title: Anti-IL6 bio rep 3

city: Boston

first: Sonu

last: Subudhi

state: MA

address: 100 Blossom St, Cox 7

department: Radiation Oncology

institute: Massachusetts General Hospital

description: sample 6

data_processing:
raw sequencing reads aligned to mm10 using STAR
Gene expression was quantified using featurecounts
Assembly: mm10
Supplementary files format and content: count matrix

source_name: sorted out 5*10^5 macrophage from tumor

extract_protocol:
RNAeasy Qiagen kit
RNA NEB PolyA kit

value: tumor

value: macrophage


title: WGBS Ctrl hippocampal microglia p3w replication1

status: Public on Jan 30 2026

type: SRA

city: Shanghai

first: Zhu

last: wei

address: siping road 1239

country: China

institute: tongji university

description: Library name: Ctrl_WGBS_1

library_source: genomic

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5)
clean data were mapped to the genome of the mouse genome (mm10) using Bismark, mapping rate and bisulfite conversion rate of each sample were then calculated.
Differentially Methylated Site (DMS) and Differentially Methylated Regions (DMR) analysis were performed by methylKit (v1.28.0).
Assembly: mm10
Supplementary files format and content: txt file including the numbers of T and C and the methylation ratio in methylation site, BigWig

molecule: genomic DNA

organism: Mus musculus

source_name: hippocampus microglia

extract_protocol:
Then genomic DNA was extract by Wizard Genomic DNA purification Kit(Promega, A1120). And DNA fragmented by sonication to a mean size of approximately 250bp (Covaris, M220)
the ligated DNA was bisulfite-converted using the MethylCode™ Bisulfite Conversion Kit (Invitrogen, MECOV50), and the construction of library follow the protocol of  EpiArt® DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103)

tag: tissue

value: hippocampus microglia

tag: age

value: postpartum 3 weeks

tag: genotype


title: Anti-IL6 bio rep 1

country: USA

description: sample 4

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: treatment


title: B6 5-1 mouse embryonic stem cells, H3K27ac (HiChIP), biological replicate2

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Library name: B6-51-k27-8cyc

data_processing:
HiChIP reads were processed using HiC-Pro (v2.11.4) with the following parameters: N_CPU = 4, SORT_RAM = 768M REFERENCE_GENOME = mm10 LIGATION_SITE = GATCGATC MIN_FRAG_SIZE = 30 MAX_FRAG_SIZE =100000 MIN_INSERT_SIZE = 30 MAX_INSERT_SIZE = 600. Long-range interactions were called with hichipper (v.0.7.8b0) using H3K27ac ChIP-seq peaks generated in this paper. PET counts were imported into RStudio (version 4.1) using diffloop (v1.22.0). Before filtering data, read matrices were TMM-normalized. Anchors of interactions were not merged and interactions less than 5,000 bp were filtered out. P-values were adjusted using an FDR cutoff of 0.01. Interactions were filtered for at least four read counts in at least two samples before identifying differential interactions using DESeq2 within the diffloop package. Significant differential interactions were cutoff at FDR < 0.2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: HiChIP

growth_protocol: Cells were grown in DMEM high glucose base medium supplemented with 15% fetal bovine serum, 1X Pen/Strep, 2 mM GlutaMAX, 1 mM sodium pyruvate, 0.1 mM MEM NEAA, 0.1 mM 2-Mercaptoethanol, 103 IU LIF, 1 μM PD0325901, and 3 μM CHIR99021

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.
Samples were processed as described in Mumbach, et al., 2016, using DpnII (NEB, R05443) with the following modifications. 1) biotin incorporation was performed at 23°C for 4 hours with interval shaking (10 sec at 900 rpm, 5 min off). 2) Ligation was performed at 16°C for 4 hours with interval shaking (1 min at 500 rpm, 4 min off). 3) Samples were sheared using a Diagenode Biorupter with the following parameters: tube size = 1.5 mL, time on = 30 sec, time off = 30 sec, cycle # = 8. 4) A total of 3 µL of H3K27ac antibody (Abcam #ab4729) was added to the sample and incubated at 4°C overnight with rotation. 5) After ChIP washes, samples were resuspended in 20 µL removal of biotin-dATP master mix: 5 µL 10X NEB Buffer 2.1, 0.125 µL of dATP and dGTP at 10 mM each, 5 µL T4 DNA polymerase (NEB, M0203), and 39.8 µL distilled water. Samples were incubated at 20°C for 4 hours with interval shaking (1 min at 400 rpm, 4 min off). Lastly, size selection of libraries was performed using a two-sided selection with AMPureXP beads. Briefly, 22.5 µL of beads were added to the sample to capture fragments less than 700 bp. Supernatant was transferred to a new tube and 13.5 µL of beads were added to the supernatant sample to capture fragments greater than 300 bp. Libraries were eluted in 50 µL 10 mM Tris pH 8.0. Libraries were quantified using qPCR against Illumina primers and then paired end sequenced with read length of 75 bp to a sequencing depth of 200 million reads per sample over two Illumina NextSeq runs.

