genome with Gencode v27 annotations using STAR (v2.6.1) [PMID: 23104886]. Read complexity was assessed with PRINSEQ Lite (v0.20.3) [PMID: 21278185], and low-complexity reads (DUST score > 4) were excluded from the BAM files. The alignment results were parsed via the SAMtools [PMID: 19505943] to generate SAM files. Gene-level counts were then obtained using featureCounts (v1.6.5) [PMID: 24227677] using the default option along with a minimum quality cut-off (Phred > 10), and transcripts per million (TPM) reads values were calculated. T cell receptor (TCR) transcripts were aggregated into four groups: TCR-α, TCR-β, TCR-γ, and TCR-δ. B cell receptor (BCR) transcripts were aggregated into light chains (IGK and IGL) and heavy chains (IGH-), with isotype transcripts (IGHG1-4, IGHM, IGHD, IGHE, IGHA1-2) analyzed separately. Transcripts were filtered using EdgeR’s filterByExpr function (v4.2.2) [PMID: 39844453] with “participants + timepoint” as the design. For each participant, baseline TPMs were averaged and raw counts were summed. Differential expression was assessed using the DESeq2 package (v1.44.0) [PMID: 25516281] for NPS and EdgeR for PBMCs in an R (v4.4.0) environment, with gene expression called differential with an FDR<0.05. Gene set enrichment analysis (GSEA) was performed using Metascape [PMID: 30944313] and GSEA (v4.4.0) [PMID: 16199517], both with the Gene Ontology (GO) gene sets [PMID: 36866529].
Assembly: GRCh38
Supplementary files format and content: "PBMC_counts.tsv" contains raw count values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm.tsv" contains TPM values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm_baseline_means_BCR_TCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were averaged.
Supplementary files format and content: "PBMC_counts_baseline_sums_BCR_TCR_aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were summed.
Supplementary files format and content: "NPS_counts.csv" contains raw count values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm.csv" contains TPM values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm_baseline_means_TCR_BCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were averaged.
Supplementary files format and content: NPS_counts_baseline_sums_BCR.TCR.aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were summed.
Supplementary files format and content: "participant_metadata_filtered.csv" contains metadata per participant.

molecule: polyA RNA

source_name: Nose

extract_protocol:
NPS: RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA was quantified by qPCR using the housekeeping gene B2M.
PBMC: 500K cells were stored in 750 μL TRIzol at -80°C. RNA until further processing. RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NPS: For cDNA synthesis, 10 ng of RNA was reverse-transcribed and pre-amplified (14 cycles) according to the Smart-Seq2 protocol. cDNA was purified with AMPure XP beads (Beckman Coulter), and 0.5 ng was used for Nextera XT sequencing library preparation with 8-bp Unique Dual Index (UDI) barcodes (IDT, Illumina) and the Nextera XT DNA Library Preparation Kit (Illumina). To minimize inter-assay variability, all purification steps were performed using an EpMotion 5075 (Eppendorf), and sequencing libraries were prepared in a 96-well format using a Mantis microfluidics liquid dispenser (Formulamatrix). Quality control included assessment of total RNA quality and quantity, optimization of pre-amplification cycle numbers, and fragment size analysis by capillary electrophoresis (5300 Fragment Analyzer, Agilent). cDNA and final libraries were quantified with the Quant-iT PicoGreen assay (Thermo Fisher Scientific). All samples passed quality thresholds, with >70% of fragments ranging from 300–700 bp and <5% primer dimers. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche), normalized to equimolar concentrations, and loaded onto a NovaSeq X Plus sequencing platform (Illumina) with a 25B flow cell. Paired-end sequencing (150 bp) yielded 4.2 billion total reads, corresponding to an average depth of ~15 million reads per sample.
PBMC: Quantabio Sparq mRNA-Seq kit was used to prepare stranded libraries using 8 ng of high-quality total RNA as input, except in 10 samples where the yield was below 8 ng. Libraries underwent 16-18 PCR amplification cycles and libraries were indexed with xGen 10 nt Unique Dual Indexes (UDIs). Paired-end (50x50) sequencing was performed on a NovaSeq 6000 targeting 40 million reads per library.

value: Nose

value: NPS

tag: days post_challenge

tag: Sex

value: female


title: MDA-MB-231/4175 Mock(#1)

