title: scRNA_CROPtimecourse_amplicon_CROP_4

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description:
Library name: scRNA_CROPtimecourse_amplicon_CROP_4
10X Genomics

data_processing:
10X Genomics Cellranger
Assembly: mm10/hg38
Supplementary files format and content: Tab separated values and counts matrix file

source_name: hiPSC

extract_protocol:
Dissociation of DS1 and DS2U at hiPSC stage (Day 0) was achieved using Accutase, whereas Day 2, Day 4, Day 6, Day 8, Day 10, Day 20 cardiomyocytes were treated with 0.25% Trypsin. Preparation of CROP-seq samples was similar at both hiPSC and Day 20 cardiomyocyte stages and CROP-seq amplicon library preparation was prepared as previously described46,57. Briefly, after the cDNA isolation step of 10X scRNA-seq library preparation, 10 ng of cDNA was separated from the remaining library and subjected to three rounds of nested PCR steps using primers listed below. Amplicon library purity was assessed by bioanalyzer HS DNA kit and purified using SPRI clean up beads. Amplicon libraries were pooled and sequenced on Illumina NextSeq 500 (Illumina, software 4.0.2) using similar cycling conditions as the endogenous transcriptome libraries mentioned above. Embryonic day 11.5 (E11.5) mouse embryos were harvested from timed pregnant females, and genotyping was conducted using yolk sac DNA to identify wild-type, Dp1Tyb, Hmgn1+/−, and Dp1Tyb; Hmgn1+/− genotypes. For each embryo, the heart was micro-dissected in ice-cold phosphate-buffered saline (PBS) under a stereomicroscope. Individual hearts were enzymatically dissociated using TrypLE Express (Thermo Fisher Scientific), with samples incubated at 37°C in a water bath for 10 minutes. Gentle trituration was performed using a 200 µL pipette at both the 5-minute and 10-minute time points to promote dissociation. The enzymatic reaction was quenched by adding ice-cold PBS containing 1% fetal bovine serum (FBS). Each sample was then passed through a 40 µm cell strainer to obtain a single-cell suspension, followed by centrifugation at 400 × g for 10 minutes at 4°C. The cell pellet was washed once with 1% FBS in PBS and resuspended in 50 µL of the same buffer. Cell viability and concentration were assessed using trypan blue exclusion. Samples with greater than 85% viability were used for library preparation. Approximately 10,000 cells per sample were loaded onto the 10x Genomics Chromium platform using the 3' v4 chemistry.
10X Genomics v3 and v4 3' scRNAseq

tag: cell line

value: hiPSC

value: Day 4 cardiomyocytes

value: WT CRISPR-A CROPseq


title: scRNA_CROPtimecourse_amplicon_CROP_10

status: Public on Aug 28 2025

type: SRA

country: USA

description:
Library name: scRNA_CROPtimecourse_amplicon_CROP_10
10X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Day 10 cardiomyocytes

tag: genotype


title: scRNA_CROPtimecourse_amplicon_CROP_2

description:
Library name: scRNA_CROPtimecourse_amplicon_CROP_2
10X Genomics

value: Day 2 cardiomyocytes


title: HPSC128 cells, siRNA MYOF, 48hrs

city: Liège

first: Olivier

last: Peulen

address: Av Hippocrate 13

country: Belgium

institute: University of Liège

description: Library name: HSPC128.MYOF

library_source: transcriptomic

data_processing:
Novaseq reads were processed using the nf-core RNAseq pipeline.
Assembly: Read alignment and quantification were performed with the “STAR-Salmon” option, using the human GRCh38 genome build associated with annotations from the Ensembl release 097
Supplementary files format and content: CSV file include raw counts for each sample

source_name: Pancreas

growth_protocol: HPSCs were maintained in DMEM/F12 with 10% FBS, without antibiotics.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA plus kit (740984, Macherey-Nagel)
mRNA library was generated using the Illumina stranded mRNA Prep Ligation kit (20040532, Illumina) according to manufacturer’s instructions

tag: tissue

value: Pancreas

value: CAF

value: MYOF knockdown

tag: treatment

value: MYOF-specific siRNA

tag: batch


title: scRNA_CROPtimecourse_amplicon_CROP_8

description:
Library name: scRNA_CROPtimecourse_amplicon_CROP_8
10X Genomics

value: Day 8 cardiomyocytes


title: scRNA_CROPtimecourse_amplicon_CROP_0

description:
Library name: scRNA_CROPtimecourse_amplicon_CROP_0
10X Genomics

value: Day 0 hiPSC


title: scRNA_CROPtimecourse_amplicon_CROP_6

description:
Library name: scRNA_CROPtimecourse_amplicon_CROP_6
10X Genomics

value: Day 6 cardiomyocytes


title: HPSC21 cells, siRNA control, 48hrs

description: Library name: HPSC21.GL3

value: WT

value: control siRNA


title: D3 TIR1 rep4

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

description: Library name: d3_degradation_E530_IGO_15393_9_S125

library_source: genomic

data_processing:
ATAC-seq was aligned using bowtie2 to mm10. Peaks were called using MACS2  with a p-value cutoff of .05, --nomodel, --shift=-100, and --extsize of 200. IDR was run on replicates with an IDR threshold of .2. Reproducible peaks were merged into a single peak atlas, and peak summits overlapping these peaks (n=248805) were used for quantification. Reads were quantified with FeatureCounts and differential peaks were called with DESeq2.
Assembly: mm10
Supplementary files format and content: Counts matrices, .tsv

molecule: genomic DNA

organism: Mus musculus

source_name: Spleen & lymph nodes

extract_protocol:
50,000 cells were washed in ice cold PBS and lysed in 50 µL of ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Following lysis, nuclei were peletted and incubated in 1x transposition buffer (Nextera TD buffer) containing 2.5 μL Nextera Tn5 transposase for 30 min at 37 degrees.
Transposed DNA fragments were isolated using QIAGEN MinElute Reaction Cleanup kit and amplified using barcoded primers with Illumina adaptor sequences. The number of cycles used for library amplification was determined using a quantitative PCR side-reaction. Amplified libraries were purified and size selected using Ampure XP beads using consecutive purifications with bead-to-sample ratios of 0.5 and 1.8. After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were sequenced on a on a NovaSeq 6000 in a PE100 run using the NovaSeq 6000 S4 Reagent Kit (200 cycles).

value: Spleen & lymph nodes

value: Treg

value: Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 3 Days


title: Tonsil sample D1 RNA

city: Chicago

first: Junjie

last: Xia

state: IL

address: 10th floor of KCBD, 900 E. 57th Street

department: Chemistry

institute: University of Chicago

description:
Library name: Sample D1 RNA
Fresh frozen Spatial transcriptome sequencing

data_processing:
The sequencing data of PLA were aligned with a custom Java program which is deposited at https://github.com/tay-lab/Prox-seq.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in JSON format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: PLA_count_matrix.txt.gz: matrix containing detected proximity ligation events
Library strategy: Spatial Transcriptomics

source_name: Human tonsil tissue

growth_protocol: Samples are collected from The University of Chicago Medicine in accordance with institutional guidelines.

extract_protocol:
Embedded tissue blocks were sectioned into 10-μm slices and mounted on Visium slides for Spatial prox-seq experiments.
Spatial transcriptome sequencing libraries were prepared with 10XGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacture's construction; Spatial PLA sequencing libaries were prepared similar as  Vistain L et al., 2022, see the Supplementary Information for the detailed protocol.

treatment_protocol: The samples were embedded in optimal cutting temperature (OCT) compound and stored in a sealed container at –80°C.

value: Human tonsil tissue

value: No treatment


title: D3 WT rep4

description: Library name: d3_degradation_E521_IGO_15393_4_S122

value: Foxp3-AID ROSA26-WT


title: Tonsil sample B1 RNA

description:
Library name: Sample B1 RNA
Fresh frozen Spatial transcriptome sequencing


title: scRNA_CROPtimecourse_endogenous_CROP_10

description:
Library name: scRNA_CROPtimecourse_endogenous_CROP_10
10X Genomics

value: hiPSC

value: Day 10 cardiomyocytes

value: WT CRISPR-A CROPseq


title: D7 WT rep3

description: Library name: d7_degradation_AC379_IGO_15393_13_S115

value: 5-ph-IAA 7 Days


title: DSP.1001660012998.D.A04.dcc

city: London

first: Jack

last: Wood

state: County

address: Gower Street

department: Neuroscience, Physiology and Pharmacology

country: United Kingdom

institute: University College London

description: Library name: DSP.1001660012998.D.A04.dcc

data_processing:
Demultiplex to FASTQ and convert to DCC with GeoMx NGS Pipeline/GUI.
Map oligo barcodes to human gene symbols using the GeoMx Human WTA PKC annotation.
AOI QC thresholds: ≥1,000 reads/AOI; ≥80% trimmed; ≥80% stitched; ≥75% aligned; ≥50% sequencing saturation. Failing AOIs were excluded.
Assembly: Gene identifiers derived from the GeoMx Human Whole Transcriptome (WTA) probe annotation (PKC file): Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: dcc/ - one .dcc file per AOI (barcode counts). dcc_stats/ - per-AOI .stats.txt files generated by GeoMx NGS.
Library strategy: Spatial Transcriptomics

source_name: Hippocampus

extract_protocol:
FFPE blocks were sectioned at 8 μm using a rotary microtome. Three of these tissue squares were mounted per SuperFrost Plus slide within the designated GeoMx scan area.
Slide preparation followed the standard GeoMx Slide Preparation protocol . Probe mic: GeoMx Whole Transcriptome Probe Mix. Library quality was verified on an Agilent TapeStation D1000. Sequencing was performed on an Illumina NextSeq 2000 (X-LEAP chemistry), paired-end.

value: Hippocampus

value: Microglia

value: P

tag: group

value: AD

tag: age

tag: braak

tag: pmd

tag: ph

tag: weight

tag: csf

tag: area

tag: slide

tag: apoe

tag: Sex

value: F


title: HPSC21 cells, siRNA MYOF, 48hrs

description: Library name: HPSC21.MYOF

value: Pancreas

tag: cell line

value: CAF

value: MYOF knockdown

value: MYOF-specific siRNA


title: HPSC130 cells, siRNA control, 48hrs

description: Library name: HPSC130.GL3

tag: cell type

value: WT

value: control siRNA


title: Tonsil sample B1 PLA

description:
Library name: Sample B1 PLA
Fresh frozen Spatial PLA sequencing

library_source: other

data_processing:
*library strategy: Spatial Proximity-Sequencing (Sprox-seq)
The sequencing data of PLA were aligned with a custom Java program which is deposited at https://github.com/tay-lab/Prox-seq.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in JSON format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: PLA_count_matrix.txt.gz: matrix containing detected proximity ligation events

molecule: other

value: Human tonsil tissue

value: No treatment


title: BATF3_KO_LA21_Rep1[RNA_Seq]

city: San Antonio

first: Hui

last: Yan

state: TX

address: 7703 Floyd Curl Dr.