tag: strain

tag: cell line

value: mouse embryonic stem cells

tag: chip antibody

value: H3K27ac (abcam, #ab4729)


title: ATAC-seq FGR hippocampal microglia p3w replication1

description: Library name: FGR_ATAC_1

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5)
reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.4.5).
Duplicates were marked with SAMtools (v1.3.1)
callpeak were execute by MACS2 (v2.2.7.1).
Differentially accessible regions analysis was performed using Diffbind (v3.12.0). Annotation of peaks was performed by ChIPpeakAnno(v3.36.1)
Assembly: mm10
Supplementary files format and content: narrowPeaks, BigWig

extract_protocol:
The interruption and extraction of DNA follow the protocol of Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).
Library construction follow the protocol of Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).


title: hypoxia, wt, rep1

city: Qingdao

first: Chengdong

last: Liu

state: Shandong

address: 5 Yushan Rd

institute: Ocean University of China

description:
Library name: Sample 7
hyp_wt_1

data_processing:
Raw sequencing data (FASTQ format) were processed using fastp to remove low-quality reads and obtain clean reads.
HISAT2 (v2.2.1) was used to build an index of the reference genome, and paired-end clean reads were aligned to the reference genome using HISAT2.
featureCounts (v2.0.6) was employed to quantify the number of reads mapped to each gene. Gene expression levels were subsequently calculated as fragments per kilobase of transcript per million mapped reads (FPKM) based on gene length and mapped read counts.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

molecule: polyA RNA

organism: Danio rerio

source_name: whole larvae

growth_protocol: Zebrafish embryos and larvae were raised at 28.5 °C in embryo rearing solution.

extract_protocol:
Total RNA was extracted using TRIzol reagent, and mRNA was purified from total RNA using poly(T) oligo–attached magnetic beads.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: whole larvae

value: WT

value: hypoxia


title: VECs, siCtrl, rep3

city: BEIJING

first: YINGCHUN

last: HAN

address: No.2, Anzhen Road, Chaoyang District

institute: ANZHEN HOSPITAL

data_processing:
Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2 , which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes
Assembly: Homo_sapiens.GRCh38.84
Supplementary files format and content: FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes

organism: Homo sapiens

source_name: primary cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed

value: primary cells

value: valvular endothelial cells

value: siCtrl


title: normoxia, wt, rep3

description:
Library name: Sample 3
nor_wt_3

value: normoxia


title: WGBS Ctrl hippocampal microglia p3w replication2

description: Library name: Ctrl_WGBS_2


title: hypoxia, wt, rep3

description:
Library name: Sample 9
hyp_wt_3


title: normoxia, wt, rep2

description:
Library name: Sample 2
nor_wt_2


title: B6 4-1 mouse embryonic stem cells, H3K27ac (HiChIP), biological replicate1

description: Library name: B6-41-k27-8cyc


title: Anti-IL6 bio rep 2

description: sample 5


title: AML_patient_sample_254

status: Public on Jan 29 2026

city: Milan

first: Serena

last: Ghisletti

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Library name: sample_254

data_processing:
After demultiplexing with bcl2fastq v2.20 (Illumina, Inc.), raw data quality checks were performed with FastQC v0.11.8. Adapters removal and dynamic trimming of low-quality bases were performed using Trimmomatic v0.39 with parameters “ILLUMINACLIP:adapters.fa:2:30:10, LEADING:30, MAXINFO:50:0.7, MINLEN:40. Paired-end reads were aligned to the UCSC hg38 human genome using STAR v2.7 22 with parameters “--outSAMtype BAM SortedByCoordinate, --outFilterMultimapNmax 20. Uniquely mapped pairs were selected for downstream analysis using SAMtools v1.9. Alignments quality controls were carried out using Qualimap v2.2.2a 23. Gene-level quantification was performed using featureCounts of the Rsubread package v1.34 according to Human GRChg38 annotation. Gene-level counts were then processed with the edgeR  R-package 24 to perform sample normalization using the ‘relative-log-expression’ (RLE) method.
Assembly: GRCh38 assembly version
Supplementary files format and content: Gene raw count matrix and log-normalized CPM (Counts per Million) matrix are provided in compressed tab-delimited format.

