title: Tsc2-/-/NRas_4

description: Library name: Samples 12

value: Tsc2 KO plus overexpression of acvtivated NRas

value: 23.3 weeks post-injection


title: Tsc2-/-/NRas_3

status: Public on Sep 01 2025

type: SRA

city: San Francisco

first: Guofei

last: Cui

state: CALIFORNIA

country: USA

institute: UCSF

description: Library name: Samples 11

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts (Novogene). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (version 1.24.0).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: liver tumor tissue

extract_protocol:
Total RNA was extracted from frozen mouse liver specimens (Akt/NRas 5-6 weeks post-injection (w.p.i.), sgGSK3a&b/NRas 9.4w.p.i., Tsc2-/-/sgGSK3α&β/NRas 6-9w.p.i., Tsc2-/-/NRas 20-24w.p.i., and normal liver -14.9 weeks) using the Quick-RNA™ Miniprep Kit (Cat# R1055, Zymo Research, Irvine, CA, USA). >6 µg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

tag: tissue

value: liver tumor tissue

tag: genotype

tag: time

tag: Sex

value: M

tag: tumor stage

value: late stage


title: NTVE lysate-1_ISBM-014

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description:
Library name: L1
Stable NTVE line

data_processing:
Deduplication via czid-dedup (paired-end mode)
featurecounts_harmonized.csv: Paired-end reads were aligned to the combined human-murine index via STAR  (star --readFilesCommand zcat --genomeDir {COMBINED_INDEX_STAR} --readFilesIn {R1} {R2} --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {OUTPUT_NAME} --quantMode GeneCounts TranscriptomeSAM))
featurecounts_harmonized.csv: Gene level feature counting via featurecounts (featureCounts -a {COMBINED_INDEX_GTF} -o {OUTPUT_FILE}  -g gene_id -t exon -s 2 -p)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: featurecounts_harmonized.csv: comma seperated plaintext file containing the raw counts mapping to features and metadata for all samples
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

tag: cell line

tag: cell type

value: immortalised cell line

value: NTVE Gag:PABP(ZF); Pgk-TetON3g (ISBM-014)

tag: rna origin

value: Cell Lysate

tag: spike-in

tag: treatment

value: doxycycline 500ng/ul


title: Tsc2-/-/NRas_2

description: Library name: Samples 10


title: Supernatant of transient transfection of Gag:PABP

description:
Library name: DJJT01_s2-gag
Transient expression of NTVE

value: WT

value: Supernatant

value: transfection with NTVE construct


title: Tsc2-/-/NRas_1

description: Library name: Samples 9

value: 20.3 weeks post-injection


title: NTVE lysate-2_ISBM-014

description:
Library name: L2
Stable NTVE line


title: Neutrophil_R5

city: Guangzhou

first: Penghan

last: Huang

address: 107 Yan Jinag West Road

country: China

institute: Sun Yat-Sen University

data_processing:
Data analysis was performed by R (v.4.2.1) software and limma (v.3.54.2) software packages.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes rwa counts for each sample

source_name: Neutrophil

extract_protocol:
Total RNA was extracted using Trizol rent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).

tag: group

value: Resistant

value: Neutrophil


title: Akt/NRas_4

description: Library name: Samples 8

value: Overexpression of acvtivated AKT and NRas

value: 5.1 weeks post-injection


title: Akt/NRas_2

description: Library name: Samples 6

value: 5.3 weeks post-injection


title: Neutrophil_R3


title: Akt/NRas_3

description: Library name: Samples 7


title: Akt/NRas_1

description: Library name: Samples 5


title: Neutrophil_R2


title: Neutrophil_R4


title: Normal liver_4

description: Library name: Samples 4

source_name: normal liver tissue

value: normal liver tissue

value: 14.9 weeks post-injection


title: Neutrophil_R1


title: Neutrophil_S5

value: Sensitive


title: Normal liver_2

description: Library name: Samples 2

value: M


title: Normal liver_3

description: Library name: Samples 3


title: Neutrophil_S3


title: Normal liver_1

description: Library name: Samples 1


title: E2-TR rep1

city: Lexington

first: Jessica

middle: L.

last: Funnell

state: Kentucky

address: 392 Chase Pl

department: Physiology

institute: University of Kentucky

description:
Library name: S10
10x Genomics

library_source: transcriptomic single cell

data_processing:
Samples were aligned with STAR aligner to the mm10 mouse reference genome using the Cell Ranger 6.1.1 pipeline. The expression matrix was loaded into R for further analysis and visualization using Seurat (v.5.0.3).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole Brain

extract_protocol:
Mice were anesthetized via 5.0% isoflurane before exsanguination and transcardial perfusion with ice-cold Dulbecco’s phosphate buffered saline (DPBS; Gibco cat. #14040133). Following perfusion, brains were quickly removed and whole right hemispheres sans brainstem and cerebellum were quickly minced using forceps on top of an ice-chilled petri dish. Minced tissue from the hemispheres (n=3 APOE4s2G, n=3 APOE4s2A, n=1 APOE4s2, n=2 E2-TR, and n=1 E4-TR) were immediately transferred into gentleMACS C-tube (Miltenyi cat. #130–093-237) containing Adult Brain Dissociation Kit (ADBK) enzymatic digest reagents (Miltenyi cat. #130–107-677) prepared according to manufacturer’s protocol. Tissues were dissociated using the “37C_ABDK” protocol on the gentleMACS Octo Dissociator instrument (Miltenyi cat. #130–095-937) with heaters attached. After tissue digestion, cell suspensions were filtered through 70 μm mesh cell filters to remove debris following the manufacturer’s suggested ABDK protocol. The resultant suspension was sequentially filtered (x2) using fresh 30 μm mesh filters.
Cell viability was checked using Acridine Orange/Propidium Iodide (AO/PI) viability kit (Logos Biosystems cat. #LGBD10012). Following viability and counting, cells were diluted to achieve a concentration of ~ 1000 cells/100uL. The diluted cell suspensions were loaded onto the 10x Chromium. Each sample was loaded into a separate channel on the Single Cell 3′ Chip and libraries were prepared using the Chromium v3 Single Cell 3′ Library and Gel Bead Kit (10x Genomics). Final library quantification and quality check was performed using BioAnalyzer (Agilent).

value: Whole Brain

value: Female

tag: age

value: Tamoxifen


title: E4-TR

description:
Library name: S12
10x Genomics


title: E2-TR rep2

description:
Library name: S11
10x Genomics


title: Neutrophil_S1


title: 4s2 no Cre

description:
Library name: S9
10x Genomics


title: Neutrophil_S2


title: SLE Patient – Mon 21

city: Heraklion

first: George

last: Bertsias

address: Andrea Kalokerinou 13

department: Medical School

country: Greece

institute: University of Crete

data_processing:
Raw fastQ files were pre-processed by assessing quality control (QC) with FASTQC. Low-quality 3’ read ends (minimum two-colour chemistry score of 20), N tails, and adapter remains were trimmed/clipped using cutadapt, allowing reads of at least 25 nucleotide length. Filtered reads were then mapped against the UCSC hg19 human reference transcriptome using STAR aligner by setting the “-- outFilterMultimapNmax” parameter to 5. Μapped reads were filtered in order to discard chimeric alignments, alignments with more than 2 mismatches, and keep only uniquely aligned reads (MAPQ = 255).
Counting on Ensembl genes and statistical analysis (differential expression analysis) was performed with metaseqR using DESeq2 for normalization and differential testing, and applying default settings for each assay (exon count summarization for RNA-seq and 3’ UTR summarization for Quant-seq). For paired-samples comparisons, ‘donor id’ was included in the DESeq2 model.
Assembly: hg19
Supplementary files format and content: count_matrix_SLEpatients_wholeblood20.txt: contains raw counts for each individual.
Supplementary files format and content: normalized_counts_silencing.txt: contains normalized gene expression counts for each donor across different conditions, using deseq2 normalization.
Supplementary files format and content: normalized_counts_SLEvsHealthy_monocytes.txt: includes normalized counts using deseq2 package.
Supplementary files format and content: metaseqr_all_out_untr_female_vs_untr_male.txt: includes normalized read counts for all analyzed genes for female and male SLE patients, extracting from metaseq.

source_name: peripheral blood

growth_protocol: RPMI-1640, GlutaMAX Supplement (Gibco) including 10% heat-inactivated FBS (Gibco), 100 IU/mL penicillin and 100 μg/mL streptomycin (Gibco)

extract_protocol:
RNA was isolated using the NucleoSpin RNA extraction kit (Macherey-Nagel). RNA was quantitated with the Nanodrop photometric method and quality control was performed with the Agilent Bioanalyzer RNA nano kit.
RNA libraries for RNA-seq were prepared with Illumina TruSeq RNA library prep kit following manufacturer 's protocol.

treatment_protocol: Cultured monocytes were stimulated with 10 ng/ml human macrophage colony-stimulating factor (M-CSF; Peprotech), 10ng/ml recombinant human TNF (Peprotech), 100 IU/ml IFN-α (PBL Science) overnight at 37oC/5% CO2, followed by 10ng/ml LPS (Sigma) challenge for 1-4 hours

value: peripheral blood

value: monocytes

value: female

value: untreated

tag: disease state

value: SLE


title: SLE Patient – Mon 22


title: 4s2 Astrocyte Cre, rep1

description:
Library name: S4
10x Genomics


title: 4s2 Astrocyte Cre, rep2

description:
Library name: S5
10x Genomics


title: SLE Patient – Mon 24


title: Lysate of transient transfection of Gag:PABP

description:
Library name: DJJT01_s1-cellular
Transient expression of NTVE

value: immortalised cell line

value: WT

value: Cell Lysate

value: transfection with NTVE construct


title: 4s2 Global Cre, rep3

description:
Library name: S3
10x Genomics


title: SLE Patient – Mon 19


title: 4s2 Global Cre, rep2

description:
Library name: S2
10x Genomics


title: Healthy – Mon 3

value: Healthy


title: 4s2 Global Cre, rep1

description:
Library name: S1
10x Genomics


title: Healthy – Mon 4


title: PS-ZT20-4

city: Shanghai

first: Baoyin

last: Ren

state: -- None selected --

address: No. 500 Dongchuan Road, Minhang District, Shanghai, China

institute: East China Normal University

description:
Library name: Sample  48
Phase shift

data_processing:
Total RNA extracted from the liver tissue was used as input material for RNA sample preparation of the transcriptome sequencing libraries.
The RNA sequencing, read mapping, and gene/transcript quantification were performed by Novogene (China, Beijing).
To select cDNA fragments of 370-420 bp in length, AMPure XP system (Beckman Coulter, Beverly, USA) was used to purify library fragments.
Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) primers were then used for PCR.
At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: liver

growth_protocol: Liver samples were rapidly frozen from mice, ground into a fine powder in liquid nitrogen, and stored at -80°C for further analysis.