department: MIMG

institute: UTHSCSA

data_processing:
RNA samples were scored by FastQC
RNA samples were trimed by trim_galore
RNA samples were mapped by HISAT2
RNA samples were sored by samtools, removed duplicates
Reads counts were extracted and normalized
Assembly: mm10
Supplementary files format and content: Normalized reads count in csv format. Processed_data_BATF3_KO_RNA_Seq.csv

source_name: B cell

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA was processed using an Illumina TruSeq RNA sample prep kit v2 (Illumina)

value: B cell

tag: genotype

value: Batf3 knockout


title: Tonsil sample D1 PLA

description:
Library name: Sample D1 PLA
Fresh frozen Spatial PLA sequencing

tag: tissue


title: scRNA_CROPtimecourse_endogenous_CROP_8

description:
Library name: scRNA_CROPtimecourse_endogenous_CROP_8
10X Genomics

value: hiPSC

value: Day 8 cardiomyocytes

value: WT CRISPR-A CROPseq


title: D3 WT rep3

description: Library name: d3_degradation_AC363_IGO_15393_3_S121

value: Spleen & lymph nodes

value: Treg

value: Foxp3-AID ROSA26-WT

tag: treatment

value: 5-ph-IAA 3 Days


title: D3 TIR1 rep3

description: Library name: d3_degradation_E515_IGO_15393_8_S124

value: Foxp3-AID ROSA26-TIR1(F74G)


title: D7 WT rep1

description: Library name: d7_degradation_AC326_IGO_15393_10_S113

value: 5-ph-IAA 7 Days


title: Tonsil sample A1 PLA

description:
Library name: Sample A1 PLA
Fresh frozen Spatial PLA sequencing


title: HPSC130 cells, siRNA MYOF, 48hrs

description: Library name: HPSC130.MYOF

value: Pancreas

value: CAF

value: MYOF knockdown

tag: batch


title: HPSC128 cells, siRNA control, 48hrs

description: Library name: HPSC128.GL3

value: WT

value: control siRNA


title: D3 WT rep2

description: Library name: d3_degradation_AC321_IGO_15393_2_S120


title: CnR_HMGN1_rep1

description: Library name: CnR_HMGN1_rep1

data_processing:
All data were processed through the Nfcore pipeline
Assembly: Hg38
Supplementary files format and content: Tab separated values and counts matrix file
Library strategy: CUT&RUN

extract_protocol:
Cut and Run samples for HMGN1-Flag. Cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs) were collected at day 20 for CUT&RUN analysis. Cells were dissociated using 0.25% Trypsin-EDTA (1X) (Gibco, 25200-072) and neutralized with 1% FBS in PBS. For each condition, 150,000 cells per sample were processed according to the manufacturer’s instructions using the CUTANA™ CUT&RUN Kit (Epicypher, 14-1048). Cells were first washed and bound to activated Concanavalin A (ConA)–coated magnetic beads in the Bead Activation Buffer. Nuclei were permeabilized with Digitonin-containing buffer, and all buffers were supplemented with cOmplete™ Mini, EDTA-free Protease Inhibitor Cocktail (Millipore Sigma, 11836170001).
CUTANA CUT&RUN Epicypher

value: D20 hiPSC cardiomyocytes


title: CnR_HMGN1_rep2

description: Library name: CnR_HMGN1_rep2


title: scRNA_CROPtimecourse_endogenous_CROP_2

description:
Library name: scRNA_CROPtimecourse_endogenous_CROP_2
10X Genomics

value: Day 2 cardiomyocytes


title: scRNA_CROPtimecourse_endogenous_CROP_4

description:
Library name: scRNA_CROPtimecourse_endogenous_CROP_4
10X Genomics

value: Day 4 cardiomyocytes


title: scRNA_CROPtimecourse_endogenous_CROP_0

description:
Library name: scRNA_CROPtimecourse_endogenous_CROP_0
10X Genomics

value: hiPSC

value: Day 0 hiPSC


title: Tonsil sample A1 RNA

description:
Library name: Sample A1 RNA
Fresh frozen Spatial transcriptome sequencing

value: Human tonsil tissue

value: No treatment


title: D3 WT rep1

description: Library name: d3_degradation_AC315_IGO_15393_1_S20

value: Spleen & lymph nodes

value: Treg


title: HPSC127 cells, siRNA MYOF, 48hrs

description: Library name: HPSC127.MYOF

value: MYOF-specific siRNA


title: scRNA_HMGN1_allele_edit_F4_rep2

description:
Library name: scRNA_HMGN1_allele_edit_F4_rep2
10X Genomics

value: Day 20 cardiomyocytes

value: Trisomy 21, HMGN1 rescue


title: scRNA_HMGN1_allele_edit_F4_rep1

description:
Library name: scRNA_HMGN1_allele_edit_F4_rep1
10X Genomics


title: Panc-1 cells, WJ460, 48hrs, replicate 2

description: Library name: Panc1.WJ460.2

data_processing:
Novaseq reads were processed using the nf-core RNAseq pipeline.
Assembly: Read alignment and quantification were performed with the “STAR-Salmon” option, using the human GRCh38 genome build associated with annotations from the Ensembl release 097
Supplementary files format and content: XLSX  file include raw counts for each sample

growth_protocol: PANC-1 were maintained in DMEM with 10% FBS, without antibiotics.

value: Pancreas

value: PDAC cells


title: Active_Treg_GFP_plusFoxp3_rep2

description: Library name: aTreg_GFP_rep2_IGO_14687_B_44

data_processing:
RNA-seq was aligned to mm39 with bowtie2 and read counts were calculated using FeatureCounts. Differential gene expression was calculated using DESeq2
Assembly: mm39
Supplementary files format and content: Counts matrices, .tsv

molecule: polyA RNA

extract_protocol:
RNA extraction was  performed according to the manufacturer’s instructions. Briefly, phase separation in cells lysed in 1mL TRIzol Reagent was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 15-18 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1-2 ng total RNA with RNA integrity numbers ranging from 5.5 to 9.3 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. 4.5-8 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Roche 07962363001) using 8 cycles of PCR.

value: Active Treg

value: no treatment


title: scRNA_WiCell_M1

description:
Library name: scRNA_WiCell_M_rep1
10X Genomics
scRNA_aggr_WiCell_B1_proc_barcodes.tsv.gz
scRNA_aggr_WiCell_B1_proc_features.tsv.gz
scRNA_aggr_WiCell_B1_proc_matrix.mtx.gz

value: Trisomy 21


title: LNCaPAR_R1881_6hr_112222_CWRU

city: Cleveland

first: Hyunmin

last: Kim

state: OH

address: 10900 Euclid Ave.

department: genetics and genome sciences

institute: Case western reserve university

description: Library name: LNCaPAR_R1881_6hr_112222_CWRU

data_processing:
RNA-seq reads were aligned to the hg38 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Assembly: hg38
Supplementary files format and content: RSEM gene FPKM, TPM

source_name: Prostate cancer cell line

growth_protocol: Cell lines were grown in DMEM (LNCaP-XIP, LAMP), RPMI-1640 (LNCaP, 22Rv1) or Haim's F-12K medium (PC3) supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from cell lines using the RNeasy mini kit (Qiagen catalogue # 74136) with QiaShredder (Qiagen catalogue # 79654).
Dual-Index Illumina barcodes were introduced during library preparation (Dovetails catalogue # 25010).

treatment_protocol: For all cell line sequencing studies, cells were grown in complete medium overnight then underwent treatment as described above. Collection was performed in complete media with centrifugation and taken directly into assay steps.

value: Prostate cancer cell line


title: LNCaPAR_R1881_1hr_112222_CWRU

description: Library name: LNCaPAR_R1881_1hr_112222_CWRU


title: LNCaPAR_R1881_24hr_112222_CWRU

description: Library name: LNCaPAR_R1881_24hr_112222_CWRU


title: scRNA_WiCell_M2

description:
Library name: scRNA_WiCell_M_rep2
10X Genomics
scRNA_aggr_WiCell_B1_proc_barcodes.tsv.gz
scRNA_aggr_WiCell_B1_proc_features.tsv.gz
scRNA_aggr_WiCell_B1_proc_matrix.mtx.gz


title: Active_Treg_GFP_plusFoxp3_rep1

description: Library name: aTreg_GFP_rep1_IGO_14687_B_22


title: D3 TIR1 rep1

description: Library name: d3_degradation_AC314_IGO_15393_5_S123

value: Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 3 Days


title: scRNA_CROPtimecourse_endogenous_CROP_6

description:
Library name: scRNA_CROPtimecourse_endogenous_CROP_6
10X Genomics

value: hiPSC

value: Day 6 cardiomyocytes

value: WT CRISPR-A CROPseq


title: Panc-1 cells, WJ460, 48hrs, replicate 3

description: Library name: Panc1.WJ460.3

value: WT


title: Panc-1 cells, WJ460, 48hrs, replicate 1

description: Library name: Panc1.WJ460.1


title: LNCaPAR_Enza_6hr_112222_CWRU

description: Library name: LNCaPAR_Enza_6hr_112222_CWRU


title: LNCaPAR_NT_24hr_112222_CWRU

description: Library name: LNCaPAR_NT_24hr_112222_CWRU


title: LNCaPAR_Enza_24hr_112222_CWRU

description: Library name: LNCaPAR_Enza_24hr_112222_CWRU


title: Resting_Treg_GFP_plusFoxp3_rep2

description: Library name: nTreg_GFP_rep2_IGO_14687_B_43

value: Spleen & lymph nodes

value: Resting Treg


title: Resting_Treg_GFP_plusFoxp3_rep1

description: Library name: nTreg_GFP_rep1_IGO_14687_B_21


title: D3 TIR1 rep2

description: Library name: d3_degradation_AC337_IGO_15393_6_S21

value: Treg


title: Resting_KIKO_D28_plusFoxp3_rep2

description: Library name: nKIKO_28_p_rep2_IGO_14687_B_41

value: Resting Treg wannabe

value: 4-hydroxytamoxifen 28 days


title: scRNA_WiCell_B1

description:
Library name: scRNA_WiCell_B_rep1
10X Genomics
scRNA_aggr_WiCell_B1_proc_barcodes.tsv.gz
scRNA_aggr_WiCell_B1_proc_features.tsv.gz
scRNA_aggr_WiCell_B1_proc_matrix.mtx.gz

value: Day 20 cardiomyocytes


title: Panc-1 cells, DMSO, 48hrs, replicate 2

description: Library name: Panc1.CTRL.2

value: Pancreas

value: PDAC cells

value: Vehicle


title: Panc-1 cells, DMSO, 48hrs, replicate 1

description: Library name: Panc1.CTRL.1


title: LNCaPAR_Enza_1hr_112222_CWRU

description: Library name: LNCaPAR_Enza_1hr_112222_CWRU


title: Panc-1 cells, siRNA MYOF, 48hrs, replicate 3

description: Library name: Panc1.SiMyof.3

value: MYOF knockdown

value: MYOF-specific siRNA


title: LNCaPAR_DMSO_6hr_112222_CWRU

description: Library name: LNCaPAR_DMSO_6hr_112222_CWRU

value: Prostate cancer cell line


title: scRNA_VPR_DYRK1A_rep2

description:
Library name: scRNA_VPR_DYRK1A_rep2
10X Genomics

value: WT CRISPR-A


title: Resting_KIKO_D28_minusFoxp3_rep2

description: Library name: nKIKO_28_n_rep2_IGO_14687_B_31


title: HPSC127 cells, siRNA control, 48hrs

description: Library name: HPSC127.GL3

value: CAF

value: control siRNA


title: LNCaPAR_DMSO_24hr_112222_CWRU

description: Library name: LNCaPAR_DMSO_24hr_112222_CWRU


title: scRNA_VPR_DYRK1A_rep1

description:
Library name: scRNA_VPR_DYRK1A_rep1
10X Genomics

value: hiPSC


title: Resting_KIKO_D28_minusFoxp3_rep1

description: Library name: nKIKO_28_n_rep1_IGO_14687_B_9


title: Panc-1 cells, DMSO, 48hrs, replicate 3

description: Library name: Panc1.CTRL.3

value: WT


title: LNCaPAR_DMSO_1hr_112222_CWRU

description: Library name: LNCaPAR_DMSO_1hr_112222_CWRU


title: Resting_KIKO_D14_plusFoxp3_rep2

description: Library name: nKIKO_14_p_rep2_IGO_14687_B_39

value: Spleen & lymph nodes

value: 4-hydroxytamoxifen 14 days


title: Panc-1 cells, siRNA MYOF, 48hrs, replicate 2

description: Library name: Panc1.SiMyof.2


title: scRNA_VPR_DSCAM_rep1

description:
Library name: scRNA_VPR_DSCAM_rep1
10X Genomics


title: Panc-1 cells, siRNA control, 48hrs, replicate 3

description: Library name: Panc1.GL3.3


title: scRNA_VPR_DSCAM_rep2

description:
Library name: scRNA_VPR_DSCAM_rep2
10X Genomics


title: scRNA_WiCell_B2

description:
Library name: scRNA_WiCell_B_rep2
10X Genomics
scRNA_aggr_WiCell_B1_proc_barcodes.tsv.gz
scRNA_aggr_WiCell_B1_proc_features.tsv.gz
scRNA_aggr_WiCell_B1_proc_matrix.mtx.gz


title: Panc-1 cells, siRNA control, 48hrs, replicate 2

description: Library name: Panc1.GL3.2


title: LNCaPAR_Bica_6hr_112222_CWRU

description: Library name: LNCaPAR_Bica_6hr_112222_CWRU


title: Resting_KIKO_D28_plusFoxp3_rep1

description: Library name: nKIKO_28_p_rep1_IGO_14687_B_19


title: Resting_KIKO_D14_minusFoxp3_rep2

description: Library name: nKIKO_14_n_rep2_IGO_14687_B_29


title: Resting_KIKO_D14_plusFoxp3_rep1

description: Library name: nKIKO_14_p_rep1_IGO_14687_B_17


title: LNCaPAR_Bica_24hr_112222_CWRU

description: Library name: LNCaPAR_Bica_24hr_112222_CWRU


title: Panc-1 cells, siRNA control, 48hrs, replicate 1

description: Library name: Panc1.GL3.1


title: Resting_KIKO_D14_minusFoxp3_rep1

description: Library name: nKIKO_14_n_rep1_IGO_14687_B_7


title: SMS1_B2, GEX

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

description:
Library name: Sample 8
10X Genomics

data_processing:
Droplet libraries were processed using cellranger pipeline (or cellranger-arc for multiome libraries). Sequencing reads were aligned to the GRCh38 human reference genome, and transcript counts were quantified for each annotated gene within every cell.
Assembly: GRCh38
Supplementary files format and content: An h5 file containing Cell Ranger count pipeline output for filtered cell-feature data: columns contain UMI counts across cells; rows contain features.

