title: D7+11 samples treated with FGF8b and FGF10

description: Library name: D7_11_F10_F8bHC


title: D7+11 samples treated with FGF10

status: Public on Jun 12 2025

type: SRA

city: Melbourne

first: Allara

last: Zylberberg

state: VIC

address: Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville VIC 3052

department: Stem Cell Medicine

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: D7_11_F10HC

library_source: other

data_processing:
10x Genomics cellranger-8.0.0 for data demultiplexing. Sample QC, integration and analysis was performed in Python using Scanpy (v.1.10.2)
Assembly: GRCh38
Supplementary files format and content: D7_5.h5ad = processed and integrated D7+5 single cell samples. D7_11.h5ad = processed and integrated D7+11 samples.

molecule: other

organism: Homo sapiens

source_name: Kidney organoid

extract_protocol:
Suspension kidney organoids at D7+5 or D7+11 were transferred into a 15ml falcon for dissociation in 4ml of 1:1 TrypLE/Accutase solution (STEMCELL Technologies) at 37°C with occasional agitation (flicking) until large clumps were no longer visible. If the organoids were not dissociated after 20 minutes, mechanical dissociation was undertaken. The TrypLE/Accutase solution was quenched using an equal amount of TeSR-E6 and cells were run through a pre-wet 40µm cell strainer to make them into single cell suspension.
Library was constructed according to manufacturer's protocol, 10x Chromium Single Cell Expression Flex Protocol (CG00527, Revision E).

tag: tissue

value: Kidney organoid

tag: cell line

tag: cell type


title: D7+5 samples treated with FGF9

description: Library name: D7_5_F9HC


title: D7+5 samples treated with FGF10

description: Library name: D7_5_F10HC


title: HCT15NC_1

city: Guangzhou

first: Chao

last: Qin

address: Guangdong Province

country: China

institute: sun yat-sen university

description:
Library name: sample 1
HCT15NC_1

library_source: transcriptomic

data_processing:
Total RNA was extracted using Trizol reagent kit
RNA quality was assessed on an Agilent 2100 Bioanalyzer
mRNA was enriched by Oligo(dT)beads.
Shorten fragments using fragmentation buffer and reverslytranscribed into cDNA by  NEBNext Ultra RNA Library Prep Kit for Illumina
The resulting cDNA library was sequenced using Illumina Novaseq6000
Assembly: Ensembl_release104
Supplementary files format and content: processed data.txt

molecule: total RNA

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) accordingto 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 gelelectrophoresis.
After total RNA was extracted, mRNA was enriched by Oligo(dT)beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverslytranscribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction(PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 byGene Denovo Biotechnology Co. (Guangzhou, China).

value: colon

tag: disease state

value: Adenocarcinoma

value: CRC cell line

tag: treatment

value: Empty vector-transfected cells

tag: batch


title: HCT15OE_2

description:
Library name: sample 4
HCT15OE_2

value: Stably transfected cells with the lentiviral vector for the overexpression of NSUN5.


title: D7+5 samples treated with FGF8b

description: Library name: D7_5_F8bHC


title: HCT15NC_2

description:
Library name: sample 2
HCT15NC_2


title: AB18668

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample92

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Blood

extract_protocol:
Synovial fluid mononuclear cells and blood mononuclear cells were isolated within maximum 4 hours of sample collection. Synovial fluid samples were first filtered by 100-micron strainer into 50 ml tube and diluted 1:1 with ice cold FACS buffer (2mM EDTA, Ph 8.0, 0.5% bovine serum albumin in PBS). Blood samples were diluted 1:1 with ice cold FACS buffer. Synovial fluid and blood mononuclear cell separation was performed using density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with the diluted synovial fluid or blood sample. Centrifugation (460g, 25min) was performed at 10◦C and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After a short centrifuge (360g, 5min), we resuspended the cell pellet in cryopreservation media (FCS+10%DMSO) and stored the samples in cryotube at -80◦C. Prior to single-cell sorting, samples were quickly defrosted at 37◦C bath and washed with heated (37 ◦C) RPMI-1640. We resuspended the cells in FACS buffer for staining and sorting.
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)

tag: gating

tag: diagnosis

value: PsA

value: Blood

tag: pid


title: HCT15OE_1

description:
Library name: sample 3
HCT15OE_1


title: AB18664

description: Library name: Sample90

source_name: SF

value: SF


title: AB18659

description: Library name: Sample85


title: AB18663

description: Library name: Sample89


title: AB18654

description: Library name: Sample83


title: AB18660

description: Library name: Sample86


title: AB18661

description: Library name: Sample87


title: AB18665

description: Library name: Sample91


title: AB18573

description: Library name: Sample78


title: AB18662

description: Library name: Sample88


title: KOA-3

city: Stockholm

first: Sören

last: Lehmann

address: Blickagången 16

department: the Department of Medicine

country: Sweden

institute: Karolinska Institute

description:
Library name: UA-2818-KOA-3_S6
other

data_processing:
Samples were analysed with the nf-core rnaseq pipeline release 1.4.2. In short, the pipeline does the following: The workflow processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts and performs extensive quality-control on the results. For information regarding the pipeline, folder structure and how to interpret results, please refer to the pipeline documentation: https://github.com/nf-core/rnaseq. Detailed information about standard outputs from the pipeline can be found here: https://github.com/nf-core/rnaseq/tree/1.4.2
Assembly: hg19
Supplementary files format and content: MALNC_RNAseq_merged_gene_counts.txt

source_name: Hematopoietic system

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer protocol.
Sequencing libraries were prepared from 500ng total RNA using TruSeq stranded total RNA library preparation kit with ribosomal depletion using RiboZero Gold (Illumina Inc.) and samples were paired-end sequenced (150 cycles in one NovaSeq 6000 SP flowcell).

treatment_protocol: NB4 KOB clones and NB4 WT clones were treated with ATRA (1µM) for 72h

value: Hematopoietic system

value: Promyelocytic leukemia cells

tag: genotype

value: carry the t(15;17) PML-RARA fusion gene, Deletion of MALNC Exon 1.1 and exon 1.2


title: AB18575

description: Library name: Sample79


title: AB18658

description: Library name: Sample84


title: AB18588

description: Library name: Sample81


title: AB18571

description: Library name: Sample77


title: AB18577

description: Library name: Sample80


title: AB18569

description: Library name: Sample75


title: AB18669

description: Library name: Sample93


title: AB18554

description: Library name: Sample68


title: AB18553

description: Library name: Sample67


title: AB18552

description: Library name: Sample66


title: AB18556

description: Library name: Sample69


title: AB18565

description: Library name: Sample72


title: AB18560

description: Library name: Sample71


title: AB18558

description: Library name: Sample70


title: AB18550

description: Library name: Sample65


title: AB18568

description: Library name: Sample74


title: AB18589

description: Library name: Sample82


title: AB18546

description: Library name: Sample61


title: AB18545

description: Library name: Sample60


title: AB18538

description: Library name: Sample54


title: AB18537

description: Library name: Sample53


title: AB18541

description: Library name: Sample56


title: AB18536

description: Library name: Sample52


title: AB18544

description: Library name: Sample59


title: AB18547

description: Library name: Sample62


title: AB18533

description: Library name: Sample49


title: AB18548

description: Library name: Sample63


title: AB18534

description: Library name: Sample50


title: AB18566

description: Library name: Sample73


title: AB18542

description: Library name: Sample57


title: AB18531

description: Library name: Sample47


title: AB18532

description: Library name: Sample48


title: AB18535

description: Library name: Sample51


title: AB18570

description: Library name: Sample76


title: AB18540

description: Library name: Sample55


title: AB18528

description: Library name: Sample44


title: AB18549

description: Library name: Sample64


title: AB18526

description: Library name: Sample43


title: AB18520

description: Library name: Sample39


title: AB18521

description: Library name: Sample40


title: AB18530

description: Library name: Sample46


title: AB18523

description: Library name: Sample41


title: AB18529

description: Library name: Sample45


title: AB18524

description: Library name: Sample42


title: AB18519

description: Library name: Sample38


title: AB18518

description: Library name: Sample37


title: AB18543

description: Library name: Sample58


title: AB18516

description: Library name: Sample35


title: AB18515

description: Library name: Sample34


title: AB18513

description: Library name: Sample32


title: AB18512

description: Library name: Sample31


title: AB18511

description: Library name: Sample30


title: AB18514

description: Library name: Sample33


title: AB18507

description: Library name: Sample27


title: AB18510

description: Library name: Sample29


title: AB18506

description: Library name: Sample26


title: AB18504

description: Library name: Sample24


title: AB18502

description: Library name: Sample23


title: AB18501

description: Library name: Sample22


title: AB18498

description: Library name: Sample19


title: AB18499

description: Library name: Sample20


title: AB18500

description: Library name: Sample21


title: AB18489

description: Library name: Sample15


title: AB18495

description: Library name: Sample16


title: AB18505

description: Library name: Sample25


title: AB18497

description: Library name: Sample18


title: AB18435

description: Library name: Sample10


title: AB18496

description: Library name: Sample17


title: AB18434

description: Library name: Sample9


title: AB18433

description: Library name: Sample8


title: AB18448

description: Library name: Sample13


title: AB18517

description: Library name: Sample36


title: AB18437

description: Library name: Sample12


title: AB18449

description: Library name: Sample14


title: AB18432

description: Library name: Sample7


title: AB18430

description: Library name: Sample5


title: AB18508

description: Library name: Sample28


title: AB18431

description: Library name: Sample6


title: AB18427

description: Library name: Sample3


title: AB18425

description: Library name: Sample1


title: PTGIR_CD4+IFNG-IL10-_3

city: Bethesda

first: Ayden

last: Case

state: MD

address: 10 Center Dr

country: USA

institute: NHLBI

description: Library name: 9

data_processing:
Raw data quality were checked with FastQC (v0.12.1) and summarised with multiqc (v1.20)
Data were merged across lanes with cat
Alignment was performed using STAR (v2.7.11b)
Quantification was performed with featureCounts (subread v2.0.3)
Downstream analysis was performed in R (v4.3) using edgeR (v3.42.4) for filtering, normalisation and statistical analysis
Assembly: hg38
Supplementary files format and content: ptgir_ptgis_sirna_counts.txt contains the raw output from featureCounts
Supplementary files format and content: ptgir_ptgis_sirna_normalised_data.csv contains filtered and TMM-CPM normalised data

extract_protocol:
RNA was extracted from activated or non-activated CD4T cells (human or mouse) with the RNAqueous Micro Kit (Invitrogen, # AM1931,) followed by DNase digestion (TURBO DNA-free™ Kit, # AM1907)
RNA was quantified and applied to the TapeStation (Agilen) for quality assessment. RNA was subjected to library preparation using poly(A) mRNA capture (NEB, # E7770 and #E7490) according to manufacturer’s protocol

tag: stimulation

tag: sirna

value: PTGIR


title: PTGIS_CD4+IFNG-IL10-_3

description: Library name: 6

value: PTGIS


title: PTGIR_CD4+IFNG-IL10-_2

description: Library name: 8


title: PTGIR_CD4+IFNG-IL10-_1

description: Library name: 7


title: PTGIS_CD4+IFNG-IL10-_2

description: Library name: 5


title: AB18436

description: Library name: Sample11


title: Scramble_CD4+IFNG-IL10-_3

description: Library name: 3

value: Scramble


title: PTGIS_CD4+IFNG-IL10-_1

description: Library name: 4


title: Scramble_CD4+IFNG+IL10-_3

description: Library name: 12


title: PTGIR_CD4+IFNG+IL10-_2

description: Library name: 13


title: Scramble_CD4+IFNG-IL10-_2

description: Library name: 2


title: Scramble_CD4+_1

description: Library name: 10


title: Scramble_CD4+_3

description: Library name: 15


title: PC9_RG7388

city: Weifang

first: lei

last: sun

address: 151 Guangwen Street

institute: shandong second medical university

description: Library name: Sample 4

data_processing:
Basecalls performed using CASAVA version 1.8
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Raw_gene_counts_matrix.xls

source_name: Lung

extract_protocol:
RNA was harvested using RNA isolation kit (Sharebio). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared  using Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following manufacture's protocols.