extract_protocol:
Total RNA was extracted by TRIzol reagent. The RNA quantification and identification were assessed using the RNA Nano 6000 Assay Kit on the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) to evaluate RNA integrity.
Total RNA extracted from the liver tissue was used as input material for RNA sample preparation of the transcriptome sequencing libraries. The RNA sequencing, read mapping, and gene/transcript quantification were performed by Novogene (China, Beijing).

treatment_protocol: Liver and plasma samples were collected every 4 hours over a 24-hour period, starting from the midpoint of the 6th day post-phase shift and ending at the midpoint of the 7th day.

value: liver

value: Phase shift


title: PS-ZT20-3

description:
Library name: Sample  47
Phase shift


title: Neutrophil_S4

value: Sensitive

value: Neutrophil


title: Healthy – Mon 1


title: PS-ZT20-2

description:
Library name: Sample  46
Phase shift


title: Healthy – Mon 2


title: 4s2 Astrocyte Cre, rep3

description:
Library name: S6
10x Genomics

value: Whole Brain


title: PS-ZT20-1

description:
Library name: Sample  45
Phase shift


title: SLE Patient – Mon 23


title: siControl untreated Donor3 (D3CU)

value: male

value: Si-Control


title: PS-ZT16-2

description:
Library name: Sample  42
Phase shift


title: siSMC1A treated with I-T-L Donor3 (D3SITL)

value: peripheral blood

value: Si-SMC1A & I-T-L


title: PS-ZT16-4

description:
Library name: Sample  44
Phase shift


title: siSMC1A untreated Donor3 (D3SU)

value: monocytes


title: PS-ZT16-3

description:
Library name: Sample  43
Phase shift


title: SLE Patient – Mon 20

value: female

value: untreated


title: siControl treated with I-T-L Donor3 (D3CITL)

value: Si-Control & I-T-L


title: siSMC1A untreated Donor2 (D2SU)


title: PS-ZT12-4

description:
Library name: Sample  40
Phase shift

value: WT


title: PS-ZT16-1

description:
Library name: Sample  41
Phase shift


title: PS-ZT12-3

description:
Library name: Sample  39
Phase shift


title: siControl untreated Donor2 (D2CU)


title: siSMC1A treated with I-T-L Donor2 (D2SITL)


title: Healthy – Mon 5


title: PS-ZT12-2

description:
Library name: Sample  38
Phase shift


title: PS-ZT12-1

description:
Library name: Sample  37
Phase shift


title: siSMC1A untreated Donor1 (D1SU)


title: PS-ZT8-3

description:
Library name: Sample  35
Phase shift


title: siControl treated with I-T-L Donor2 (D2CITL)


title: siSMC1A treated with I-T-L Donor1 (D1SITL)


title: PS-ZT8-4

description:
Library name: Sample  36
Phase shift


title: siControl untreated Donor1 (D1CU)


title: PS-ZT8-2

description:
Library name: Sample  34
Phase shift


title: siControl treated with I-T-L Donor1 (D1CITL)


title: PS-ZT8-1

description:
Library name: Sample  33
Phase shift


title: Input_H3K27AC_untr

library_source: genomic

data_processing:
Raw fastQ files were pre-processed by assessing quality control (QC) with FASTQC. Low-quality 3’ read ends (minimum two-colour chemistry score of 20), N tails, and adapter remains were trimmed/clipped using cutadapt, allowing reads of at least 25 nucleotide length. Filtered reads were then mapped against the UCSC hg19 human reference genome using bwa-mem aligner with default parameters. Mapped reads were further filtered using samtools, in order to discard chimeric alignments, alignments with more than 2 mismatches, and alignments with MAPQ quality lower than 10. A deduplicated version of alignments was also created using samtools markdup command, in order to eliminate the effect of PCR over-amplification during visualization. Alignment QC was further accessed using deeptools.
For each SMC1A ChIP-seq IP-INPUT pair, peaks were called by macs2 with the following custom parameters enabled: “--nomodel”, “--shift 100”, and “--extsize 200”. H3K27ac ChIP-seq peak calling was performed by epic2, keeping duplicates (-kd parameter), using a bin of 400 base pairs (bps), allowing 1 gap, and a fragment size of 150 bps. Peaks spanning ENCODE blacklisted regions or including less than 10 mapped reads were excluded.
Assembly: hg19
Supplementary files format and content: Peak files for each sample of each experiment.

molecule: genomic DNA

growth_protocol: RPMI-1640, GlutaMAX Supplement, 10% heat-inactivated FBS, 100 IU/mL penicillin and 100 μg/mL streptomycin (Gibco). Cells were cultured at 37 C, at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde  for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
ChIP-seq  libraries were prepared at the Greek Genome Center of the Biomedical Research Foundation Academy of Athens (BRFAA), according to a previously published protocol (Ford, Ethan, et al. BMC Research Notes 7 (2014): 1-5).

treatment_protocol: 10 ng/ml M-CSF, 10 ng/ml recombinant human TNF, 100 IU/ml IFN-α overnight at 37 C/ 5% CO2. Next day, 10ng/ml LPS 1h challenge .

tag: chip antibody


title: PS-ZT4-4

description:
Library name: Sample  32
Phase shift


title: PS-ZT4-3

description:
Library name: Sample  31
Phase shift


title: H3K27AC_untr_3

value: H3K27ac (Abcam, #ab4729)


title: PS-ZT0-4

description:
Library name: Sample  28
Phase shift


title: H3K27AC_untr_2


title: PS-ZT4-2

description:
Library name: Sample  30
Phase shift


title: PS-ZT4-1

description:
Library name: Sample  29
Phase shift


title: PS-ZT0-1

description:
Library name: Sample  25
Phase shift


title: PS-ZT0-2

description:
Library name: Sample  26
Phase shift


title: H3K27AC_ITL_2

value: IFNa-TNF-LPS


title: H3K27AC_ITL_3


title: PS-ZT0-3

description:
Library name: Sample  27
Phase shift


title: Input_H3K27AC_ITL_1


title: H3K27AC_untr_1


title: Input_SMC1A_ITL_3


title: Control-ZT20-2

description:
Library name: Sample  22
Control


title: Control-ZT20-4

description:
Library name: Sample  24
Control


title: Input_SMC1A_ITL_2


title: Control-ZT16-4

description:
Library name: Sample  20
Control


title: SMC1A_ITL_3

value: SMC1A (Bethyl Laboratories, #A300-055A)


title: Control-ZT20-3

description:
Library name: Sample  23
Control

value: liver


title: SMC1A_ITL_2


title: Control-ZT16-3

description:
Library name: Sample  19
Control

value: Phase shift


title: Control-ZT16-2

description:
Library name: Sample  18
Control


title: Input_SMC1A_ITL_1


title: SMC1A_ITL_1


title: H3K27AC_ITL_4


title: Input_H3K27AC_ITL_2


title: Control-ZT16-1

description:
Library name: Sample  17
Control


title: Input_SMC1A_untr_2


title: H3K27AC_ITL_1


title: Input_SMC1A_untr_1


title: Control-ZT12-2

description:
Library name: Sample  14
Control


title: Control-ZT12-3

description:
Library name: Sample  15
Control


title: SMC1A_untr_1


title: Control-ZT12-4

description:
Library name: Sample  16
Control


title: HaCaT, Dacomitinib 3

city: 杭州市

first: zhou

middle: wan

last: ying

state: 浙江省

address: Banshan street

institute: 浙江省肿瘤医院

description: treated with Dacomitinib for 48h

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp（0.12.2）
Trimmed sequence reads were mapped toGRCh38 using hisat2（2.0.5）
Read count extraction and normalization were performed using featureCounts（1.5.0-p3）
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HaCaT

growth_protocol: HaCaT cells were cultured in DMEM (Gibco, California, USA) supplemented with 10% FBS (Gibco, California, USA), 100 U/mL penicillin, and 10 μg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Dacomitinib treated HaCaT for 48 hours

value: HaCaT

value: Human Keratinocytes Cells

value: Dacomitinib


title: Control-ZT20-1

description:
Library name: Sample  21
Control


title: SMC1A_untr_2

value: male


title: Control-ZT12-1

description:
Library name: Sample  13
Control


title: HaCaT, Dacomitinib 2

description: treated with Dacomitinib for 48h


title: HaCaT, Control 3

description: Control

value: Control


title: Control-ZT8-1

description:
Library name: Sample  9
Control


title: Control-ZT4-4

description:
Library name: Sample  8
Control


title: Control-ZT8-3

description:
Library name: Sample  11
Control


title: Control-ZT4-3

description:
Library name: Sample  7
Control


title: HaCaT, Control 2

description: Control


title: Control-ZT8-4

description:
Library name: Sample  12
Control


title: Control-ZT8-2

description:
Library name: Sample  10
Control


title: CD4+ DR+, Healthy control, 7

city: Erlangen

first: Giulia

last: Benintende

address: Ulmenweg 18

institute: Universitaetsklinikum Erlangen Medizinische Klinik 5

data_processing:
The multiple pairwise differential expression workflow was generated using Searchlight 2 (v2.0.3).
Assembly: homo sapiens
Supplementary files format and content: tsv file includes read counts for each sample and gene

source_name: PBMC

extract_protocol:
RNA was extracted with RNeasy kit (Qiagen, USA), according to manufacturer´s protocol.
The prepared libraries were then quality-checked, pooled and sequenced on an Illumina platform (Illumina NovaSeq6000, PE150 mode).

value: PBMC

tag: condition

value: Healthy control, 7

value: CD4+ DR+


title: Control-ZT0-4

description:
Library name: Sample  4
Control


title: HaCaT, Dacomitinib 1

description: treated with Dacomitinib for 48h


title: Control-ZT4-2

description:
Library name: Sample  6
Control


title: CD4+ DR+, Healthy control, 8

value: Healthy control, 8


title: CD4+ DR+, Healthy control, 4

value: Healthy control, 4


title: Control-ZT4-1

description:
Library name: Sample  5
Control


title: CD4+ DR+, Healthy control, 5

value: Healthy control, 5


title: Control-ZT0-2

description:
Library name: Sample  2
Control

value: WT


title: CD4+ DR+, Healthy control, 6

value: Healthy control, 6


title: OH_3

city: Wuhan

first: Jinzhou

last: Xu

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital

description: Library name: Sample6

data_processing:
The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on Illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE150 read length.
Fastp (v0.23. 1) was used to trim primer sequence and low quality bases of raw reads and collect the basic statistics.
Assembly: mm10
Supplementary files format and content: matrix files for each sample

source_name: subcutaneous transplanted tumor

extract_protocol:
After harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Multitissue dissociation kit 2(Miltenyi Catalog No.XXX) from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI 1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
Single- cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet(SeekOne® DD) Single Cell 3’ library preparation kit (SeekGene Catalog No.). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® DD Chip S3 (Chip S3). Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in Chip S3. After emulsion droplet generation reverse transcription were performed at 42℃ for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, Atailed and ligated to sequencing adaptor. Finally the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index.