source_name: cortical organoids

growth_protocol: Patterned human cortical organoids were generated using the AggreWell system36 (StemCell technologies) according to manufacturer instructions. Briefly, hiPSCs were dissociated into single cells using Gentle Cell Dissociation Reagent (GCDR) (StemCell Technologies) and cells from each well were centrifuged with 500 µl Anti-Adherence Rinsing Solution at 1300 × g for 3 min. 1.5-3 million cells were seeded in each prepared well by spinning for 100 × g for 5 min in 1.5 mL STEMdiff Seeding Medium I with ROCK inhibitor Y-27632 (10 µM). For the next 5 days, 1 ml per well of fresh STEMdiff Forebrain Organoid Formation Medium I was carefully exchanged. On day 6, one Aggrewell of embryoid bodies were filtered through a 37 µM strainer and transferred to six wells of a 6-Well Ultra-Low Adherent Plate (Corning) containing 2 ml STEMdiff Forebrain Organoid Expansion Medium. STEMdiff™ Forebrain Organoid Expansion Medium was changed every other day until day 25, at which point the medium was changed to STEMdiff Forebrain Organoid Differentiation Medium. Organoids were cultured in differentiation media until day 43. Following day 43, organoids were cultured in STEMdiff™ Forebrain Organoid Maintenance Medium indefinitely. Maintenance media was changed every 2–3 days, the volume was increased to 2.2-3 ml when necessary.

extract_protocol:
Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec) with gentle MACS Dissociation and C tubes.
Nuclei from day-75 cortical organoids (3 control libraries Ctrl 1-3 and 3 SMS libraries SMS 1-3, n=5 organoids per library, all snRNA-seq libraries were derived from female samples) were isolated using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec), following the manufacturer’s guidelines with gentle MACS Dissociation and C tubes. Upon isolation, the nuclei were counted on the Nexcelom Cellaca MX. Single nuclei RNA libraries were generated using 10X Genomics’ Single Cell Gene Expression kits (RNA-seq and ATAC bundle for Ctrl2, Ctrl3, SMS2 and RNA-seq for Ctrl1, SMS1, SMS3) and loaded onto the Chromium instrument for downstream analysis and processed according to the standard manufacturer’s specifications.

treatment_protocol: No additional treatments

value: cortical organoids

tag: developmental stage

value: female

tag: condition

value: SMS


title: SMS3_B2, GEX

description:
Library name: Sample 9
10X Genomics


title: CTRL1_B2, GEX

description:
Library name: Sample 7
10X Genomics

value: Control


title: LNCaPAR_BG15n_6hr_112222_CWRU

description: Library name: LNCaPAR_BG15n_6hr_112222_CWRU


title: Resting_KIKO_D7_plusFoxp3_rep2

description: Library name: nKIKO_7_p_rep2_IGO_14687_B_37

value: Resting Treg wannabe

value: 4-hydroxytamoxifen 7 days


title: HDF_NaNO2_1

city: Moscow

first: Vadim

last: Chechekhin

address: Leninskie gory 1

country: Russia

institute: Lomonosov Moscow State University

description: Library name: mgu10

data_processing:
SТАR aligner v2.7.10b, Subrеаd v2.0.6, and DЕSеq2 v1.38.3 in R 4.2.1 software tools
Quality control was assesed using FASTQC v0.12.0 and MultiQC v1.16
Assembly: hg38
Supplementary files format and content: fastq files includes raw counts for each sample

source_name: HDF #1

growth_protocol: Primary isolated human dermal fibroblasts were cultured in Dulbecco's Modified Eagle’s Medium (DMEM) containing high glucose (Gibco, #11965092), supplemented with 10% fetal bovine serum (FBS) (ThermoFisher Scientific, #26140079), 1x antibiotic/antimycotic mixture (Gibco, #15240062) and 1x L-Gln (Gibco, #11539876).

extract_protocol:
Total RNA was isolated from cell lysates using the Direct-zol RNA Miniprep kit (Zymo Research, USA, #R2052) according to the manufacturer's instructions.
About 800 ng of total RNA (for each group) was utilized for library construction employing the NЕВNext® Poly(А) mRNА Magnetiс Isоlatiоn Mоdulе alongside the NЕВNext® Ultra II™ Dirесtiоnal RNА Librаry Prер Kit for Illuminа (Nеw Еnglаnd Biоlаbs), following the manufacturer’s guidelines.

treatment_protocol: We used cultures of primary human dermal fibroblasts of 5-8 passages of 80-90% confluent. In experimental groups growth medium was replaced with the non-concentrated secretome of primary MSCs or immortalized MSCs. In the negative control group, cells were cultured in complete fibroblast growth medium, and in the positive control groups mutagen solutions (3mM sodium nitrite or 0.01% DMS in complete fibroblast growth medium) were used. In the DMS group, 6 hours after the start of the experiment, the DMS solution was re-placed with the complete fibroblast growth medium. Test solutions were renewed every 3 days, and 7 days after the start of the experiment.

value: HDF #1

value: primary human dermal fibroblasts #1

value: 3mM sodium nitrite #1

tag: time

value: 7 days


title: LNCaPAR_Bica_1hr_112222_CWRU

description: Library name: LNCaPAR_Bica_1hr_112222_CWRU

value: Prostate cancer cell line


title: LNCaPAR_BG15n_24hr_112222_CWRU

description: Library name: LNCaPAR_BG15n_24hr_112222_CWRU


title: Panc-1 cells, siRNA MYOF, 48hrs, replicate 1

description: Library name: Panc1.SiMyof.1

value: Pancreas

value: PDAC cells

value: MYOF knockdown

value: MYOF-specific siRNA


title: Resting_KIKO_D7_plusFoxp3_rep1

description: Library name: nKIKO_7_p_rep1_IGO_14687_B_15

value: Spleen & lymph nodes


title: HDF_С_2

description: Library name: mgu9

source_name: HDF #2

value: HDF #2

value: primary human dermal fibroblasts #2

value: WT

value: culture medium


title: Multiome, SMS2_B1, GEX

description:
Library name: Sample 5
10X Genomics

value: cortical organoids

value: female

value: SMS


title: Multiome, SMS2_B1, ATAC

description:
Library name: Sample 6
10X Genomics

library_source: genomic single cell


title: LNCaPAR_BG15n_1hr_112222_CWRU

description: Library name: LNCaPAR_BG15n_1hr_112222_CWRU


title: Multiome, CTRL3_B1, ATAC

description:
Library name: Sample 4
10X Genomics

value: Control


title: LNCaPAR_BG15a_6hr_112222_CWRU

description: Library name: LNCaPAR_BG15a_6hr_112222_CWRU


title: Resting_KIKO_D7_minusFoxp3_rep1

description: Library name: nKIKO_7_n_rep1_IGO_14687_B_5

value: Resting Treg wannabe

value: 4-hydroxytamoxifen 7 days


title: HDF_NaNO2_2

description: Library name: mgu7

value: 3mM sodium nitrite #2

value: 7 days


title: Multiome, CTRL3_B1, GEX

description:
Library name: Sample 3
10X Genomics


title: Resting_KIKO_D3_plusFoxp3_rep2

description: Library name: nKIKO_3_p_rep2_IGO_14687_B_35

value: 4-hydroxytamoxifen 3 days


title: HDF_С_1

description: Library name: mgu6

value: HDF #1

value: primary human dermal fibroblasts #1


title: LNCaPAR_BG15a_24hr_112222_CWRU

description: Library name: LNCaPAR_BG15a_24hr_112222_CWRU

value: Prostate cancer cell line


title: LNCaPAR_BG15a_1hr_112222_CWRU

description: Library name: LNCaPAR_BG15a_1hr_112222_CWRU


title: Resting_KIKO_D3_plusFoxp3_rep1

description: Library name: nKIKO_3_p_rep1_IGO_14687_B_13

value: Spleen & lymph nodes


title: Multiome, CTRL2_B1, ATAC

description:
Library name: Sample 2
10X Genomics


title: Multiome, CTRL2_B1, GEX

description:
Library name: Sample 1
10X Genomics


title: HDF_MSCwt_1

description: Library name: mgu5

value: secretome of wild type MSCs #1


title: HDF_MSCwt_2

description: Library name: mgu4

value: HDF #2

value: primary human dermal fibroblasts #2

value: secretome of wild type MSCs #2


title: CWRR1_EnzR_2R-L_100623_NextSeq

description: Library name: CWRR1_EnzR_2R-L_100623_NextSeq


title: CWRR1_EnzR_NT_081122_CWRU

description: Library name: CWRR1_EnzR_NT_081122_CWRU


title: Resting_KIKO_D3_minusFoxp3_rep2

description: Library name: nKIKO_3_n_rep2_IGO_14687_B_25


title: HDF_DMS_1

description: Library name: mgu8

value: WT

value: dimethyl sulfate #1


title: scRNA_E115_tg_rep2

description:
Library name: scRNA_E115_tg_rep2
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz

source_name: E11.5 cardiac regions

value: E11.5 cardiac regions

value: dissociated cells from cardiac region

value: Dp1Tyb tg/+


title: scRNA_E115_tg_rep3

description:
Library name: scRNA_E115_tg_rep3
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz


title: HDF_MSCimmort_2

description: Library name: mgu3

value: secretome of immortalized MSCs #2


title: CWRR1_EnzR_2L-R_100623_NextSeq

description: Library name: CWRR1_EnzR_2L-R_100623_NextSeq


title: Resting_KIKO_D3_minusFoxp3_rep1

description: Library name: nKIKO_3_n_rep1_IGO_14687_B_3

value: Resting Treg wannabe


title: HDF_MSCimmort_1

description: Library name: mgu1

value: secretome of immortalized MSCs #1

value: 7 days


title: CWRR1_EnzR_2L_L_100623_NextSeq

description: Library name: CWRR1_EnzR_2L_L_100623_NextSeq


title: scRNA_E115_tg_rep1

description:
Library name: scRNA_E115_tg_rep1
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz


title: Resting_KIKO_D0_plusFoxp3_rep1

description: Library name: nKIKO_0_p_rep1_IGO_14687_B_11

value: no treatment


title: scRNA_E115_het_rep2

description:
Library name: scRNA_E115_het_rep2
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz

value: Dp1Tyb tg/+;Hmgn1 +/-


title: CWRR1_EnzR_1R_L_100623_NextSeq

description: Library name: CWRR1_EnzR_1R_L_100623_NextSeq

value: Prostate cancer cell line


title: Resting_KIKO_D7_minusFoxp3_rep2

description: Library name: nKIKO_7_n_rep2_IGO_14687_B_27

value: Spleen & lymph nodes

value: 4-hydroxytamoxifen 7 days


title: HDF_DMS_2

description: Library name: mgu2

value: HDF #2

value: 0.01% dimethyl sulfate #2


title: Whole exome sequencing of lung tumor tissue from patient 4

city: Irvine

first: Stephanie

middle: Jeanelle

last: Hachey

address: 2400 Biological Sciences III

institute: UC Irvine

description: Library name: P004_WES

data_processing:
Raw WES reads were aligned to the human reference genome (GRCh38) using BWA-MEM, and somatic variants were identified using GATK Mutect2. RNA-seq reads were aligned to GRCh38 using STAR, and gene expression levels were quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab separated values (normalized counts and DE results, RNAseq; copy number variations, WES), png chromosomal view CNV WES

source_name: pT4N1(1/28)+11R, stage IIIA, adenocarcinoma

extract_protocol:
DNA and RNA were extracted from freshly collected primary tumor and matched adjacent normal tissues using the QIAGEN Quick-DNA and Quick-RNA Microprep Kits, respectively.
Whole-exome sequencing (WES) was performed on tumor and matched normal DNA using the Agilent SureSelect Human All Exon V7 kit for library preparation, followed by 150 bp paired-end sequencing on the Illumina NovaSeq 6000 platform. Bulk RNA sequencing (RNA-seq) was conducted on tumor tissue using the Clontech SMARTer Stranded Total RNA-Seq Pico Input Mammalian v3 Kit and paired-end sequenced on the Illumina NovaSeq X Plus.