value: Lung

value: epithelial cell

value: WT


title: PC9_Controle

description: Library name: Sample 3

value: DMSO


title: HCC827_Control

description: Library name: Sample 1


title: HCC827_RG7388

description: Library name: Sample 2


title: Scramble_CD4+IFNG-IL10-_1

description: Library name: 1


title: P3HR1 E2F1 WT(+ DOX) control

city: Kolkata

first: Joyanta

last: Biswas

state: West Bengal

address: Street-358, Action Area-1, Newtown

department: Institute of Health Sciences

country: India

institute: Presidency University

description: Library name: Sample3

data_processing:
High-quality reads were processed through Trimmomatic v0.35 to eliminate adapter sequences
The trimmed sequences were then aligned to the Human reference genome (Homo sapiens.GRCh37) using BWA v0.7.12 with default parameters.
Read counts were determined using featureCounts v2.0.3, followed by differential expression analysis conducted with DESeq v1.8.1
Assembly: hg38
Supplementary files format and content: Excel sheets containing DESeq output

extract_protocol:
RNA was extracted using the PureZOL™ RNA Isolation Reagent (Bio-Rad, USA).
A total of 5µg of RNA that passed quality control (QC) was utilized for library preparation employing the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760S/L).

value: EBV positive Burkitt's lymphoma cells

value: E2F1 KD (plus DOX)

tag: time

value: untreated


title: P3HR1 E2F1 WT(+ DOX) TPA-NaBu

description: Library name: Sample4

value: treated


title: AB18429

description: Library name: Sample4

value: PsA


title: P3HR1 E2F1 WT(-DOX) TPA-NaBu

description: Library name: Sample2

value: E2F1 WT (minus DOX) / E2F1 KD (plus DOX)


title: AB18426

description: Library name: Sample2

value: Blood


title: P3HR1 E2F1 WT(- DOX) control

description: Library name: Sample1


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, epidermis, lesion B, biopsy 1

city: Copenhagen

first: Terkild

middle: Brink

last: Buus

address: Blegdamsvej 3

department: ISIM

country: Denmark

institute: University of Copenhagen

description: Library name: PT23_Skin_Erythroderma_Epidermis_B.1

data_processing:
Sequencing reads from HTO and ADT libraries were counted using the Kallisto-KITE workflow [https://github.com/pachterlab/kite]. Sequencing reads from GEX and TCRαβ libraries were aligned and assembled using the CellRanger (v7.0.0) software. Ambient signal from GEX, ADT and HTO libraries was removed using CellBender (Fleming et al.). Initially cell barcodes having less than 100 genes detected or more than 50% of unique molecular identifiers (UMIs) derived from mitochondrial transcripts were removed. Further filtering was done following “overclustering” with scran::clusterCells clustering (NNGraphParam with k=5) and removal of clusters that consistently have low UMI counts, low number of genes detected and high fraction of UMIs derived from mitochondrial transcripts. Hashtagged cells were demultiplexed into their respective samples and cross-sample doublets were removed using the hashsolo function from the solo python library (Bernstein et al.). Some samples (primarily skin) were combined from multiple reaction wells (due to high cell numbers) during processing and each demultiplexed sample was exported as individual h5 files using DropletUtils::write10xCounts(type="HDF5") to make samples more accessible to the community.
Assembly: GRCh38
Supplementary files format and content: HDF5 Feature-Barcode Matrix (10X Genomics h5) containing unique molecular identifier counts for mRNA (GEX) and antibody derived tags (ADT) tagged with the feature types "Gene Expression" and "Antibody Capture", respectively.
Supplementary files format and content: Per barcode (cell) level filtered contig annotations of T cell receptor alpha and beta chains (in gzipped 10X Genomics csv format)

source_name: Skin

extract_protocol:
Lesional skin biopsies from L-CTCL patients were either processed as whole-skin or separated into dermis and epidermis by overnight incubation in 2.4mg/mL Dispase II in Phosphate-buffered Saline (PBS) at 4ºC. For whole-skin and dermis samples, the sample was cut into four equal size chunks and enzymatically digested using Miltenyi Whole Skin Dissociation (WSD) kit following manufacturer’s instructions with the exception that enzyme P was omitted to better preserve surface epitopes. Epidermis was digested using the Miltenyi WSD kit following manufacturer instructions with the same exception as above and only incubating 30 minutes at 37ºC.  Peripheral blood mononuclear cells (PBMCs) from blood of patients with L-CTCL were isolated by density gradient centrifugation following manufacturers protocol (StemCell Technologies). In most cases, PBMCs were cryopreserved in RPMI-1640 media containing 30% human serum and 10% DMSO. Cryopreserved PBMCs were thawed in 37ºC water bath and washed twice in RPMI-1650 containing 10% human serum and allowed to recover overnight before setting up experiments.  Samples from multiple compartments (dermis, epidermis and blood) as well as multiple donors were multiplexed using cell hashing and stained with oligo-conjugated antibodies targeting surface antigens (for CITE-seq) before proceeding to fluorescence activated cell sorting (FACS; for matched skin and blood samples) and subsequent single-cell segmentation using the 10X Chromium (Chromium Next GEM Single Cell 5’ reagent kit v2, 10X Genomics) following manufacturers instructions.
After cDNA synthesis, emulsion recovery and clean up following manufacturers instructions (Chromium Next GEM Single Cell 5’ reagent kit v2, 10X Genomics), full length cDNA was amplified by 13 cycles of PCR with addition of 25 nM of primers targeting the PCR handle present on all the hashtag oligo (HTO) antibodies (HTO_add: GTGACTGGAGTTCAGACGTGTGC*T*C) and antibody-derived tags (ADT; TotalSeq-C) antibodies (ADT_add: CTCGTGGGCTCGGAGATGTGTATAAGAG*A*C) together with the cDNA primers included in the Chromium Next GEM Single Cell 5’ reagent kit v2 (10X Genomics). Following size selection, HTO and ADT sequencing libraries were constructed separately from the small cDNA fraction by 9 and 12 cycles of PCR using TruSeq/TruSeq and TruSeq/Nextera P5/P7 indexing primers, respectively. Gene expression (GEX) and TCRαβ sequencing libraries were constructed from the large cDNA fraction following manufacturer’s instructions. HTO, ADT, GEX and TCRαβ libraries were sequencing together on Illumina NovaSeq 6000 aiming to reach at least 4000, 10000, 25000, and 3000 paired-end reads per cell for the respective libraries.

treatment_protocol: PBMCs cultured in the presence or absence of S. aureus enterotoxins or Romidepsin were kept in RPMI-1640 media supplemented with 10% human serum and 1% antibiotics (penicillin and streptomycin) in U-bottom 96-well plates containing up to 200x10^3 cells in 200µl

value: cutaneous T-cell lymphoma (L-CTCL)

value: Skin

value: Skin cells


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, dermis, lesion B, biopsy 2

description: Library name: PT23_Skin_Erythroderma_Dermis_B.2


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, epidermis, lesion B, biopsy 2

description: Library name: PT23_Skin_Erythroderma_Epidermis_B.2


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, dermis, lesion B, biopsy 1

description: Library name: PT23_Skin_Erythroderma_Dermis_B.1


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, epidermis, lesion A, biopsy 2

description: Library name: PT23_Skin_Erythroderma_Epidermis_A.2


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, dermis, lesion A, biopsy 1

description: Library name: PT23_Skin_Erythroderma_Dermis_A.1


title: L-CTCL Patient 23, PBMCs ex vivo

description: Library name: PT23_Blood

value: Peripheral Blood Mononuclear Cells


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, epidermis, lesion A, biopsy 2

description: Library name: PT22_Skin_Erythroderma_Epidermis_A.2


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, epidermis, lesion B, biopsy 1

description: Library name: PT22_Skin_Erythroderma_Epidermis_B.1


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, dermis, lesion A, biopsy 2

description: Library name: PT23_Skin_Erythroderma_Dermis_A.2


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, epidermis, lesion B, biopsy 2

description: Library name: PT22_Skin_Erythroderma_Epidermis_B.2


title: PTGIR_CD4+IFNG+IL10-_3

description: Library name: 14

value: PTGIR


title: Scramble_CD4+IFNG+IL10-_2

description: Library name: 11

value: Scramble


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, dermis, lesion A, biopsy 1

description: Library name: PT22_Skin_Erythroderma_Dermis_A.1


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, dermis, lesion B, biopsy 1

description: Library name: PT22_Skin_Erythroderma_Dermis_B.1


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, epidermis, lesion A, biopsy 1

description: Library name: PT22_Skin_Erythroderma_Epidermis_A.1


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, dermis, lesion A, biopsy 2

description: Library name: PT22_Skin_Erythroderma_Dermis_A.2


title: L-CTCL Patient 21, second timepoint +126 days, PBMCs ex vivo

description: Library name: PT21_Day126_Blood


title: L-CTCL Patient 21, first timepoint, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT21_Day0_Blood_PBS_72h

value: PBS

value: 72 hours


title: L-CTCL Patient 21, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT21_Day0_Blood_SE_72h

value: S. aureus enterotoxins


title: L-CTCL Patient 21, first timepoint, PBMCs ex vivo

description: Library name: PT21_Day0_Blood


title: L-CTCL Patient 20, PBMCs, cultured as PBS control for 144 hours

description: Library name: PT20_Blood_PBS_144h

value: 144 hours


title: L-CTCL Patient 20, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT20_Blood_SE_72h


title: L-CTCL Patient 20, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT20_Blood_PBS_72h


title: L-CTCL Patient 20, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT20_Blood_SE_48h

value: 48 hours


title: L-CTCL Patient 23, Skin biopsy from erythrodermic lesion, epidermis, lesion A, biopsy 1

description: Library name: PT23_Skin_Erythroderma_Epidermis_A.1


title: L-CTCL Patient 20, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT20_Blood_PBS_48h


title: L-CTCL Patient 20, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 24 hours