treatment_protocol: 5% PBS/OH2 intervention for 3 times

value: subcutaneous transplanted tumor

value: Protate cancer


title: HaCaT, Control 1

description: Control


title: Control-ZT0-1

description:
Library name: Sample  1
Control

value: liver


title: CD4+ DR+, Healthy control, 2

value: Healthy control, 2


title: Control-ZT0-3

description:
Library name: Sample  3
Control

value: Phase shift


title: OH_1

description: Library name: Sample4


title: CD4+ DR+, Case, 15

value: Case, 15


title: OH_2

description: Library name: Sample5


title: CD4+ DR+, Case, 14

value: Case, 14


title: NC_3

description: Library name: Sample3


title: CD4+ DR+, Healthy control, 1

value: Healthy control, 1


title: CD4+ DR+, Case, 12

value: Case, 12


title: NC_2

description: Library name: Sample2


title: NC_1

description: Library name: Sample1


title: CD4+ DR+, Case, 10

value: PBMC

value: Case, 10


title: Whole testis, KO RAD21L, scRNAseq

city: Cerdanyola del Vallès

first: Laia

last: Marín-Gual

address: Campus UAB

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: KO_scRNAseq

data_processing:
Cell Ranger (version 6.1.2) was used to map the single-cell RNAseq reads against the mouse annotation (version GRCm39) using default settings. Mapped data was subsequently analysed with the Seurat package (version 4.3).
Assembly: GRCm39
Supplementary files format and content: features.tsv, barcodes.tsv, matrix.mtx

source_name: Testis

extract_protocol:
Testicular disaggregation from 55 days post-partum Rad21l+/+ and Rad21l-/- mice was conducted as previously described (1). An aliquot of the single-cell solution was loaded into a ChromiumTM Single Cell Chip (10x Genomics®), aiming to recover between 5,000 and 6,000 cells.
Libraries were prepared following manufacturer’s instructions and sequenced on Illumina NovaSeq 6000 (50bp pair ends).

value: Testis

value: RAD21L KO

value: Male


title: CD4+ DR+, Case, 9

value: Case, 9

value: CD4+ DR+


title: Whole testis, WT RAD21L, scRNAseq

description: Library name: WT_scRNAseq

value: WT


title: LZ, RAD21L KO, HiC, rep3

description:
Library name: LZ_KO_HiC_rep3
lz_ko_raw.tsv

data_processing:
BBDuk (version 09/2019) was used for quality check and trimming. Basically, adapters and low-quality reads (i.e. reads with a minimum length of 35 bp and a minimum Phred quality score of 20) were removed. High-quality reads were then mapped against the mouse genome (version mm10) using the GEM (version 3.6.1) mapper from TADbit (version 1.0.1).
Assembly: mm10
Supplementary files format and content: GInteraction tables of Hi-C data at a 50 Kbp resolution, which include interaction values between all genomic bins genome-wide.

source_name: Leptotene/Zygotene

extract_protocol:
Hi-C libraries were generated following standard procedures (1). Briefly, crosslinked populations were incubated in lysis buffer for 30 min in ice and then centrifuged at 2,000 xg for 5 min. Cells were subsequently washed twice with 1xNEBuffer 2 and resuspended in 0.5% SDS in 1xNEBuffer 2. After incubating cells for 10 min at 65ºC, 10% Triton X-100 in 1xNEBuffer 2 was added and incubated for 30 min at 37ºC. Cells were then centrifuged at 2,000 xg for 5 min and washed twice with 1xNEBuffer 2. Following, chromatin was digested by incubating cells overnight with 400U of MboI (NEB) at 37ºC. An aliquot for the ND (Non-Digested) control was taken before the restriction enzyme addition, and another aliquot for the NL (Non-Ligated) control was taken from the digested sample the following day. A digestion control was performed by incubating the ND and NL controls with proteinase K (1 mg/ml) for 1 h at 65ºC, followed by Phenol:Chloroform purification. The digestion quality was checked by running DNA from both controls on a 0.8% agarose gel. After digestion, cells were centrifuged at 2,000 xg for 5 min and washed twice with 1xNEBuffer 2. Chromatin ends were then repaired and biotinylated by resuspending cells with reparation mix (1xNEBuffer 2, 0.05mM dCTP, 0.05mM dTTP, 0.5mM dGTP, 0.05mM biotin-dATP, 50U Klenow) and incubating them for 45 min at 37ºC. Following, cells were incubated for 10 min at 65ºC and centrifuged at 2,000 xg for 5 min. An aliquot for the 3C control was taken before adding the reparation mix. Both the 3C control and the sample were resuspended with ligation buffer (1xNEB T4 ligase buffer, 0.8% Triton X-100, 0.1 mg/ml BSA, 10,000U T4 DNA ligase) and incubated overnight at 16ºC. The following day, cells were centrifuged at 2,000 xg for 5 min and resuspended in 1xNEBuffer 2 with 0.25 mg/ml RNAse A. After incubating cells for 15 min at 37ºC, 0.5 mg/ml proteinase K was added. Cells were then incubated at 65ºC overnight to reverse the crosslink. DNA was subsequently purified with Phenol:Chloroform. DNA quality from the 3C control and the Hi-C sample was assessed by running a 0.8% agarose gel and DNA concentration was measured by a Qubit.
For library preparation, samples were first sonicated 30 s ON, 90 s OFF, 4 cycles, low mode (3 times). Subsequently, biotinylated fragments were pulled down using Dynabeads MyOne Streptavidin T1 beads. Briefly, beads were washed with 2xbinding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl) and 0.05% Tween 20 in 1xbinding buffer. Beads were then resuspended with 1xbinding buffer, mixed with the sonicated samples and incubated for 30 min at RT under rotation. After two washes with 1xbinding buffer, samples were resuspended with the end repair mix (1xNEB T4 DNA ligase buffer with 10mM ATP, 0.5mM dNTP mix, 50U NEB T4 PNK, 12U T4 DNA polymerase I, 5U Klenow) and incubated for 30 min at RT to repair ends and remove biotin from unligated ends. Beads were then washed twice with 1xbinding buffer, resuspended with the dATP attachment mix (1xNEBuffer 2, 0.5mM dATP, 2.5U NEB Klenow exo minus) and incubated at 37ºC for 30 min. Subsequently, beads were washed twice with 1xbinding buffer, resuspended in 1xNEB Quick ligation reaction buffer together with the NEBNext adapter and Illumina adapters and incubated 15 min at RT to ligate adapters to chromatin ends. Following, beads were washed twice with 1xbinding buffer, resuspended with Tris buffer and mixed with 1 µM primer P5, 1 µM primer P7 and cocktail master mix (NEB). A final amplification was performed following the PCR program: 98ºC 30 s; 98ºC 10 s, 60ºC 30 s, 72ºC 30 s x 8 cycles; 72ºC 5 min. The beads were then captured on a magnet and the supernatant with the amplification products were transferred to a new tube. A 1:1 amount of AmpureBeads was added to the samples and incubated for 10 min at RT. The beads were then washed twice with 70% ethanol, eluded with Tris buffer and incubated for 5 min at RT. AmpureBeads were finally separated on a magnet and the solution was transferred to a new tube. The quality and concentration of the libraries was checked by Qubit and the Agilent Bioanalyzer System. Libraries were submitted for Illumina sequencing (paired-end 150bp each side on NovaSeq 6000).

value: Leptotene/Zygotene


title: CD4+ DR+, Case, 8

value: Case, 8


title: LZ, RAD21L KO, HiC, rep2

description:
Library name: LZ_KO_HiC_rep2
lz_ko_raw.tsv


title: LZ, RAD21L KO, HiC, rep1

description:
Library name: LZ_KO_HiC_rep1
lz_ko_raw.tsv


title: CD4+ DR+, Case, 7

value: Case, 7


title: CD4+ DR+, Healthy control, 3

value: Healthy control, 3


title: CD4+ DR+, Case, 5

value: Case, 5


title: Spermatogonia, RAD21L KO, HiC, rep3

description:
Library name: Spermatogonia_KO_HiC_rep3
spg_ko_raw.tsv

source_name: Spermatogonia

value: Spermatogonia


title: CD4+ DR+, Case, 6

value: Case, 6


title: CD4+ DR+, Case, 13

value: Case, 13


title: Spermatogonia, RAD21L KO, HiC, rep1

description:
Library name: Spermatogonia_KO_HiC_rep1
spg_ko_raw.tsv


title: CD4+ DR+, Case, 2

value: Case, 2


title: Spermatogonia, RAD21L KO, HiC, rep2

description:
Library name: Spermatogonia_KO_HiC_rep2
spg_ko_raw.tsv


title: CD4+ DR+, Case, 1

value: PBMC

value: Case, 1


title: TT-seq_BRD2_degron_1h_rep1

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

description: Library name: Sample 3

data_processing:
Raw reads with spike-in were firstly trimmed by Cutadapt software and then mapped to mm10 and dm6 genome using Bowtie2 software
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software normalized by the reads mapped to dm6 genome.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: nuclear RNA

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i/mLIF medium, which composed of DMEM containing 1 mM L-glutamine, 1× nucleosides (Sigma, ES-008), 1× nonessential amino acids (Milipore, TMS-001-C), 1× sodium pyruvate (Gibco, 11360070), 1× penicillin/ streptomycin (Gibco, 15140-122), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107), and also supplemented with 15% fetal bovine serum (FBS) (VivaCell, 04-001-1A), incubated at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
4SU is a derivative of uracil that can be recognized by the RNA polymerase in cells and incorporated into the RNA chain being synthesized. The biotin is chemically labeled on the RNA molecule containing 4SU. The newly synthesized and biotin-labeled RNA is then separated from the total RNA using magnetic beads coated with streptavidin.Extracted twice using Trizol reagent following the instruction.
The native RNAs were isolated and examined. After checked the quantity and quality and poly(A) RNA depletion, the TT-seq RNA library were generated using the no coding RNA library method with random primers and sequencing analyzed using Nova PE150 platform.

treatment_protocol: For target protein degradation, the degron cells were firstly induced with 1 μg/ml Dox in the 2i medium to express the OsTir1 for 12 h, then 500 μM auxin were added to induced the degradation for 1h, then cells were harvested for next assays.