value: tumor

value: epithelial, lung

value: age 69, F, never smoker, Hispanic


title: Whole exome sequencing of lung tumor tissue from patient 5

description: Library name: P005_WES

source_name: pT4N0(0/34), stage IIA, invasive squamous cell carcinoma

value: age 84, M, former smoker (25 pack years), White


title: Resting_KIKO_D0_minusFoxp3_rep1

description: Library name: nKIKO_0_n_rep1_IGO_14687_B_1


title: scRNA_E115_wt_rep2

description:
Library name: scRNA_E115_wt_rep2
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz

value: E11.5 cardiac regions

value: dissociated cells from cardiac region

value: WT


title: Whole exome sequencing of lung tumor tissue from patient 3

description: Library name: P003_WES

source_name: pT1cN0(0/9),stage IA3,  adenocarcinoma

value: age 63, F, former smoker (10 pack years), White


title: CWRR1_EnzaR_R1881_6hr_060123_CWRU

description: Library name: CWRR1_EnzaR_R1881_6hr_060123_CWRU


title: CWRR1_EnzaR_R1881_24hr_060123_CWRU

description: Library name: CWRR1_EnzaR_R1881_24hr_060123_CWRU


title: scRNA_E115_het_rep1

description:
Library name: scRNA_E115_het_rep1
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz


title: scRNA_E115_wt_rep1

description:
Library name: scRNA_E115_wt_rep1
10X Genomics
scRNA_E115_aggr_proc_barcodes.tsv.gz
scRNA_E115_aggr_proc_features.tsv.gz
scRNA_E115_aggr_proc_matrix.mtx.gz


title: Whole exome sequencing of lung tumor tissue from patient 2

description: Library name: P002_WES

source_name: pT1cN2(+7), stage IIIA, adenosquamous carcinoma

value: age 64, F, never smoker, White


title: CWRR1_EnzaR_Enza_6hr_060123_CWRU

description: Library name: CWRR1_EnzaR_Enza_6hr_060123_CWRU


title: Whole exome sequencing of lung tumor tissue from patient 1

description: Library name: P001_WES

source_name: stage pT3N0(0/6), NSCLC, invasive papillary adenocarcinoma

value: age 49, F, never smoker, Vietnamese


title: Resting_KIKO_D0_plusFoxp3_rep2

description: Library name: nKIKO_0_p_rep2_IGO_14687_B_33

value: Resting Treg wannabe

value: no treatment


title: Active_KIKO_D28_plusFoxp3_rep2

description: Library name: aKIKO_28_p_rep2_IGO_14687_B_42

value: Active Treg wannabe

value: 4-hydroxytamoxifen 28 days


title: Active_KIKO_D28_plusFoxp3_rep1

description: Library name: aKIKO_28_p_rep1_IGO_14687_B_20

value: Spleen & lymph nodes


title: M No PE, 16A2, Villous Tissue

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

description: Illumina HiSeq 2500

data_processing:
Reads were subjected to adapter trimming using Trimmomatic v0.39.
Reads were mapped to the University of California Santa Cruz hg38 human genome assembly using TopHat2 version 2.0.14.
Raw read counts were generated using HTseq version 0.11.2 with the iGenomes (Illumina) Homo sapiens reference file .
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw feature count values for each sample.

source_name: placenta, villous tissue

extract_protocol:
RNA was isolated using TRIzol reagent (Life Technologies), then purified using the RNA Clean-Up and Concentration Kit (Norgen Biotek).
RNA libraries for RNA-seq were prepared using using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold following manufacturer's protocols (Illumina).

value: placenta, villous tissue

tag: clinical group

value: normotensive

tag: singleton or_twin

value: twin

tag: age of_mother_(years)

tag: birthweight interval_(grams)

tag: assigned neonatal_sex

value: Male

tag: maternal ethnicity

value: Non-Hispanic

tag: maternal race

value: White


title: CWRR1_EnzaR_Enza_24hr_060123_CWRU

description: Library name: CWRR1_EnzaR_Enza_24hr_060123_CWRU

value: Prostate cancer cell line


title: M No PE, 16A1, Villous Tissue

description: Illumina HiSeq 2500


title: Active_KIKO_D28_minusFoxp3_rep2

description: Library name: aKIKO_28_n_rep2_IGO_14687_B_32


title: Active_KIKO_D28_minusFoxp3_rep1

description: Library name: aKIKO_28_n_rep1_IGO_14687_B_10


title: A673,IC50,48h,Rep3

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description: Library name: sample 3

data_processing:
RNA-SeqEZPZ pipeline were used to analyze all the samples
Briefly, low quality and adapter sequences were trimmed using Trim_galore
Trimmed sequences were mapped to hg38 using STAR with 2-pass approach
Reads were assigned to features using featureCounts
Normalization, differential analysis and statistical reports were done using DESeq2 and SARTools
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw and normalized counts, log2FoldChange, p-values adjusted and other statistics generated by DESeq2 for each sample
Supplementary files format and content: html file containing statistical report generated by RNA-SeqEZPZ

growth_protocol: A673 cells were grown in DMEM + 10% FBS + PSQ + 1% Sodium Pyruvate.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen). 300ng of total RNA was used for library prep.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were seeded at 30% confluency and left to adhere overnight. After 24 hours, cells were dosed with DMSO or Seclidemstat equating calculated IC50 for A673 cell line. Cells were harvested for RNA extraction after 48 hours.

value: Ewing sarcoma

value: wildtype


title: CWRR1_EnzaR_DMSO_6hr_060123_CWRU

description: Library name: CWRR1_EnzaR_DMSO_6hr_060123_CWRU


title: D No PE, 15B, Villous Tissue

description: Illumina HiSeq 2500

value: Female


title: A673,IC50,48h,Rep2

description: Library name: sample 2


title: CWRR1_EnzaR_DMSO_24hr_060123_CWRU

description: Library name: CWRR1_EnzaR_DMSO_24hr_060123_CWRU


title: Resting_KIKO_D0_minusFoxp3_rep2

description: Library name: nKIKO_0_n_rep2_IGO_14687_B_23


title: A673,IC50,48h,Rep1

description: Library name: sample 1


title: D No PE, 15A, Villous Tissue

description: Illumina HiSeq 2500


title: Active_KIKO_D14_plusFoxp3_rep1

description: Library name: aKIKO_14_p_rep1_IGO_14687_B_18

value: 4-hydroxytamoxifen 14 days


title: CWRR1_EnzaR_Bica_6hr_060123_CWRU

description: Library name: CWRR1_EnzaR_Bica_6hr_060123_CWRU


title: D PE, 14B, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia


title: CWRR1_EnzaR_Bica_24hr_060123_CWRU

description: Library name: CWRR1_EnzaR_Bica_24hr_060123_CWRU


title: Active_KIKO_D14_minusFoxp3_rep2

description: Library name: aKIKO_14_n_rep2_IGO_14687_B_30


title: PCa1_NEPC_Lymph node

city: Taipei

first: Pei-Ching

last: Chang

address: No. 155, Sec. 2, Linong Street, Beitou District

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

description:
Library name: PCa1
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) and analyzed using Partek Flow software (Partek, Cat. No. 4485102).
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-seperated matrix file

source_name: Lymph node

extract_protocol:
Single-cell suspensions with viability greater than 90% were resuspended at a density of 1,000 cells/μL. Approximately 8,000–10,000 cells per sample were encapsulated into individual droplets using the 10x Genomics Chromium Single Cell-A Chip platform. Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the manufacturer's protocol.
Sequencing was performed on an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads with a target sequencing depth of ~150 million reads per sample.

value: Lymph node

value: Prostate cancer cell


title: D PE, 14A, Villous Tissue

description: Illumina HiSeq 2500


title: CWRR1_EnzaR_BG15n_6hr_060123_CWRU

description: Library name: CWRR1_EnzaR_BG15n_6hr_060123_CWRU


title: M PE, 13A2, Villous Tissue

description: Illumina HiSeq 2500


title: cuttag_Smad4_Smad4KO_replicate2

city: Beijing

first: Ming

middle: han

last: wang

address: Haidian road

country: China

institute: Tsinghua university

description:
Library name: Smad4-4
CUT& Tag of Smad4（CST#46535） in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).

data_processing:
Original fastq data were trimmed using Trim Galore software(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version: 0.4.4) to remove adapters and low-quality reads (parameters: --trim1 -paired).
Trimmed reads were filtered for repeat elements using sequences obtained from RepBase (v26.08) with Bowtie2 (v.2.3.5.1). The filtered reads were aligned with Bowtie2 (v.2.3.5.1) using -I 25 -X 900 -N 1 -L 25 and Samtools (v1.10).
BAM files were deduplicated with Picard (https://broadinstitute.github.io/picard/, v2.23.4) MarkDuplicates.
Normalized coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 10 --normalizeUsing RPKM and the respective genome size.
Peaks were called with MACS2 (v2.2.6) (parameters: callpeak -f BAMPE --nomodel --nolambda).
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
Minute ™  Cytodynamic and Nuclear Extraction Kits for Cells were used to extract cell nuclei from mouse liver tissue. Cell nuclei were resuspended in the Wash Buffer, and after counting, 100K cells were added to each sample for CUT&Tag experiment.
The CUT&Tag library was constructed using the reagent kit from Hefei STM Biotechnology Co., Ltd.. Libraries were amplified using 18 cycles on the thermocycler.  Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: disease state

value: liver fibrosis

value: liver

value: BDL


title: cuttag_Smad4_Smad4KO_replicate1

description:
Library name: Smad4-3
CUT& Tag of Smad4（CST#46535） in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).


title: cuttag_Smad4_Smad4WT_replicate2

description:
Library name: Smad4-2
CUT& Tag of Smad4（CST#46535） in fibrotic livers of CREPTflox/flox mice with bile duct ligation (BDL).


title: Active_KIKO_D7_plusFoxp3_rep2

description: Library name: aKIKO_7_p_rep2_IGO_14687_B_38

source_name: Spleen & lymph nodes

value: Spleen & lymph nodes

value: Active Treg wannabe

value: 4-hydroxytamoxifen 7 days


title: M PE, 13A1, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: twin


title: CWRR1_EnzaR_BG15n_24hr_060123_CWRU

description: Library name: CWRR1_EnzaR_BG15n_24hr_060123_CWRU

tag: cell line


title: Active_KIKO_D7_plusFoxp3_rep1

description: Library name: aKIKO_7_p_rep1_IGO_14687_B_16

tag: cell type


title: CWRR1_EnzaR_BG15a_6hr_060123_CWRU

description: Library name: CWRR1_EnzaR_BG15a_6hr_060123_CWRU


title: M No PE, 12A2, Villous Tissue

description: Illumina HiSeq 2500

value: normotensive

value: Male

value: Non-Hispanic

value: White


title: Active_KIKO_D14_plusFoxp3_rep2

description: Library name: aKIKO_14_p_rep2_IGO_14687_B_40

tag: genotype


title: CWRR1_EnzaR_BG15a_24hr_060123_CWRU

description: Library name: CWRR1_EnzaR_BG15a_24hr_060123_CWRU

value: Prostate cancer cell line


title: M No PE, 12A1, Villous Tissue

description: Illumina HiSeq 2500

tag: tissue


title: cuttag_Smad4_Smad4WT_replicate1

description:
Library name: Smad4-1
CUT& Tag of Smad4（CST#46535） in fibrotic livers of CREPTflox/flox mice with bile duct ligation (BDL).

tag: treatment


title: CWRR1_ctrl_R1881_6hr_060123_CWRU

description: Library name: CWRR1_ctrl_R1881_6hr_060123_CWRU


title: cuttag_Smad2/3_Smad2/3KO_replicate2

description:
Library name: Smad23-4
CUT& Tag of Smad2/3（ab202445） in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).


title: D No PE, 11B, Villous Tissue

description: Illumina HiSeq 2500

value: Female


title: Active_KIKO_D7_minusFoxp3_rep2

description: Library name: aKIKO_7_n_rep2_IGO_14687_B_28


title: Active_KIKO_D7_minusFoxp3_rep1

description: Library name: aKIKO_7_n_rep1_IGO_14687_B_6


title: cuttag_Smad2/3_Smad2/3KO_replicate1

description:
Library name: Smad23-3
CUT& Tag of Smad2/3（ab202445） in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).


title: Active_KIKO_D3_plusFoxp3_rep2

description: Library name: aKIKO_3_p_rep2_IGO_14687_B_36

value: 4-hydroxytamoxifen 3 days


title: cuttag_Smad2/3_Smad2/3WT_replicate2

description:
Library name: Smad23-2
CUT& Tag of Smad2/3（ab202445） in fibrotic livers of CREPTflox/flox mice with bile duct ligation (BDL).


title: Active_KIKO_D14_minusFoxp3_rep1

description: Library name: aKIKO_14_n_rep1_IGO_14687_B_8

value: 4-hydroxytamoxifen 14 days


title: Active_KIKO_D3_plusFoxp3_rep1

description: Library name: aKIKO_3_p_rep1_IGO_14687_B_14


title: cuttag_Smad2/3_Smad2/3WT_replicate1

description:
Library name: Smad23-1
CUT& Tag of Smad2/3（ab202445） in fibrotic livers of CREPTflox/flox mice with bile duct ligation (BDL).