description: Library name: Sample 1


title: AB6488

status: Public on Jul 21 2026

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample840
MARS

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: BM

tag: gate

value: PC


title: AB6489

description:
Library name: Sample841
MARS


title: AB6487

description:
Library name: Sample839
MARS


title: AB6486

description:
Library name: Sample838
MARS


title: AB6484

description:
Library name: Sample836
MARS


title: AB6485

description:
Library name: Sample837
MARS


title: AB6483

description:
Library name: Sample835
MARS


title: AB6481

description:
Library name: Sample833
MARS


title: AB6482

description:
Library name: Sample834
MARS


title: AB6479

description:
Library name: Sample831
MARS


title: AB6480

description:
Library name: Sample832
MARS


title: AB6364

description:
Library name: Sample830
MARS


title: AB6361

description:
Library name: Sample827
MARS


title: AB6363

description:
Library name: Sample829
MARS


title: AB6362

description:
Library name: Sample828
MARS


title: AB6275

description:
Library name: Sample826
MARS


title: AB6274

description:
Library name: Sample825
MARS


title: AB6273

description:
Library name: Sample824
MARS


title: AB6270

description:
Library name: Sample821
MARS


title: AB6272

description:
Library name: Sample823
MARS


title: AB6269

description:
Library name: Sample820
MARS


title: AB6268

description:
Library name: Sample819
MARS


title: AB6267

description:
Library name: Sample818
MARS


title: AB6266

description:
Library name: Sample817
MARS


title: AB6265

description:
Library name: Sample816
MARS


title: AB6263

description:
Library name: Sample814
MARS


title: AB6264

description:
Library name: Sample815
MARS


title: AB6262

description:
Library name: Sample813
MARS


title: AB6261

description:
Library name: Sample812
MARS


title: AB6260

description:
Library name: Sample811
MARS


title: AB6271

description:
Library name: Sample822
MARS


title: AB6258

description:
Library name: Sample809
MARS


title: AB6259

description:
Library name: Sample810
MARS


title: AB6257

description:
Library name: Sample808
MARS


title: AB6256

description:
Library name: Sample807
MARS


title: AB6255

description:
Library name: Sample806
MARS


title: AB6254

description:
Library name: Sample805
MARS


title: AB6253

description:
Library name: Sample804
MARS


title: AB6252

description:
Library name: Sample803
MARS


title: AB6251

description:
Library name: Sample802
MARS


title: AB6250

description:
Library name: Sample801
MARS


title: AB6249

description:
Library name: Sample800
MARS


title: AB6248

description:
Library name: Sample799
MARS


title: AB6247

description:
Library name: Sample798
MARS


title: AB6245

description:
Library name: Sample796
MARS


title: AB6244

description:
Library name: Sample795
MARS


title: AB6246

description:
Library name: Sample797
MARS


title: AB6069

description:
Library name: Sample792
MARS


title: AB6071

description:
Library name: Sample794
MARS


title: AB6070

description:
Library name: Sample793
MARS


title: AB6068

description:
Library name: Sample791
MARS


title: AB6067

description:
Library name: Sample790
MARS


title: AB6066

description:
Library name: Sample789
MARS


title: AB6065

description:
Library name: Sample788
MARS


title: AB6064

description:
Library name: Sample787
MARS


title: AB6063

description:
Library name: Sample786
MARS


title: AB6062

description:
Library name: Sample785
MARS


title: AB6061

description:
Library name: Sample784
MARS


title: AB6060

description:
Library name: Sample783
MARS


title: AB6059

description:
Library name: Sample782
MARS


title: AB6058

description:
Library name: Sample781
MARS


title: AB6056

description:
Library name: Sample779
MARS


title: AB6057

description:
Library name: Sample780
MARS


title: AB6055

description:
Library name: Sample778
MARS


title: AB6053

description:
Library name: Sample776
MARS


title: AB6054

description:
Library name: Sample777
MARS


title: AB6051

description:
Library name: Sample774
MARS


title: AB6052

description:
Library name: Sample775
MARS


title: AB6050

description:
Library name: Sample773
MARS


title: AB6049

description:
Library name: Sample772
MARS


title: AB6048

description:
Library name: Sample771
MARS


title: Optic nerve_Sham-injected_S1

description:
Library name: AMf20
10x Genomics

value: Optic Nerve

value: CD45+ cells


title: AB6005

description:
Library name: Sample770
MARS


title: AB6004

description:
Library name: Sample769
MARS


title: AB6003

description:
Library name: Sample768
MARS


title: AB6001

description:
Library name: Sample766
MARS


title: AB6002

description:
Library name: Sample767
MARS


title: AB5999

description:
Library name: Sample764
MARS


title: AB5998

description:
Library name: Sample763
MARS


title: AB6000

description:
Library name: Sample765
MARS


title: AB5997

description:
Library name: Sample762
MARS


title: AB5994

description:
Library name: Sample759
MARS


title: AB5995

description:
Library name: Sample760
MARS


title: AB5996

description:
Library name: Sample761
MARS


title: AB5982

description:
Library name: Sample757
MARS


title: AB5993

description:
Library name: Sample758
MARS


title: AB5980

description:
Library name: Sample755
MARS


title: AB5981

description:
Library name: Sample756
MARS


title: AB5979

description:
Library name: Sample754
MARS


title: AB5978

description:
Library name: Sample753
MARS


title: AB5977

description:
Library name: Sample752
MARS


title: AB5975

description:
Library name: Sample750
MARS


title: AB5976

description:
Library name: Sample751
MARS


title: AB5973

description:
Library name: Sample748
MARS


title: AB5972

description:
Library name: Sample747
MARS


title: AB5974

description:
Library name: Sample749
MARS


title: AB5971

description:
Library name: Sample746
MARS


title: AB5788

description:
Library name: Sample744
MARS


title: AB5787

description:
Library name: Sample743
MARS


title: AB5789

description:
Library name: Sample745
MARS


title: AB5473

description:
Library name: Sample742
MARS


title: AB5472

description:
Library name: Sample741
MARS


title: AB5471

description:
Library name: Sample740
MARS


title: AB5423

description:
Library name: Sample738
MARS


title: AB5470

description:
Library name: Sample739
MARS


title: AB5421

description:
Library name: Sample736
MARS


title: AB5422

description:
Library name: Sample737
MARS


title: AB5420

description:
Library name: Sample735
MARS


title: AB5419

description:
Library name: Sample734
MARS


title: AB14635

description:
Library name: Sample465
MARS


title: AB14634

description:
Library name: Sample464
MARS


title: AB14637

description:
Library name: Sample466
MARS


title: AB14633

description:
Library name: Sample463
MARS


title: AB14626

description:
Library name: Sample460
MARS


title: AB14630

description:
Library name: Sample462
MARS


title: AB14624

description:
Library name: Sample458
MARS


title: AB14625

description:
Library name: Sample459
MARS


title: AB14627

description:
Library name: Sample461
MARS


title: AB14623

description:
Library name: Sample457
MARS


title: AB14622

description:
Library name: Sample456
MARS


title: AB14621

description:
Library name: Sample455
MARS


title: AB14620

description:
Library name: Sample454
MARS


title: AB14619

description:
Library name: Sample453
MARS


title: AB14618

description:
Library name: Sample452
MARS


title: AB14617

description:
Library name: Sample451
MARS


title: AB14616

description:
Library name: Sample450
MARS


title: AB14590

description:
Library name: Sample449
MARS


title: AB14589

description:
Library name: Sample448
MARS


title: AB14588

description:
Library name: Sample447
MARS


title: AB14574

description:
Library name: Sample445
MARS


title: AB14572

description:
Library name: Sample443
MARS


title: AB14573

description:
Library name: Sample444
MARS


title: AB14587

description:
Library name: Sample446
MARS


title: AB14571

description:
Library name: Sample442
MARS


title: AB14569

description:
Library name: Sample440
MARS


title: AB14570

description:
Library name: Sample441
MARS


title: AB14568

description:
Library name: Sample439
MARS


title: AB14567

description:
Library name: Sample438
MARS


title: AB14566

description:
Library name: Sample437
MARS


title: AB14565

description:
Library name: Sample436
MARS


title: AB14564

description:
Library name: Sample435
MARS


title: AB14563

description:
Library name: Sample434
MARS


title: AB14562

description:
Library name: Sample433
MARS


title: AB14561

description:
Library name: Sample432
MARS


title: AB14560

description:
Library name: Sample431
MARS


title: AB14559

description:
Library name: Sample430
MARS


title: AB14555

description:
Library name: Sample427
MARS


title: AB14557

description:
Library name: Sample428
MARS


title: AB14554

description:
Library name: Sample426
MARS


title: AB14558

description:
Library name: Sample429
MARS


title: AB14553

description:
Library name: Sample425
MARS


title: AB14551

description:
Library name: Sample423
MARS


title: AB14552

description:
Library name: Sample424
MARS


title: AB14546

description:
Library name: Sample422
MARS


title: AB14544

description:
Library name: Sample420
MARS


title: AB14542

description:
Library name: Sample418
MARS


title: AB14541

description:
Library name: Sample417
MARS


title: AB14540

description:
Library name: Sample416
MARS


title: AB14537

description:
Library name: Sample413
MARS


title: AB14528

description:
Library name: Sample412
MARS


title: AB14526

description:
Library name: Sample410
MARS


title: AB14538

description:
Library name: Sample414
MARS


title: AB14527

description:
Library name: Sample411
MARS


title: AB14524

description:
Library name: Sample408
MARS


title: AB14523

description:
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title: AB14525

description:
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title: AB14522

description:
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title: AB14521

description:
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title: AB14545

description:
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title: AB14443

description:
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title: AB14445

description:
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title: AB14444

description:
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title: AB14438

description:
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title: AB14442

description:
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title: AB14441

description:
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title: AB14440

description:
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title: AB14439

description:
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title: AB14437

description:
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title: AB14436

description:
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title: AB14434

description:
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title: AB14435

description:
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title: AB14433

description:
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title: AB14432

description:
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title: AB14431

description:
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title: AB14430

description:
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title: AB14429

description:
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title: AB14427

description:
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title: AB14426

description:
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title: AB14428

description:
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title: AB14348

description:
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title: AB14345

description:
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title: AB14332

description:
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title: AB14346

description:
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title: AB14347

description:
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title: AB14330

description:
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title: AB14329

description:
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title: AB14331

description:
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title: AB14324

description:
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title: AB14323

description:
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title: AB14322

description:
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title: AB14321

description:
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title: AB14254

description:
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title: AB14253

description:
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title: AB14255

description:
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title: AB14252

description:
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title: AB14251

description:
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title: AB14250

description:
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title: AB14185

description:
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title: AB14182

description:
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title: AB14184

description:
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title: AB14183

description:
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title: AB14180

description:
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title: AB14181

description:
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title: AB14179

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title: AB14178

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title: AB14177

description:
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title: AB14175

description:
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title: AB14176

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title: AB14174

description:
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title: AB14543

description:
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title: AB14173

description:
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title: AB14172

description:
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title: AB14170

description:
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title: AB14171

description:
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title: AB14539

description:
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title: AB14169

description:
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title: AB14167

description:
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title: AB14168

description:
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title: AB14166

description:
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title: AB14165

description:
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title: AB14163

description:
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title: AB14164

description:
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title: AB14162

description:
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title: AB14161

description:
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title: AB14160

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title: AB14085

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title: AB14084

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title: AB14083

description:
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title: AB14082

description:
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title: AB14081

description:
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title: AB14079

description:
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title: AB14080

description:
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title: AB14077

description:
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title: AB14078

description:
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title: AB14075

description:
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title: AB14076

description:
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title: AB14074

description:
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title: AB14073

description:
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title: AB14072

description:
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title: AB14071

description:
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title: AB14069

description:
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description:
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description:
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title: AB14067

description:
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title: AB14066

description:
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title: AB14023

description:
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title: AB14026

description:
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title: AB14025

description:
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title: AB14022

description:
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title: AB14020

description:
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title: AB14024

description:
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title: AB14021

description:
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title: AB14019

description:
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title: AB14017

description:
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title: AB14018

description:
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title: AB14016

description:
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title: AB14015

description:
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title: AB13903

description:
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title: AB13901

description:
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title: AB13745

description:
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title: AB13743

description:
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title: AB13902

description:
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title: AB13742

description:
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title: AB13116

description:
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title: AB13114

description:
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title: AB13740

description:
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title: AB12840

description:
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title: AB12839

description:
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title: AB12838

description:
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title: AB12837

description:
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title: AB12836

description:
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title: AB12835

description:
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title: AB12834

description:
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MARS


title: AB12831

description:
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MARS


title: MuSC RNA-seq III control 1h biol rep 2

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: Cultured adult mouse MuSC, serum starved, control-treated for 1h, biological replicate 2
TPM_joined.tab: TPM_wt2control1h
FPKM_joined.tab: FPKM_wt2control1h

data_processing:
After removing the sequencing adapters, the resulting FASTQ files were filtered for the desired length of 150 bp and for quality scores of Phred+33. FASTQ files were aligned to the mouse genome (GENCODE GRCm39) using STAR v2.7.11a with the following settings: --runThreadN 80 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 75 --outFilterMatchNmin 250 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 80 -e. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into two tables: output.tpm.csv and output.fpkm.csv.
Assembly: GENCODE M32 (GRCm39)
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.xlsx, TPM_joined.tab, TPM_joined.xlsx => fused tables with all the samples of the experiment in TAB and XLSX format provided as TPM and FPKM values, gene_count.csv => fused tables with the fragment counts for all the samples of the experiment

source_name: skeletal muscle

growth_protocol: Muscle stem cells were isolated from forelimb, hindlimb, dorsal, and breast muscles of female 8-week-old mice by autoMACS and cultured in DMEM (Gibco, 41966029), 15% FBS (Gibco), 2.5 ng/mL basic FGF (Sigma, F3133), 10 ng/mL leukemia inhibitory factor (Sigma, ESG1106), and 1% Pen/Strep (Gibco) in Matrigel® (Corning, 356231)-coated dishes at 3% O2 and 5% CO2 at 37 °C for 48 hours. After the first 24 hours, 1x B27 without vitamin A (Gibco, 12587010) was added. In order to eliminate the effect of BMPs in the culture medium (e.g. from serum supplements), cells were then cultured in serum-free medium containing soluble BMP receptor (recombinant mouse BMPR-1A-Fc Chimera, R&D Systems, 437-MR) at a concentration of 200 ng/mL for 6 h.