value: mouse embryonic stem cells

value: BRD2 degron 1h


title: CD4+ DR+, Active control, 7

value: Active control, 7


title: CD4+ DR+, Case, 3

value: Case, 3


title: Fibroblasts, RAD21L KO, HiC, rep1

description:
Library name: Fibroblasts_KO_HiC_rep1
fib_ko_raw.tsv

source_name: Fibroblasts

value: Fibroblasts

value: RAD21L KO

value: Male


title: CD4+ DR+, Case, 11

value: Case, 11

value: CD4+ DR+

value: WT


title: CD4+ DR+, Active control, 8

value: Active control, 8


title: TT-seq_BRD2_degron_1h_rep2

description: Library name: Sample 4


title: Cut&Tag_SRCAP_BRD2_degron_1h_rep2

description: Library name: Sample 46

data_processing:
Raw reads were firstly trimmed by Cutadapt software and then mapped to mm10 and genome by Bowtie2 software. Reads with spike-in were mapped to both mm10 and hg19 genome.
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software using RPGC as the normalization method. Bam files with spike-in were normalized by the reads mapped to hg19 genome.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Cut&Tag

extract_protocol:
DNA was purified through the Tris saturated equilibrium phenol (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0) for ChIP-Seq, and gel extraction using DNA extract kit for Cut&Tag
ChIP-seq, briefly, the pretreated cells were harvested by trypsinization following 1% formaldehyde (final concentration, wt/vol) crosslinked and stored at -80 °C for downstream experiments. For chromatin immunoprecipitation, 20 million crosslinked cells (5% HEK293T cell were added as spikein) were lysed gently for chromatin isolation with ice-cold NP-40 lysis buffer and glycerol / urea buffer, finally centrifugated at 12,000 rpm for 1 min at 4 °C, the pellet of chromatin were resuspended in 1 ml sonication buffer, 1000 U MNase (NEB, M0247) and 5 mM CaCl2 were added and incubated for 15 min at 37 °C with 750 rpm shaking. After quenched by 20 μl 0.5 M EDTA and 40 μl 0.5 M EGTA in ice bath, the chromatin was sonicated using Qsonica Q800R3 DNA Shearing Sonicator for 15 min with 60% AMPL. Soluble chromatin was isolated by centrifugation at 1,2000 rpm for 10 min at 4 °C, 20 μl supernatant were sampled as input, the rest supernatant was transferred into 2 new DNase free tube for immunoprecipitation. 1 μl GFP abs (ABcam, ab290), 1 μg RPB1 NTD abs (CST, 14958S), and equal isotype IgG control for each ChIP reaction, respectively. After incubation overnight at 4 °C with low-speed rotation, 30 μl Protein G magnetic beads were added into the mixture to capture for 4 h, then washed beads once with sonication buffer, twice with high-salt wash buffer, twice with LiCl wash buffer and finally three times with TE buffer. For ChIP-seq, beads were eluted and then decrosslinked with 4 μl proteinase K (Sigma, 20 mg/ml) at 65 °C overnight, DNA was purified through the Tris saturated equilibrium phenol (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0), and the ChIP library was prepared following the instruction of VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608-01); Cut&Tag was performed according to the manufacture of Hyperactive Universal Cut&Tag Assay Kit for Illumina (Vazyme, TD903-01), with 5% spikein 293T cells


title: CD4+ DR+, Active control, 6

value: Active control, 6


title: CD4+ DR+, Active control, 5

value: Active control, 5


title: CD4+ DR+, Active control, 4

value: Active control, 4


title: Cut&Tag_SRCAP_BRD2_degron_0h_rep2

description: Library name: Sample 44

value: BRD2 degron 0h


title: CD4+ DR+, Active control, 3

value: PBMC

value: Active control, 3


title: Cut&Tag_SRCAP_BRD2_degron_1h_rep1

description: Library name: Sample 45

value: mouse embryonic stem cells


title: CD4+ DR+, Active control, 2

value: Active control, 2


title: CD4+ DR+, Case, 4

value: Case, 4


title: Cut&Tag_P400_BRD2_degron_1h_rep2

description: Library name: Sample 42

value: BRD2 degron 1h


title: Cut&Tag_SRCAP_BRD2_degron_0h_rep1

description: Library name: Sample 43


title: MDSCs, Healthy control, 8

value: Healthy control, 8

value: CD14+ HLA-DR low


title: Cut&Tag_P400_BRD2_degron_0h_rep2

description: Library name: Sample 40


title: Cut&Tag_P400_BRD2_degron_1h_rep1

description: Library name: Sample 41


title: MDSCs, Healthy control, 7

value: Healthy control, 7


title: Cut&Tag_P400_BRD2_degron_0h_rep1

description: Library name: Sample 39


title: TT-seq_BRD2_degron_0h_rep2

description: Library name: Sample 2


title: MDSCs, Healthy control, 6

value: Healthy control, 6


title: Cut&Tag_INO80_BRD2_degron_1h_rep2

description: Library name: Sample 38


title: MDSCs, Healthy control, 5

value: Healthy control, 5


title: MDSCs, Healthy control, 4

value: Healthy control, 4

value: WT


title: Cut&Tag_INO80_BRD2_degron_1h_rep1

description: Library name: Sample 37


title: TT-seq_BRD2_degron_0h_rep1

description: Library name: Sample 1


title: Cut&Tag_INO80_BRD2_degron_0h_rep2

description: Library name: Sample 36


title: MDSCs, Healthy control, 2

value: Healthy control, 2


title: Cut&Tag_H2AZ_SRCAP_degron_24h_rep2

description: Library name: Sample 34

value: SRCAP degron 1h


title: MDSCs, Healthy control, 1

value: Healthy control, 1


title: Cut&Tag_H2AZ_P400_degron_24h_rep2

description: Library name: Sample 32

value: P400 degron 24h


title: MDSCs, Case, 15

value: PBMC

value: Case, 15


title: Cut&Tag_H2AZ_SRCAP_degron_24h_rep1

description: Library name: Sample 33

value: mouse embryonic stem cells


title: Cut&Tag_H2AZ_P400_degron_24h_rep1

description: Library name: Sample 31


title: Cut&Tag_H2AZ_P400_degron_24h_0h_rep2

description: Library name: Sample 30

value: P400 degron 0h


title: MDSCs, Case, 13

value: Case, 13


title: CD4+ DR+, Active control, 1

value: Active control, 1

value: CD4+ DR+


title: MDSCs, Case, 12

value: Case, 12

value: CD14+ HLA-DR low


title: MDSCs, Case, 11

value: Case, 11


title: Cut&Tag_H2AZ_P400_degron_24h_0h_rep1

description: Library name: Sample 29


title: Cut&Tag_H2AZ_P400_degron_1h_rep2

description: Library name: Sample 28

value: P400 degron 1h


title: Cut&Tag_H2AZ_P400_degron_1h_rep1

description: Library name: Sample 27


title: MDSCs, Case, 8

value: Case, 8


title: MDSCs, Case, 10

value: Case, 10

value: WT


title: Cut&Tag_H2AZ_P400_degron_0h_rep1

description: Library name: Sample 25


title: MDSCs, Case, 9

value: Case, 9


title: MDSCs, Healthy control, 3

value: Healthy control, 3


title: Cut&Tag_H2AZ_INO80_degron_24h_rep2

description: Library name: Sample 24

value: INO80 degron 24h


title: Cut&Tag_INO80_BRD2_degron_0h_rep1

description: Library name: Sample 35

value: BRD2 degron 0h


title: MDSCs, Case, 7

value: PBMC

value: Case, 7


title: MDSCs, Case, 6

value: Case, 6


title: MDSCs, Case, 5

value: Case, 5


title: Cut&Tag_H2AZ_INO80_degron_24h_0h_rep2

description: Library name: Sample 22

value: mouse embryonic stem cells

value: INO80 degron 0h


title: MDSCs, Case, 4

value: Case, 4


title: Cut&Tag_H2AZ_INO80_degron_24h_rep1

description: Library name: Sample 23


title: MDSCs, Case, 14

value: Case, 14

value: CD14+ HLA-DR low


title: Cut&Tag_H2AZ_INO80_degron_24h_0h_rep1

description: Library name: Sample 21


title: MDSCs, Case, 3

value: Case, 3


title: MDSCs, Case, 2

value: Case, 2


title: MDSCs, Case, 1

value: Case, 1


title: Cut&Tag_H2AZ_BRD2_degron_1h_rep1

description: Library name: Sample 19

value: BRD2 degron 1h


title: Cut&Tag_H2AZ_BRD2_degron_0h_rep2

description: Library name: Sample 18


title: Cut&Tag_H2AZ_BRD2_degron_0h_rep1

description: Library name: Sample 17


title: Cut&Tag_H2AZ_P400_degron_0h_rep2

description: Library name: Sample 26

value: P400 degron 0h


title: MDSCs, Active control, 7

value: Active control, 7

value: WT


title: Cut&Tag_H2AZac_BRD2_degron_0h_rep2

description: Library name: Sample 14

value: BRD2 degron 0h


title: MDSCs, Active control, 5

value: PBMC

value: Active control, 5


title: Cut&Tag_H2AZac_BRD2_degron_1h_rep1

description: Library name: Sample 15


title: MDSCs, Active control, 6

value: Active control, 6


title: Cut&Tag_H2AZac_BRD2_degron_0h_rep1

description: Library name: Sample 13


title: ChIP-seq_RPB1_SRCAP_degron_24h_rep2

description: Library name: Sample 12

data_processing:
Raw reads were firstly trimmed by Cutadapt software and then mapped to mm10 and genome by Bowtie2 software. Reads with spike-in were mapped to both mm10 and hg19 genome.
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software using RPGC as the normalization method. Bam files with spike-in were normalized by the reads mapped to hg19 genome.
Assembly: mm10
Supplementary files format and content: bigwig

value: SRCAP degron 24h


title: MDSCs, Active control, 3

value: Active control, 3


title: Cut&Tag_H2AZac_BRD2_degron_1h_rep2

description: Library name: Sample 16

value: mouse embryonic stem cells


title: MDSCs, Active control, 1

value: Active control, 1


title: ChIP-seq_RPB1_SRCAP_degron_24h_0h_rep2

description: Library name: Sample 10

value: SRCAP degron 0h


title: MDSCs, Active control, 4

value: Active control, 4

value: CD14+ HLA-DR low


title: OH4

first: Yohan

last: Choi

state: KY

address: 800 Rose St

department: OB/GYN

data_processing:
fastq.gz files were generated and demultiplexed with the bcl2fast1 v1.8.4 Conversion Software (Illumina). Adaptor sequences were trimmed from raw RNA sequencing reads.
The quality of raw data was checked on the fastq.gz files using fastq.gzC (version 0.11.4) software.
Trimmomatic (version 0.33) was used to trim any residual adapter content and low-quality bases, and trimmed data were qualified again on the trimmed fastq.gz files using fastq.gzC (version 0.11.4) software.
Each set of RNA sequencing reads was aligned with the NCBI annotation of the human genome reference sequence (GRCh38.p6_genomic.fna) using the alignment software, STAR (version 2.5.0a).
RNA sequencing data were analyzed in R (version 3.3.1) using packages as described below. Briefly, the number of reads per genes was normalized using the trimmed mean of M-values (TMM values) normalization method in the edgeR package (version 3.15.0). Principal components analysis (PCA) was performed for the clustering of the samples to determine whether any samples are outliers and/or if there are overall treatment differences or batch effects. Next, statistical analysis was applied to the 13,539 genes left after filtering and performed to determine differential expression between the treatments using edgeR (version 3.15.0).
Assembly: GRCh38
Supplementary files format and content: .txt

source_name: Ovary

growth_protocol: Cells were obatined from IVF patients at the time of oocyte retrieval and subjected to a Percoll gradient. Isolated granulosa cells were plated and incubated in Opti-MEM + 1x antibiotics/antimycotics and 10% fetal bovine serum for 6 days to regain the responsiveness to hCG.