title: D No PE, 11A, Villous Tissue

description: Illumina HiSeq 2500


title: CWRR1_ctrl_NT_081122_CWRU

description: Library name: CWRR1_ctrl_NT_081122_CWRU


title: CWRR1_ctrl_Enza_6hr_060123_CWRU

description: Library name: CWRR1_ctrl_Enza_6hr_060123_CWRU


title: Active_KIKO_D3_minusFoxp3_rep2

description: Library name: aKIKO_3_n_rep2_IGO_14687_B_26


title: D No PE, 10A, Villous Tissue

description: Illumina HiSeq 2500


title: cuttag_crept_creptKO_replicate2

description:
Library name: CREPT4
CUT& Tag of CREPT（Change Lab） in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).


title: Active_KIKO_D3_minusFoxp3_rep1

description: Library name: aKIKO_3_n_rep1_IGO_14687_B_4


title: cuttag_crept_creptKO_replicate1

description:
Library name: CREPT3
CUT& Tag of CREPT（Change Lab） in fibrotic livers of hepatocyte-specific deletion (CREPThep-/-) mice with bile duct ligation (BDL).


title: CWRR1_ctrl_Enza_24hr_060123_CWRU

description: Library name: CWRR1_ctrl_Enza_24hr_060123_CWRU


title: CWRR1_ctrl_DMSO_6hr_060123_CWRU

description: Library name: CWRR1_ctrl_DMSO_6hr_060123_CWRU


title: D PE, 9B, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia


title: D PE, 9A, Villous Tissue

description: Illumina HiSeq 2500


title: cuttag_crept_creptWT_replicate2

description:
Library name: CREPT2
CUT& Tag of CREPT（Change Lab） in fibrotic livers of CREPTflox/flox mice with bile duct ligation (BDL).

value: liver fibrosis


title: D No PE, 8B, Villous Tissue

description: Illumina HiSeq 2500

value: Other


title: CWRR1_ctrl_DMSO_24hr_060123_CWRU

description: Library name: CWRR1_ctrl_DMSO_24hr_060123_CWRU


title: Active_KIKO_D0_minusFoxp3_rep2

description: Library name: aKIKO_0_n_rep2_IGO_14687_B_24

value: no treatment


title: CWRR1_ctrl_R1881_24hr_060123_CWRU

description: Library name: CWRR1_ctrl_R1881_24hr_060123_CWRU


title: Active_KIKO_D0_plusFoxp3_rep1

description: Library name: aKIKO_0_p_rep1_IGO_14687_B_12

value: Spleen & lymph nodes


title: D No PE, 8A, Villous Tissue

description: Illumina HiSeq 2500


title: iPSC-derived renal tubular epithelial cells, WDR72C6  (mutant), day 14 of differentiation_No 3

city: Khon Kaen

first: ์Narissara

last: Kaewboonlert

state: Khon Kaen

address: Mittraphap Rd

department: Department of Biochemistry, Faculty of Medicine

country: Thailand

institute: Khon Kaen University

description:
Library name: WDR72C6_No3
Column name in read count_RPKM_TPM_differential expression_all.csv: EXP:WDR72_No3:ReadCount

data_processing:
Raw RNA-seq reads were preprocessed to remove low-quality sequences and adapter contamination. Low-quality reads and adapter sequences were trimmed using cutadapt v2.8.
Filtered reads were aligned to the Homo sapiens reference genome (GRCh38.p13, GCA_000001405.28) from Ensembl, gene model version 99, using STAR v2.7.1a (Reference 2) following ENCODE standard options.
Gene and transcript abundance estimation was performed using RSEM v1.3.1, featureCounts v2.0.0, HTSeq-count v0.11.2, and Cufflinks v2.2.1.
Differential expression analysis was performed using TCC v1.26.0, edgeR v3.28.1 , DESeq v1.38.0, and DESeq2 v1.26.0.
Functional enrichment analysis of differentially expressed genes (DEGs) was performed using goseq v1.38 and GOplot v1.0.2.
Assembly: Homo sapiens (GRCh38.p13)
Supplementary files format and content: csv file include TPM for values for each sample.

growth_protocol: iPSC-derived renal tubular epithelial cells were cultured in REGMTM Renal Epithelial Cell Growth Medium Bullet Kit (REGM) at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted from iPSC-derived renal tubular epithelial cells using the RNeasy Mini Kit protocol.
"RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the TruSeq Stranded mRNA Reference Guide #1000000040498 v00.

value: WDR72C6 mutation (variants c.1777A>G and c.2522T>A)

value: Renal tubular epithelial cell treatment


title: CWRR1_ctrl_Bica_24hr_060123_CWRU

description: Library name: CWRR1_ctrl_Bica_24hr_060123_CWRU


title: cuttag_crept_creptWT_replicate1

description:
Library name: CREPT1
CUT& Tag of CREPT（Change Lab） in fibrotic livers of CREPTflox/flox mice with bile duct ligation (BDL).

value: liver

value: BDL


title: D No PE, 10B, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: normotensive

value: twin


title: Active_KIKO_D0_minusFoxp3_rep1

description: Library name: aKIKO_0_n_rep1_IGO_14687_B_2

value: Active Treg wannabe


title: CWRR1_ctrl_BG15n_6hr_060123_CWRU

description: Library name: CWRR1_ctrl_BG15n_6hr_060123_CWRU

value: Prostate cancer cell line


title: iPSC-derived renal tubular epithelial cells, WDR72C6  (mutant), day 14 of differentiation_No 1

description:
Library name: WDR72C6_No1
Column name in read count_RPKM_TPM_differential expression_all.csv: EXP:WDR72_No1:ReadCount


title: WT.infant.rep4

description: Library name: WT-4_IGO_16168_B_4_S74

source_name: Spleen & Lymph nodes

value: Spleen & Lymph nodes

value: Treg

value: Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 7 Days


title: D No PE, 7A, Villous Tissue

description: Illumina HiSeq 2500

value: Female

value: Non-Hispanic

value: White


title: D No PE, 7B, Villous Tissue

description: Illumina HiSeq 2500

value: Male


title: WT.infant.rep3

description: Library name: WT-3_IGO_16168_B_3_S73


title: D No PE, 6B, Villous Tissue

description: Illumina HiSeq 2500


title: iPSC-derived renal tubular epithelial cells, WDR72C6  (mutant), day 14 of differentiation_No 2

description:
Library name: WDR72C6_No2
Column name in read count_RPKM_TPM_differential expression_all.csv: EXP:WDR72_No2:ReadCount

value: WDR72C6 mutation (variants c.1777A>G and c.2522T>A)


title: Active_KIKO_D0_plusFoxp3_rep2

description: Library name: aKIKO_0_p_rep2_IGO_14687_B_34

value: Spleen & lymph nodes

value: no treatment


title: CWRR1_ctrl_BG15n_24hr_060123_CWRU

description: Library name: CWRR1_ctrl_BG15n_24hr_060123_CWRU


title: WT.infant.rep2

description: Library name: WT-2_IGO_16168_B_2_S72


title: iPSC-derived renal tubular epithelial cells, WTC13 (wild-type), day 14 of differentiation_No 3

description:
Library name: WTC13_No3
Column name in read count_RPKM_TPM_differential expression_all.csv: EXP:WTC13_No3:ReadCount

value: wild-type

value: Renal tubular epithelial cell treatment


title: CWRR1_ctrl_BG15a_6hr_060123_CWRU

description: Library name: CWRR1_ctrl_BG15a_6hr_060123_CWRU


title: CWRR1_ctrl_BG15a_24hr_060123_CWRU

description: Library name: CWRR1_ctrl_BG15a_24hr_060123_CWRU


title: iPSC-derived renal tubular epithelial cells, WTC13 (wild-type), day 14 of differentiation_No 2

description:
Library name: WTC13_No2
Column name in read count_RPKM_TPM_differential expression_all.csv: EXP:WTC13_No2:ReadCount


title: CWRR1_ctrl_Bica_6hr_060123_CWRU

description: Library name: CWRR1_ctrl_Bica_6hr_060123_CWRU


title: WT.infant.rep1

description: Library name: WT-1_IGO_16168_B_1_S71


title: D No PE, 6A, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: normotensive


title: Tir1.infant.rep4

description: Library name: TIR1-4_IGO_16168_B_8_S78

value: Foxp3-AID ROSA26-WT


title: NK92_PD-1_PPI_BioRep4

city: Abingdon

first: Alice

last: Newey

address: 92 Park Dr, Milton

institute: Immunocore

description: Library name: ID_9178

data_processing:
Following RNA sequencing, raw fastq files were trimmed with Trim galore (v0.6.7) with --nextseq-trim option enabled. Quality was then assessed using FastQC and MultiQC (v1.12). Transcript mapping and quantification was then performed by the QIAGEN OmicSoft Suite software, version 10.0.1.81, including use of the QIAGEN Omicsoft Aligner
Assembly: grch38
Supplementary files format and content: tab-delimited text files contain raw counts for each sample.

growth_protocol: The NK92 cell line was from the Basel Institute for Immunology and maintained in GMP SCGM medium (Sartorius Stedim, 20802-0500) supplemented with 20% heat inactivated FBS, pen/strep (50 U/mL penicillin and 50 µg/mL strep, Gibco, 15070-063) and IL-2 (500 U/mL Peprotech, 200-02).

extract_protocol:
Cell pellets containing 1 to 2 million cells were lysed with Buffer RLT Lysis buffer (Qiagen, 1015762, 350 µL) then stored at -80⁰C. RNA was prepped with the RNEasy mini Qiagen kit.
The RNA samples were submitted for paired-end RNA sequencing by GENEWIZ, and they were sequenced on the Illumina Nextseq to a depth of ~20 million reads per sample.

treatment_protocol: NK92-PD-1 cells were incubated with K562-HLA-A*02-PPI/ImmTAAIs target cells for 20 hours and were sorted on the Sony SH800 for the NK-92 cells.

value: Nk cell line

tag: genetic modification

value: PPI


title: D No PE, 5A, Villous Tissue

description: Illumina HiSeq 2500

value: twin


title: D No PE, 5B, Villous Tissue

description: Illumina HiSeq 2500


title: iPSC-derived renal tubular epithelial cells, WTC13 (wild-type), day 14 of differentiation_No 1

description:
Library name: WTC13_No1
Column name in read count_RPKM_TPM_differential expression_all.csv: EXP:WTC13_No1:ReadCount


title: NK92_PD-1_UntargtedControl_BioRep4

description: Library name: ID_9177

value: UntargtedControl


title: NK92_PD-1_UntreatedControl_BioRep4

description: Library name: ID_9176

value: UntreatedControl


title: CR23CART_3

city: Guangzhou

first: Fan

last: Xing

address: Zhongshan Road

institute: Guangdong Provincial People's Hospital

description: Library name: CR23CART_3

data_processing:
Raw fastq were quality-controlled using fastp(v0.23.4) with default parameters.
The clean fastqas were mapped to reference genome(GRCh38) by STAR(v2.7.11a) with parameter "--quantMode GeneCounts".
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file with expression counts matrix

source_name: cell line

extract_protocol:
RNA libraries for RNA-seq were prepared using mRNA-seq library Prep Kit following manufacturer's protocols
RNA libraries for RNA-seq were prepared using mRNA-seq library Prep Kit following manufacturer's protocols

value: cell line

value: CR23/B7H3_CAR_T cels

value: CD3 T cells

value: loading VSVΔ51


title: CR23CART_2

description: Library name: CR23CART_2


title: D PE, 4B, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia

value: Male

value: Non-Hispanic

value: White


title: CR23CART_1

description: Library name: CR23CART_1


title: D PE, 4A, Villous Tissue

description: Illumina HiSeq 2500

value: Female


title: Tir1.infant.rep1

description: Library name: TIR1-1_IGO_16168_B_5_S75

value: Spleen & Lymph nodes

value: Treg

value: 5-ph-IAA 7 Days


title: Thymus_Cd73negTreg_TIR1_rep3

description: Library name: 6_T_IGO_14532_B_6

source_name: Thymus

value: Thymus

value: Thymic Treg

value: Foxp3-AID ROSA26-TIR1(F74G)


title: NK92_PD-1_UntargtedControl_BioRep3

description: Library name: ID_9174

value: Nk cell line

value: UntargtedControl


title: CART_2

description: Library name: CART_2

value: cell line

value: B7H3_CAR_T cels


title: D PE, 3A, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: twin


title: Tir1.infant.rep3

description: Library name: TIR1-3_IGO_16168_B_7_S77

value: Foxp3-AID ROSA26-WT


title: M PE, 2A2, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia

value: Hispanic


title: NK92_PD-1_UntreatedControl_BioRep3

description: Library name: ID_9173

value: UntreatedControl


title: Thymus_Cd73negTreg_TIR1_rep1

description: Library name: 4_T_IGO_14532_B_4


title: NK92_PD-1_PPI_BioRep2

description: Library name: ID_9172

value: PPI


title: M PE, 2A1, Villous Tissue

description: Illumina HiSeq 2500

value: Female

value: White


title: NK92_PD-1_PPI_BioRep3

description: Library name: ID_9175


title: b-Orgs HEP generation T0 LM481H

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Library name: 27
b-Orgs HEP generation T0 LM481H