extract_protocol:
Cells were washed, trypsinized, centrifuged, and frozen at -80 °C for later RNA extraction. RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, 740955). RNA quantity and quality were assessed using a NanoDrop® 2000c spectrophotometer (Thermo Fisher Scientific)
The construction of the eukaryotic strand-specific transcriptome library was performed according to the "DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing" protocol of the  Beijing Genetics Institute (BGI). Briefly, 500 ng total RNA was enriched for poly(A)-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized using dUTP instead of dTTP and the synthesized cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR. After quality control, the library was circularized and amplified to produce DNA nanoballs (DNBs).

treatment_protocol: Depending on the condition, cells were optionally pretreated with 20 µM DAPT or 10 µM cycloheximide for 10 minutes and subsequently stimulated with 100 ng/mL BMP6 or treated with vehicle (4 mM HCl containing 0.1% BSA) for 1 or 3 hours.

value: skeletal muscle

value: muscle stem cells

value: control

tag: time

value: biol rep 2


title: AB12829

description:
Library name: Sample285
MARS


title: AB12828

description:
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title: AB12827

description:
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title: AB12826

description:
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title: AB12825

description:
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title: AB12824

description:
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title: AB12823

description:
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title: AB12821

description:
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title: AB12819

description:
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title: AB12771

description:
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title: AB12830

description:
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title: AB12766

description:
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title: AB12765

description:
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title: AB12764

description:
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title: AB12756

description:
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title: AB12757

description:
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title: AB12754

description:
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title: AB12755

description:
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title: AB12770

description:
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title: AB12456

description:
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title: AB12454

description:
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title: AB12424

description:
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title: AB12453

description:
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title: AB12423

description:
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title: AB12421

description:
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title: AB12379

description:
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title: AB12378

description:
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title: AB12377

description:
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title: AB12376

description:
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title: AB12375

description:
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title: AB12422

description:
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title: AB12374

description:
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title: AB12373

description:
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title: AB12372

description:
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title: AB12352

description:
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title: AB12299

description:
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title: AB12296

description:
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title: AB12297

description:
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title: AB12371

description:
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title: AB12293

description:
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title: AB12292

description:
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title: AB12294

description:
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title: AB12291

description:
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title: AB12290

description:
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title: AB12287

description:
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title: AB12286

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title: AB12285

description:
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title: AB12100

description:
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title: AB12289

description:
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title: AB12098

description:
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title: AB12097

description:
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title: AB12099

description:
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title: AB12096

description:
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title: AB12095

description:
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title: AB12093

description:
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title: AB12092

description:
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title: AB12094

description:
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title: AB12090

description:
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title: AB12091

description:
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title: AB12087

description:
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title: AB12085

description:
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title: AB12084

description:
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title: AB12082

description:
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title: AB12080

description:
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title: AB12295

description:
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title: AB12081

description:
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title: AB12079

description:
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title: AB12083

description:
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title: AB12078

description:
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MARS


title: AB12077

description:
Library name: Sample210
MARS


title: FFPE, EarlyProgressive,nr43

city: Bergen

first: Tony

last: Chen

address: Haukelandsveien 22

country: Norway

institute: Haukeland University Hospital

description:
Library name: EP_43
Novogene

data_processing:
Alignment using Hisat2 v2.0.5
Adapter contamination, uncertain nucleotides constitute more than 10% of reads and low base quality  were filtered for clean reads.
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: raw_gene_count.csv

source_name: Formalin Fixed Paraffin embedded kidney tissue

extract_protocol:
For RNA bulk sequencing, the RNA was extracted using miRNeasy extraction kit. 10 ng/ul was used for library construction.
For bulk RNA sequencing, RNA libraries was prepared according to the Truseq Exome library prep kit following manufacturers protocol.


title: AB12075

description:
Library name: Sample208
MARS


title: AB11793

description:
Library name: Sample207
MARS


title: AB12076

description:
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MARS


title: AB11792

description:
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MARS


title: AB11791

description:
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MARS


title: AB11789

description:
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title: AB11788

description:
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title: AB11787

description:
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title: AB11711

description:
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title: AB11786

description:
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title: AB11710

description:
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title: AB12822

description:
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title: AB11709

description:
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title: AB12820

description:
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title: AB11707

description:
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title: AB11708

description:
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title: AB12818

description:
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title: AB11706

description:
Library name: Sample194
MARS


title: AB11684

description:
Library name: Sample193
MARS


title: BulkCA1_H1_008, WT male, ZT6

city: Austin

first: Laura

middle: K

last: Fonken

state: TX

address: 107 W Dean Keeton St

department: Pharmacy

institute: The University of Texas at Austin

description:
Library name: BulkCA1_H1_008
Column name in bulkCA1_counts.csv: H1-008

data_processing:
Samples were sequenced on a NovaSeq S1, SR100.
FASTQ files from multiple sequencing lanes were combined, if needed, and PCR-duplicate sequences were collapsed (deduplicated). The 5' inline barcode Tag, adapter, and polyA tail were removed.
Reads were mapped to the mm39 genome using STAR with default settings and quantMode to produce transcript quantifications.
Library quality and mapping performance was assessed on each sample using the STAR Log.final.out file and by viewing the read alignments using Interactive Genome Viewer. Microglia samples were excluded from analysis if any of the following criteria were met: input reads<1000000, uniquely mapped reads < 900000, uniquely mapped percentage < 85%, mismatch rate per base > 0.85, or if mapping coverage was judged to be poor by a blinded observer in Interactive Genome Viewer.
The counts matrix was created using column 3 (first read strand aligned with RNA) from the ReadsPerGene.out.tab file. Genes with >10 counts in at least 80% (CA1) or 20% (microglia) of samples were considered for analysis.
A PCA was performed on the filtered data to check for outliers. None were detected or excluded here.
Differential gene expression was modelled using limma-voom with TMM normalization. False discovery rate was determined by Benjamini-Hochberg multiplicity correction  (microglia) or permutation analysis (CA1).
Assembly: mm39
Supplementary files format and content: csv file contains raw counts for each sample

source_name: hippocampus, area CA1

extract_protocol:
Mice were intracardially perfused with PBS on postnatal day 28 at zeitgeber time 6. Brains were removed, flash-frozen whole on dry ice and stored at -80C. The hippocampus was sectioned into 100um-thick coronal slices on a cryostat at 20C, and tissue from area CA1 was collected via micropunch and stored at -80C until RNA extraction. RNA extractions were performed using the RNeasy kit (Qiagen) with on-column DNase digestion according to the manufacturer’s instructions.  300ng total RNA was used for library construction.
Mice were intracardially perfused with PBS on postnatal day 28 at zeitgeber time 6 or 18. Brains were removed and hippocampi were incubated for 15min at 37C in digestion mix containing HBSS, 5% FBS, 10uM HEPES, 2mg/mL collagenase A, and 28U/mL DNase I. Tissue was dissociated using a series of fire-polished glass pipettes, and myelin was removed using Miltenyi Biotec's Debris Removal Kit. Cells were incubated with Miltenyi CD11b microbeads, and microglia were isolated using Mintenyi MACS Separation Columns with MACS MultiStand magnet. Microglia were stored in PBS at -80C until RNA extractions. RNA was extracted using TRizol/chloroform, according to manufacturer's instructions. 150ng total RNA was used for library construction.
Total RNA was fragmented with Mg+ buffer via hydrolysis. cDNA was synthesized with a poly-dT oligo, PCR-amplified, and purified with DNA-binding magnetic beads. Among-sample concentrations were normalized and sample-specific barcodes were added via PCR. Samples were pooled to select a small range of fragment sizes via automated gel extraction (400-500bp). Postextraction products were quantified by Qubit and normalized among pools.