source_name: Bone marrow-CD34+

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cells were grown at 37°C and 5%CO2 and treated with 3uM DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time.
Libraries for CD34+ mRNA sequencing were prepared by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Libraries for MDS-L mRNA sequencing were prepared by using the Illumina Stranded mRNA Prep (Illumina). All samples were sequenced at an average of 40 million 50-bp pair-end reads with Novaseq 6000.
All RNA-seq data sets were processed in paired-end.

value: Bone marrow-CD34+

tag: disease state

value: AML


title: ATAC-seq FGR hippocampal microglia p3w replication2

description: Library name: FGR_ATAC_2


title: Control bio rep 3

description: sample 3

value: Control


title: hypoxia, gcn2, rep1

description:
Library name: Sample 10
hyp_gcn2_1

value: gcn2 knockout


title: AML_patient_sample_78

description: Library name: sample_78

growth_protocol: Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen. Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA).


title: AML_patient_sample_253

description: Library name: sample_253


title: normoxia, gcn2, rep1

description:
Library name: Sample 4
nor_gcn2_1


title: normoxia, wt, rep1

description:
Library name: Sample 1
nor_wt_1


title: normoxia, gcn2, rep2

description:
Library name: Sample 5
nor_gcn2_2


title: VECs, siPALMD, rep1

value: siPALMD


title: AML_patient_sample_255

description: Library name: sample_255


title: AML_patient_sample_77

description: Library name: sample_77


title: AML_patient_sample_62

description: Library name: sample_62


title: AML_patient_sample_252

description: Library name: sample_252


title: VECs, siCtrl, rep1


title: AML_patient_sample_44

description: Library name: sample_44


title: Control bio rep 2

description: sample 2

value: tumor

value: macrophage


title: ATAC-seq Ctrl hippocampal microglia p3w replication2

description: Library name: Ctrl_ATAC_2

value: hippocampus microglia

value: postpartum 3 weeks


title: AML_patient_sample_39

description: Library name: sample_39


title: AML_patient_sample_80

description: Library name: sample_80


title: AML_patient_sample_256

description: Library name: sample_256


title: VECs, siCtrl, rep2


title: AML_patient_sample_42

description: Library name: sample_42


title: AML_patient_sample_45

description: Library name: sample_45


title: AML_patient_sample_68

description: Library name: sample_68


title: ATAC-seq Ctrl hippocampal microglia p3w replication1

description: Library name: Ctrl_ATAC_1


title: AML_patient_sample_64

description: Library name: sample_64


title: AML_patient_sample_35

description: Library name: sample_35


title: AML_patient_sample_79

description: Library name: sample_79


title: AML_patient_sample_63

description: Library name: sample_63


title: AML_patient_sample_251

description: Library name: sample_251


title: AML_patient_sample_250

description: Library name: sample_250


title: AML_patient_sample_57

description: Library name: sample_57


title: AML_patient_sample_7

description: Library name: sample_7


title: Control bio rep 1

description: sample 1


title: AML_patient_sample_16

description: Library name: sample_16


title: AML_patient_sample_37

description: Library name: sample_37


title: HR_patient_sample_247

description: Library name: sample_247

value: HR


title: AML_patient_sample_38

description: Library name: sample_38


title: HR_patient_sample_248

description: Library name: sample_248


title: AML_patient_sample_6

description: Library name: sample_6


title: HR_patient_sample_246

description: Library name: sample_246


title: HR_patient_sample_241

description: Library name: sample_241


title: HR_patient_sample_243

description: Library name: sample_243


title: HR_patient_sample_244

description: Library name: sample_244


title: HR_patient_sample_249

description: Library name: sample_249


title: HR_patient_sample_239

description: Library name: sample_239


title: AML_patient_sample_27

description: Library name: sample_27


title: HR_patient_sample_242

description: Library name: sample_242


title: HR_patient_sample_237

description: Library name: sample_237


title: AML_patient_sample_34

description: Library name: sample_34


title: HR_patient_sample_234

description: Library name: sample_234


title: HR_patient_sample_238

description: Library name: sample_238


title: HR_patient_sample_236

description: Library name: sample_236


title: HR_patient_sample_240

description: Library name: sample_240


title: AML_patient_sample_20

description: Library name: sample_20


title: AML_patient_sample_28

description: Library name: sample_28


title: HR_patient_sample_229

description: Library name: sample_229


title: HR_patient_sample_245

description: Library name: sample_245


title: AML_patient_sample_36

description: Library name: sample_36


title: HR_patient_sample_223

description: Library name: sample_223


title: HR_patient_sample_225

description: Library name: sample_225


title: HR_patient_sample_221

description: Library name: sample_221


title: HR_patient_sample_233

description: Library name: sample_233