description: Library name: PT20_Blood_SE_24h

value: 24 hours


title: L-CTCL Patient 20, PBMCs, cultured as PBS control for 24 hours

description: Library name: PT20_Blood_PBS_24h


title: L-CTCL Patient 19, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT19_Blood_PBS_72h


title: L-CTCL Patient 19, PBMCs, cultured as PBS control for 144 hours

description: Library name: PT19_Blood_PBS_144h


title: L-CTCL Patient 19, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT19_Blood_PBS_48h


title: L-CTCL Patient 19, PBMCs, cultured as PBS control for 24 hours

description: Library name: PT19_Blood_PBS_24h


title: L-CTCL Patient 20, PBMCs, cultured as PBS control for 4 hours

description: Library name: PT20_Blood_PBS_4h

value: 4 hours


title: L-CTCL Patient 22, Skin biopsy from erythrodermic lesion, dermis, lesion B, biopsy 2

description: Library name: PT22_Skin_Erythroderma_Dermis_B.2


title: L-CTCL Patient 19, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 4 hours

description: Library name: PT19_Blood_SE_4h


title: L-CTCL Patient 19, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT19_Blood_SE_72h


title: L-CTCL Patient 22, PBMCs ex vivo

description: Library name: PT22_Blood


title: L-CTCL Patient 19, PBMCs, cultured as PBS control for 4 hours

description: Library name: PT19_Blood_PBS_4h


title: L-CTCL Patient 18, PBMCs ex vivo

description: Library name: PT18_Blood


title: L-CTCL Patient 20, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 4 hours

description: Library name: PT20_Blood_SE_4h


title: L-CTCL Patient 17, Skin biopsy from erythrodermic lesion_Whole-skin, cultured as PBS control for 36 hours

description: Library name: PT17_Skin_Erythroderma_Whole-skin_PBS_36h

value: 36 hours


title: L-CTCL Patient 17, PBMCs, cultured as PBS control for 36 hours

description: Library name: PT17_Blood_PBS_36h


title: L-CTCL Patient 15, PBMCs ex vivo

description: Library name: PT15_Blood


title: L-CTCL Patient 17, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 36 hours

description: Library name: PT17_Blood_SE_36h


title: L-CTCL Patient 19, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 24 hours

description: Library name: PT19_Blood_SE_24h


title: L-CTCL Patient 14, first timepoint, PBMCs ex vivo

description: Library name: PT14_Day0_Blood


title: L-CTCL Patient 19, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT19_Blood_SE_48h


title: L-CTCL Patient 20, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 144 hours

description: Library name: PT20_Blood_SE_144h


title: L-CTCL Patient 14, second timepoint +43 days, PBMCs ex vivo

description: Library name: PT14_Day43_Blood


title: L-CTCL Patient 11, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 144 hours

description: Library name: PT11_Blood_SE_144h


title: L-CTCL Patient 17, PBMCs_Romidepsin for 36 hours

description: Library name: PT17_Blood_Romidepsin_36h

value: Romidepsin


title: L-CTCL Patient 11, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT11_Blood_PBS_72h


title: L-CTCL Patient 11, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT11_Blood_SE_72h


title: L-CTCL Patient 11, PBMCs, cultured as PBS control for 144 hours

description: Library name: PT11_Blood_PBS_144h


title: L-CTCL Patient 11, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT11_Blood_SE_48h


title: L-CTCL Patient 19, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 144 hours

description: Library name: PT19_Blood_SE_144h


title: L-CTCL Patient 11, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT11_Blood_PBS_48h


title: L-CTCL Patient 11, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 24 hours

description: Library name: PT11_Blood_SE_24h


title: L-CTCL Patient 11, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 4 hours

description: Library name: PT11_Blood_SE_4h


title: L-CTCL Patient 11, PBMCs, cultured as PBS control for 4 hours

description: Library name: PT11_Blood_PBS_4h


title: L-CTCL Patient 12, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 144 hours

description: Library name: PT12_Blood_SE_144h


title: L-CTCL Patient 12, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT12_Blood_PBS_72h


title: L-CTCL Patient 12, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT12_Blood_SE_72h


title: L-CTCL Patient 12, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 24 hours

description: Library name: PT12_Blood_SE_24h


title: L-CTCL Patient 12, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT12_Blood_SE_48h


title: L-CTCL Patient 12, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT12_Blood_PBS_48h


title: L-CTCL Patient 12, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 4 hours

description: Library name: PT12_Blood_SE_4h


title: L-CTCL Patient 12, PBMCs, cultured as PBS control for 24 hours

description: Library name: PT12_Blood_PBS_24h


title: L-CTCL Patient 12, PBMCs, cultured as PBS control for 4 hours

description: Library name: PT12_Blood_PBS_4h


title: L-CTCL Patient 10, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT10_Blood_PBS_48h


title: L-CTCL Patient 10, PBMCs ex vivo

description: Library name: PT10_Blood


title: L-CTCL Patient 10, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT10_Blood_SE_48h


title: L-CTCL Patient 12, PBMCs, cultured as PBS control for 144 hours

description: Library name: PT12_Blood_PBS_144h


title: L-CTCL Patient 13, second timepoint +294 days, PBMCs ex vivo

description: Library name: PT13_Day294_Blood


title: L-CTCL Patient 08, second timepoint +266 days, PBMCs ex vivo

description: Library name: PT08_Day266_Blood


title: L-CTCL Patient 08, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT08_Day0_Blood_SE_72h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 144 hours

description: Library name: PT13_Day0_Blood_SE_144h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT13_Day0_Blood_SE_72h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT13_Day0_Blood_PBS_72h


title: L-CTCL Patient 08, first timepoint, PBMCs ex vivo

description: Library name: PT08_Day0_Blood


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT13_Day0_Blood_SE_48h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured as PBS control for 144 hours

description: Library name: PT13_Day0_Blood_PBS_144h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT13_Day0_Blood_PBS_48h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 24 hours

description: Library name: PT13_Day0_Blood_SE_24h


title: L-CTCL Patient 11, PBMCs, cultured as PBS control for 24 hours

description: Library name: PT11_Blood_PBS_24h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 4 hours

description: Library name: PT13_Day0_Blood_SE_4h


title: L-CTCL Patient 09, Skin biopsy from erythrodermic lesion, epidermis, lesion A

description: Library name: PT09_Skin_Erythroderma_Epidermis_A


title: L-CTCL Patient 09, PBMCs ex vivo

description: Library name: PT09_Blood


title: L-CTCL Patient 09, Skin biopsy from plaque lesion, dermis, lesion B

description: Library name: PT09_Skin_Plaque_Dermis_B


title: L-CTCL Patient 06, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT06_Blood_PBS_48h


title: L-CTCL Patient 06, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT06_Blood_SE_48h


title: L-CTCL Patient 04, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT04_Blood_SE_72h


title: L-CTCL Patient 07, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT07_Blood_SE_48h


title: L-CTCL Patient 04, PBMCs ex vivo

description: Library name: PT04_Blood


title: L-CTCL Patient 16, PBMCs ex vivo

description: Library name: PT16_Blood


title: L-CTCL Patient 16, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT16_Blood_SE_48h


title: L-CTCL Patient 07, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT07_Blood_PBS_48h


title: L-CTCL Patient 03, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT03_Blood_SE_48h


title: L-CTCL Patient 08, first timepoint, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT08_Day0_Blood_PBS_72h


title: L-CTCL Patient 03, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT03_Blood_PBS_72h


title: L-CTCL Patient 03, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 72 hours

description: Library name: PT03_Blood_SE_72h


title: L-CTCL Patient 03, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 144 hours

description: Library name: PT03_Blood_SE_144h


title: L-CTCL Patient 03, PBMCs, cultured as PBS control for 144 hours

description: Library name: PT03_Blood_PBS_144h


title: L-CTCL Patient 07, PBMCs ex vivo

description: Library name: PT07_Blood


title: L-CTCL Patient 16, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT16_Blood_PBS_48h


title: L-CTCL Patient 05, PBMCs ex vivo

description: Library name: PT05_Blood


title: L-CTCL Patient 09, Skin biopsy from erythrodermic lesion, dermis, lesion A

description: Library name: PT09_Skin_Erythroderma_Dermis_A


title: L-CTCL Patient 03, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 24 hours

description: Library name: PT03_Blood_SE_24h


title: L-CTCL Patient 03, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT03_Blood_PBS_48h


title: L-CTCL Patient 03, PBMCs, cultured as PBS control for 24 hours

description: Library name: PT03_Blood_PBS_24h


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured as PBS control for 24 hours

description: Library name: PT13_Day0_Blood_PBS_24h


title: L-CTCL Patient 03, PBMCs, cultured as PBS control for 4 hours

description: Library name: PT03_Blood_PBS_4h


title: L-CTCL Patient 09, Skin biopsy from plaque lesion, epidermis, lesion B

description: Library name: PT09_Skin_Plaque_Epidermis_B


title: L-CTCL Patient 13, first timepoint, PBMCs, cultured as PBS control for 4 hours

description: Library name: PT13_Day0_Blood_PBS_4h


title: L-CTCL Patient 04, PBMCs, cultured as PBS control for 72 hours

description: Library name: PT04_Blood_PBS_72h


title: L-CTCL Patient 06, PBMCs ex vivo

description: Library name: PT06_Blood


title: L-CTCL Patient 02, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT02_Blood_SE_48h


title: L-CTCL Patient 01, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT01_Blood_PBS_48h


title: L-CTCL Patient 01, PBMCs ex vivo

description: Library name: PT01_Blood


title: AB9853_SB201

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

value: Control


title: AB9856_SB201

value: Blood


title: AB9855_SB201


title: AB9851_SB201


title: L-CTCL Patient 02, PBMCs ex vivo

description: Library name: PT02_Blood

value: cutaneous T-cell lymphoma (L-CTCL)


title: L-CTCL Patient 03, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 4 hours

description: Library name: PT03_Blood_SE_4h


title: AB9854_SB201


title: L-CTCL Patient 02, PBMCs, cultured as PBS control for 48 hours

description: Library name: PT02_Blood_PBS_48h


title: AB9846_SB201


title: AB9845_SB201


title: AB9848_SB201


title: AB9847_SB201


title: AB9852_SB201


title: L-CTCL Patient 01, PBMCs, cultured in presence of Staphylococcus aureus enterotoxis for 48 hours

description: Library name: PT01_Blood_SE_48h


title: AB9850_SB201


title: AB9849_SB201


title: AB9841_SB201


title: AB9844_SB201


title: AB8937_SB195

value: PsA

value: Synovial fluid (SF)