extract_protocol:
Total RNA was isolated from the cultured cells using a Rneasy mini kit (Qiagen) and eluted in 40 ul of nuclease-free water.
The strand-specific RNA sequencing libraries for 8 individual samples were prepared using a TruSeq Stranded RNA Sample Prep Kit (Illumina). These samples represent four independent experiments for each of the two conditions examined. Libraries were pooled in equimolar concentration, and the pool was quantitated by quantitative PCR and sequenced on three lanes for 101 cycles on a HiSeq6000 (Illumina) using a HiSeq SBS sequencing kit version 2.

treatment_protocol: After the acclimation period, the cells were incubated without serum and treated with hCG. Then, 12h later, rhOSM was added to the culture. The cells were further cultured for 24h (36h in total)

value: Ovary

value: Primary human granulosa-lutein cells

value: hCG+rhOSM

value: RNA


title: ChIP-seq_RPB1_P400_degron_24h_rep2

description: Library name: Sample 8

value: P400 degron 24h


title: MDSCs, Active control, 2

value: Active control, 2

value: WT


title: ChIP-seq_RPB1_SRCAP_degron_24h_0h_rep1

description: Library name: Sample 9


title: Cut&Tag_H2AZ_BRD2_degron_1h_rep2

description: Library name: Sample 20

value: BRD2 degron 1h


title: ChIP-seq_RPB1_P400_degron_24h_rep1

description: Library name: Sample 7


title: OH3


title: H4

value: hCG


title: ChIP-seq_RPB1_SRCAP_degron_24h_rep1

description: Library name: Sample 11


title: ChIP-seq_RPB1_P400_degron_24h_0h_rep2

description: Library name: Sample 6

value: P400 degron 0h


title: MDSCs, Active control, 8

value: PBMC

value: Active control, 8


title: H3


title: ChIP-seq_RPB1_P400_degron_24h_0h_rep1

description: Library name: Sample 5

value: mouse embryonic stem cells


title: H1


title: Jurkat cell stimulated ATAC-seq rep1

first: Mulin Jun

last: Li

state: Guangdong

address: No. 9 Jinsui Road, Guangzhou

institute: Guangzhou Women and Children's Medical Center

data_processing:
The ATAC-seq analysis sequences, including adapters and low-quality reads, were trimmed for all 150-bp paired-end ATAC-seq reads.
The clean reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 (v2.2.1) with the default parameters.
All the samples were processed separately, and duplicate reads were removed.
The ATAC-seq peak regions of each sample were called using MACS2 (v2.1.1) with default parameters.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig

source_name: Jurkat cell

growth_protocol: Jurkat (Clone E6-1) cell line (ATCC, CRL-9855) was cultured in Iscove’s Modified Eagle’s Medium (IMDM; Thermo Fisher Scientific, 31980030) containing 10% FBS and Penicillin and Streptomycin. All cell lines were authenticated by Short Tandem Repeat (STR) and tested no mycoplasma contamination utilizing the Quantiative PCR mycoplasma detection kit (Sigma-Aldrich, MP0040A).

extract_protocol:
Jurkat cells were pretreated with DNase I (Thermo Fisher Scientific, EN0521) to digest DNA from dead cells and to eliminate free-floating DNA. The cells were counted using Crystal Violet (Sigma-Aldrich, C0775), and approximately 50,000 cells from each sample were resuspended in 1 ml of cold ATAC-Resuspension Buffer (RSB), which contained 3 mM MgCl2 (Sigma-Aldrich, M2670), 10 mM Tris-HCl (pH 7.5) (Thermo Fisher Scientific, 15567027), and 10 mM NaCl (Sigma-Aldrich, S7653) in sterile H2O. After centrifugation, the supernatant was discarded, and the cell pellets were resuspended in 50 μl of cold RSB containing 0.1% Tween-20 (Sigma-Aldrich, P1379), 0.1% NP-40 (Thermo Fisher Scientific, FNN0021), and 0.01% Digitonin (Sigma-Aldrich, D141). Following lysis, 1 ml of RSB containing 0.1% Tween-20 was added, and the tube was inverted several times to ensure thorough mixing. After centrifugation, the supernatant was removed, and the nuclei were resuspended in 50 μl of Transposition Mix (Vazyme, TD501). The transposition reaction was then incubated at 37°C for 25 minutes with shaking at 1,500 x g. The reaction products were purified using the QIAquick PCR Purification Kit (QIAGEN, 28106).
The ATAC-seq library was prepared with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) and the TruePrep Index Kit V2 for Illumina (Vazyme, TD202), following the kit’s instructions.

treatment_protocol: Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

value: Jurkat cell

value: Cells derived from human T cells

value: anti-CD3/CD28 stimulated


title: Jurkat cell resting ATAC-seq rep1

value: resting


title: ChIP-seq_RPB1_INO80_degron_24h_rep1

description: Library name: Sample 3

value: INO80 degron 24h


title: ChIP-seq_RPB1_INO80_degron_24h_0h_rep2

description: Library name: Sample 2

value: INO80 degron 0h


title: ChIP-seq_RPB1_INO80_degron_24h_0h_rep1

description: Library name: Sample 1


title: Jurkat cell stimulated RNA-seq replicate 2

data_processing:
RNA-seq reads were filtered by removing reads containing adapter and low quality.
The reference genome (GRCh37/hg19) was index using STAR, and 150-bp paired-end reads were mapped to the human reference genome using STAR with the default parameters.
GENCODE v28 annotation file was used to guide the STAR alignment step, and RSEM was used to quantify the reads count of each gene in the genome assembly GRCh37/hg19.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text files includes gene expression for each Sample

extract_protocol:
For RNA isolation, total RNA was extracted by TRIzol (ThermoFisher, 15596018) according to the manufacturer’s instructions.
The freshly extracted total RNAs with high qualities were sent to the Novogene (Beijing, China) for constructing libraries and sequencing.


title: Jurkat cell stimulated RNA-seq replicate 1


title: SMA mouse spinal cord, E14.5, rep2

city: Trento

first: Gabriella

last: Viero

address: Via Sommarive 18

department: Institute of Biophysics

country: Italy

institute: CNR

description:
Library name: sma spinal cord rep2
E145_SC_RS_T_SMA_2

data_processing:
Trimming of reads was performed with Cutadapt (v4.1). The first three nucleotides (5’ end) were trimmed and the adapter sequence of 15 As was removed (3’end). Reads shorter than 15 nucleotides were discarded. Maximum error rate and minimum overlap parameters were set at 0.15 and 10, respectively. Reads Alignment. Reads mapping on the collection of Mus musculus rRNAs (from the SILVA rRNA database, release 119) and tRNAs (from the Genomic tRNA database: gtrnadb.ucsc.edu/) were removed. The remaining reads were mapped on the mouse genome (using the Gencode M22 annotations ensembl 97) allowing a maximum of 5 multiple alignments for each read. All alignments were performed with STAR (v2.5.3a) employing default settings. Reads mapping on the same position with respect to transcript coordinates were then removed before proceeding with positional analyses. The identification of reads Psite position on the transcript was performed using riboWaltz. Duplicated reads mapping on the same position with respect to transcript coordinates were also removed. Remaining raw counts were computed for each gene.
Assembly: Gencode M22 (GRCm38.p6)
Supplementary files format and content: tab delimited text file containing transcript-specific ribosome protected fragment counts for each sample
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

source_name: spinal cord

growth_protocol: The Taiwanese model of SMA has been originally obtained from Jackson Laboratories (strain 005058). We refer to Smn+/−; SMN2tg/0 embryos as healthy controls, and Smn−/−; SMN2tg/0 as SMA embryos. The morning of vaginal plug  discovery was counted as embryonic day 0.5 (E0.5), and the embryos were collected when they reached the age of interest.

extract_protocol:
Brain and spinal cord were collected from control and SMA embryos at E14.5, snap frozen and then stored at -80℃ until used. Cytoplasmic lysates were prepared as it follows. Briefly, the tissues were pulverised with a sterile pestle and mortar in liquid nitrogen, and then 400-800 μL of tissue was added to ribosome lysis buffer (10mM Tris-HCl pH 7.5, 10mM MgCl2, 10mM NaCl, 1% w/V TritonX-100, 5 U/mL DNAseI, 800 U/ml RiboLock RNAse Inhibitor, 1mM DTT, 200μg/mL cycloheximide, 1% w/V Na-deoxycholate). To facilitate cell lysis, lysates were incubated on ice for 17-20 minutes followed by centrifuging twice at 12,000 rpm for 10 min at 4°C to remove tissue debris, mitochondria, and nuclei. Supernatants was measured for the 260nm absorbance, the final NaCl salt concentration of the lysate was adjusted to a final salt concentration of 100 mM.
Ribosome purification was achieved by treating lysates with 10 U/Abs RNAse at room temperature for 45 minutes followed by addition of 5μL of SUPERase-In RNase inhibitor (Thermo Fisher Scientific) to halt the reaction. Lysates were loaded onto 13.2 mL polyallomer ultracentrifuge tubes (Beckman) containing a 10%-40% (w/v) linear sucrose gradient (10mM Tris-HCl ph7.5, 10mM MgCl2, 10mM NaCl). The fraction was then used for RNA purification using the phenol/chloroform protocol. Ribosome-protected fragments (RPFs) measuring 28-32bp were separated and purified using a 15% Urea-TBE gel. After RNA extraction from the gel, RPFs were then dephosphorylated using 120U T4 polynucleotide kinase (New England Biolabs #M0201S) and 20U of SUPERase-InTM Rnase inhibitor in T4 PNK polynucleotide kinase buffer (New England Biolabs) at 37 °C for 1 hour followed by 10 minutes incubation at 70 °C to inactivate the enzymes. After RPFs purification, the libraries were prepared. Experiments were performed in triplicate. Libraries from E14.5 brain and spinal cord tissues of Taiwanese mouse embryos were sequenced at the CIBIO NGS facility of the University of Trento, Italy, using an Illumina NovaSeq6000 system.

treatment_protocol: The morning of vaginal plug discovery was counted as embryonic day 0.5 (E0.5), and the embryos were collected when they reached the age of interest. Tail tips were collected during the dissection and kept for genotyping. Pregnant dams were sacrificed at the desired time point and then embryos were collected individually. Each embryo was weighed, and the stage of development was assessed following the Theiler Staging Criteria for Mouse Embryo Development. Prior to fixation, embryos’heads were separated from the bodies.