treatment_protocol: Microglia-specific Bmal1 conditional knockout mice (Tmem119wt/CreER2::Bmal1fl/fl, KO ) and wildtype (Tmem119wt/wt::Bmal1fl/fl , WT) littermates were administered 50ug tamoxifen i.p. on postnatal days 3-5.

value: hippocampus, area CA1

value: wt

value: M

tag: zeitgeber time


title: AB11683

description:
Library name: Sample192
MARS


title: AB11549

description:
Library name: Sample190
MARS


title: AB11550

description:
Library name: Sample191
MARS


title: AB11548

description:
Library name: Sample189
MARS


title: PBMC_8782_CD_3

description:
Library name: PBMC_8782_CD_3
RNA-Seq of CHIM PBMC

source_name: Blood

value: Blood

value: PBMC


title: AB12768

description:
Library name: Sample270
MARS


title: AB12769

description:
Library name: Sample271
MARS


title: AB11547

description:
Library name: Sample188
MARS


title: AB11408

description:
Library name: Sample187
MARS


title: AB11406

description:
Library name: Sample185
MARS


title: AB11407

description:
Library name: Sample186
MARS


title: AB11405

description:
Library name: Sample184
MARS


title: AB12767

description:
Library name: Sample269
MARS


title: AB11404

description:
Library name: Sample183
MARS


title: AB11403

description:
Library name: Sample182
MARS


title: AB11401

description:
Library name: Sample180
MARS


title: AB11402

description:
Library name: Sample181
MARS


title: FFPE, LateProgressive,nr67, nr68, nr100

description:
Library name: LP_spatial
10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files and bam files.
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger deafult settings.
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: aligned_tissue_image.jpg: image of tissue and spots.
Supplementary files format and content: cytassist_image.tiff: image of image in Cytassist
Supplementary files format and content: tissue_hires_image.jpg: high res image of tissue
Supplementary files format and content: tissue_lowres_image.jpg: low res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions.csv: spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv list of gene Ids
Supplementary files format and content: matrix.mtx gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

extract_protocol:
Spatial transcriptomics, ffpe tissue with the 5 um sections was mounted onto glass slides for cytassist imaging and library construction.
Spatial transcriptome sequencing  libraries were prepared with 10X genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: Formalin Fixed Paraffin embedded kidney tissue


title: AB11400

description:
Library name: Sample179
MARS


title: AB11399

description:
Library name: Sample178
MARS


title: AB11397

description:
Library name: Sample176
MARS


title: AB11398

description:
Library name: Sample177
MARS


title: AB11395

description:
Library name: Sample174
MARS


title: AB11396

description:
Library name: Sample175
MARS


title: AB11394

description:
Library name: Sample173
MARS


title: AB11393

description:
Library name: Sample172
MARS


title: AB11392

description:
Library name: Sample171
MARS


title: AB11391

description:
Library name: Sample170
MARS


title: AB11390

description:
Library name: Sample169
MARS


title: AB11388

description:
Library name: Sample167
MARS


title: AB11387

description:
Library name: Sample166
MARS


title: AB11385

description:
Library name: Sample164
MARS


title: AB11389

description:
Library name: Sample168
MARS


title: AB11386

description:
Library name: Sample165
MARS


title: AB11384

description:
Library name: Sample163
MARS


title: AB11790

description:
Library name: Sample204
MARS


title: AB11383

description:
Library name: Sample162
MARS


title: AB11382

description:
Library name: Sample161
MARS


title: AB11381

description:
Library name: Sample160
MARS


title: AB11378

description:
Library name: Sample157
MARS


title: AB11379

description:
Library name: Sample158
MARS


title: AB11376

description:
Library name: Sample155
MARS


title: AB11375

description:
Library name: Sample154
MARS


title: AB11377

description:
Library name: Sample156
MARS


title: AB11374

description:
Library name: Sample153
MARS


title: AB11380

description:
Library name: Sample159
MARS


title: AB11373

description:
Library name: Sample152
MARS


title: AB11372

description:
Library name: Sample151
MARS


title: AB11371

description:
Library name: Sample150
MARS


title: AB11368

description:
Library name: Sample147
MARS


title: AB11367

description:
Library name: Sample146
MARS


title: AB11366

description:
Library name: Sample145
MARS


title: AB11370

description:
Library name: Sample149
MARS


title: AB11369

description:
Library name: Sample148
MARS


title: AB11365

description:
Library name: Sample144
MARS


title: AB11364

description:
Library name: Sample143
MARS


title: AB11363

description:
Library name: Sample142
MARS


title: AB11361

description:
Library name: Sample140
MARS


title: CeA_snRNAseq_Sensitive_M2

last: Osterndorff-Kahanek

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: M2

data_processing:
Fastq files were processed using the CellRanger (v7.0.0) pipeline. CellRanger outputs were imported to Seurat (v4.3.0) for further processing.
Assembly: mRatBN7
Supplementary files format and content: Tab-separated values files, comma-separated values files, matrix files

organism: Rattus norvegicus

source_name: central amygdala (CeA)

extract_protocol:
Rats were immediately sacrificed after last footshock session, and brains were fresh frozen and then stored at −80°C until further processing. We sectioned the brains at a cryostat (Leica CM3050s) and collected 300 µm slices from approximately bregma -1.6mm to -2.8mm based on the rat brain in stereotaxic coordinates. Then CeA tissue was harvested bilaterally from the brain slices using a 1.5 mm diameter biopsy punch and tissue blocks were stored at −80°C. Nuclei were isolated using the Chromium Nuclei Isolation Kit with RNase inhibitor (10X Genomics) following the manufacturer's instructions with a lysis time of 6.5 minutes and a single wash following debris removal. The nuclei were resuspended in a final volume of 50–100 µL at a target concentration of 500–1,200 nuclei/µL.
Single-nucleus RNA-seq libraries were generated using the Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics), targeting 10,000 nuclei per sample. Libraries were sequenced on an  Illumina NovaSeq 6000 system using an S1 flow cell, producing approximately 500 million reads per sample.

value: central amygdala (CeA)