title: AML_patient_sample_33

description: Library name: sample_33


title: HR_patient_sample_230

description: Library name: sample_230


title: HR_patient_sample_222

description: Library name: sample_222


title: HR_patient_sample_60

description: Library name: sample_60


title: HR_patient_sample_217

description: Library name: sample_217


title: HR_patient_sample_232

description: Library name: sample_232


title: HR_patient_sample_231

description: Library name: sample_231


title: HR_patient_sample_224

description: Library name: sample_224


title: HR_patient_sample_227

description: Library name: sample_227


title: HR_patient_sample_235

description: Library name: sample_235


title: HR_patient_sample_66

description: Library name: sample_66


title: HR_patient_sample_226

description: Library name: sample_226


title: HR_patient_sample_49

description: Library name: sample_49


title: HR_patient_sample_228

description: Library name: sample_228


title: HR_patient_sample_220

description: Library name: sample_220


title: HR_patient_sample_29

description: Library name: sample_29


title: HR_patient_sample_43

description: Library name: sample_43


title: HR_patient_sample_218

description: Library name: sample_218


title: HR_patient_sample_81

description: Library name: sample_81


title: HR_patient_sample_219

description: Library name: sample_219


title: HR_patient_sample_11

description: Library name: sample_11


title: HR_patient_sample_8

description: Library name: sample_8


title: LR_patient_sample_213

description: Library name: sample_213

value: LR


title: HR_patient_sample_19

description: Library name: sample_19


title: LR_patient_sample_215

description: Library name: sample_215


title: LR_patient_sample_216

description: Library name: sample_216


title: LR_patient_sample_211

description: Library name: sample_211


title: LR_patient_sample_212

description: Library name: sample_212


title: LR_patient_sample_209

description: Library name: sample_209


title: LR_patient_sample_207

description: Library name: sample_207


title: LR_patient_sample_210

description: Library name: sample_210


title: LR_patient_sample_208

description: Library name: sample_208


title: LR_patient_sample_204

description: Library name: sample_204


title: LR_patient_sample_206

description: Library name: sample_206


title: LR_patient_sample_202

description: Library name: sample_202


title: LR_patient_sample_200

description: Library name: sample_200


title: LR_patient_sample_201

description: Library name: sample_201


title: LR_patient_sample_203

description: Library name: sample_203


title: LR_patient_sample_197

description: Library name: sample_197


title: LR_patient_sample_214

description: Library name: sample_214


title: LR_patient_sample_199

description: Library name: sample_199


title: LR_patient_sample_192

description: Library name: sample_192


title: LR_patient_sample_195

description: Library name: sample_195


title: LR_patient_sample_198

description: Library name: sample_198


title: LR_patient_sample_190

description: Library name: sample_190


title: LR_patient_sample_194

description: Library name: sample_194


title: LR_patient_sample_186

description: Library name: sample_186


title: LR_patient_sample_196

description: Library name: sample_196


title: LR_patient_sample_183

description: Library name: sample_183


title: LR_patient_sample_193

description: Library name: sample_193


title: LR_patient_sample_185

description: Library name: sample_185


title: LR_patient_sample_189

description: Library name: sample_189


title: LR_patient_sample_191

description: Library name: sample_191


title: LR_patient_sample_182

description: Library name: sample_182


title: LR_patient_sample_180

description: Library name: sample_180


title: LR_patient_sample_181

description: Library name: sample_181


title: LR_patient_sample_205

description: Library name: sample_205


title: LR_patient_sample_188

description: Library name: sample_188


title: LR_patient_sample_187

description: Library name: sample_187


title: LR_patient_sample_178

description: Library name: sample_178


title: LR_patient_sample_184

description: Library name: sample_184


title: LR_patient_sample_177

description: Library name: sample_177


title: LR_patient_sample_174

description: Library name: sample_174


title: LR_patient_sample_173

description: Library name: sample_173


title: LR_patient_sample_171

description: Library name: sample_171


title: LR_patient_sample_175

description: Library name: sample_175


title: LR_patient_sample_165

description: Library name: sample_165


title: LR_patient_sample_172

description: Library name: sample_172


title: LR_patient_sample_164

description: Library name: sample_164


title: LR_patient_sample_161

description: Library name: sample_161


title: LR_patient_sample_166

description: Library name: sample_166


title: LR_patient_sample_159

description: Library name: sample_159


title: LR_patient_sample_167

description: Library name: sample_167


title: LR_patient_sample_163

description: Library name: sample_163


title: LR_patient_sample_179