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and eventually filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter if necessary.
Mapping of the reads were obtained using the STAR program against human genome (GRCh38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE.v26 database .
Assembly: Homo Sapiens (GRCh38)
Supplementary files format and content: Expected counts (RSEM)

source_name: Liver biopsy tissue

growth_protocol: b-Orgs and Chol-Orgs were grown embedded in Matrigel (Corning). HEP medium used for b-Orgs generation was previously described by H. Hu et al. Cell 2018. BEC medium used for b-Orgs and Cho-Orgs generation was previously described by L. Broutier et al. Nat Protoc 2016.

extract_protocol:
Total RNA was extracted from total liver tissue and from cultured organoids using the commercial RNeasy Micro and Mini Kits (Qiagen) following manufacturer’s instructions.
Sequencing libraries were prepared using NuGEN Universal Plus mRNA-Seq kit (PART NO. 0508, 9133, 9134) and following the user guides (M01442v2 and M01485v8).

treatment_protocol: To model disease progression, b-Orgs generated with HEP medium were treated for 5 days with AH-medium. AH-medium consisted of HEP-medium with 100ng/mL LPS (Sigma, L2637), 20ng/mL rhTNFa (Genscript, Z01001), 10ng/mL rhIL1b (Preprotech, 200-01B) and 100mM EtOH. Vehicle group was just cultured with HEP-medium.

value: Liver biopsy tissue

value: b-Orgs HEP generation T0


title: NK92_PD-1_UntargtedControl_BioRep2

description: Library name: ID_9171


title: NK92_PD-1_UntreatedControl_BioRep2

description: Library name: ID_9170


title: Thymus_Cd73negTreg_WT_rep2

description: Library name: 2_T_IGO_14532_B_2

value: Thymus

value: Thymic Treg

value: 5-ph-IAA 7 Days


title: Thymus_Cd73negTreg_WT_rep3

description: Library name: 3_T_IGO_14532_B_3


title: D PE, 1B, Villous Tissue

description: Illumina HiSeq 2500

value: Male

value: Non-Hispanic

value: Black


title: b-Orgs HEP generation T0 LM488H

description:
Library name: 26
b-Orgs HEP generation T0 LM488H


title: Tir1.infant.rep2

description: Library name: TIR1-2_IGO_16168_B_6_S76

value: Spleen & Lymph nodes

value: Treg


title: D PE, 3B, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: twin


title: D PE, 1A, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia


title: b-Orgs HEP generation T0 LM484H

description:
Library name: 25
b-Orgs HEP generation T0 LM484H


title: Thymus_Cd73negTreg_WT_rep1

description: Library name: 1_T_IGO_14532_B_1

value: Foxp3-AID ROSA26-WT


title: NK92_PD-1_PPI_BioRep1

description: Library name: ID_9169

value: Nk cell line

value: PPI


title: CART_3

description: Library name: CART_3

value: cell line

value: B7H3_CAR_T cels

value: CD3 T cells

value: loading VSVΔ51


title: b-Orgs HEP generation T0 LM476H

description:
Library name: 21
b-Orgs HEP generation T0 LM476H

value: Liver biopsy tissue

value: b-Orgs HEP generation T0


title: CART_1

description: Library name: CART_1


title: NK92_PD-1_UntargtedControl_BioRep1

description: Library name: ID_9168

value: UntargtedControl


title: b-Orgs HEP generation T0 LM477H

description:
Library name: 20
b-Orgs HEP generation T0 LM477H


title: Thymus_Cd73negTreg_TIR1_rep2

description: Library name: 5_T_IGO_14532_B_5

value: Thymus

value: Thymic Treg

value: Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 7 Days


title: S PE, 39, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: singleton

value: Female

value: Non-Hispanic

value: White


title: Resting_Treg_TIR1_rep3

description: Library name: 6_SLO_R_IGO_14532_B_18

value: Spleen & lymph nodes

value: Resting Treg (CD62L high)


title: NK92_PD-1_UntreatedControl_BioRep1

description: Library name: ID_9167

value: Nk cell line

value: UntreatedControl


title: Resting_Treg_TIR1_rep2

description: Library name: 5_SLO_R_IGO_14532_B_16


title: b-Orgs HEP generation T0 LM500H

description:
Library name: 19
b-Orgs HEP generation T0 LM500H


title: S PE, 38, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia


title: aorta, IgG control

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description: Library name: IgG

data_processing:
Fastq files were trimmed using trim_galore (version 0.6.10) with default paired settings
Paired trimmed reads were aligned to the mouse genome (mm10) using bowtie2 with the following parameters "-N 1" and this SAM output was piped into samtools view (version 1.6)  with the parameters "-bSF4"
BAM files were then sorted, duplicate reads were removed, reads that could not be uniquely mapped were dropped, and the file was indexed
Bigwig files were generated using bamCompare from deeptools (version 3.2.2.) comparing the sample files to the IgG bam file with specification of -binSize 20 –smoothLength 60 –extendReads 150 –scaleFactorsMethod readcount –operation subtract and the parameter –center for Prdm16
HOMER (version 4.11) was used for peak calling where Tag directories were first created for each sample utilizing makeTagDirectory with the parameters "-single -genome mm10" specified. The function findpeaks was used for peakcalling with parameters "-size 200 -F 2 -L 2 -fdr 0.01 -center -region" specified for Prdm16 compared to the IgG input tag directory. The same parameters were run for IgG without calling -i -center and -region and the H3K27ac sample was run with just -style set to histone.
Assembly: mm10
Supplementary files format and content: bigWigs generated using deeptools bamcompare function

source_name: Cleaned Aorta

growth_protocol: Animals were raised at room temperature on standard chow (LabDiet, 5010) with a 12-h light–dark cycle at room temperature (22 °C).

extract_protocol:
For PRDM16 ChIP in C57Bl6/J aortae, 12 were dissected, dual-crosslinked with 1.5mM EGS for 20 min followed by 1% formaldehyde for 10 min, then washed and snap frozen in liquid nitrogen.  Aortae were pooled into a 2mL safe-lock tube with a 3mm stainless steel bead and cryo-milled into a powder using 2 cycles of 5Hz for 30 sec and 23 Hz for 30 sec.  The pulverized aortas were placed on wet ice, allowed to thaw slightly and then resuspended in 0.6% SDS lysis buffer.  Chromatin was sheared using a microtip probe sonicator at 25% Amplitude, 30 sec on, 20 sec off for 5 minutes.  After the first minute of shearing the insoluble ECM clump was removed with a pipet tip and shearing resumed for the remaining 4 minutes.  Dilution buffer was added to make a 0.1% SDS final IP concentration and the sample was split into 3 separate immunoprecipitations with approximately 10ug chromatin per IP.
ChIP DNA was purified using Active Motif Chromatin IP Purification Kit and used for downstream library prep. Sequencing libraries were made according to manufacturer’s recommendations using the Roche KAPA HyperPrep Kit and Roche Universal Dual-Index Adapters.  Size selection was performed using Beckman Coulter SPRI Select beads for an 800 bp upper limit cut-off

value: Cleaned Aorta

tag: chip antibody

value: control

tag: Sex

value: male


title: aorta, Prdm16

description: Library name: Prdm16

value: Prdm16 (in house)


title: Hermes 4B melanocytes, siCDH3AS1_2

city: Tampa

first: Alex

middle: M

last: Jaeger

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: Moffitt Cancer Center

description:
Library name: AJ058
riboseq on siCDH3AS1 treated melanocytes

data_processing:
The first 3 5' nucleotides were removed along with polyA tracts that are artifacts from library generation
Trimmed RPF sequences were then, deduplicated, aligned to rRNA and tRNA, keeping unaligned reads
Reads unaligned to rRNA/tRNA were then aligned to the genome and transcriptome to generate alignment files for further analysis
3 nt periodicity of reads was performed with RiboWaltz in R
differential expression was performed with DEseq2
Assembly: hg38
Supplementary files format and content: csv files containing raw read counts and RPKM calcluations for 5'UTRs, CDS, and 3'UTRs for all transcripts
Library strategy: Ribo-Seq

source_name: skin

growth_protocol: Hermes cells were cultured in RPMI1640+10% FBS, 200 nM TPA, 10 nM endothelin-1, 200 pM cholera toxin, and 10 ng/mL human stem cell factor.

extract_protocol:
Cells grown in 10 cm dishes were washed with 5 mL of ice-cold PBS containing 100 μg/mL cycloheximide (Millipore, Cat. #239764) and immediately harvested by scraping. The cells were collected by centrifugation at 5,000 × g for 5 minutes, and the pellet was resuspended in 400 μL of lysis buffer. The lysate was homogenized by vortexing and incubated on ice for 10 minutes. Clarification was performed by centrifugation at 15,000 × g for 10 minutes at 4°C, and the supernatant was kept on ice. For RNA digestion, 40–60 μg of RNA from the lysate were treated with RNAse I (Lucigen, Cat. #N6901K) for 50 minutes at room temperature while rotating. Following digestion, 5 μL of RNasin™ Plus RNAse inhibitor (Promega, Cat. #PRN2615) was added to the RNA. Monosome isolation was performed with Microspin S-400 HR columns (Cytiva, Cat. #GE27-5140-01). Columns were washed six times with 500 μL of column wash buffer, followed by centrifugation at 600 × g for 4 minutes. Subsequently, 100 μL of digested sample was applied to the resin in each column and centrifuged at 600 × g for 2 minutes. Approximately 125 μL of eluate was collected per column, and eluates from the same sample were pooled. To precipitate Ribosome-Protected Fragment (RPF) RNA, an equal volume of acid phenol:chloroform was added to the eluate, vortexed, and incubated at room temperature for 5 minutes. The mixture was centrifuged at 15,000 × g for 10 minutes at 4°C. The aqueous phase was collected, and 1:10 volume of 3 M NaOAc (pH 5.2), 2 μL of glycogen, and 1 volume of ice-cold isopropanol were added. The RPF RNA was precipitated overnight at −80°C. The samples were centrifuged at 15,000 × g for 15 minutes at 4°C, the supernatant was discarded, and the pellet was washed with 80% ethanol. Following another centrifugation at 15,000 × g for 10 minutes at 4°C, the pellet was air-dried and resuspended in 15 μL of nuclease-free water. To select for the appropriate size RNA, the samples were run on a Novex 12% TBE Urea precast gel (Thermo Fisher Scientific). 5uL of Gel Loading Buffer (Thermo Fisher, Cat # AM8547) was added to the resuspended RNA and loaded into one or two wells of the gel alongside a 30nt RNA oligo marker and small RNA ladder (Zymo Cat # R1090). The gel was then washed with TBE, stained with Sybr Gold Nucleic Acid Stain (Thermo Fisher, Cat. #S11494), and imaged. RNA species of 30nt using the marker as reference were then excised, crushed, and suspended in 400uL RNA Binding Buffer (Zymo RNA Clean & Concentrator Kit, Cat. # R1016) and left to diffuse at room temperature overnight. Following overnight diffusion, samples were centrifuged at 10,000 x g for 10min to pellet the gel and ~350uL of RNA binding buffer was removed. The RNA was then isolated using the RNA Clean & Concentrator™ column (Zymo Research), following the manufacturer’s instructions and eluted in 30uL of nuclease free water.
Following elution, samples were transferred to PCR tubes, mixed with 1uL (10 units) of T4 Polynucleotide Kinase (NEB, Cat #M0201L), 5uL T4 Polynucleotide Kinase Reaction Buffer (NEB, Cat #B0201S) and 5uL 10mM ATP, and the volume was brought up to 50uL. Samples were then incubated at 37C for 1 hour. A modified protocol for the RNA Clean & Concentrator™ column was then used to isolate RNA. 100uL adjusted binding buffer (1:1 RNA Binding buffer and ethanol) was mixed with the phosphorylated RNA and added to the column. After centrifugation, 150uL of ethanol was then added to the flow through and this solution was loaded added to a new column and washed according to the manufacturer’s instructions, eluting in 7uL of nuclease free water. Library preparation was performed using the Takara SMARTer® smRNA-Seq Kit for Illumina® (Takara). Samples received 17 PCR cycles and were sequenced at 50-bp single end reads on a NovaSeq6000

treatment_protocol: Cells at 50% confluency were transfected with 25-50 nM of Dharmacon siRNAs using JetPRIME transfection reagent.