value: spinal cord

value: tissue

value: Smn-/-; SMN2tg/0

value: disease state


title: Jurkat cell resting RNA-seq replicate 2


title: SMA mouse spinal cord, E14.5, rep3

description:
Library name: sma spinal cord rep3
E145_SC_RS_T_SMA_3


title: Jurkat cell resting RNA-seq replicate 1


title: OH2

value: Ovary

value: Primary human granulosa-lutein cells

value: hCG+rhOSM

value: RNA


title: control mouse spinal cord, E14.5, rep3

description:
Library name: ctrl spinal cord rep3
E145_SC_RS_T_WT_3

value: Smn+/-; SMN2tg/0

value: control


title: SMA mouse spinal cord, E14.5, rep1

description:
Library name: sma spinal cord rep1
E145_SC_RS_T_SMA_1


title: ChIP-seq_RPB1_INO80_degron_24h_rep2

description: Library name: Sample 4

value: mouse embryonic stem cells


title: SMA mouse brain, E14.5, rep2

description:
Library name: SMA brain rep2
E145_B_RS_T_SMA_2

source_name: brain

value: brain


title: control mouse brain, E14.5, rep2

description:
Library name: ctrl brain rep2
E145_B_RS_T_WT_2


title: LuCaP70CR_docetaxel_resistant_8

city: Boston

first: Steven

middle: P

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School

data_processing:
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters.
cufflinks v2.2.1 was used to generate FPKM values.
Assembly: hg19
Supplementary files format and content: Comma-separated values file includes FPKM values for each sample.
Supplementary files format and content: Comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values).

source_name: Prostate

growth_protocol: Mice with LuCaP35CR or LuCaP70CR xenograft tumors. Mice with LNCaP FOXJ1_OE and LNCaP EV xenografts.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
Transcriptome library construction with polyA selection (with Novogene for LuCaP70CR and FOXJ1 libraries; with GENWIZ for LuCaP35CR).

treatment_protocol: Mice with LuCaP35CR or LuCaP70CR xenograft tumors were treated with either vehicle or docetaxel (DTX) at 30 mg/kg by i.p. injection every 21 days starting at day 0 as indicated. Docetaxel and vehicle treated xenografts were harvested when they reached ~1500 mm3. The treated tumors were harvested 2 weeks after their final dose of docetaxel. Mice bearing LNCaP FOXJ1_OE and LNCaP EV xenografts were treated with docetaxel (DTX, 30 mg/kg). The first dose was administered when tumors reached ~250 mm3 (Day 9), and a second dose was given on Day 30. Mice for both groups were  sacrificed 5 days after the second dose, and the tumors were harvested for RNA sequencing.

value: Prostate

value: LuCaP70CR xenograft

value: prostate cancer

value: WT

value: docetaxel at 30 mg/kg by i.p. injection every 21 days


title: control mouse spinal cord, E14.5, rep1

description:
Library name: ctrl spinal cord rep1
E145_SC_RS_T_WT_1

value: spinal cord


title: LuCaP70CR_docetaxel_resistant_7


title: SMA mouse brain, E14.5, rep3

description:
Library name: SMA brain rep3
E145_B_RS_T_SMA_3

value: tissue


title: H2

value: hCG


title: LuCaP70CR_docetaxel_resistant_5


title: LuCaP70CR_docetaxel_sensitive_10

value: vehicle at 30 mg/kg by i.p. injection every 21 days


title: LuCaP70CR_docetaxel_resistant_6


title: LuCaP70CR_docetaxel_resistant_4


title: control mouse spinal cord, E14.5, rep2

description:
Library name: ctrl spinal cord rep2
E145_SC_RS_T_WT_2


title: CUT&Tag of IgG in mouse VSMCs (vasostatin-2)

first: Jingmeng

last: Liu

address: No. 197, Ruijin 2nd Road, Huangpu District, Shanghai

department: Department of Cardiovascular Medicine

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: VS2_IgG
Primary VSMCs treated with VS2 and IgG control antibody

data_processing:
Raw sequencing reads were first processed using Trimmomatic v0.39 with default parameters to remove sequencing adapters and low-quality bases, as described in Bolger et al., Bioinformatics, 2014, 30(15):2114–2120. The quality of both raw and clean reads was assessed using Q20/Q30 metrics, where Q = -10 log₁₀(p), with p representing the base calling error rate. A Q20 score corresponds to 99% accuracy, and Q30 to 99.9% accuracy. Clean reads were aligned to the mouse reference genome (mm10, GENCODE annotation) using BWA v0.7.17 with default parameters. Uniquely mapped reads were used to generate BAM files. Peak calling was performed using MACS2 v2.2.7.1 with the following parameters: macs2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B --SPMR. Only peaks with q-value < 0.05 were retained. Signal intensity tracks (bigWig files) were generated from BAM files normalized to signal per million reads (SPMR). Processed data include .bw (bigWig) signal tracks and .narrowPeak files containing peak locations.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for IgG sample)
Library strategy: CUT&Tag

source_name: aorta

growth_protocol: Primary vascular smooth muscle cells were isolated from mouse aortas and cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin under standard conditions (37°C, 5% CO₂).

extract_protocol:
CUT&Tag was performed following the standard protocol using the NR1D1 antibody. Briefly, permeabilized nuclei were incubated with primary antibody followed by secondary antibody and pA-Tn5 adapter complex. DNA fragments released after tagmentation were extracted using a DNA purification kit.
DNA fragments were amplified using indexed primers and a limited-cycle PCR. Libraries were purified using AMPure XP beads and quality-checked using Bioanalyzer. Sequencing was performed on Illumina NovaSeq 6000 with paired-end 150 bp reads.

treatment_protocol: Cells were treated with vasostatin-2 for 24 hours. The control group was treated with PBS under identical conditions.

value: aorta

value: vascular smooth muscle cells

tag: batch


title: LuCaP70CR_docetaxel_sensitive_1


title: LuCaP70CR_docetaxel_sensitive_3


title: LNCaP_FOXJ1_EV_xenograft_6

value: LNCaP xenograft

value: FOXJ1 EV

value: 30 mg/kg docetaxel (day 9, day 30)


title: CUT&Tag of NR1D1 in mouse VSMCs (vasostatin-2)

description:
Library name: VS2_NR1D1
Primary VSMCs treated with VS2 and anti-NR1D1 antibody


title: control mouse brain, E14.5, rep3

description:
Library name: ctrl brain rep3
E145_B_RS_T_WT_3

value: Smn+/-; SMN2tg/0

value: control


title: Bone marrow DAPI-lineage-cKit+ cells, Mx1-cre;Pex5fl/fl, Mutant 2

city: NEW YORK

first: Yue

last: Zhang

state: NY

address: 650 W 168th St, New York, NY 10032, black building 1108

institute: Columbia University

description:
Library name: LY004
10x Genomics

data_processing:
scRNA-seq data were analyzed with CellRanger.
Assembly: Mouse mm10
Supplementary files format and content: HDF5 files

source_name: Bone marrow

extract_protocol:
Bone marrow cells were isolated by flushing long bones.The cells were passed through 25G syringes at least twice in Ca²⁺- and Mg²⁺-free HBSS containing 2% heat-inactivated bovine serum to obtain a single-cell suspension. The cells were filtered through a 70-μm nylon mesh.The following antibodies were used for staining cells (all from Biolegend): lineage markers (anti-Ter119, anti-B220 (6B2), anti-Gr1 (8C5), anti-CD2 (RM2-5), anti-CD3 (17A2), anti-CD5 (53-7.3) and anti-CD8 (53-6.7)), anti-Sca-1 (E13-161.7), and anti-cKit (2B8). DAPI-lineage-cKit+ cells from bone marrow  were double-sorted in a yield-purity order of sorting modes on BD SORP FACSAria. The sorted cells were resuspended in Ca²⁺- and Mg²⁺-free HBSS.
10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 were used to prepare the library according to the manufacturer’s instructions.

value: Bone marrow

value: primary cells

value: DAPI-lineage-cKit+ cells

value: pIpC


title: LNCaP_FOXJ1_OE_xenograft_1

value: Prostate

value: prostate cancer

value: FOXJ1 OE


title: control mouse brain, E14.5, rep1

description:
Library name: ctrl brain rep1
E145_B_RS_T_WT_1

value: brain

value: tissue


title: Bone marrow DAPI-lineage-cKit+ cells, Mx1-cre;Pex5fl/fl, Mutant 1

description:
Library name: LY002
10x Genomics


title: LuCaP70CR_docetaxel_resistant_9

value: LuCaP70CR xenograft

value: WT

value: docetaxel at 30 mg/kg by i.p. injection every 21 days


title: LuCaP70CR_docetaxel_sensitive_2

value: vehicle at 30 mg/kg by i.p. injection every 21 days


title: BMM_ATAC-seq

city: Yinchuan

first: Qu

last: XU

state: Ningxia Hui Autonomous Region

address: 804 Shengli South Street, Yinchuan, Ningxia Hui Autonomous Region 750004

institute: Ningxia Medical University

description: Library name: BMM_ATAC-seq

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.The library preparations weresequenced on Illumina Novaseq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.
Assembly: GRCm39.110
Supplementary files format and content: bigWig

source_name: Mouse bone marrow macrophages

extract_protocol:
Take out the cryovial and shake it in 37℃ water to quickly thaw it within 1-2 min.Cells were centrifuged at 4 ℃ 500×g for 5 min. Cell activity was detected with LUNA-FL and counted.50000 live cells were centrifuged with 500 g for 5 minutes, supernatant was discarded, The precipitation was resuspended with 50 ul lysis buffer,and placed on ice for 5 minutes, then 1ml wash buffer was added, mixed, 500 g centrifuged for 5 minutes, supernatant was discarded, and nucleus was collected.
Briefly, nucleus was extracted from samples, and the nucleus pellet was resuspended in the Tn5 transposase reaction mix.The transposition reaction was incubated at 37 ℃ for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library(ATAC-seq_Novogene Kit). After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit

value: Mouse bone marrow macrophages


title: BMM_Cut&Tag

description: Library name: DMM_CutandTag

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina)according to the manufacturer’s instructions.The library preparations weresequenced on Illumina Novaseq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd.(Beijing, China)and 150 bp paired-end reads were generated.
Assembly: GRCm39.110
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Take out the cryovial and shake it in 37 °C water to quickly thaw it within 1-2 min.Cells were centrifuged for 5 min at 500×g at 4 ℃ Cell activity was detected with LUNA-FL and counted
Briefly, the cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation. DNA sequence is tagmented,with adapters added at the same time at both ends, which can be enriched by PCR to form thesequencing-ready libraries(CUT&Tag_Novogene Kit). After the PCR reaction, libraries were.purified with the AMPurebeads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: antibody


title: LNCaP_FOXJ1_EV_xenograft_7

tag: tissue

value: LNCaP xenograft

value: FOXJ1 EV

value: 30 mg/kg docetaxel (day 9, day 30)


title: SMA mouse brain, E14.5, rep1

description:
Library name: SMA brain rep1
E145_B_RS_T_SMA_1

tag: genotype

value: Smn-/-; SMN2tg/0

value: disease state


title: CUT&Tag of IgG in mouse VSMCs (control)

description:
Library name: PBS_IgG
Primary VSMCs treated with PBS and IgG control antibody