title: AB9842_SB201


title: AB9840_SB201


title: AB9843_SB201


title: AB8932_SB195


title: AB9839_SB201


title: AB8936_SB195


title: AB8934_SB195


title: AB8931_SB195


title: AB8935_SB195


title: AB8933_SB195


title: AB8926_SB195


title: AB8930_SB195


title: AB8927_SB195


title: AB8929_SB195


title: AB8928_SB195


title: AB8924_SB195


title: AB8919_SB195

value: OA


title: AB8922_SB195


title: AB8917_SB195


title: AB8913_SB195


title: AB8912_SB195


title: AB8923_SB195


title: AB8914_SB195


title: AB8921_SB195


title: AB8915_SB195


title: AB8910_SB195


title: AB8918_SB195


title: AB8920_SB195


title: AB8909_SB195


title: AB8911_SB195


title: AB8906_SB195


title: AB8908_SB195


title: AB8899_SB195


title: AB8925_SB195


title: AB8905_SB195


title: AB8900_SB195


title: AB8901_SB195


title: AB8902_SB195


title: AB8896_SB195


title: AB8897_SB195


title: AB8898_SB195


title: AB8916_SB195


title: AB8755_SB194


title: AB8903_SB195


title: AB8751_SB194


title: AB8895_SB195


title: AB8904_SB195


title: AB8752_SB194


title: AB8894_SB195


title: AB8753_SB194


title: AB8557_SB193


title: AB8757_SB194


title: AB8756_SB194


title: AB8758_SB194


title: AB8750_SB194


title: AB8555_SB193


title: AB8907_SB195


title: AB8554_SB193


title: AB8754_SB194


title: AB8558_SB193


title: AB8556_SB193


title: AB8553_SB193


title: AB8551_SB193


title: AB8548_SB193


title: AB8549_SB193


title: AB8547_SB193


title: AB8550_SB193


title: AB8541_SB193


title: AB8546_SB193


title: AB8542_SB193


title: AB8538_SB193


title: AB8537_SB193


title: AB8544_SB193


title: AB8543_SB193


title: AB8533_SB193


title: AB8539_SB193


title: AB8552_SB193


title: AB8527_SB193


title: AB8534_SB193


title: AB8536_SB193


title: AB8531_SB193


title: AB8532_SB193


title: AB8530_SB193


title: AB8529_SB193


title: AB8540_SB193


title: AB8519_SB193


title: AB8520_SB193


title: AB8528_SB193


title: AB8526_SB193


title: AB8515_SB193


title: AB8514_SB193


title: AB8525_SB193


title: AB8524_SB193


title: AB8510_SB193


title: AB8512_SB193


title: AB8523_SB193


title: AB8522_SB193


title: AB8502_SB193


title: AB8518_SB193


title: AB8503_SB193


title: AB8501_SB193


title: AB8507_SB193


title: AB8511_SB193


title: AB8521_SB193


title: AB8504_SB193


title: AB8517_SB193


title: AB8513_SB193


title: AB8498_SB193


title: AB8495_SB193


title: AB8506_SB193


title: AB8505_SB193


title: AB8500_SB193


title: AB8499_SB193


title: AB8497_SB193


title: AB8516_SB193


title: AB8509_SB193


title: AB8508_SB193


title: AB8496_SB193


title: AB8487_SB193


title: AB8318_SB192


title: AB8494_SB193


title: AB8323_SB192


title: AB8316_SB192


title: AB8491_SB193


title: AB8314_SB192


title: AB8488_SB193


title: AB8307_SB192


title: AB8310_SB192


title: AB8486_SB193


title: AB8493_SB193


title: AB8489_SB193


title: AB8303_SB192


title: AB8485_SB193


title: AB8301_SB192


title: AB8336_SB192


title: AB8337_SB192


title: AB8335_SB192


title: AB8297_SB192


title: AB8293_SB192


title: AB8294_SB192


title: AB8321_SB192


title: AB8320_SB192


title: AB8312_SB192


title: AB8311_SB192


title: AB8317_SB192


title: AB8492_SB193


title: AB8490_SB193


title: AB8305_SB192


title: AB8298_SB192


title: AB8304_SB192


title: AB7606_SB187


title: AB7607_SB187


title: AB8300_SB192


title: AB7602_SB187


title: AB7604_SB187


title: AB7605_SB187


title: AB8302_SB192


title: AB7601_SB187


title: AB8299_SB192


title: AB8296_SB192


title: AB7597_SB187


title: AB7430_SB186


title: AB7427_SB186


title: AB8295_SB192


title: AB7425_SB186


title: AB7598_SB187


title: AB8535_SB193


title: AB7609_SB187


title: AB7608_SB187


title: AB7424_SB186


title: AB7600_SB187


title: AB7421_SB186


title: AB7599_SB187


title: AB7419_SB186


title: AB7428_SB186


title: AB7426_SB186


title: AB7416_SB186


title: AB7610_SB187


title: AB7411_SB186


title: AB7410_SB186


title: AB7603_SB187


title: AB7408_SB186


title: AB7423_SB186


title: AB7409_SB186


title: AB7402_SB186


title: AB7422_SB186


title: AB7420_SB186


title: AB7418_SB186


title: AB7429_SB186


title: AB7400_SB186


title: AB7414_SB186


title: AB7415_SB186


title: AB7413_SB186


title: AB7396_SB186


title: AB7392_SB186


title: AB7412_SB186


title: AB7406_SB186


title: AB7404_SB186


title: AB7388_SB186


title: AB7387_SB186


title: AB7405_SB186


title: AB7403_SB186


title: AB7401_SB186


title: AB7384_SB186


title: AB7383_SB186


title: AB6941_SB183


title: AB6940_SB183


title: AB7417_SB186


title: AB7399_SB186


title: AB6938_SB183


title: AB7397_SB186


title: AB7394_SB186


title: AB7395_SB186


title: AB7393_SB186


title: AB6933_SB183


title: AB6934_SB183


title: AB7391_SB186


title: AB7407_SB186


title: 1mM-DSG_G2

city: New York

first: Axel

last: Delamarre

state: NY

address: 411 E 67th st

institute: MSKCC

description: Library name: 1mM-DSG_G2

library_source: genomic

data_processing:
Alignment - deduplication - groupy - pairwise interaction
Assembly: saccer3
Supplementary files format and content: .hic or .mcool

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT

extract_protocol:
Cells were broken using Freezer/Mill (Spex SamplePrep ,6875D) for 5 cycles, 2 min, 15cps. After verification of the breakage under the microscope, cells were resuspended in 450µL of XLB3 (supplemented with Protease inhibitors, A32955, Pierce) and cross-linked by addition of DSG at 6mM final (Disuccinimidyl glutarate, A35392, ThermoFisher) for 30min at 30˚C. DSG was quenched by addition of 50µL of Tris 1M for 1min. Cells where wash 3 times HS buffer (Sorbitol 1M, Hepes pH 7.5 10mM) and resuspended in CAD-buffer (Sorbitol 1M, Hepes pH 7.5 10mM, DTT 5mM, IGEPAL 0.1%, MgCl2 1mM, Protease inhibitors A32955, Pierce ) and supplemented with pre activated CAD. Digestion reaction for 1hr at 37C with 1000 rpm agitation. Cells were placed on ice for 2 min and washed twice in SB buffer (10mM Hepes pH 7.5, 0.1% IGEPAL, 1mM EDTA, 1mM DTT) and resuspended in 300µL of SB. 100µL of cells were diluted in 300µL of SB and added to 50µL of pre-activated NHS beads (Pierce, 88827) and agitated for 10min at RT. Beads binding was quenched by addition of 30µL of TrisHCl 1M for 1 min. Beads were resuspended in 500µL of SB and supplemented with 3mM ZnCl2 final for 2min. Beads were washed twice in SB and resuspended in 500µL of SB. End-Repair and A-tailing was performed with the NEBNext Ultra II DNA library Prep Kit (NEB, E7645). 30min 20˚C 1 krpm, then 30min 65˚C 1 krpm. Cells were incubated 2 min on ice and washed twice in HB ( 10mM Hepes pH7.5, 1M NaCl, 0.5% Na-deoxycholate, 0.5% Triton X-100, 0.5% IGEPAL) and twice in SB buffer. Beads were resuspended in 100 µL of Hepes pH 7.5 10mM. 20µL of beads were incubated with 2µL of linker mixture at desired ratio at 25µM and 22µL Blunt/TA ligase (NEB, M0367L) for 40min at 20˚C. Beads were washes twice in HB and twice in SB. Beads were resuspended in 20µL of Hepes pH 7.5 10mM with 2µL of seed at 10ng.µL and 22µL of Blunt/TA ligase (NEB, M0367L) for 40min at 20˚C. Beads were washes twice in HB and twice in SB and resuspended in 20µL of Hepes pH 7.5 10mM. PCP reaction were realized on 1µL and 0.25µL of beads mixture in PCP buffer (HEPES pH 7.5 40mM, 6mM MgCl2,  2.5mM dNTP, 2.5 mM rMTP, 1mM DTT, 2.5% PEG 20K, 0.5 µL RNase inhibitor (Pierce, AM2694), 1µL of Reverse Transcriptase (ProtoScript II, NEB M0368), 3µL of T7 RNA Polymerase (NEB, M0251)) for 1hr at 30˚C. PCP reaction was supplemented 20µL Tris HCl pH 7.5 100M with 0.1 µL of RNAse cocktail (Invitrogen, AM2286) for at least 2 hours at 65˚C. The decrosslinked chromatin was supplemented with 17 µL of H2O, 1.5 µL of each of the PCR primers (any of the Illumina NEBNext primers, E6440S) at 10 µM and 50µL of KAPA RM (Roche, 07958927001) and incubated in the PCR reaction for 12 cycles ( 5min 95˚C, [20 sec 98˚C, 15 sec 71˚C, 1min 72˚C] x12, 2 min 72˚C, 4˚C).
Following PCP, the library was produced using Illumina P5 and P7 primer from NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7103)

value: WT


title: AB7390_SB186


title: AB7386_SB186


title: AB7385_SB186


title: AB6929_SB183


title: AB6939_SB183


title: AB6937_SB183


title: AB6942_SB183


title: AB6931_SB183


title: AB7389_SB186


title: AB6935_SB183


title: 6mM-DSG_G2

description: Library name: 6mM-DSG_G2


title: AB6924_SB183


title: AB6932_SB183


title: AB7398_SB186


title: WT-G2_rep2


title: 3mM-DSG_G2

description: Library name: 3mM-DSG_G2


title: AB6921_SB183


title: Rpb1AA_Rpb3AA_G1_test_rep1

description: Library name: Rpb1AA_Rpb3AA_G1_test_rep1

value: With Rapamycin


title: AB6930_SB183


title: AB6928_SB183


title: Rpb1AA_Rpb3AA_G1_control_rep2

description: Library name: Rpb1AA_Rpb3AA_G1_control_rep2

value: No rapamycin


title: AB6936_SB183


title: AB6927_SB183


title: Rpb1AA_Rpb3AA_G1_control_rep1

description: Library name: Rpb1AA_Rpb3AA_G1_control_rep1


title: AB6918_SB183


title: VAS5_8WK_WL_batch3

city: Newark

first: Kiloni

last: Quiles

state: NJ

address: 205 South Orange Avenue

department: Medicine

institute: Rutgers New Jersey Medical School

description: Library name: SAMPLE_30

data_processing:
Raw FastQ files of single paired-end reads were trimmed based on minimum Illumina phred scores of 33 using the Trimmomatic package version 0.36.
The trimmed sequences were aligned to bacterial, fungal, viral, and miscellaneous microbial gene indices downloaded from Refseq while filtering out samples that also aligned to human and mouse gene index hg19 from Refseq. Rsubread was used to align the same sequences to the Refseq mouse gene index mm10.
Raw RNA sequences feature counts and the pre-processing and sequence alignment code written by our lab is available on our Github repository.
Supplementary files format and content: Features combined text files show raw mouse gene counts annotated by ensemble IDs
Supplementary files format and content: Comma-separated value files show normalized microbiome expression for each sample

organism:
Mus musculus
lung metagenome

extract_protocol: Mice were euthanized and whole lungs were extracted and homogenized. Host and microbial RNA was extracted using our proprietary protocol, with a combination of Purelink RNA extraction and Dnase digest, Qiashredder, and Qiagen Rneasy mini kit.