value: male

tag: strain

value: Wistar

tag: phenotpe

value: Sensitive


title: AB11360

description:
Library name: Sample139
MARS

value: BM


title: AB11356

description:
Library name: Sample135
MARS

value: PC


title: AB11358

description:
Library name: Sample137
MARS


title: AB11359

description:
Library name: Sample138
MARS


title: AB11362

description:
Library name: Sample141
MARS


title: AB11354

description:
Library name: Sample133
MARS


title: AB11357

description:
Library name: Sample136
MARS


title: AB11352

description:
Library name: Sample131
MARS


title: AB11350

description:
Library name: Sample129
MARS


title: AB11355

description:
Library name: Sample134
MARS


title: AB11351

description:
Library name: Sample130
MARS


title: AB11348

description:
Library name: Sample127
MARS


title: AB11346

description:
Library name: Sample125
MARS


title: AB11347

description:
Library name: Sample126
MARS


title: AB11343

description:
Library name: Sample122
MARS


title: AB11342

description:
Library name: Sample121
MARS


title: AB11344

description:
Library name: Sample123
MARS


title: FFPE, LateStable,nr59.nr66,nr99

description:
Library name: LS_spatial
10X Genomics


title: AB11289

description:
Library name: Sample118
MARS


title: AB11287

description:
Library name: Sample116
MARS


title: AB11288

description:
Library name: Sample117
MARS


title: AB11185

description:
Library name: Sample111
MARS


title: AB11186

description:
Library name: Sample112
MARS


title: AB11284

description:
Library name: Sample113
MARS


title: AB11184

description:
Library name: Sample110
MARS


title: AB11182

description:
Library name: Sample108
MARS


title: PBMC_8779_CD_8

description:
Library name: PBMC_8779_CD_8
RNA-Seq of CHIM PBMC

value: female


title: AB11181

description:
Library name: Sample107
MARS


title: AB11180

description:
Library name: Sample106
MARS


title: AB11177

description:
Library name: Sample103
MARS


title: AB11173

description:
Library name: Sample99
MARS


title: AB11172

description:
Library name: Sample98
MARS


title: AB11170

description:
Library name: Sample96
MARS


title: AB11171

description:
Library name: Sample97
MARS


title: AB11169

description:
Library name: Sample95
MARS


title: AB11168

description:
Library name: Sample94
MARS


title: AB11167

description:
Library name: Sample93
MARS


title: AB11165

description:
Library name: Sample91
MARS


title: AB11164

description:
Library name: Sample90
MARS


title: AB11162

description:
Library name: Sample88
MARS


title: AB11161

description:
Library name: Sample87
MARS


title: AB11160

description:
Library name: Sample86
MARS


title: AB11157

description:
Library name: Sample83
MARS


title: AB11159

description:
Library name: Sample85
MARS


title: AB11156

description:
Library name: Sample82
MARS


title: AB11154

description:
Library name: Sample80
MARS


title: AB11155

description:
Library name: Sample81
MARS


title: AB11153

description:
Library name: Sample79
MARS


title: AB11151

description:
Library name: Sample77
MARS


title: AB11149

description:
Library name: Sample75
MARS


title: AB11148

description:
Library name: Sample74
MARS


title: AB11146

description:
Library name: Sample72
MARS


title: AB11145

description:
Library name: Sample71
MARS


title: AB11353

description:
Library name: Sample132
MARS


title: AB11349

description:
Library name: Sample128
MARS


title: AB11143

description:
Library name: Sample69
MARS


title: AB11142

description:
Library name: Sample68
MARS


title: AB11340

description:
Library name: Sample119
MARS


title: AB11141

description:
Library name: Sample67
MARS


title: AB11285

description:
Library name: Sample114
MARS


title: AB11286

description:
Library name: Sample115
MARS


title: AB11139

description:
Library name: Sample65
MARS


title: AB11140

description:
Library name: Sample66
MARS


title: AB11136

description:
Library name: Sample62
MARS


title: AB11137

description:
Library name: Sample63
MARS


title: AB11138

description:
Library name: Sample64
MARS


title: AB11179

description:
Library name: Sample105
MARS


title: AB11135

description:
Library name: Sample61
MARS


title: AB11134

description:
Library name: Sample60
MARS


title: AB10753

description:
Library name: Sample58
MARS


title: AB11174

description:
Library name: Sample100
MARS


title: AB11133

description:
Library name: Sample59
MARS


title: AB10751

description:
Library name: Sample56
MARS


title: AB10654

description:
Library name: Sample55
MARS


title: AB10653

description:
Library name: Sample54
MARS


title: AB10651

description:
Library name: Sample53
MARS


title: AB10650

description:
Library name: Sample52
MARS


title: AB10649

description:
Library name: Sample51
MARS


title: AB10647

description:
Library name: Sample49
MARS


title: AB10622

description:
Library name: Sample46
MARS


title: AB10620

description:
Library name: Sample44
MARS


title: AB10619

description:
Library name: Sample43
MARS


title: AB10618

description:
Library name: Sample42
MARS


title: AB10617

description:
Library name: Sample41
MARS


title: AB10616

description:
Library name: Sample40
MARS


title: AB10614

description:
Library name: Sample38
MARS


title: AB10613

description:
Library name: Sample37
MARS


title: AB10612

description:
Library name: Sample36
MARS


title: AB10611

description:
Library name: Sample35
MARS


title: AB10610

description:
Library name: Sample34
MARS


title: AB10609

description:
Library name: Sample33
MARS


title: AB10607

description:
Library name: Sample31
MARS


title: AB10606

description:
Library name: Sample30
MARS


title: AB10605

description:
Library name: Sample29
MARS


title: AB10604

description:
Library name: Sample28
MARS


title: AB10602

description:
Library name: Sample26
MARS


title: AB10601

description:
Library name: Sample25
MARS


title: AB10600

description:
Library name: Sample24
MARS


title: AB10648

description:
Library name: Sample50
MARS


title: AB10599

description:
Library name: Sample23
MARS


title: AB10646

description:
Library name: Sample48
MARS


title: AB10645

description:
Library name: Sample47
MARS


title: AB10598

description:
Library name: Sample22
MARS


title: AB10597

description:
Library name: Sample21
MARS


title: AB10621

description:
Library name: Sample45
MARS


title: AB10596

description:
Library name: Sample20
MARS


title: AB10595

description:
Library name: Sample19
MARS


title: AB10593

description:
Library name: Sample17
MARS


title: AB10592

description:
Library name: Sample16
MARS


title: AB10594

description:
Library name: Sample18
MARS


title: AB10615

description:
Library name: Sample39
MARS


title: AB10591

description:
Library name: Sample15
MARS


title: AB10590

description:
Library name: Sample14
MARS


title: AB10589

description:
Library name: Sample13
MARS


title: AB10588

description:
Library name: Sample12
MARS


title: AB10587

description:
Library name: Sample11
MARS


title: AB10586

description:
Library name: Sample10
MARS


title: AB10585

description:
Library name: Sample9
MARS


title: AB11345

description:
Library name: Sample124
MARS


title: AB10584

description:
Library name: Sample8
MARS


title: AB10583

description:
Library name: Sample7
MARS


title: AB11341

description:
Library name: Sample120
MARS


title: AB10608

description:
Library name: Sample32
MARS


title: AB10582

description:
Library name: Sample6
MARS


title: AB10581

description:
Library name: Sample5
MARS


title: AB10580

description:
Library name: Sample4
MARS


title: KO_Rep2

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

description: Library name: VEL7002A6

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (version 3.4) before alignment.
Reads were mapped and subsequent gene-level counted using RSEM 1.3.1 and STAR 2.7.10a against the human genome GRCh38 using annotation release 95, both from Ensembl.
Assembly: GRCh38
Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.

growth_protocol: Complete RPMI medium (RPMI 1640 with 10% heat-inactivated FBS, 100 U ml−1 penicillin, 100 μg ml−1 streptomycin sulfate, 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 1X minimal essential medium nonessential amino acids and 50 μM 2-mercaptoethanol) supplemented with 100 U mL-1 of rhIL-2

extract_protocol:
RNA extraction using RNeasy® Plus Micro Kit - QIAGEN
NEBNext_Low_Input_w_NEB_Ultra_II_FS

treatment_protocol: Labelled with anti-Vδ1-PE antibody and sorted by FACS prior to RNA extraction.

value: Vdelta1 T cells

value: TRDV1 KO


title: AB10578

description:
Library name: Sample2
MARS


title: AB11183

description:
Library name: Sample109
MARS


title: AB10577

description:
Library name: Sample1
MARS


title: KO_Rep1

description: Library name: VEL7002A4


title: WT_Rep2

description: Library name: VEL7002A5

value: WT


title: AB10579

description:
Library name: Sample3
MARS


title: AB10603

description:
Library name: Sample27
MARS


title: AB11178

description:
Library name: Sample104
MARS


title: D458_shHSPA5_5-5_ISRIB

city: Orsay

first: Sabine

last: Druillennec

address: Bat 110 centre universitaire

country: France

institute: Institut Curie

description: Library name: D725T24

data_processing:
Raw sequencing reads were first checked for quality with Fastqc (0.11.8) and trimmed for adapter sequences with cutadapt using the TrimGalore (0.6.2) wrapper.
Trimmed reads were subsequently aligned to the complete human ribosomal RNA sequence with bowtie1.
Reads that did not align to rRNA were then mapped to the human reference genome hg38 and read counts per gene were generated with STAR mapper (2.6.1a_08-27).
The bioinformatics pipelines used for these tasks are available online (RNAseq v3.1.8: https://gitlab.curie.fr/data-analysis/RNA-seq, doi: 10.5281/zenodo.7443721).
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: D458Med cells transduced with shCtrl, shHSPA5#2 and shHSPA5#5 encoding lentiviral particles were seeded 72h after infection. RNA was isolated 6h after DMSO or ISRIB (0,5µM) treatment.

extract_protocol:
Total RNAs were isolated using the NucleoSpin RNA, Mini kit for RNA purification (Macherey-Nagel). RNA Quality was evaluated by Bioanalyzer (Agilent Technologies) and samples with RNA integrity > 7 were used for library construction.
RNA-sequencing libraries were prepared from 1µg of total RNA following the Illumina stranded mRNA prep Ligation protocol.

value: Medulloblastoma cell line

value: HSPA5 knockdown

value: ISRIB


title: WT_Rep1

description: Library name: VEL7002A3


title: D458_shHSPA5_2-5_ISRIB

description: Library name: D725T22


title: AB11175

description:
Library name: Sample101
MARS


title: AB11176

description:
Library name: Sample102
MARS


title: SRRM2-depleted HEK293T replicate 2

city: Hangzhou

first: jinghan

last: rong

state: Zhejiang

address: westlake university

institute: westlake university

description:
Library name: SR_2
Biological replicate 2 of SRRM2-depleted HEK293T cells generated using small interfering RNA.

data_processing:
Raw reads in FASTQ format were processed using fastp to remove adapter-containing reads, reads containing poly-N sequences, and low-quality reads.
High-quality paired-end reads were aligned to the human reference genome using HISAT2 version 2.0.5.
Alternative splicing events were detected and quantified using replicate Multivariate Analysis of Transcript Splicing version 3.2.5.
Skipped-exon events were compared between VRK1-KO and wild-type cells and between SRRM2-depleted and wild-type cells.
Complete rMATS results for all quantified skipped-exon events were retained, and significant differential skipped-exon events were defined using a false discovery rate cutoff of 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing complete rMATS skipped-exon results for VRK1-knockout versus wild-type cells.
Supplementary files format and content: Tab-delimited text file containing complete rMATS skipped-exon results for SRRM2-depleted versus wild-type cells.