value: skin

value: Hermes 4B

value: melanocytes

value: WT

tag: batch


title: Resting_Treg_WT_rep3

city: Princeton

first: Yuri

last: Pritykin

address: 245 Carl Icahn Lab

institute: Princeton

description: Library name: 3_SLO_R_IGO_14532_B_12

value: Foxp3-AID ROSA26-WT

value: 5-ph-IAA 7 Days


title: Resting_Treg_WT_rep2

description: Library name: 2_SLO_R_IGO_14532_B_10


title: Hermes 4B melanocytes, siCDH3AS1_1

description:
Library name: AJ050
riboseq on siCDH3AS1 treated melanocytes


title: aorta, H3K27ac

description: Library name: H3K27ac

value: Active Motif 39133


title: Resting_Treg_WT_rep1

description: Library name: 1_SLO_R_IGO_14532_B_8


title: S PE, 40, Villous Tissue

city: Chicago

description: Illumina HiSeq 2500

value: placenta, villous tissue

tag: clinical group

value: singleton

value: Female

value: Non-Hispanic

value: White


title: Hermes 4B melanocytes, siCtrl_2

description:
Library name: AJ057
riboseq on control treated melanocytes


title: S PE, 35, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia

tag: singleton or_twin

value: Male

value: Hispanic


title: S PE, 34, Villous Tissue

description: Illumina HiSeq 2500

tag: age of_mother_(years)


title: Hermes 4B melanocytes, siCtrl_1

description:
Library name: AJ049
riboseq on control treated melanocytes

value: control


title: Active_Treg_TIR1_rep3

description: Library name: 6_SLO_A_IGO_14532_B_17

value: Spleen & lymph nodes

value: Active Treg (CD62 low)

value: Foxp3-AID ROSA26-TIR1(F74G)


title: patient 4 PolyIC

city: St. Louis

first: Daniel

middle: Andre

last: Veronese-Paniagua

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St. Louis

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University in St. Louis
Assembly: refdata-gex-GRCh38-2020-A_pCVB-eGFP_paniagua
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Pacnreatic Islet

growth_protocol: Primary human islets were cultured in CMRL+10% FBS

extract_protocol:
cells were single cell dispersed
Library construction for single cell was constructed using 10X Chromium Protocol.

treatment_protocol: Cells were treated with CVB3-eGFP at MOI 20, 500 ng/mL poly(I:C), or endotoxin-free water (control) for 24 hr and 48 hr

value: Pacnreatic Islet

value: 500 ng/mL poly(I:C)


title: Resting_Treg_TIR1_rep1

description: Library name: 4_SLO_R_IGO_14532_B_14

value: Resting Treg (CD62L high)


title: patient 4 control

value: Endotoxin-free water


title: S PE, 32, Villous Tissue

description: Illumina HiSeq 2500

tag: birthweight interval_(grams)


title: Active_Treg_TIR1_rep1

description: Library name: 4_SLO_A_IGO_14532_B_13

value: 5-ph-IAA 7 Days


title: Vehicle_S4, rep2

city: Houston

first: Zhenzhen

last: Xun

address: 7007 Bertner Ave

institute: MD Anderson Cancer Center

description:
Library name: sample22
2_V4

data_processing:
Raw fastq files were mapped to mouse transcriptome mm10 using PIPseeker V3.2
Assembly: Mouse mm10
Supplementary files format and content: matrix, features, and barcodes files

source_name: tumor

extract_protocol:
Tumors were dissected from mice and single-cell suspensions were obtained.CD45+ cells were sorted for sequencing
Cells were processed accroding to the manufacturer's protocol and sequenced on a PIPseekerTM 3' Single Cell RNA (scRNA-seq) Kits.

value: tumor

value: CD45+ cells

value: Vehicle


title: S PE, 37, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: singleton

tag: assigned neonatal_sex

value: Female

value: Non-Hispanic

value: Black


title: Vehicle_S4, rep4

description:
Library name: sample24
4_V4


title: S PE, 31, Villous Tissue

description: Illumina HiSeq 2500

value: preeclampsia

value: Male

tag: maternal ethnicity

value: White


title: patient 4 48hr CVB3

value: CVB3-eGFP at MOI 20


title: Vehicle_S4, rep1

description:
Library name: sample21
1_V4


title: Vehicle_S2, rep4

description:
Library name: sample20
4_V3


title: S PE, 36, Villous Tissue

description: Illumina HiSeq 2500

tag: maternal race


title: Active_Treg_WT_rep3

description: Library name: 3_SLO_A_IGO_14532_B_11

data_processing:
RNA-seq was aligned to mm39 with bowtie2 and read counts were calculated using FeatureCounts. Differential gene expression was calculated using DESeq2
Assembly: mm39
Supplementary files format and content: Counts matrices, .tsv

extract_protocol:
RNA extraction was  performed according to the manufacturer’s instructions. Briefly, phase separation in cells lysed in 1mL TRIzol Reagent was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 15-18 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1-2 ng total RNA with RNA integrity numbers ranging from 5.5 to 9.3 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. 4.5-8 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Roche 07962363001) using 8 cycles of PCR.

value: Spleen & lymph nodes

value: Active Treg (CD62 low)

value: Foxp3-AID ROSA26-WT


title: patient 4 24hr CVB3

value: Pacnreatic Islet


title: S PE, S20, Villous Tissue

description: Illumina HiSeq 2500

value: early-onset preeclampsia


title: S PE, S18, Villous Tissue

description: Illumina HiSeq 2500


title: Active_Treg_WT_rep2

description: Library name: 2_SLO_A_IGO_14532_B_9

value: 5-ph-IAA 7 Days


title: Vehicle_S2, rep3

description:
Library name: sample19
3_V3

value: tumor

value: CD45+ cells


title: Vehicle_S4, rep3

description:
Library name: sample23
3_V4

value: Vehicle


title: Active_Treg_WT_rep1

description: Library name: 1_SLO_A_IGO_14532_B_7


title: Vehicle_S2, rep2

description:
Library name: sample18
2_V3


title: S PE, S06, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: singleton


title: S PE, 33, Villous Tissue

description: Illumina HiSeq 2500

value: Non-Hispanic


title: Skeletal muscle, satellite cell retained 2, 28 month old

city: Fayetteville

first: Kevin

last: Murach

state: Arkansas

address: 155 Stadium Drive

institute: University of Arkansas

description: Library name: veh_2_4d_mov

data_processing:
Alignment was performed using mm10 genome and CellRanger version 7.1.0
Assembly: mm10
Supplementary files format and content: .h5 files

source_name: Plantaris skeletal muscle

extract_protocol:
Single cell suspensions were made from fresh muscle using collagenase followed by collagenase and dispase. Suspended cells were then filtered through a 40μm strainer and pelletted by centrifugation at 500 x g for 5 minutes and resuspended in dPBS with 0.04% BSA to reduce ambient RNA and cell aggregation per 10X Genomics recommendation. Debris, doublets, and dead cells were gated out during fluorescence activated cell sorting (FACS) using forward/side-scatter profiles and DAPI fluorescent intensity. Cells were sorted directly into reverse transcription buffer. After loading into the 10X Chromium Controller, the Single Cell 3' reagent kit was applied according to the manufacturer's protocol.
Libraries were prepared using version 3.0 chemistry.

treatment_protocol: SC-/tam/t mice: daily intraperitoneal injection of tamoxifen (2mg/injection) in sunflowerseed oil with 15% ethanol for 5 days. SC+/veh/v mice: daily intraperitoneal injection of sunflowerseed oil with 15% ethanol for 5 days. Two week washout period prior to bilateral synergist ablation surgery including removal of the gastrocnemius and soleus muscles. Plantaris muscles were collected 96 hours after surgery.

value: Plantaris skeletal muscle

value: Sunflowerseed oil


title: Vehicle_S2, rep1

description:
Library name: sample17
1_V3


title: Skeletal muscle, satellite cell retained 1, 28 month old

description: Library name: veh_1_4d_mov


title: Output sample of replicate 3 of synthetic bZIP bindingPCA

city: Basel

first: Alexandra

middle: Michaela

last: Bendel

address: Maulbeerstr. 66

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Library name: Synthetic_bZIPs - Output 3
TableS3_synthetic_bZIPs.txt

data_processing:
Reads were processed with mutscan (Soneson et al. 2023)
Supplementary files format and content: tab-deliminated text files; contains read counts (barcode-association data) logFC (binding PCA) and further information, depending on dataset

organism: Saccharomyces cerevisiae

extract_protocol:
For the barcode variant association, DNA was extracted from the transformed E. coli cells using the NucleoBond® PC 500 kit (Macherey-Nagel, Düren, Germany). For the yeast libraries, DNA was extracted using a custom yeast Midiprep protocol
Sequencing libraries were constructed by PCR with primers cotaining the illumina adapters


title: Skeletal muscle, satellite cell depleted 1, 28 month old

description: Library name: tam_1_4d_mov

value: Tamoxifen


title: Vehicle_S1, rep2

description:
Library name: sample14
2_V2


title: patient 2 24hr

description: multiplexed


title: Active_Treg_TIR1_rep2

description: Library name: 5_SLO_A_IGO_14532_B_15

value: Foxp3-AID ROSA26-TIR1(F74G)


title: Vehicle_S1, rep4

description:
Library name: sample16
4_V2


title: Output sample of replicate 4 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Output 4
TableS3_synthetic_bZIPs.txt


title: patient 3 24hr

description: multiplexed


title: Skeletal muscle, satellite cell depleted 2, 28 month old

description: Library name: tam_2_4d_mov


title: patient 1 48hr

description: multiplexed


title: Output sample of replicate 1 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Output 1
TableS3_synthetic_bZIPs.txt


title: patient 2 48hr

description: multiplexed


title: Output sample of replicate 2 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Output 2
TableS3_synthetic_bZIPs.txt


title: Vehicle_S1, rep3

description:
Library name: sample15
3_V2


title: patient 1 24hr

description: multiplexed


title: Vehicle_S1, rep1

description:
Library name: sample13
1_V2


title: Input sample of replicate 4 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Input 4
TableS3_synthetic_bZIPs.txt


title: BV2_CC_hyp_rep2_ATACseq

city: Warsaw

first: Monika

last: Dzwigonska

address: 3 Pasteur Street

country: Poland

institute: Nencki Institute of Experimental Biology, PAS

data_processing:
Reads were trimmed using Trimmomatic (version 0.36) to remove adapter, transposase sequence short reads, and low quality 5′ and 3′ bases. Paired-end reads were then aligned to mm10 reference genome using Hisat2 (version 2.1.0) with parameters -X 2000. Duplicate reads were subsequently removed with Picard's MarkDuplicates tool (version 2.26.2) and reads mapping to the mitochondrial genome were also excluded. Only properly paired and uniquely mapped reads were kept for downstream analysis using samtools view with the options -q 30 -f 2 -F 256.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated from BAM files using Deeptools (bamCoverage) and were normalized to genome coverage (RPGC).
Supplementary files format and content: Peaks were called using MACS2 (version 2.1.1.2) with parameters set to -f BAPME -q 0.01 –nomodel –shift 0.

growth_protocol: GL261 cells were seeded in DMEM supplemented with 10% FBS and antibiotics. After 24 h, the medium was changed to a microglia culture medium DMEM with GlutaMAX™ supplemented with 2% FBS and antibiotics  and the BV2 cells were co-seeded onto GL261 cells at a 1:2 ratio relative to GL261 cells. Following 24h, the cells were cultured under normoxic or hypoxic conditions for another 16 hours and used in further assays. The control BV2 and GL261 cells were grown as monoculture.

extract_protocol:
ATACseq was performed as previously described with some modifications (Chen et al., 2016). While still in hypoxic conditions, cells were fixed with 1% formaldehyde (Thermo Scientific) for 10 min and then quenched with 0.125 M glycine for 5 min at room temperature. After returning to normal conditions (21% O2), cells were washed with PBS and incubate in 3% BSA (Sigma) with CD16/CD32 Fc Block™ (1:250, BD Pharmingen, Cat#553142) for 15 min. Next the CD45 (Clone 30-F11) labeled with PE, (1:400, BD Pharmingen, Cat#553081) was added for 40 min, washed with PBS, and CD45+ cells or GFP+ cells were sorted to 1% BSA in PBS using Cell Sorter BD FACSAriaII. After sort, cells were counted and 50,000 cells lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 5 min on ice. Cells were then centrifuged at 500xg for 8min, and cell pellets were resuspended in transposition reaction according to the standard ATACseq protocol using 2.5 ul of Tn5 enzyme per 50 000 of cells (Buenrostro et al., 2015). After transposition, cells were centrifuged and reverse crosslinked (50 mM Tris-Cl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 200 μg/ml proteinase K) at 65°C with an overnight shaking at 1200 rpm. Zymo DNA Clean & Concentrator-5 columns (ZymoResearch) were used to purify DNA.
Sequencing libraries were prepared according to the original ATACseq protocol (Buenrostro et al., 2015). The ATACseq libraries were assessed for appropriate quality using a Bioanalyzer 2100 and subjected to paired-end sequencing (2x151bp) using NovaSeq 6000 (Illumina). Two biological replicates per condition were analysed.