treatment_protocol: Mice were maintained on VAS or VAD diets for 3 weeks and 8 weeks respectively.

value: Lung

tag: diet

tag: cell types

value: Eukaryote, Prokaryote

value: VAS


title: AB6926_SB183


title: AB6919_SB183


title: sth1aa_WR_pooled


title: snf2aa_WR


title: AB6925_SB183


title: AB6917_SB183


title: Rpb1AA_Rpb3AA_G1_test_rep2

description: Library name: Rpb1AA_Rpb3AA_G1_test_rep2


title: sth1aa_noR_pooled


title: AB6922_SB183


title: AB6923_SB183


title: VAS7_8WK_WL_batch3

description: Library name: SAMPLE_31


title: AB6914_SB183


title: VAS9_8WK_WL_batch3

description: Library name: SAMPLE_32


title: AB6920_SB183


title: HC_M3

city: Zhengzhou City

first: Xue

last: Cao

state: Henan Province

address: No. 7, Weiwu Road, Zhengzhou City, Henan Province

institute: Henan Provincial People's Hospital

description: Library name: Sample12

data_processing:
Long-read RNA sequencing was performed on AS and HC samples using ONT. Raw off-machine data were obtained in POD5 format containing signal-level information. Basecalling was carried out using Dorado (v0.8.2), which converted POD5 files into FASTQ sequences with associated quality scores.
Full-length reads were identified and trimmed using Pychopper (v2.7.9), and low-quality reads (mean Q score <10 or length <50 bp) were filtered with Chopper (v0.7.0). Clean reads were aligned to the Ensembl GRCh38_v45 reference genome using Minimap2 (v2.27-r1193) in spliced alignment mode with parameters -ax splice -uf -k14.
Isoform-level transcript detection and correction were performed with the Pinfish pipeline, and the resulting polished transcripts were output in GTF format. To create a comprehensive, non-redundant transcriptome across all samples, individual transcript assemblies were merged using StringTie (v2.1.6).
Annotation comparison against reference transcripts was conducted using GffCompare (v0.12.6) with parameters -G and -R, allowing classification of novel transcripts and genes. Transcript class codes [u, x, i, j, o] were considered novel, while [=, c] indicated known isoforms. All transcripts were merged and retained for downstream quantification and analysis.
Assembly: GRCh38_v45
Supplementary files format and content: tab delimited text file including the expression level (TPM values) of all samples at gene level.
Supplementary files format and content: tab delimited text file including the expression level (TPM values) of all samples at transcript level.

source_name: peripheral blood

extract_protocol:
Whole blood samples were obtained from 6 patients with AS (3 males and 3 females) who met the modified New York classification criteria, had comparable disease duration and inflammatory levels, and a Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) score ≥ 4. Age- and sex-matched healthy controls (HC) (n = 6) were included. Approximately 3~4 mL of whole blood was collected from each individual, and total RNA was extracted for subsequent long-read RNA sequencing using the ONT platform.
For each sample, 500 ng of total RNA was adjusted to 9 μL with nuclease-free water and mixed with 1 μL of 10 μM VNP primer and 1 μL of 10 mM dNTPs. The mixture was incubated at 65°C for 5 minutes and then immediately snap-cooled. Strand-switching buffer containing 5 × RT buffer, RNaseOUT, nuclease-free water, and a 10 μM strand-switching primer was added, followed by incubation at 42°C for 2 minutes. Subsequently, 1 μL of Maxima H Minus Reverse Transcriptase was added, and the reaction proceeded at 42°C for 90 minutes, followed by heat inactivation at 85°C for 5 minutes and cooling to 4°C. For cDNA amplification, 20 μL of first-strand product was combined with 2 μL each of PR1 and PR2 primers, 25 μL of LongAmp Taq 2 × Master Mix, and 1 μL of water. The PCR conditions were: 94°C for 3 minutes; 12 cycles of 94°C for 15 seconds, 50°C for 15 seconds, and 65°C for 2 minutes; and a final extension at 65°C for 10 minutes. Barcoding was performed using the ONT Native Barcoding Expansion Kit (SQK-NBD114.96) according to the manufacturer's protocol. Barcoded DNA was purified using 1 × AMPure XP beads, eluted in 20 μL of nuclease-free water, and quantified using a Qubit fluorometer. Finally, 300 fmol of adapter-ligated library was loaded onto a PromethION R10.4.4 flow cell and sequenced on the ONT platform.

value: peripheral blood


title: VAS4_3WK_WL_batch2

description: Library name: SAMPLE_26


title: HC_M2

description: Library name: Sample11

value: Age- and sex-matched healthy controls (HC)


title: VAS3_8WK_WL_batch3

description: Library name: SAMPLE_25


title: AB6912_SB183


title: WT-G2_rep1


title: WT-G1_rep2


title: VAS4_8WK_WL_batch3

description: Library name: SAMPLE_28


title: WT-G1_rep1


title: AB6916_SB183


title: HC_F3

description: Library name: Sample9


title: AB6907_SB183


title: AB6915_SB183


title: AB6913_SB183


title: AB6911_SB183


title: AB6904_SB183


title: VAS10_8WK_WL_batch3

description: Library name: SAMPLE_19


title: AB6910_SB183


title: HC_M1

description: Library name: Sample10


title: HC_F1

description: Library name: Sample7


title: VAS1_3WK_WL_batch3

description: Library name: SAMPLE_18


title: VAS3_3WK_WL_batch3

description: Library name: SAMPLE_24


title: AB6909_SB183


title: AB6908_SB183


title: AB6902_SB183


title: AB6901_SB183


title: AB6906_SB183


title: VAD7_8WK_WL_batch3

description: Library name: SAMPLE_15

value: Deficient

value: VAD


title: VAS2_3WK_WL_batch3

description: Library name: SAMPLE_21


title: AS_M1

description: Library name: Sample4

value: Ankylosing spondylitis (AS)


title: VAD5_8WK_WL_batch3

description: Library name: SAMPLE_14


title: AB6897_SB183


title: HC_F2

description: Library name: Sample8


title: VAS4_3WK_WL_batch3

description: Library name: SAMPLE_27

value: Control


title: AB6905_SB183


title: VAD5_3WK_WL_batch3

description: Library name: SAMPLE_13


title: VAD4_8WK_WL_batch3

description: Library name: SAMPLE_12


title: AS_M3

description: Library name: Sample6


title: AS_F1

description: Library name: Sample1


title: AB6903_SB183


title: VAD8_8WK_WL_batch3

description: Library name: SAMPLE_16


title: AS_M2

description: Library name: Sample5


title: AB6899_SB183


title: AB6702_SB181


title: AB6900_SB183


title: AB6701_SB181


title: AB6898_SB183


title: AB6698_SB181


title: AB6896_SB183


title: AB6895_SB183


title: AS_F2

description: Library name: Sample2


title: AB6894_SB183


title: AB6893_SB183


title: Mammary WildType, FVB/N mice, rep 7

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

country: United Kingdom

institute: CRUK Scotland Institute

description: Library name: CCR20190326_S18_CC37_10_4h

data_processing:
Quality Control with FastQC and FastQ Screen. Aligned to genome with version 2.1 of HiSat2 and sorted with Samtools version 1.2 using code following the format of `hisat2 -x path/to/index_hisat2/ --known-splicesite-infile path/to/mouse_38.95_splice_sites.txt --rna-strandness RF -1 path/to/{read1} -2 path/to/{read2} | samtools sort -o path/to/{samplename}.bam`. Counts tables for each bam file produced with version 0.11.2 of HTSeq Count. Format of code `htseq-count /path/to/{sample name}.bam -s reverse --mode=intersection-nonempty --type=exon --idattr=gene_id -f bam /path/to/Mus_musculus_GeneAnnot.GRCh38.95.gtf '>' tables/{sample name}.tsv`. Individual tables merged using base Linux commands.
Assembly: Ensemble 38.95 Mus Musculus.
Supplementary files format and content: raw_count_table.tsv file is a tab separated flat text file table of the counts for each sample of the Ensembl IDs.

organism: Mus musculus

source_name: Mammary

extract_protocol:
RNA was prepared from ~25mg of frozen tissue using Trizol (ThermoFisher) as per manufacturer instructions. For PyMT+ cell lines, cells lines were previously generated by Gounis et al., (Gounis et al, 2024), and plated at 0.5x106 - 1x106 cells per 10cm dish, 37°C/5% CO2 for 24 hours to achieve 80% confluence the next day. Cells were washed twice in ice-cold PBS, lysed into 1mL Trizol, and RNA prepped as manufacturer instructions.
Illumina TruSeq RNA Library Prep kit v2

value: Mammary


title: AB6696_SB181


title: AB6704_SB181


title: VAD2_3WK_WL_batch3

description: Library name: SAMPLE_5


title: AB6695_SB181


title: AB6694_SB181


title: VAD4_3WK_WL_batch3

description: Library name: SAMPLE_11


title: Mammary WildType, FVB/N mice, rep 8

description: Library name: CCR20190326_S19_CC39_11_4h


title: VAD3_8WK_WL_batch3

description: Library name: SAMPLE_9


title: AS_F3

description: Library name: Sample3


title: AB6691_SB181


title: AB6700_SB181


title: AB6699_SB181


title: Mammary WildType, FVB/N mice, rep 6

description: Library name: CCR20190326_S17_CC35_11_1f


title: AB6697_SB181


title: AB6688_SB181


title: AB6687_SB181


title: VAD2_8WK_WL_batch3

description: Library name: SAMPLE_6


title: AB6703_SB181


title: VAS2_3WK_BALF_batch1

description: Library name: SAMPLE_35

source_name: BALF

value: BALF


title: Mammary WildType, FVB/N mice, rep 5

description: Library name: CCR20190326_S16_CC33_8_3g


title: VAD7_3WK_BALF_batch1

description: Library name: SAMPLE_34


title: Mammary tumor, MMTV-PyMT, rep 31

description: Library name: CCR20190326_S15_CC30_12_5i


title: VAD10_8WK_WL_batch3

description: Library name: SAMPLE_3


title: AB6692_SB181

value: PsA


title: AB6684_SB181

value: Synovial fluid (SF)