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 °C in a humidified incubator with 5% carbon dioxide.

extract_protocol:
Total RNA was extracted using TRIzol RNA extraction reagent. RNA integrity was assessed using the Agilent Bioanalyzer 2100 system.
Messenger RNA was purified from total RNA using poly-T oligonucleotide-attached magnetic beads. After fragmentation, first-strand complementary DNA was synthesized using random hexamer primers, followed by second-strand complementary DNA synthesis. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit, real-time polymerase chain reaction, and the Bioanalyzer, followed by paired-end sequencing on an Illumina platform.

treatment_protocol: Vaccinia-related kinase 1-knockout cells were generated using the CRISPR-Cas9 system. HEK293T cells were transfected with 20 nM SRRM2-targeting siRNA using Lipofectamine RNAiMAX and harvested 48 h after transfection.

value: wild-type

value: SRRM2-targeting small interfering RNA


title: D458_shHSPA5_5-5_DMSO

description: Library name: D725T23

value: dmso


title: D458_shHSPA5_2-5_DMSO

description: Library name: D725T21


title: D458_shCtrl-5_ISRIB

description: Library name: D725T20


title: D458_shHSPA5_2-4_DMSO

description: Library name: D725T15


title: D458_shHSPA5_2-4_ISRIB

description: Library name: D725T16


title: D458_shHSPA5_5-4_DMSO

description: Library name: D725T17


title: D458_shHSPA5_5-4_ISRIB

description: Library name: D725T18


title: D458_shCtrl-5_DMSO

description: Library name: D725T19


title: D458_shCtrl-4_ISRIB

description: Library name: D725T14


title: D458_shHSPA5_5-3_ISRIB

description: Library name: D725T12


title: AB11166

description:
Library name: Sample92
MARS


title: D458_shHSPA5_2-3_ISRIB

description: Library name: D725T10


title: D458_shCtrl-4_DMSO

description: Library name: D725T13


title: D458_shHSPA5_5-3_DMSO

description: Library name: D725T11


title: AB11163

description:
Library name: Sample89
MARS


title: D458_shCtrl-3_ISRIB

description: Library name: D725T08


title: D458_shHSPA5_2-3_DMSO

description: Library name: D725T09


title: D458_shCtrl-3_DMSO

description: Library name: D725T07


title: D458_shHSPA5_5-2_ISRIB

description: Library name: D725T06


title: D458_shHSPA5_5-2_DMSO

description: Library name: D725T05


title: AB11158

description:
Library name: Sample84
MARS


title: Microglia_C6_043, KO female, ZT18

description:
Library name: Microglia_C6_043
Column name in microglia_counts.csv: C6-043

source_name: brain

value: brain

value: microglia

value: ko

value: F


title: D458_shHSPA5_2-1_ISRIB

description: Library name: D725T04


title: D458_shCtrl-1_DMSO

description: Library name: D725T01


title: shCtrl_3

description:
Library name: D495T85
D495T85

data_processing:
Raw sequencing reads were first checked for quality with Fastqc (0.11.8) and trimmed for adapter sequences with cutadapt using the TrimGalore (0.6.2) wrapper.
Trimmed reads were subsequently aligned to the complete human ribosomal RNA sequence with bowtie1.
Reads that did not align to rRNA were then mapped to the human reference genome hg38 and read counts per gene were generated with STAR mapper (2.6.1a_08-27).
The bioinformatics pipelines used for these tasks are available online (RNAseq v3.1.7: https://gitlab.curie.fr/data-analysis/RNA-seq, doi: 10.5281/zenodo.7443721).
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: D425Med cells transduced with shCtrl, shHSPA5#2 and shHSPA5#5 encoding lentiviral particles. Transduced cells were seeded 72h after infection and RNA was isolated 48h later.

extract_protocol:
Total RNAs were isolated using the NucleoSpin RNA, Mini kit for RNA purification (Macherey-Nagel). RNA Quality was evaluated by Bioanalyzer (Agilent Technologies) and samples with RNA integrity > 7 were used for library construction.
RNA-sequencing libraries were prepared from 1µg of total RNA using the TruSeq Stranded mRNA kit following manufacturer's protocols.


title: shHSPA5_2-3

description:
Library name: D495T86
D495T86


title: D458_shHSPA5_2-1_DMSO

description: Library name: D725T03


title: shHSPA5_5-2

description:
Library name: D495T84
D495T84


title: shHSPA5_5-3

description:
Library name: D495T87
D495T87


title: D458_shCtrl-1_ISRIB

description: Library name: D725T02


title: shCtrl_2

description:
Library name: D495T82
D495T82


title: shHSPA5_2-1

description:
Library name: D495T80
D495T80


title: shHSPA5_2-2

description:
Library name: D495T83
D495T83


title: shCtrl_1

description:
Library name: D495T79
D495T79


title: A549_CC_3

city: Tianjin

first: Xiaoling

last: Tian

state: Tianjin

address: Tianjin Medical University 22 Qixiangtai Road, Heping Distric

institute: Tianjin Medical University

description: Library name: A549_CC_3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
HTseq was used to quantify gene count.
Assembly: hg38
Supplementary files format and content: Matrix table with different expression genes in indicated cells.

growth_protocol: A549(G/G) and A549(C/C) cells were cultred in RPMI1640 medium containg 10%FBS, H1155(G/G) and H1155(C/C) cells were cultred in DMEM medium containg 10%FBS.

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.

value: Lung cancer cell

value: C/C


title: shHSPA5_5-1

description:
Library name: D495T81
D495T81


title: A549_GG_3

description: Library name: A549_GG_3

value: G/G


title: A549_CC_1

description: Library name: A549_CC_1


title: A549_CC_2

description: Library name: A549_CC_2


title: AB11152

description:
Library name: Sample78
MARS

value: BM

value: PC


title: porcine alveolar macrophages infected with ASFV ΔD250R, rep2

city: Harbin, Heilongjiang Province

first: Linfei

last: Song

address: 678 Haping Road, Xiangfang District

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

description:
Library name: P73-2
Column name in raw_counts_All_Samples.txt: P73-2

data_processing:
Illumina Bcltofastq 1.8.4 ver software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default parameters.
Trimmed sequence reads were mapped to Sscrofa11.1 and ASM2981691v1 using HISAT2 (version-2.2.1).
Read count extraction and normalization were performed using featureCounts(version-2.0.6).
Assembly: Sscrofa11.1 and ASM2981691v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files FPKM values for each Sample

organism: Sus scrofa

source_name: porcine alveolar macrophages

extract_protocol:
RNA was harvested using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: porcine alveolar macrophages


title: A549_GG_1

description: Library name: A549_GG_1


title: H1155_CC_1

description: Library name: H1155_CC_1


title: A549_GG_2

description: Library name: A549_GG_2


title: H1155_CC_3

description: Library name: H1155_CC_3


title: H1155_GG_1

description: Library name: H1155_GG_1


title: AB11150

description:
Library name: Sample76
MARS


title: H1155(C/C)_H3K27ac_input_2

description:
Library name: H1155(C/C)_H3K27ac_input_2
H1155CC-H3K27ac-2.bw

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: Bigwig

molecule: genomic DNA

growth_protocol: All cell lines were cultred in DMEM medium containg 10%FBS.

extract_protocol:
1 × 10^7cells were washed with PBS and fixed with 37 °C pre-heated 10% FBS DMEM/1% formaldehyde at room temperature for 10 min, and quenched with 0.125 M glycine for 5 min, and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina sequencer following the manufacturer's protocols.