value: aorta

value: vascular smooth muscle cells

value: PBS


title: LNCaP_FOXJ1_EV_xenograft_8

value: Prostate

value: prostate cancer


title: LNCaP_FOXJ1_OE_xenograft_2

value: FOXJ1 OE


title: MPC5 cells,sh_METTL3

city: Kunming

first: Yihua

last: Bai

state: 云南省

address: No. 374, Dianmian Road, WuhuaDistrict

institute: The Second Affiliated Hospital of Kunming Medical University

description: Library name: MPC5_sh_METTL3

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: eg GRCH38
Supplementary files format and content: MPC5_IPVSMPC5_input_peak.xlsx,MPC5sh_METTL3_G_IPVSMPC5sh_METTL3_G_input_peak.xlsx,MPC5sh_METTL3_IPVSMPC5sh_METTL3_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: MPC5sh_METTL3_GVSMPC5_diffPeak_result.xlsx,MPC5sh_METTL3VSMPC5_diffPeak_result.xlsx,MPC5sh_METTL3VSMPC5sh_METTL3_G_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)

source_name: Kidney

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: Kidney

value: Mouse Podocyte Clone5(MPC5)

value: podocytes

value: METTL3 knockdown

value: Cultured in a standard medium


title: CUT&Tag of NR1D1 in mouse VSMCs (control)

description:
Library name: PBS_NR1D1
Primary VSMCs treated with PBS and anti-NR1D1 antibody

value: WT


title: Bone marrow DAPI-lineage-cKit+ cells, Pex5fl/fl, Control 2

description:
Library name: LY003
10x Genomics

value: Bone marrow

value: primary cells

value: DAPI-lineage-cKit+ cells

value: pIpC


title: Bone marrow DAPI-lineage-cKit+ cells, Pex5fl/fl, Control 1

description:
Library name: LY001
10x Genomics


title: IgG410

city: Ube

first: Keishiro

last: Isayama

state: 山口県

country: Japan

institute: Yamaguchi　University

data_processing:
FASTQ files produced by Illumina NovaSeq 6000 were imported to CLC Genomics Workbench software.
The reads were trimmed and mapped to the reference genome by using the CLC Genomics Workbench.
Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software.
Assembly: GRCh37 (hg19) release-75
Supplementary files format and content: tab-delimited text file include log2(TPM+1) values for each sample.

source_name: orbital

extract_protocol:
Fresh tissues were stored at -80°C in RNA later RNA Stabilization Reagent (QIAGEN, Hilden, Germany). The tissues were then homogenized using a bead mill at 3,200 rpm for 30 seconds in homogenization solution equipped with Maxwell RSC simply RNA tissue kit (Promega, Madison, WI). The Maxwell RSC simply RNA tissue kit (Promega) was used to extract total RNA, and mRNA was purified using Oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB).
The NEBNext Ultra II RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) were used to generate cDNA libraries for Illumina sequencing. An Agilent 4200 TapeStation. The confirmed libraries were mixed in equal molecular amounts for clustering and sequencing on an Illumina NovaSeq 6000 DNA sequencer with a 50 bp paired-end cycle sequencing kit (Illumina, San Diego, CA).

value: orbital

value: orbital IgG4ROD


title: IgG49


title: IgG48


title: IgG46


title: IgG411


title: MPC5 cells,sh_METTL3_G

description: Library name: MPC5_sh_METTL3_G

value: Treated with 25 μmol/L glucose for 72 hours.


title: IgG47


title: MPC5 cells,control

description: Library name: MPC5


title: IgG45


title: IgG44


title: IgG43


title: MPC5 cells,sh_METTL3_G_input RNA,rep1

description: Library name: MPC5sh_METTL3_G_1_input

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: eg GRCH38
Supplementary files format and content: MPC5_IPVSMPC5_input_peak.xlsx,MPC5sh_METTL3_G_IPVSMPC5sh_METTL3_G_input_peak.xlsx,MPC5sh_METTL3_IPVSMPC5sh_METTL3_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: MPC5sh_METTL3_GVSMPC5_diffPeak_result.xlsx,MPC5sh_METTL3VSMPC5_diffPeak_result.xlsx,MPC5sh_METTL3VSMPC5sh_METTL3_G_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)
Library strategy: MeRIP-Seq


title: MPC5 cells,sh_METTL3_G_IP RNA,rep2

description: Library name: MPC5sh_METTL3_G_2_IP


title: MPC5 cells,sh_METTL3_G_input RNA,rep2

description: Library name: MPC5sh_METTL3_G_2_input


title: IgG41


title: IgG42


title: MALT9

value: orbital MALT lymphoma


title: MPC5 cells,sh_METTL3_G_IP RNA,rep1

description: Library name: MPC5sh_METTL3_G_1_IP


title: MPC5 cells,sh_METTL3_input RNA,rep2

description: Library name: MPC5sh_METTL3_2_input


title: MPC5 cells,sh_METTL3_IP RNA,rep2

description: Library name: MPC5sh_METTL3_2_IP


title: MALT8


title: MALT7


title: MPC5 cells,sh_METTL3_input RNA,rep1

description: Library name: MPC5sh_METTL3_1_input


title: MPC5 cells,control_IP RNA,rep2

description: Library name: MPC5_2_IP


title: MALT6


title: regeneration_6 time-point

first: yue

last: chen

state: Shanghai

address: 320 Yue-Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
library strategy: Spatial transcriptome
Spatial transcriptome data of regenerated fragments was generated by Stereo-seq (BGI) (Chen et al., 2022), aligned to S. mediterranea transcriptome smed_20140614 as the SAW pipeline.
Assembly: Schmidtea mediterranea transcriptome is available from GSE72389

organism: Schmidtea mediterranea

source_name: neck

growth_protocol: Asexual S. mediterranea (strain CIW4) anamials were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol:
Samples of different treatments were fixed using methacarn (6 mL methanol, 3 mL chloroform, 1 mL glacial acetic acid).
Tissue sections adhered to the Stereo-seq chip surface (Chen et al., 2022), and then incubated at 37 °C for 3 min. After 30 min fixation at -20 °C by methanol (Sigma, 34860), ssDNA of tissues was stained with nucleic acid dye (Thermo fisher, Q10212) and imaged under a fluorescence microscope. Tissue sections were permeabilized using 0.1% pepsin (Sigma, P7000) in 0.01M HCl buffer and incubated at 37°C for 15 min. DNA nanoballs (DNBs) on the chip captured released RNA from tissues, then were reverse transcribed at 42 °C overnight. After reverse transcription, tissues were digested with tissue removal buffer (10 mM Tris-HCl, 25 mM EDTA, 100 mM NaCl, 0.5% SDS) at 37 °C for 30 min, and then cDNA-containing chips were subjected to Exonuclease I (NEB, M0293L) at 37 °C for 1h. PCR reactions with KAPA HiFi Hotstart Ready Mix (Roche, KK2602) were performed to amplify cDNAs. Qubit™ dsDNA Assay Kit (Thermo, Q32854) was used to quantify the concentrations of PCR products. cDNAs were fragmented with in-house Tn5 transposase at 55 °C for 10 min, which were stopped by adding 0.02% SDS, followed by amplifying using KAPA HiFi Hotstart Ready Mix. PCR products were purified and used to generate DNBs. Finally, DNBs were sequenced (50 bp for read 1, 100 bp for read 2) on the MGI DNBSEQ-Tx sequencer.

value: neck

tag: strain

value: asexual strain CIW4

value: wild type

value: amputation


title: MPC5 cells,sh_METTL3_IP RNA,rep1

description: Library name: MPC5sh_METTL3_1_IP

value: Kidney

value: Mouse Podocyte Clone5(MPC5)


title: MALT5


title: intact and RNAi (mixed dample)

data_processing:
library strategy: Spatial transcriptome
Spatial transcriptome data of both intact and RNAi-treated samples were generated by Stereo-seq (BGI) (Chen et al., 2022), aligned to S. mediterranea transcriptome smed_20140614 as the SAW pipeline.
Assembly: Schmidtea mediterranea transcriptome is available from GSE72389

source_name: intact and tail

value: intact and tail

value: wild type and RNAi


title: MPC5 cells,control_input RNA,rep2

description: Library name: MPC5_2_input

value: podocytes

value: WT

value: Cultured in a standard medium


title: MPC5 cells,control_IP RNA,rep1

description: Library name: MPC5_1_IP


title: MALT4


title: LX-2 cells, transfected with NAT10 SiRNA,TGF-β24h,SiNAT10_TGFB_1

first: An

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

description:
Library name: SiNAT10_TGFB_1
Transcriptome profile of LX-2 cells transfected with NAT10 SiRNA and treated with human recombinant TGF beta,,biological rep1

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Rawdata (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome.
Assembly: hg38
Supplementary files format and content: CSV file includes raw counts for each Sample
Supplementary files format and content: CSV file includes FPKM values for each Sample

growth_protocol: LX-2 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and  1% antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was harvested using TRIzol reagent, and a minimum of 2 μg of total RNA per sample was used for the construction of sequencing libraries .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LX-2 was stimulated by 5ng/ml TGF-β1 (PeproTech, USA) and after 24 hours we extracted the total RNA. siRNA specific to NAT10 was transfected into cells using Lipofectamine 2000 (Invitrogen, USA).After 48 hours of transfection,the cells were treated with 5ng/ml of TGF-β1 and after 24 hours we extracted the total RNA.

value: hepatic stellate cells

value: transfected with NAT10 SiRNA and treated with human recombinant TGF-β1


title: LX-2 cells, transfected with NAT10 SiRNA,TGF-β24h,SiNAT10_TGFB_3

description:
Library name: SiNAT10_TGFB_3
Transcriptome profile of LX-2 cells transfected with NAT10 SiRNA and treated with human recombinant TGF beta,,biological rep3


title: LX-2 cells, transfected with NAT10 SiRNA,SiNAT10_3

description:
Library name: SiNAT10_3
Transcriptome profile of LX-2 cells transfected with NAT10 SiRNA,biological rep3

value: transfected with NAT10 SiRNA


title: MPC5 cells,control_input RNA,rep1

description: Library name: MPC5_1_input


title: LX-2 cells, transfected with NAT10 SiRNA,SiNAT10_2

description:
Library name: SiNAT10_2
Transcriptome profile of LX-2 cells transfected with NAT10 SiRNA,biological rep2


title: LX-2 cells, transfected with NAT10 SiRNA,TGF-β24h,SiNAT10_TGFB_2

description:
Library name: SiNAT10_TGFB_2
Transcriptome profile of LX-2 cells transfected with NAT10 SiRNA and treated with human recombinant TGF beta,,biological rep2


title: LX-2 cells, transfected with NAT10 SiRNA,SiNAT10_1

description:
Library name: SiNAT10_1
Transcriptome profile of LX-2 cells transfected with NAT10 SiRNA,biological rep1


title: MALT2

value: orbital


title: LX-2 cells,TGF-β24h,TGFB2

description:
Library name: TGFB2
Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep2

value: treated with human recombinant TGF-β1


title: LX-2 cells,TGF-β24h,TGFB1

description:
Library name: TGFB1
Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep1


title: LX-2 cells,TGF-β24h,TGFB3

description:
Library name: TGFB3
Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep3


title: E14_RS_vSP_diff_Biol_rep_2

city: New York

first: Esteban

middle: O.