title: Mammary tumor, MMTV-PyMT, rep 30

description: Library name: CCR20190326_S14_CC27_34_3d


title: AB6682_SB181


title: VAD3_3WK_WL_batch3

description: Library name: SAMPLE_8


title: VAD1_3WK_WL_batch3

description: Library name: SAMPLE_2


title: Mammary tumor, MMTV-PyMT, rep 29

description: Library name: CCR20190326_S13_CC26_10_3i


title: AB6690_SB181


title: AB6689_SB181


title: VAS3_3WK_BALF_batch1

description: Library name: SAMPLE_36


title: AB6686_SB181


title: AB6693_SB181


title: VAS3_3WK_WL_batch2

description: Library name: SAMPLE_23


title: Mammary tumor, MMTV-PyMT, rep 24

description: Library name: CCR20190326_S08_CC15_33_5h


title: Mammary tumor, MMTV-PyMT, rep 27

description: Library name: CCR20190326_S11_CC22_11_1d


title: Mammary tumor, MMTV-PyMT, rep 23

description: Library name: CCR20190326_S07_CC14_10_4j


title: Mammary tumor, MMTV-PyMT, rep 22

description: Library name: CCR20190326_S06_CC12_34_3e


title: Mammary tumor, MMTV-PyMT, rep 26

description: Library name: CCR20190326_S10_CC20_10_4f


title: VAD5_3WK_BALF_batch1

description: Library name: SAMPLE_33


title: AB6683_SB181


title: Mammary tumor, MMTV-PyMT, rep 25

description: Library name: CCR20190326_S09_CC18_34_3a


title: AB6681_SB181


title: Mammary tumor, MMTV-PyMT, rep 28

description: Library name: CCR20190326_S12_CC24_11_4k


title: VAS5_3WK_WL_batch3

description: Library name: SAMPLE_29


title: AB6685_SB181


title: AB6680_SB181


title: VAD4_3WK_WL_batch2

description: Library name: SAMPLE_10


title: AB6658_SB181


title: VAS2_8WK_WL_batch3

description: Library name: SAMPLE_22


title: AB6666_SB181


title: VAD3_3WK_WL_batch2

description: Library name: SAMPLE_7


title: AB6665_SB181


title: AB6678_SB181


title: VAS2_3WK_WL_batch2

description: Library name: SAMPLE_20


title: Mammary tumor, MMTV-PyMT, rep 18

description: Library name: CCR20190326_S02_CC4_9_6b


title: AB6664_SB181


title: AB6663_SB181


title: Mammary tumor, MMTV-PyMT, rep 17

description: Library name: CCR20190326_S01_CC2_33_4g


title: AB6655_SB181


title: AB6656_SB181


title: Mammary WildType, FVB/N mice, rep 4

description: Library name: CCR20190325_S20_CC38_10_4i


title: Mammary tumor, MMTV-PyMT, rep 21

description: Library name: CCR20190326_S05_CC9_11_1c


title: AB6662_SB181


title: Mammary tumor, MMTV-PyMT, rep 20

description: Library name: CCR20190326_S04_CC8_38_1g


title: AB6660_SB181


title: AB6661_SB181


title: AB6679_SB181


title: hypoxia,input

city: Beijing

first: Yubing

last: Zeng

address: 9 Dongdan Santiao, Dongcheng District,

institute: Peking union medical college

description: HYP input

data_processing:
After getting  Raw data , we will do each bioinformitics analysis as the client appoints on contract. After sequencing data was delivered, we did data filtering first, which could remove low quality reads, N reads and adaptor sequences, and get clean data.
Then, we mapped clean data to reference genome when we made sure the data quantity of clean data was qualified. Also, we needed to make a quality test about the alignment.
Then we used the alignment result to calling peak.
Later, we used the peak information for standard bioinformatics analysis and personalized bioinformatics analysis.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: peak-gene.txt

source_name: lung

extract_protocol:
lung tissues were fixed with 1.5% formaldehyde for 20minutes.After nucleus preparation and chromatin digestion, samples were sonicated using Agilent2200 and add primary antibody and beads.
(1) DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. (2) PCR amplification and size selection (usually 100-300bp, including adaptor sequence). (3) Qualified library for sequencing.

value: lung

value: hypoxia


title: AB6659_SB181


title: Mammary tumor, MMTV-PyMT, rep 19

description: Library name: CCR20190326_S03_CC7_36_1e


title: AB6652_SB181


title: Mammary WildType, FVB/N mice, rep 2

description: Library name: CCR20190325_S18_CC34_8_3j


title: normoxia,input

description: CON input

value: normoxia


title: AB6651_SB181


title: AB6657_SB181


title: knock down Hif-1α after hypoxia,input

description: HIF-KD input

value: knock down Hif-1α after hypoxia


title: VAD1_3WK_WL_batch2

description: Library name: SAMPLE_1

value: Lung

value: WT


title: VAD2_3WK_WL_batch2

description: Library name: SAMPLE_4

value: Eukaryote, Prokaryote


title: knock down Hif-1α after hypoxia,Kla,ChIP,rep1

description: HIF-KD


title: AB6654_SB181


title: vHip,Social Isolation_Nr3c1 shRNA,rep3

first: Zhuo

last: Wang

address: 382 Waihuan East Road, Panyu District, Guangzhou City, Guangdong Province

institute: South China University of Technology

description: Library name: SI-Nr3c1-shRNA-3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating raw counts and FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCm39
Supplementary files format and content: xlsx file includes FPKM values for each Sample
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: ventral hippocampus

growth_protocol: Male Camk2a-Cre C57BL/6 mice aged 8–12 weeks were housed in specific pathogen-free (SPF) conditions under a 12-hour light/dark cycle, with ambient temperature maintained at 20–24°C an d relative humidity at 50–60%, while food and water were provided ad libitum.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were 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 then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. 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. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: At the beginning of model establishment, mice in the GL-SC-shRNA group were stereotactically injected with AAV5-CAG-DIO-SC-shRNA (200 μl, 2.00E+2 vg/mL, brainVTA) into the ventral hippocampus. Mice in the SI-SC-shRNA group were also stereotactically injected with AAV5-CAG-DIO-SC-shRNA (200 μl, 2.00E+12 vg/mL, brainVTA) into the ventral hippocampus. Mice in the SI-Nr3c1-shRNA group were stereotactically injected with AAV5-CAG-DIO-Nr3c1-shRNA (200 μl, 2.00E+12 vg/mL, brainVTA) into the ventral hippocampus. During the model - building period, mice in the GL group were housed in cages with 5 mice per cage, while mice in the social isolation (SI) group were individually housed in cages with 1 mouse per cage. The model - building process lasted for four weeks.

value: ventral hippocampus

value: Nr3c1 knockdown

value: Social Isolation


title: VAS1_3WK_WL_batch2

description: Library name: SAMPLE_17

value: VAS


title: hypoxia,Kla,ChIP,rep1

description: HYP


title: Mammary WildType, FVB/N mice, rep 1

description: Library name: CCR20190325_S17_CC32_8_3f


title: Mammary tumor, MMTV-PyMT, rep 16

description: Library name: CCR20190325_S16_CC31_9_6g


title: AB6650_SB181


title: AB6649_SB181


title: vHip,Social Isolation_Nr3c1 shRNA,rep1

description: Library name: SI-Nr3c1-shRNA-1


title: Mammary tumor, MMTV-PyMT, rep 14

description: Library name: CCR20190325_S14_CC28_10_4k


title: normoxia,Kla,ChIP,rep1

description: CON


title: AB6653_SB181


title: vHip,Social Isolation_Nr3c1 shRNA,rep2

description: Library name: SI-Nr3c1-shRNA-2


title: Mammary tumor, MMTV-PyMT, rep 12

description: Library name: CCR20190325_S12_CC23_34_2d


title: AB6648_SB181


title: Mammary WildType, FVB/N mice, rep 3

description: Library name: CCR20190325_S19_CC36_10_4g


title: Mammary tumor, MMTV-PyMT, rep 15

description: Library name: CCR20190325_S15_CC29_11_4j


title: Mammary tumor, MMTV-PyMT, rep 11

description: Library name: CCR20190325_S11_CC21_36_1d


title: vHip,Social Isolation_Scramble shRNA,rep1

description: Library name: SI-SC-shRNA-1

value: Scramble shRNA control


title: Mammary tumor, MMTV-PyMT, rep 10

description: Library name: CCR20190325_S10_CC19_9_6h


title: Male Inha KO, DEHP 500, rep 2

city: Clayton

first: Kate

last: Loveland

state: Victoria

address: 27-31 Wright St

institute: Hudson Institute of Medical Research

data_processing:
Parsing and base calling performed using Dragen BCLConvert 3.10.11
Data processed using nf-core/rnaseq 3.0.1 pipeline
Assembly: Reference genome: Mus musculus/Ensembl/GRCm39.release-109
Supplementary files format and content: Excel file containing raw counts for all samples

source_name: Male E15.5 placenta

extract_protocol:
RNA for all samples extracted using the RNeasy mini kit (Qiagen), 25ng of RNA from each sample used for library preparation
Novel RNA-Seq pipeline (version 01/09/2021) developed by the MHTP Genomics facility

treatment_protocol: 500 mg/kg/day of DEHP dissolved in corn oil, or equivalent volume of corn oil, delivered orally to pregnant dams from E12.5-14.5

value: Male E15.5 placenta

value: Inha KO

value: DEHP 500 mg/kg/day


title: Mammary tumor, MMTV-PyMT, rep 9

description: Library name: CCR20190325_S09_CC17_34_2h

value: Mammary


title: AB6644_SB181

value: PsA

value: Synovial fluid (SF)


title: vHip,Group Living_Scramble shRNA,rep3

description: Library name: GL-SC-shRNA-3

value: Group Living


title: AB6643_SB181


title: Male Inha KO, DEHP 500, rep 1


title: vHip,Group Living_Scramble shRNA,rep2

description: Library name: GL-SC-shRNA-2


title: vHip,Group Living_Scramble shRNA,rep1

description: Library name: GL-SC-shRNA-1


title: Mammary tumor, MMTV-PyMT, rep 8

description: Library name: CCR20190325_S08_CC16_12_5g


title: Female Inha KO, DEHP 500, rep 2

source_name: Female E15.5 placenta

value: Female E15.5 placenta


title: AB6642_SB181


title: Female Inha KO, DEHP 500, rep 1


title: Female Inha KO, DEHP 500, rep 3


title: vHip,Social Isolation_Scramble shRNA,rep2

description: Library name: SI-SC-shRNA-2


title: AB6640_SB181


title: A_LDHB inhibition3

city: Jinan

first: Tiantian

middle: tian

last: Deng

address: Jinan Qianfoshan street

institute: Shandong University

description: Library name: Sample6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38.V101
Supplementary files format and content: Excel file includes FPKM values for each Sample