treatment_protocol: Cells were incubated at <0.1% in a M35 Hypoxystation (Don Whitley) hypoxic chamber in the presence of 5% CO2 at 37°C for 16h.

value: Murine microglial

tag: condition

value: Co-culture

value: hypoxia <0.1% O2


title: patient 3 48hr

description: multiplexed


title: AMG510_S3, rep4

description:
Library name: sample12
4_AMG3


title: BV2_CC_hyp_rep1_ATACseq

tag: cell line


title: b-Orgs AH-medium (487OH)

source_name: Liver Organoids

value: Liver Organoids

tag: sample group

value: b-Orgs AH-medium


title: Input sample of replicate 3 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Input 3
TableS3_synthetic_bZIPs.txt

tag: cell type


title: Input sample of replicate 2 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Input 2
TableS3_synthetic_bZIPs.txt


title: AMG510_S3, rep3

description:
Library name: sample11
3_AMG3

tag: tissue


title: BV2_CC_norm_rep2_ATACseq

tag: treatment

value: normoxia 21% O2


title: b-Orgs AH-medium (474OH)


title: b-Orgs AH-medium (486OH)


title: BV2_Ctrl_norm_rep2_ATACseq

value: Monoculture


title: Input sample of replicate 1 of synthetic bZIP bindingPCA

description:
Library name: Synthetic_bZIPs - Input 1
TableS3_synthetic_bZIPs.txt


title: AMG510_S2, rep4

description:
Library name: sample8
4_AMG2

value: tumor


title: b-Orgs AH-medium (471OH)


title: BV2_Ctrl_hyp_rep1_ATACseq


title: BV2_Ctrl_hyp_rep2_ATACseq


title: BV2_CC_norm_rep1_ATACseq


title: Output sample of replicate 2 of bindingPCA screen of Batch 4

description:
Library name: Batch 4 - Output 2
TableS1_all_unfiltered_data.txt


title: b-Orgs Vehicle (487VEH)

value: b-Orgs Vehicle


title: AMG510_S2, rep3

description:
Library name: sample7
3_AMG2

value: CD45+ cells


title: b-Orgs Vehicle (474VEH)


title: AMG510_S3, rep1

description:
Library name: sample9
1_AMG3


title: AMG510_S2, rep2

description:
Library name: sample6
2_AMG2


title: AMG510_S3, rep2

description:
Library name: sample10
2_AMG3


title: Output sample of replicate 1 of bindingPCA screen of Batch 4

description:
Library name: Batch 4 - Output 1
TableS1_all_unfiltered_data.txt


title: b-Orgs Vehicle (486VEH)


title: BV2_Ctrl_norm_rep1_ATACseq


title: AMG510_S2, rep1

description:
Library name: sample5
1_AMG2


title: GL261_CC_hyp_rep2_RNAseq

data_processing:
Low-quality reads and adapters were trimmed using Trimmomatic (version 0.36) The resulting RNA sequencing reads were mapped to mm10 reference genome sequence using STAR aligner (version 2.6). Read duplicates were marked with Picard Tools (version 2.17.1) and only uniquely maped reads were kept for the downstream analysis with samtools view -q 255. Quantification of mapped reads and summarisation by gene was performed using HTSeq-count (version 0.9.1), with overlap mode set to union and stranded mode to reverse (-m union -s reverse).
Assembly: mm10
Supplementary files format and content: Bigwig files were generated from BAM files using Deeptools (bamCoverage) and were normalized to genome coverage (RPKM).
Supplementary files format and content: raw counts

source_name: GL261 stably expressing pEGFP-N1

growth_protocol: For direct co-culture experiment GL261 cells were seeded in DMEM supplemented with 10% FBS and antibiotics (100 U/mL penicillin, 100 µg/mL streptomycin). After 24 h, the medium was changed to a BV2 culture medium (DMEM with GlutaMAX? supplemented with 2% FBS and antibiotics) or BMDM culture medium (DMEM with GlutaMAX? supplemented with 10% FBS and antibiotics). Following 24h, either BV2 cells or BMDM cell were co-seeded onto GL261 cell at a ratio of 1:2 (BV2:GL261) or 1:1 (BMDM:GL261), cultured under normoxic or hypoxic conditions for another 16 hours and used in further assays. The control BV2, BMDMs or GL261 were grown as monoculture. For the HDAC inhibitor (HDACi) treatment experiments, BV2 or BMDM were seeded in DMEM with GlutaMAX supplemented with 2% or 10% FBS, respectively. Following 24h cells were cultured under normoxic or hypoxic conditions and treated with Panobinostat or DMSO.

extract_protocol:
For RNAseq cells from hypoxia or normoxia conditions were fixed on ice with 3% Glyoxal fixation solution as was described previously (Channathodiyil, PLoS One. 2021). RNA was isolated using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions and the quality was assessed with the Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies).
PolyA enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems). The RNAseq libraries were sequenced at 2x151 bp paired-end on NovaSeq 6000. Two biological replicates per condition were analysed.

value: GL261 stably expressing pEGFP-N1

value: Murine glioma


title: Input sample of replicate 2 of bindingPCA screen of Batch 4

description:
Library name: Batch 4 - Input 2
TableS1_all_unfiltered_data.txt


title: b-Orgs HEP passage 3 (511P3)

value: b-Orgs HEP passage 3


title: b-Orgs Vehicle (471VEH)


title: AMG510_S1, rep4

description:
Library name: sample4
4_AMG1


title: GL261_CC_hyp_rep1_RNAseq


title: Input sample of replicate 1 of bindingPCA screen of Batch 4

description:
Library name: Batch 4 - Input 1
TableS1_all_unfiltered_data.txt


title: b-Orgs HEP passage 3 (487P3)


title: AMG510_S1, rep3

description:
Library name: sample3
3_AMG1


title: GL261_CC_norm_rep2_RNAseq


title: AMG510_S1, rep2

description:
Library name: sample2
2_AMG1


title: Input sample of replicate 3 of bindingPCA screen of Batch 4

description:
Library name: Batch 4 - Input 3
TableS1_all_unfiltered_data.txt


title: b-Orgs HEP passage 1 (511P1)

value: b-Orgs HEP passage 1


title: GL261_Ctrl_hyp_rep2_RNAseq


title: GL261_CC_norm_rep1_RNAseq


title: b-Orgs HEP passage 3 (486P3B)


title: Input sample of replicate 3 of bindingPCA screen of Batch 3

description:
Library name: Batch 3 - Input 3
TableS1_all_unfiltered_data.txt


title: b-Orgs HEP passage 1 (486P1B)


title: Input sample of replicate 2 of bindingPCA screen of Batch 3

description:
Library name: Batch 3 - Input 2
TableS1_all_unfiltered_data.txt


title: Output sample of replicate 3 of bindingPCA screen of Batch 4

description:
Library name: Batch 4 - Output 3
TableS1_all_unfiltered_data.txt


title: b-Orgs HEP passage 1 (487P1)


title: Output sample of replicate 3 of bindingPCA screen of Batch 3

description:
Library name: Batch 3 - Output 3
TableS1_all_unfiltered_data.txt


title: WT3_Th1_2

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

institute: Broad Institute

description: Library name: WT3_Th1_2_S18

data_processing:
Demultiplexed fastq files were pseudoaligned and counted with kallisto
Assembly: GRCm38
Supplementary files format and content: Abundance files for individual isoforms as produced by kallisto, as tsv files

source_name: T cell

extract_protocol:
Cells were lyzed in RLT buffer (Qiagen)
Libraries were constructed from lysates using 10 ng of total RNA according to the standard Smart-Seq protocol (Ramsköld et al., 2012) before indexing and sequencing on a NextSeq 500.

treatment_protocol: Naïve CD4+ T cells were isolated by using EasySep Mouse Naïve CD4+ T Cell isolation Kit and 1 million/mL of cells was cultured in 2 μg/mL anti-CD3/anti-CD28-coated 96-well plates under different cytokine conditions for 3 days: Th0: no added cytokines, Th1: 10ng/mL IL-12, Th17n: 25ng/mL IL-6 and 2ng/mL TGF-b1, Th17p: 25ng/mL IL-6 and 20ng/mL IL-1b and 20ng/mL IL-23, Treg: 3ng/mL TGF-b1.

value: T cell

tag: genotype

tag: animal


title: Output sample of replicate 2 of bindingPCA screen of Batch 3

description:
Library name: Batch 3 - Output 2
TableS1_all_unfiltered_data.txt


title: Output sample of replicate 1 of bindingPCA screen of Batch 3

description:
Library name: Batch 3 - Output 1
TableS1_all_unfiltered_data.txt


title: Input sample of replicate 1 of bindingPCA screen of Batch 3

description:
Library name: Batch 3 - Input 1
TableS1_all_unfiltered_data.txt


title: GL261_Ctrl_hyp_rep1_RNAseq


title: b-Orgs HEP generation T0C (511T0C)

value: b-Orgs HEP generation T0C


title: WT3_Th1_1

description: Library name: WT3_Th1_1_S17


title: WT3_Treg_2

description: Library name: WT3_Treg_2_S54

value: Treg


title: AMG510_S1, rep1

description:
Library name: sample1
1_AMG1


title: GL261_Ctrl_norm_rep1_RNAseq


title: GL261_Ctrl_norm_rep2_RNAseq


title: WT3_Treg_1

description: Library name: WT3_Treg_1_S53


title: BV2_CC_hyp_rep2_RNAseq

value: Murine microglial


title: Output sample of replicate 3 of bindingPCA screen of Batch 2

description:
Library name: Batch 2 - Output 3
TableS1_all_unfiltered_data.txt


title: Output sample of replicate 2 of bindingPCA screen of Batch 2

description:
Library name: Batch 2 - Output 2
TableS1_all_unfiltered_data.txt


title: BV2_CC_hyp_rep1_RNAseq

value: Co-culture


title: b-Orgs HEP generation T0C (487T0C)


title: BV2_Ctrl_hyp_rep2_RNAseq

value: hypoxia <0.1% O2


title: BV2_Ctrl_hyp_rep1_RNAseq


title: BV2_Ctrl_norm_rep2_RNAseq


title: BV2_CC_norm_rep2_RNAseq


title: BV2_Ctrl_norm_rep1_RNAseq


title: Output sample of replicate 1 of bindingPCA screen of Batch 2

description:
Library name: Batch 2 - Output 1
TableS1_all_unfiltered_data.txt


title: b-Orgs HEP generation T0C (486T0C)

value: Liver Organoids


title: WT3_Th17n_1

description: Library name: WT3_Th17n_1_S29


title: b-Orgs HEP generation T0B  (487T0B)

value: b-Orgs HEP generation T0B


title: Input sample of replicate 3 of bindingPCA screen of Batch 2

description:
Library name: Batch 2 - Input 3
TableS1_all_unfiltered_data.txt


title: WT3_Th17p_1

description: Library name: WT3_Th17p_1_S41


title: b-Orgs HEP generation T0  (487T0)

value: b-Orgs HEP generation T0


title: BV2_CC_norm_rep1_RNAseq

value: normoxia 21% O2


title: WT3_Th17n_2

description: Library name: WT3_Th17n_2_S30


title: b-Orgs HEP generation T0B  (511T0B)


title: WT3_Th17p_2

description: Library name: WT3_Th17p_2_S42


title: b-Orgs HEP generation T0B  (486T0B)


title: b-Orgs HEP generation T0  (511T0)


title: WT2_Treg_2

description: Library name: WT2_Treg_2_S52


title: Output sample of replicate 3 of bindingPCA screen of Batch 1

description:
Library name: Batch 1 - Output 3
TableS1_all_unfiltered_data.txt


title: WT3_Th0_2

description: Library name: WT3_Th0_2_S6


title: Input sample of replicate 2 of bindingPCA screen of Batch 2

description:
Library name: Batch 2 - Input 2
TableS1_all_unfiltered_data.txt


title: WT3_Th0_1

description: Library name: WT3_Th0_1_S5