treatment_protocol: no treatment


title: H1155_GG_3

description: Library name: H1155_GG_3


title: H1155(C/C)_H3K27ac_input_1

description:
Library name: H1155(C/C)_H3K27ac_input_1
H1155CC-H3K27ac-1.bw


title: H1155(C/C)_H3K27ac_IP_1

description:
Library name: H1155(C/C)_H3K27ac_IP_1
H1155CC-H3K27ac-1.bw


title: H1155(C/C)_H3K27ac_IP_2

description:
Library name: H1155(C/C)_H3K27ac_IP_2
H1155CC-H3K27ac-2.bw


title: H1155(G/G)_H3K27ac_input_2

description:
Library name: H1155(G/G)_H3K27ac_input_2
H1155GG-H3K27ac-2.bw


title: H1155(G/G)_H3K27ac_IP_2

description:
Library name: H1155(G/G)_H3K27ac_IP_2
H1155GG-H3K27ac-2.bw


title: H1155(C/C)_H3K4me3_input_2

description:
Library name: H1155(C/C)_H3K4me3_input_2
H1155CC-H3K4me3-2.bw


title: H1155(C/C)_H3K4me3_IP_2

description:
Library name: H1155(C/C)_H3K4me3_IP_2
H1155CC-H3K4me3-2.bw


title: H1155(C/C)_H3K4me3_input_1

description:
Library name: H1155(C/C)_H3K4me3_input_1
H1155CC-H3K4me3-1.bw


title: H1155(C/C)_H3K4me3_IP_1

description:
Library name: H1155(C/C)_H3K4me3_IP_1
H1155CC-H3K4me3-1.bw


title: H1155(G/G)_H3K4me3_IP_1

description:
Library name: H1155(G/G)_H3K4me3_IP_1
H1155GG-H3K4me3-1.bw


title: H1155(G/G)_H3K4me3_IP_2

description:
Library name: H1155(G/G)_H3K4me3_IP_2
H1155GG-H3K4me3-2.bw


title: 4C_2

description: Library name: 4C_2

data_processing:
The reduced genome was generated by extracting the sequences flanking the HindIII restriction sites (30 bp on each strand from the HindIII restriction sites to downstream) using the hg38 reference human genome, called 4C frag-ends. Non-unique frag-ends are discarded in subsequent analysis.
Subsequently, the highest covered frag-end was removed from the dataset in the normalization process and data are read-depth normalized to 1 million aligned intrachromosomal reads.
A Bioconductor package ‘r3Cseq’ with 2.5 kb sliding window was used to determine significant interactions and calculate interaction difference.
Assembly: hg38
Supplementary files format and content: wig
Library strategy: 4C-seq

extract_protocol:
4C-seq was performed as previously described using Hind III for the first digestion, and Dpn II for the second digestion. In brief, cells were cross-linked in 2% formaldehyde for 10 min at room temperature and quenched with 0.2M glycine. Cells were then rinsed for 2 times with ice-cold PBS at room temperature and harvested and incubated in lysis buffer (50 mM Tris-Cl, 150 mM NaCl, 5 mM EDTA, 0.5% CA630, 0.5% Triton X-100 and protease inhibitor cocktail) while tumbling for 1 h at 4 °C. Cells were then pelleted, washed, and resuspended in Hind III buffer. SDS was added to a concentration of 0.3% for 1 h in a thermomixer at 37 °C and 400 rpm. Triton X-100 was then added to a concentration of 1.8% and cells were incubated in a thermomixer at 37 °C at 400 rpm for 3 h. 200 units of Hind III enzyme were added for a 4 h incubation in a thermomixer at 37 °C and 900 rpm; another 200 units of Hind III were added for overnight incubation. Cells were then incubated 20 min at 65 °C to heat inactivate enzyme, suspended in ligation buffer and 4,000 units of T4 ligase and incubated overnight at 16 °C. The next day, 300 μg Proteinase K was added for overnight incubation at 65 °C. Ligated DNA was purified and digested with 90 units Dpn II in Dpn II buffer overnight in a thermomixer at 37 °C and 500 rpm, followed by heat inactivation of enzyme (65 °C for 25 min). Samples were then diluted with ligation buffer and 100 units ligase were then added for overnight incubation at 16 °C. Circularized DNA was PCR-amplified using bait-specific inverse primers. Finally, PCR products were pooled and purified.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina sequencer following the manufacturer's protocols.

value: C/G


title: H1155(G/G)_H3K4me3_input_1

description:
Library name: H1155(G/G)_H3K4me3_input_1
H1155GG-H3K4me3-1.bw


title: AML primary cells, Ksuc Low, patient4

city: Hefei

first: Mengqing

last: Gao

state: Anhui

department: Department of Hematology

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

data_processing:
Raw fastq reads were processed using fastp to remove low-quality reads, resulting in clean reads for subsequent data analysis.
HISAT2 was used for alignment to the reference genome hg38.
Gene expression levels were calculated in FPKM and the read counts for each gene were obtained using HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: bone marrow

growth_protocol: U937 cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA from U937 cells was extracted with TRIzol reagent (Invitrogen, 15596026CN). RNAs from primary samples were extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, Cat# 80004) according to the manufacturer’s instructions.
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme) for AML primary samples and Fast RNA-seq Lib Prep Kit V2 (ABclonal) for cell lines according to the manufacturer's instructions

treatment_protocol: U937 NT, KO1, KO2 were deprived of glutamine for 6 hours. U937 cells were treated with 0.5 μM JQ1 for 24 hours.

value: bone marrow

value: bone marrow mononuclear cells


title: AML primary cells, Ksuc Low, patient2


title: AML primary cells, Ksuc Low, patient1


title: AML primary cells, Ksuc High, patient3


title: AML primary cells, Ksuc High, patient2


title: U937 cells, KO2, rep1

value: acute myeloid leukemia cell lines

value: SUCLG1 knockout

value: glutamine deprivation


title: U937 cells, KO1, rep3


title: U937 cells, KO1, rep1


title: U937 cells, NT, rep3

value: non-targeting


title: U937 cells, JQ1, rep3


title: U937 cells, control, rep1

value: DMSO


title: U937 KO2, Input

data_processing:
Raw fastq reads were processed using fastp, and clean reads were aligned to reference genome using BWA.
Peak calling was performed using MACS2 (version 2.2.7.1) software to identify regions of IP enrichment over background with a q-value threshold of 0.05.
Peaks were annotated using the ChIPseeker software according to their corresponding functional regions.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were lysed to obtain nuclei, which were then subjected to MNase digestion to obtain mononucleosomes.
ChIP libraries were prepared using Novagene Library DNA Prep Kit

treatment_protocol: U937 NT, KO1, KO2 were deprived of glutamine for 6 hours.

tag: chip antibody


title: U937 KO1, Input


title: U937 NT, Input


title: AB10752

description:
Library name: Sample57
MARS


title: U937 KO1, BRD4, ChIP

value: BRD4 (Bethyl lab, A301-985)


title: U937 NT, BRD4, ChIP


title: acRIP-seq NAT10 knock out IgG in K562 cell line [KO_IgG_2]

city: Beijing

first: Yanran

last: Wang

address: No.5, Dongdan Sanjiao, Dongcheng District, Beijing

department: State Key Laboratory of Medical Molecular Biology

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were aligned to the Homo sapiens transcripts using bowtie2. ac4C peaks were detected by MACS2, and filtered by log10P < -3. Input samples were used as controls for peak calling. Screening of differential peaks using BEDTools map. ac4C sites that resided in protein coding genes were analyzed for downstream analysis. ChIPseeker was used for annotating the peaks.
Assembly: GENCODE Release 36, GRCh38.p13, transcripts
Supplementary files format and content: bigWig, narrowPeak

source_name: K562 cell line

growth_protocol: NAT10 knock-out k562 cells were grown in RPMI-1640 media supplemented with 10% FBS at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNA was rRNA depleted with the NEBNext® rRNA Depletion Kit v2 (Promega) and then subjected to immunoprecipitation. Briefly, RNA was randomly fragmented to ~100 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody or Normal Rabbit IgG antibody by rotating at room temperature for 2 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
RNA extracted from IP, IgG and input samples obtained from NAT10 knock-out k562 cells was then constructed using the NEBNext® Ultra™ RNA Library Prep Kit,, following the manufacturer's instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a Novaseq 6000 platform (Illumina).

value: K562 cell line

value: NAT10 knock out


title: acRIP-seq NAT10 knock out IP of ac4C mRNA in K562 cell line [KO_IP_2]


title: acRIP-seq NAT10 knock out IgG in K562 cell line [KO_IgG_1]


title: acRIP-seq NAT10 knock out input in K562 cell line [KO_input_2]


title: acRIP-seq NAT10 knock out input in K562 cell line [KO_input_1]


title: Plasma, no Bleeding, Stroke, id560

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQC quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification (mirbase)
bowtie1 RNAcentral mapping
gtRNAdb based tRNA quantification
Assembly: GRCh38.p12
Assembly: RNAcentral version: v19.0
Assembly: mirBase version: v22.1
Supplementary files format and content: csv with tRNA quantifications (raw count)
Supplementary files format and content: csv with miRNA quantifications (raw count)