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: LDHB inhibition(AXKO-0046)


title: AB6646_SB181


title: AB6647_SB181


title: Mammary tumor, MMTV-PyMT, rep 7

description: Library name: CCR20190325_S07_CC13_36_1g


title: vHip,Social Isolation_Scramble shRNA,rep3

description: Library name: SI-SC-shRNA-3


title: AB6641_SB181


title: Male Inha Het, DEHP 500, rep 2

value: Inha Het


title: AB6645_SB181


title: Mammary tumor, MMTV-PyMT, rep 6

description: Library name: CCR20190325_S06_CC11_33_4h


title: Male Inha Het, DEHP 500, rep 3


title: Mammary tumor, MMTV-PyMT, rep 3

description: Library name: CCR20190325_S03_CC5_10_3h


title: AB6639_SB181


title: A_LDHB inhibition2

description: Library name: Sample5

value: WT


title: AB6637_SB181


title: A_LDHB inhibition1

description: Library name: Sample4


title: Mammary tumor, MMTV-PyMT, rep 2

description: Library name: CCR20190325_S02_CC3_11_4i


title: Mammary tumor, MMTV-PyMT, rep 4

description: Library name: CCR20190325_S04_CC6_9_6f


title: C_Control3

description: Library name: Sample3

value: Control


title: AB6635_SB181


title: AB6638_SB181


title: Male Inha Het, DEHP 500, rep 1


title: C_Control2

description: Library name: Sample2


title: EC, 354 EC KO_TAC, 4 weeks

city: Boston

first: Erin

last: Sanders

state: MA

address: 150 Harrison Ave

institute: Tufts University

description:
Library name: 15_354_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:15_354_TAC

data_processing:
The resulting reads in fastq format were mapped to the mouse reference genome (UCSC mm10) using HISAT2 (Version2.1.0). The resulting alignment file in BAM format was used as input to generate a raw count matrix using FeatureCounts (Subread package), with USCS mm10 GTF as the annotation. The raw read count matrix was then used as input for downstream analyses using Qlucore Omics Explorer.  The normalization, quantification, different expression analysis, and visualization were all performed using Qlucore Omics Explorer following manufacturer recommendations.
Assembly: mm10
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Heart

extract_protocol:
RNA was extracted using Quigen RNAEasy Plus kit. XXμg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNASeq were prepared using TrueSeq Library Prep kit according the manufacturers instructions.

value: Heart

value: Endothelial Cells

value: EC STING KO

value: TAC


title: AB6636_SB181


title: Mammary tumor, MMTV-PyMT, rep 1

description: Library name: CCR20190325_S01_CC1_35_5f


title: Female Inha Het, DEHP 500, rep 2


title: Chr_ABBM4307-p_pre, pBM19_ABBM4307-p_pre, pBM69_ABBM4307-p_pre rep3

city: Trondheim

first: Luciana

last: Fernandes de Brito

address: Kjemi 3, 3.237, Gløshaugen, Sem Sælandsvei 6/8

department: Department of Biotechnology and food science

country: Norway

institute: Norwegian University of Science and Technology

description:
MAPTOCHR_ABBM4307-p_pre_3
MAPTOPBM19_ABBM4307-p_pre_3
MAPTOPBM69_ABBM4307-p_pre_3

data_processing:
Paired-end reads generated from the RNA-seq were aligned to the B. methanolicus MGA3 genome reference sequences, encompassing the chromosome as well as the two plasmids pBM19 and pBM69 (GenBank accession numbers CP007739, CP007741, and CP007740, respectively). Before the alignment, the reads underwent trimming with a minimum length of 36 base pairs using the Trimmomatic v0.33 tool (doi.org/10.1093/bioinformatics/btu170). The trimmed reads were then aligned to the reference sequences using the short-read alignment software Bowtie 2 (https://doi.org/10.1038/nmeth.1923). The ReadXplorer software v2 (https://doi.org/10.1093/bioinformatics/btw541) was employed for visualizing the mapped reads, conducting read counts, and determining RPKM (reads per kilobase per million mapped reads) values.
Assembly: not provided
Supplementary files format and content: Processed data is presented in .xls format, it contains raw and normalized read counts.

organism: Bacillus methanolicus

extract_protocol:
For the total RNA extraction from the tested B. methanolicus strains, we employed the NucleoSpin RNA isolation kit (Macherey-Nagel) and the RNase-free DNase set (Qiagen), following the manufacturers’ protocols.
https://doi.org/10.3389/fmicb.2019.01725

value: bacteria

value: mutant-p

value: random mutagenesis; uninduced plasmid expression


title: AB6633_SB181


title: C_Control1

description: Library name: Sample1


title: Chr_ABBM4307-p_pre, pBM19_ABBM4307-p_pre, pBM69_ABBM4307-p_pre rep2

description:
MAPTOCHR_ABBM4307-p_pre_2
MAPTOPBM19_ABBM4307-p_pre_2
MAPTOPBM69_ABBM4307-p_pre_2


title: Female Inha Het, DEHP 500, rep 1

value: DEHP 500 mg/kg/day


title: Female Inha Het, DEHP 500, rep 3


title: Mammary tumor, MMTV-PyMT, rep 5

description: Library name: CCR20190325_S05_CC10_11_3e

value: Mammary


title: AB6634_SB181

value: PsA


title: EC, 351 EC KO_TAC, 4 weeks

description:
Library name: 12_351_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:12_351_TAC


title: EC, 352 EC KO_TAC, 4 weeks

description:
Library name: 13_352_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:13_352_TAC


title: Male Inha WT, DEHP 500, rep 3

value: Male E15.5 placenta

value: Inha WT


title: Chr_ABBM4307-p_pre, pBM19_ABBM4307-p_pre, pBM69_ABBM4307-p_pre rep1

description:
MAPTOCHR_ABBM4307-p_pre_1
MAPTOPBM19_ABBM4307-p_pre_1
MAPTOPBM69_ABBM4307-p_pre_1


title: Male Inha WT, DEHP 500, rep 1


title: AB6631_SB181

value: Synovial fluid (SF)


title: AB6632_SB181


title: Female Inha WT, DEHP 500, rep 3

value: Female E15.5 placenta


title: SeqScope_1st

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Synthetic ssDNA library

data_processing:
Sequencing by Illumina HiSeqX, HiSeq4000 and NovaSeq platforms .
Seq-Scope data were initially processed using the STtools package, utilizing STAR/STARsolo 2.7.5c, with a modification to use hexagonal array, instead of square array. The processed DGE matrix, pooled in non-overlapping hexagons with 12 μm sides, was analyzed in the Seurat V4 package.
First, we removed all genes starting with mt and Gm to remove mitochondrial genes and hypothetical gene models. Then feature number <75 was removed, and data were normalized using regularized negative binomial repression implemented in Seurat’s SCTransform function.
Clustering analysis was performed using the shared nearest neighbor modularity optimization implemented in Seurat’s FindClusters function. The clusters were visualized in the UMAP (uniform manifold approximation and projection) manifold or the histological space using ggplot functions. The markers for each cluster were identified through the FindAllMarkers function and used to annotate cell types.
The clusters identified from initial non-overlapping hexagonal array were projected onto the multiscale sliding windows (MSSW) array, which has four-times higher resolution compared to the original non-overlapping array , using FindTransferAnchors, TransferData, and GetTransferPredictions functions, so that we can achieve higher resolution for cell type predictions.
Assembly: mm10
Supplementary files format and content: Digital expression matrix with barcode featuring spatial coordinates

organism: synthetic construct

growth_protocol: Normal rearing condition

extract_protocol:
The experimental procedures were performed as we previously described, but it was adapted to HISEQ2500 flow cell system so that Seq-Scope has wider and continuous imaging area (1.5 mm × 60 mm in HISEQ2500, compared to 1 mm-diameter circles in MISEQ). A single imaging area was used for all 20 samples to minimize the experimental batch effects. In brief, HDMI32-Dral [Seed HDMI-oligo, containing the PCR/read adaptor sequences, the restriction enzyme-cleavable RNA-capture domain (olido-dT), the high-definition map coordinate identifier (HDMI), a spatial barcode composed of a 32 random nucleotide sequence] was amplified on a flow cell surface to generate HDMI-oligo cluster. The HDMI sequence and coordinates of each cluster were determined using the HISEQ2500 platform. Thumbnail images of clusters were visualized using Illumina Sequencing Analysis Viewer to inspect the cluster morphology and density. Next, the HISEQ2500 flow cell was processed to expose the oligo-dT and RNA-capture domain and generate an HDMI-encoded RNA-capturing array (HDMI-array). Subsequently, the HISEQ2500 flow cell was disassembled to expose the HDMI-array to the outside and used for tissue attachment. The OCT-mounted fresh frozen aortic tissue was sectioned 10 μm thickness in a cryostat (Leica CM3050S, -20°C) and the aortic sections were maneuvered onto the HDMI-array slide. After fixing in 4% formaldehyde for 10 min and incubating in isopropanol for 2 min, the tissue was stained with hematoxylin (Agilent, S3309) for 5 min, treated with bluing buffer (Agilent, CS702) for 2 min, and incubated with buffered eosin [1:9 = eosin (HT110216, Sigma): 0.45M Tris-Acetic buffer (pH 6.0)]. After mounting in 85% glycerol, the tissues were imaged under a digital imager (Keyence, BZ-X800).
Total RNAs released from the fixed tissues were performed as previously described13. Briefly, the fixed tissues attached on the HDMI-array slide were treated with 0.2 U/μl collagenase I (Thermo Fisher, 17018-029) at 37 °C for 20 min, and then incubated with 1mg/ml pepsin (Sigma, P7000) in 0.1M HCl at 37 °C for 10 min. The RNAs released from the tissue sections were captured by the HDMI-array and used as a template to generate cDNA footprints on the HDMI-barcoded RNA capturing molecule by reverse transcription. After overnight reverse transcription reaction at 37 °C, the tissues were incubated in exonuclease I cocktail [1U Exo I enzyme (M2903, NEB) in 1x Exo I buffer] and subsequently digested in 1x tissue digestion buffer [100 mM Tris pH8.0, 100mM NaCl, 2% SDS, 5mM EDTA, 16 U/ml Proteinase K (P8107S, NEB)]. After tissue digestion, the secondary strand, a chimeric molecule of HDMI and cDNA sequences, is synthesized on the cDNA footprint using an adaptor-tagged random primer (Truseq Read 2-conjugated Random Primer version 2 with TCA GAC GTG TGC TCT TCC GAT CTN NNN NNN NB sequence). After removing all DNAs that did not bind to the HDMI-array, the secondary strand product was eluted using NaOH, and after neutralization, purified using AMPure XP purification kit (A63881, Beckman Coulter). The secondary strand product was used as a template to construct library using Kapa HiFi Hotstart Readymix (KK2602, KAPA Biosystems) through two rounds of library PCR. After purification using Zymoclean Gel DNA recovery Kit (D4001, Zymo Research) and AMPure XP, the pooled libraries were subjected to paired-end (100-150bp) sequencing in the Illumina platform at Psomagen lnc.

treatment_protocol: Sixteen-week-old Apoe -/- male mice fed a normal diet were subcutaneously implanted minipumps to delivery AngII (1,000ng/ml, 5 mice) or saline (5 mice) for 4 weeks. No significant difference was found in body weight, TC, and TG between the two groups at 4 weeks after minipump implantation. The extraluminal diameters were significantly increased in AngII group, in which 3 mice developed AAA (60% incidence). The fresh frozen suprarenal abdominal aortas from 3 AAAs and 3 normal controls were pair-embedded in OCT and cut into 10 μm sections. A total of 20 aortic sections (10 normal aortic sections and 10 aneurysmal sections) were attached onto HDMI-array slide for histological staining, library preparation and sequencing.