last: Mazzoni

address: 430 East 29th Street 4th floor

department: Department of Cell Biology

institute: NYU Grossman School of Medicine

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw data processing, demultiplexing, and aggregation were all done with CellRanger 7.1.0. Intron reads were kept for Cell Oracle analysis.
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ventral spinal cord embryoid bodies

extract_protocol:
Cells were dissociated to single cells while alive with TrypLE (Gibco) and then frozen as routine cryopreservation (in 1:1 growth medium : FBS supplemented with 10% DMSO). Along differentiation, 6 samples of differentiation days 0, 2, 3, 4, 5, and 6 were collected. On the day of running single cell-RNA-sequencing, all samples were thawed, counted live cells, mixed in equalmolar ratios, and diluted to the desired 10k cells per replicate.
Followed exactly the 10X Genomics Chromium Next GEM Single Cell 3’ v3.1 chemistry protocol.

value: ventral spinal cord embryoid bodies


title: Rg3_3

city: changchun

first: 富强

last: 李

state: 吉林省

address: 前进

institute: 吉林大学

data_processing:
clc genomics workbench V11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited  text file include raw counts for each  sample

source_name: gastric

growth_protocol: BGC823 cells were cultured in RPMI-1640 medium (Meilunbio®, Dalian, China) containing 10% fetal bovine serum (KangYuan Biology, Tianjin, China) and 1% penicillin-streptomycin (Thermo-Fisher Scientific) and maintained at 37°C and 5% CO2. Each cell line was authenticated via short tandem repeat (STR) profiling within 3 years. All experiments were performed with mycoplasma-free cells.

extract_protocol:
Enrichment of eukaryotic mRNA with magnetic beads bearing Oligo (dT)
The first cDNA strand was synthesized with six-base random primers (random hexamers) using mRNA as a template, then the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H, and DNA polymerase I. The cDNA was purified by using AMPure XP beads; the purified double-stranded cDNA was then subjected to end repair, addition of the A tails and connected to sequencing junctions, and then fragment size selection was performed with AMPure XP beads; Finally, the cDNA library was enriched by PCR.

treatment_protocol: BGC823 cells (2 × 10^4 cells/well) were seeded and cultured overnight in 6-well plates. The culture medium was changed to contain 200 μg/mL of Rg3 every 24 hours, for a total duration of 48 hours.

value: gastric

value: gastric cancer cell

value: wt


title: E14_RS_vSP_diff_Biol_rep_1

description:
Library name: Sample 1
10x Genomics


title: LX-2 cells,con3

description:
Library name: con 3
Transcriptome profile of LX-2 cells untreated,biological rep3

value: untreated


title: Dmso_3

value: dmso


title: Retinal ganglion cells, β2KO, rep4

city: Berkeley

first: Matthew

middle: A

last: Po

state: California

address: Stanley Hall

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

description:
Library name: Sample 7
10X Genomics

data_processing:
Single-cell libraries were aligned to the UCSC mm10 genome assembly using Cellranger v7.1.0 (10X Genomics). This alignment was performed separately on each sample (three P7 WT samples, four P7 β2KO samples), and the resulting cells-by-genes expression matrices were combined to obtain an expression matrix for each condition.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files of cell barcodes and features (genes), matrix file of read counts

source_name: Retina

extract_protocol:
P7 C57BL/6J and β2KO mice were anesthetized in an isoflurane induction chamber and euthanized by decapitation. All the solutions were filtered using 0.22 µm syringe filter (Fisher #9720511). Eyes were enucleated and retinas were immediately dissected in oxygenated (95% oxygen/5% carbon dioxide) Ames’ media with L-glutamine and sodium bicarbonate (pH ~7.4) at room temperature under light scope. Retinas (6 to 8 per sample) were digested for 10 min at 37oC in 70 µl papain (Fisher #LS003126) + 50 µl DNase (Sigma #D4527-40KU) + 50 µl L-cysteine (Sigma #C1276-10G) in 5 ml Ames, which was activated at 37oC for 15 min. Samples were gently swirled once during this incubation. Following this, papain was removed and samples was gently triturated with P1000 pipette tips in 1 ml 10x ovomucoid (Fisher #NC9931428) + 50 µl DNase + 9 ml Ames. Manual trituration was performed using 2 ml of ovo solution at a time and the supernatant was filtered using 40 μm cell strainer in a new tube. This cell suspension was spun down at 450 g for 8 min. Supernatant was discarded and the pellet was resuspended in 250 μl of Ames + bovine serum albumin (BSA). This solution was prepared using 27 ml Ames + 3 ml 4% BSA (Sigma #A9418-5G) + 50 µl DNase. Cells were counted using hemocytometer (1:100 dilution factor with trypan blue). 10 million cells were incubated in 10 µl CD90.2 microbeads (Miltenyi Biotec #130-121-278) for 10 min at 4oC. Following incubation, 6 ml Ames + BSA solution was added and cells were spun down at 450 g for 8 min. Supernatant was discarded and cells were resuspended in fresh 500 µl Ames + BSA solution. Cell suspension was subjected to magnetic-activated cell sorting (MACS) using large cell columns (Miltenyi Biotec #130-042-202) to sort RGCs. To obtain a high number of RGCs, the tube containing the cells was washed with 500 µl Ames + BSA solution for 2 times. To obtain better purity, MACS was repeated one more time on eluted CD90.2+ RGCs using fresh columns. This cell suspension was spun down at 450 g for 8 min and the supernatant was removed. Pellet obtained was resuspended in ~1000 μl of Ames + BSA and cell concentration was counted using hemocytometer (dilution factor 2). This spun down strategy was employed to obtain a highly concentrated sample in a small volume of ~100 μl Ames + BSA.
Single-cell libraries on RGCs isolated were prepared using Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics, Pleasanton, CA) following manufacturer’s protocol.

value: Retina

value: Retinal ganglion cells

tag: Sex

value: pooled male and female


title: LX-2 cells,con2

description:
Library name: con 2
Transcriptome profile of LX-2 cells untreated,biological rep2


title: LX-2 cells,con1

description:
Library name: con1
Transcriptome profile of LX-2 cells untreated,biological rep1


title: Retinal ganglion cells, β2KO, rep3

description:
Library name: Sample 6
10X Genomics


title: Rg3_2


title: Dmso_2


title: MALT3

value: orbital MALT lymphoma


title: Cel5-3

city: Macau

first: Dingqi

address: Taipa

country: Macau

institute: Macau University of Science and Technology

description: Library name: Cel5-3

data_processing:
Sequencing reads were demultiplexed based on sample barcode with idemux (https://github.com/Lexogen-Tools/idemux).
Demultiplexed reads were trimmed with cutadapt to remove polyA, adaptor and low-quality sequences.
Reads were mapped to human GRCh38 reference assembly with STAR aligner.
PCR duplicates were removed based on UMI with UMI-tools. Htseq-count was used to generate read counts.
Normalized counts were generated with DESeq2, accounting for total reads counts.
Assembly: GRCh38
Supplementary files format and content: Normalized counts matrix. The column names are sample names. The row names are gene symbols.

source_name: Immortalized RAFLS

growth_protocol: Immortalized RAFLS was purchased from Meisen CTCC (Cat. #CTCC-001-0385, Pan’an, Zhejiang, China) and cultured in DMEM/F-12 supplemented with 10% FBS, 1% Insulin-Transferrin-Selenium (ITS) and 1% Penicillin-Streptomycin-Glutamate.

extract_protocol:
Total RNA was extracted with routine Trizol method.
Transcriptomic profiling was performed with an in-house, proprietary method that captures the 3’ primed end of mRNA molecules for sequencing.

treatment_protocol: All cells are simulated with 1 ng/mL TNFα for 24h, and exposed to different treatments during the last 4 hours.

value: Immortalized RAFLS

value: Rheumatoid arthritis fibroblast-like synoviocytes


title: Cel6-3

description: Library name: Cel6-3


title: Retinal ganglion cells, β2KO, rep2

description:
Library name: Sample 5
10X Genomics


title: Cel6-1

description: Library name: Cel6-1


title: Retinal ganglion cells, wild-type, rep3

description:
Library name: Sample 3
10X Genomics

value: Wild-type


title: Cel5-2

description: Library name: Cel5-2


title: Rg3_1


title: Cel5-1

description: Library name: Cel5-1


title: Cel-3

description: Library name: Cel-3

value: Cel


title: Cel-1

description: Library name: Cel-1


title: MALT1


title: DMSO-2

description: Library name: DMSO-2

value: DMSO


title: Retinal ganglion cells, β2KO, rep1

description:
Library name: Sample 4
10X Genomics


title: DMSO-3

description: Library name: DMSO-3


title: Cel-2

description: Library name: Cel-2


title: RIOK1-kd gRNA-3 REP2

city: Bronx

first: David

last: Shechter

state: New York

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

description:
salmon.merged.gene_counts_length_scaled.tsv
condition_RIOK1.3_vs_CONTROL_DESEQ2.csv

data_processing:
nf-core/rnaseq v3.9
DESeq2
Assembly: hg38
Supplementary files format and content: .tsv,salmon length normalized gene counts
Supplementary files format and content: .csv,DESeq2 output files for each knockdown

extract_protocol: non-directional, polyA capture

value: Puromycin (1ug/mL), Blasticidin S (5 ug/mL)


title: Locus Coeruleus tissue, 5xFAD transgenic, 79#

city: Shanghai

first: Ziyue

last: Zhou

address: 100 Haike Road, Zhangjiang Hi-Tech Park, Pudong

institute: The Interdisciplinary Research Center on Biology and Chemistry

description:
Library name: Sample 6
Column name in WT_vs_FAD_TPM.csv: Tg_79_clean_L006

data_processing:
The Bioinformatics pipeline [ref.1] was used to process sequencing data. STAR [ref.2] was used to align reads to mm39 genome build and RSEM was used to quantify expression at the gene level [ref.3]. Differential expression analysis was conducted using DESeq2 with default parameters [ref.4]. Differential gene expression was identified using a statistical cut-off of padj < 0.05(Additional file: gene table).   [ref.1]: https://github.com/emc2cube/Bioinformatics [ref.2]: STAR: ultrafast universal RNA-seq aligner [ref.3]: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome [ref.4]: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Assembly: mm39
Supplementary files format and content: csv file including TPM values for each Sample

source_name: Locus Coeruleus

extract_protocol:
Total RNA was isolated from tissue using the TRIzol® Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Only high-quality RNA samples (OD260 / 280 = 1.8 ~ 2.2, OD260 / 230 ≥ 1.9, RIN ≥ 9.0) were used to construct a sequencing library.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on an Illumina Novaseq 6000 by Shanghai Personal Biotechnology Cp. Ltd.

value: Locus Coeruleus


title: Retinal ganglion cells, wild-type, rep2

description:
Library name: Sample 2
10X Genomics


title: DMSO-1

description: Library name: DMSO-1


title: RIOK1-kd gRNA-3 REP1