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen)
Small RNA libraries were prepared using the RealSeq Somagenics kit

value: Plasma

tag: major bleeding

tag: stroke

value: Stroke


title: Plasma, no Bleeding, Stroke Control, id514

tag: tissue

value: Control


title: Plasma, no Bleeding, Stroke Control, id505


title: Plasma, no Bleeding, Stroke, id499


title: H1155(G/G)_H3K27ac_IP_1

description:
Library name: H1155(G/G)_H3K27ac_IP_1
H1155GG-H3K27ac-1.bw

tag: cell type

value: Lung cancer cell

tag: genotype

value: G/G


title: Plasma, no Bleeding, Stroke, id491


title: Plasma, no Bleeding, Stroke Control, id483


title: Plasma, Major Bleeding, no Stroke, id478

value: MajorBleeding


title: AML primary cells, Ksuc High, patient1


title: Plasma, no Bleeding, Stroke, id465


title: U937 cells, KO2, rep2

tag: treatment


title: Plasma, no Bleeding, Stroke Control, id455


title: U937 cells, KO1, rep2


title: Plasma, Major Bleeding, no Stroke, id435


title: Plasma, Bleeding Control, no Stroke, id407


title: U937 cells, NT, rep1


title: U937 cells, JQ1, rep1


title: AB13829

description:
Library name: Sample1523
MARS_v2

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: BM


title: AB13828

description:
Library name: Sample1522
MARS_v2

value: PC


title: AB13827

description:
Library name: Sample1521
MARS_v2


title: AB13825

description:
Library name: Sample1519
MARS_v2


title: AB13823

description:
Library name: Sample1517
MARS_v2


title: AB13824

description:
Library name: Sample1518
MARS_v2


title: AB13826

description:
Library name: Sample1520
MARS_v2


title: U937 KO2 BRD4, ChIP


title: AB13818

description:
Library name: Sample1515
MARS_v2


title: AB13817

description:
Library name: Sample1514
MARS_v2


title: AB13816

description:
Library name: Sample1513
MARS_v2


title: AB13815

description:
Library name: Sample1512
MARS_v2


title: AB13814

description:
Library name: Sample1511
MARS_v2


title: AB13813

description:
Library name: Sample1510
MARS_v2


title: AB13810

description:
Library name: Sample1507
MARS_v2


title: AB13811

description:
Library name: Sample1508
MARS_v2


title: AB13812

description:
Library name: Sample1509
MARS_v2


title: AB13808

description:
Library name: Sample1505
MARS_v2


title: AB13809

description:
Library name: Sample1506
MARS_v2


title: AB13807

description:
Library name: Sample1504
MARS_v2


title: AB13806

description:
Library name: Sample1503
MARS_v2


title: AB13805

description:
Library name: Sample1502
MARS_v2


title: AB13803

description:
Library name: Sample1500
MARS_v2


title: AB13804

description:
Library name: Sample1501
MARS_v2


title: Plasma, Bleeding Control, no Stroke, id548


title: AB13800

description:
Library name: Sample1497
MARS_v2


title: AB13801

description:
Library name: Sample1498
MARS_v2


title: AB13802

description:
Library name: Sample1499
MARS_v2


title: AB13799

description:
Library name: Sample1496
MARS_v2


title: AB13796

description:
Library name: Sample1493
MARS_v2


title: AB13797

description:
Library name: Sample1494
MARS_v2


title: AB13798

description:
Library name: Sample1495
MARS_v2


title: AB13795

description:
Library name: Sample1492
MARS_v2


title: AB13794

description:
Library name: Sample1491
MARS_v2


title: AB13792

description:
Library name: Sample1489
MARS_v2


title: AB13793

description:
Library name: Sample1490
MARS_v2


title: AB13790

description:
Library name: Sample1487
MARS_v2


title: AB13791

description:
Library name: Sample1488
MARS_v2


title: AB13788

description:
Library name: Sample1485
MARS_v2


title: AB13787

description:
Library name: Sample1484
MARS_v2


title: AB13785

description:
Library name: Sample1482
MARS_v2


title: AB13786

description:
Library name: Sample1483
MARS_v2


title: AB13784

description:
Library name: Sample1481
MARS_v2


title: AB13783

description:
Library name: Sample1480
MARS_v2


title: AB13782

description:
Library name: Sample1479
MARS_v2


title: AB13780

description:
Library name: Sample1477
MARS_v2


title: AB13781

description:
Library name: Sample1478
MARS_v2


title: AB13779

description:
Library name: Sample1476
MARS_v2


title: AB13778

description:
Library name: Sample1475
MARS_v2


title: AB13777

description:
Library name: Sample1474
MARS_v2


title: AB13776

description:
Library name: Sample1473
MARS_v2


title: AB13775

description:
Library name: Sample1472
MARS_v2


title: AB13774

description:
Library name: Sample1471
MARS_v2


title: AB13773

description:
Library name: Sample1470
MARS_v2


title: AB13772

description:
Library name: Sample1469
MARS_v2


title: AB13822

description:
Library name: Sample1516
MARS_v2


title: AB13766

description:
Library name: Sample1466
MARS_v2


title: AB13771

description:
Library name: Sample1468
MARS_v2


title: AB13770

description:
Library name: Sample1467
MARS_v2


title: AB13765

description:
Library name: Sample1465
MARS_v2


title: AB13758

description:
Library name: Sample1464
MARS_v2


title: AB13716

description:
Library name: Sample1463
MARS_v2


title: AB13714

description:
Library name: Sample1462
MARS_v2


title: AB13705

description:
Library name: Sample1460
MARS_v2


title: AB13709

description:
Library name: Sample1461
MARS_v2


title: AB13703

description:
Library name: Sample1458
MARS_v2


title: AB13704

description:
Library name: Sample1459
MARS_v2


title: AB13702

description:
Library name: Sample1457
MARS_v2


title: AB13701

description:
Library name: Sample1456
MARS_v2


title: AB13700

description:
Library name: Sample1455
MARS_v2


title: AB13697

description:
Library name: Sample1454
MARS_v2


title: AB13695

description:
Library name: Sample1452
MARS_v2


title: AB13689

description:
Library name: Sample1450
MARS_v2


title: AB13694

description:
Library name: Sample1451
MARS_v2


title: AB13696

description:
Library name: Sample1453
MARS_v2


title: AB13688

description:
Library name: Sample1449
MARS_v2


title: H1155_CC_2

description: Library name: H1155_CC_2

value: C/C


title: AB13687

description:
Library name: Sample1448
MARS_v2


title: AB13685

description:
Library name: Sample1447
MARS_v2


title: AB13683

description:
Library name: Sample1446
MARS_v2


title: H1155_GG_2

description: Library name: H1155_GG_2


title: AB13681

description:
Library name: Sample1445
MARS_v2


title: AB13679

description:
Library name: Sample1443
MARS_v2


title: AB13680

description:
Library name: Sample1444
MARS_v2


title: H1155(G/G)_H3K27ac_input_1

description:
Library name: H1155(G/G)_H3K27ac_input_1
H1155GG-H3K27ac-1.bw


title: AB13676

description:
Library name: Sample1442
MARS_v2


title: AB13675

description:
Library name: Sample1441
MARS_v2


title: AB13673

description:
Library name: Sample1440
MARS_v2


title: AB13672

description:
Library name: Sample1439
MARS_v2


title: H1155(G/G)_H3K4me3_input_2

description:
Library name: H1155(G/G)_H3K4me3_input_2
H1155GG-H3K4me3-2.bw


title: AB13671

description:
Library name: Sample1438
MARS_v2


title: AB13670

description:
Library name: Sample1437
MARS_v2


title: AB13668

description:
Library name: Sample1436
MARS_v2


title: AB13667

description:
Library name: Sample1435
MARS_v2


title: AB13789

description:
Library name: Sample1486
MARS_v2


title: AB13666

description:
Library name: Sample1434
MARS_v2


title: AB13665

description:
Library name: Sample1433
MARS_v2


title: AB13664

description:
Library name: Sample1432
MARS_v2


title: 4C_1

description: Library name: 4C_1

value: C/G


title: AB13663

description:
Library name: Sample1431
MARS_v2


title: AB13662

description:
Library name: Sample1430
MARS_v2


title: U937 cells, KO2, rep3

value: acute myeloid leukemia cell lines

value: SUCLG1 knockout


title: AML primary cells, Ksuc High, patient4

value: bone marrow

value: bone marrow mononuclear cells


title: AML primary cells, Ksuc Low, patient3


title: AB13661

description:
Library name: Sample1429
MARS_v2


title: AB13660

description:
Library name: Sample1428
MARS_v2


title: AB13659

description:
Library name: Sample1427
MARS_v2


title: AB13655

description:
Library name: Sample1425
MARS_v2


title: AB13652

description:
Library name: Sample1422
MARS_v2


title: AB13653

description:
Library name: Sample1423
MARS_v2


title: AB13654

description:
Library name: Sample1424
MARS_v2


title: AB13651

description:
Library name: Sample1421
MARS_v2


title: U937 cells, NT, rep2

value: non-targeting

value: glutamine deprivation


title: AB13650

description:
Library name: Sample1420
MARS_v2


title: AB13658

description:
Library name: Sample1426
MARS_v2


title: AB13528

description:
Library name: Sample1418
MARS_v2


title: AB13649

description:
Library name: Sample1419
MARS_v2


title: AB13527

description:
Library name: Sample1417
MARS_v2


title: AB13526

description:
Library name: Sample1416
MARS_v2


title: AB13525

description:
Library name: Sample1415
MARS_v2


title: AB13524

description:
Library name: Sample1414
MARS_v2