value: synthetic


title: AB6630_SB181

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

extract_protocol:
Synovial fluid mononuclear cells and blood mononuclear cells were isolated within maximum 4 hours of sample collection. Synovial fluid samples were first filtered by 100-micron strainer into 50 ml tube and diluted 1:1 with ice cold FACS buffer (2mM EDTA, Ph 8.0, 0.5% bovine serum albumin in PBS). Blood samples were diluted 1:1 with ice cold FACS buffer. Synovial fluid and blood mononuclear cell separation was performed using density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with the diluted synovial fluid or blood sample. Centrifugation (460g, 25min) was performed at 10◦C and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After a short centrifuge (360g, 5min), we resuspended the cell pellet in cryopreservation media (FCS+10%DMSO) and stored the samples in cryotube at -80◦C. Prior to single-cell sorting, samples were quickly defrosted at 37◦C bath and washed with heated (37 ◦C) RPMI-1640. We resuspended the cells in FACS buffer for staining and sorting.
3' end mRNA libraries were prepared for sequencing using SPID-seq (Yofe et al, Cancer Discovery 2023)


title: EC, 349 EC KO_Sham, 4 weeks

description:
Library name: 10_349_Sham
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:10_349_Sham

value: Sham


title: Chr_ABBM4307-p_post, pBM19_ABBM4307-p_post, pBM69_ABBM4307-p_post rep3

description:
MAPTOCHR_ABBM4307-p_post_3
MAPTOPBM19_ABBM4307-p_post_3
MAPTOPBM69_ABBM4307-p_post_3

value: random mutagenesis; induced plasmid expression


title: EC, 350 EC KO_Sham, 4 weeks

description:
Library name: 11_350_Sham
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:11_350_Sham

value: Heart


title: AB6629_SB181


title: EC, 353 EC KO_TAC, 4 weeks

description:
Library name: 14_353_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:14_353_TAC

value: Endothelial Cells


title: Chr_ABBM4307-p_post, pBM19_ABBM4307-p_post, pBM69_ABBM4307-p_post rep2

description:
MAPTOCHR_ABBM4307-p_post_2
MAPTOPBM19_ABBM4307-p_post_2
MAPTOPBM69_ABBM4307-p_post_2


title: Female Inha WT, DEHP 500, rep 2


title: Chr_ABBM4307-p_post, pBM19_ABBM4307-p_post, pBM69_ABBM4307-p_post rep1

description:
MAPTOCHR_ABBM4307-p_post_1
MAPTOPBM19_ABBM4307-p_post_1
MAPTOPBM69_ABBM4307-p_post_1


title: Male Inha WT, DEHP 500, rep 2


title: Female Inha WT, DEHP 500, rep 1


title: AB6628_SB181


title: EC, 138 WT_TAC, 4 weeks

description:
Library name: 8_138_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:8_138_TAC

value: WT


title: Chr_ABBM4307, pBM19_ABBM4307, pBM69_ABBM4307 rep3

description:
MAPTOCHR_ABBM4307_3
MAPTOPBM19_ABBM4307_3
MAPTOPBM69_ABBM4307_3

value: mutant

value: random mutagenesis


title: AB6627_SB181


title: Male Inha KO, corn oil, rep 2

value: Inha KO

value: Corn oil


title: EC, 137 WT_TAC, 4 weeks

description:
Library name: 7_137_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:7_137_TAC

value: TAC


title: Chr_ABBM4307, pBM19_ABBM4307, pBM69_ABBM4307 rep2

description:
MAPTOCHR_ABBM4307_2
MAPTOPBM19_ABBM4307_2
MAPTOPBM69_ABBM4307_2

value: bacteria


title: AB6626_SB181

value: PsA


title: Male Inha KO, corn oil, rep 1

value: Male E15.5 placenta


title: EC, 136 WT_TAC, 4 weeks

description:
Library name: 6_136_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:6_136_TAC


title: Chr_ABBM4307, pBM19_ABBM4307, pBM69_ABBM4307 rep1

description:
MAPTOCHR_ABBM4307_1
MAPTOPBM19_ABBM4307_1
MAPTOPBM69_ABBM4307_1


title: AB6625_SB181


title: Female Inha KO, corn oil, rep 3


title: AB6624_SB181


title: Female Inha KO, corn oil, rep 2


title: EC, 135 WT_TAC, 4 weeks

description:
Library name: 5_135_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:5_135_TAC


title: Chr_MGA3-p, pBM19_MGA3-p, pBM69_MGA3-p rep3

description:
MAPTOCHR_MGA3-p_3
MAPTOPBM19_MGA3-p_3
MAPTOPBM69_MGA3-p_3

value: wt-p

value: plasmid expression


title: EC, 134 WT_TAC, 4 weeks

description:
Library name: 4_134_TAC
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:4_134_TAC


title: Male Inha KO, DEHP 500, rep 3

value: DEHP 500 mg/kg/day


title: Female Inha KO, corn oil, rep 1

value: Female E15.5 placenta


title: Chr_MGA3-p, pBM19_MGA3-p, pBM69_MGA3-p rep1

description:
MAPTOCHR_MGA3-p_1
MAPTOPBM19_MGA3-p_1
MAPTOPBM69_MGA3-p_1


title: AB6623_SB181

value: Synovial fluid (SF)


title: EC,  133 WT_Sham, 4 weeks

description:
Library name: 3_133_Sham
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:3_133_Sham

value: Sham


title: EC, 348 EC KO_Sham, 4 weeks

description:
Library name: 9_348_Sham
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:9_348_Sham

value: Heart

value: EC STING KO


title: AB6622_SB181


title: Male Inha Het, corn oil, rep 3

value: Inha Het


title: Chr_MGA3-p, pBM19_MGA3-p, pBM69_MGA3-p rep2

description:
MAPTOCHR_MGA3-p_2
MAPTOPBM19_MGA3-p_2
MAPTOPBM69_MGA3-p_2


title: Male Inha Het, corn oil, rep 2


title: LCL89_Input

description: Library name: Sample4

data_processing:
High-quality reads were processed through Trimmomatic v0.35 to eliminate adapter sequences
The trimmed sequences were then aligned to the Human reference genome (Homo sapiens.GRCh37) using BWA v0.7.12 with default parameters.
peaks were called using MACS2 v2.2.9.1 with cut-off q-value <= 0.05
Assembly: hg38
Supplementary files format and content: bed file containg narrow peak
Supplementary files format and content: .bed

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature, after quenching and cell lysis chromatin was sonicated using Diagenode Bioruptor Plus sonicator (Diagenode Inc.) with 20 sets of 30 seconds pulses in ice.
ChIP-seq libraries were prepared using TruSeq ChIP Library Preparation Kit

tag: chip antibody


title: EC, 132 WT_Sham, 4 weeks

description:
Library name: 2_132_Sham
Column name in Processed data file_non normalized featureCountsOut_gene_combined_all samples.xlsx:2_132_Sham

value: Endothelial Cells

value: WT


title: Male Inha Het, corn oil, rep 1


title: AB6621_SB181


title: AB6620_SB181


title: LCL1_Input

description: Library name: Sample3


title: Trace Procr-CreER;tdTomato, scRNAseq

city: Shanghai

first: Dandan

address: 1239 Siping Road, Yangpu District

institute: Tongji University

description:
Library name: Procr_td_trace
CD45-Ter119-CD31-DAPI-tdTomato+ articular superficial cells from three Procr-CreER;tdTomato mice 4 weeks post tamoxifen treatment at 4 week.

data_processing:
For scRNA-seq, sequencing data from 10× Genomics were processed with CellRanger (version 3.0.1) for demultiplexing, barcode processing and single-cell 3′ gene counting. Human and mouse genome reference was used for sequence alignment. Only confidently mapped, non-PCR duplicates with valid barcodes and UMIs were used to generate the gene-barcode matrix. For quality control, only cells with more than 5000 reads and less than 10% of mitochondrial genes were retained for downstream analyses. Cell doublets were removed using Doublet Finder software implemented in R. The clustering and visualization were finished by Seurat. For RNA-seq data analysis, adapters were trimmed and the resulting data were mapped to mm10 genome using STAR. HtSeq was used to summarize read counts, and duplicated reads were removed by UMI information (in Read2) to obtain gene counts. DEGs were calculated by DESeq2. Normalized CPM value = gene counts/ total gene counts x 1,000,000.
Assembly: mm10
Supplementary files format and content: For  scRNA-seq data, we provided Tab-separated values files and matrix files.

source_name: knee joint cartilage

extract_protocol:
For scRNA-seq, intact long bones were isolated, and attached soft tissues were removed using forceps, and dissociated periosteum cells and epiphysis articular cartilage cells with enzymatic digestion solution: 3 mg/ml type I collagenase (Worthington, LS004197), 4 mg/ml Dispase II (Sigma, 04942078001) and 1 U/ml DNase I (Sigma, D4527) in HBSS with Ca2+ and Mg2+. After four rounds of enzymic digestion in 37°C water bath (20 min per round), cells were resuspended in staining buffer (Ca2+ and Mg2+ free HBSS with 2% FBS) with 2 mM EDTA to stop the digestion for flow cytometry. Dissociated cells were stained by standard protocols with the following antibodies (eBioscience, Shanghai, China). allophycocyanin (APC)-conjugated CD31 (390), CD45 (30F-11), Ter119 (TER-119). DAPI were used for viable cell gating.
For scRNA-seq library construction, harvested cells were resuspended at 1 × 103 cells/mL and loaded on Chromium Controller to obtain single cells (10× Genomics) according to the manufacturer’s protocol of Beijing SeekGene BioSciences Co., Ltd (Beijing, China). Chromium Single cell 3’ Library and Gel Bead Kit V2 (10× Genomics, PN120237) was used to generate single cell gel beads in emulsion (GEM). The captured cells were lysed, and the released RNA was reverse-transcribed with primers containing poly-(d)T, barcode, Unique Molecular Identifiers (UMIs) and read 1 primer sequence in GEMs. Barcoded cDNA was purified and amplified by PCR. The adapter ligation reaction was performed to add sample index and read 2 primer sequence. After quality control, the libraries were sequenced on Illumina Novaseq 6000 platform in 150 bp pair-ended manner.

value: knee joint cartilage

value: superficial cells

value: Procr-CreER;tdTomato

value: polyA RNA

value: paired-end


title: LCL89_E2F1_ChIP

description: Library name: Sample2


title: AB6592_SB180

city: Rehovot

value: PsA


title: Female Inha Het, corn oil, rep 3

value: Corn oil


title: LCL1_E2F1_ChIP

description: Library name: Sample1


title: AB6591_SB180


title: Female Inha Het, corn oil, rep 2


title: Pulse Procr-CreER;tdTomato, scRNAseq

description:
Library name: Procr_td_pulse
CD45-Ter119-CD31-DAPI-tdTomato+ articular superficial cells from three Procr-CreER;tdTomato mice 2 days post tamoxifen treatment at 4 week.


title: Male Inha WT, corn oil, rep 3

value: Male E15.5 placenta

value: Inha WT