description: Library name: sample_179


title: LR_patient_sample_170

description: Library name: sample_170


title: LR_patient_sample_162

description: Library name: sample_162


title: LR_patient_sample_168

description: Library name: sample_168


title: LR_patient_sample_160

description: Library name: sample_160


title: LR_patient_sample_158

description: Library name: sample_158


title: LR_patient_sample_157

description: Library name: sample_157


title: LR_patient_sample_155

description: Library name: sample_155


title: LR_patient_sample_156

description: Library name: sample_156


title: LR_patient_sample_169

description: Library name: sample_169


title: LR_patient_sample_150

description: Library name: sample_150


title: LR_patient_sample_149

description: Library name: sample_149


title: LR_patient_sample_153

description: Library name: sample_153


title: LR_patient_sample_176

description: Library name: sample_176


title: LR_patient_sample_151

description: Library name: sample_151


title: LR_patient_sample_148

description: Library name: sample_148


title: LR_patient_sample_147

description: Library name: sample_147


title: LR_patient_sample_154

description: Library name: sample_154


title: LR_patient_sample_146

description: Library name: sample_146


title: LR_patient_sample_145

description: Library name: sample_145


title: LR_patient_sample_144

description: Library name: sample_144


title: LR_patient_sample_142

description: Library name: sample_142


title: LR_patient_sample_136

description: Library name: sample_136


title: LR_patient_sample_140

description: Library name: sample_140


title: LR_patient_sample_138

description: Library name: sample_138


title: LR_patient_sample_152

description: Library name: sample_152


title: LR_patient_sample_134

description: Library name: sample_134


title: LR_patient_sample_137

description: Library name: sample_137


title: LR_patient_sample_135

description: Library name: sample_135


title: LR_patient_sample_143

description: Library name: sample_143


title: LR_patient_sample_130

description: Library name: sample_130


title: LR_patient_sample_128

description: Library name: sample_128


title: LR_patient_sample_133

description: Library name: sample_133


title: LR_patient_sample_121

description: Library name: sample_121


title: LR_patient_sample_127

description: Library name: sample_127


title: LR_patient_sample_141

description: Library name: sample_141


title: LR_patient_sample_120

description: Library name: sample_120


title: LR_patient_sample_131

description: Library name: sample_131


title: LR_patient_sample_122

description: Library name: sample_122


title: LR_patient_sample_126

description: Library name: sample_126


title: LR_patient_sample_119

description: Library name: sample_119


title: LR_patient_sample_118

description: Library name: sample_118


title: LR_patient_sample_139

description: Library name: sample_139


title: LR_patient_sample_129

description: Library name: sample_129


title: LR_patient_sample_132

description: Library name: sample_132


title: LR_patient_sample_124

description: Library name: sample_124


title: LR_patient_sample_123

description: Library name: sample_123


title: LR_patient_sample_116

description: Library name: sample_116


title: LR_patient_sample_115

description: Library name: sample_115


title: LR_patient_sample_111

description: Library name: sample_111


title: LR_patient_sample_125

description: Library name: sample_125


title: LR_patient_sample_112

description: Library name: sample_112


title: LR_patient_sample_113

description: Library name: sample_113


title: LR_patient_sample_108

description: Library name: sample_108


title: LR_patient_sample_100

description: Library name: sample_100


title: LR_patient_sample_102

description: Library name: sample_102


title: LR_patient_sample_104

description: Library name: sample_104


title: LR_patient_sample_114

description: Library name: sample_114


title: LR_patient_sample_105

description: Library name: sample_105


title: LR_patient_sample_96

description: Library name: sample_96


title: LR_patient_sample_103

description: Library name: sample_103


title: LR_patient_sample_117

description: Library name: sample_117


title: LR_patient_sample_97

description: Library name: sample_97


title: LR_patient_sample_109

description: Library name: sample_109


title: LR_patient_sample_94

description: Library name: sample_94


title: LR_patient_sample_95

description: Library name: sample_95


title: LR_patient_sample_98

description: Library name: sample_98


title: LR_patient_sample_106

description: Library name: sample_106


title: LR_patient_sample_99

description: Library name: sample_99


title: LR_patient_sample_101

description: Library name: sample_101


title: LR_patient_sample_91

description: Library name: sample_91


title: LR_patient_sample_110

description: Library name: sample_110


title: LR_patient_sample_93

description: Library name: sample_93


title: LR_patient_sample_89

description: Library name: sample_89


title: LR_patient_sample_107

description: Library name: sample_107


title: LR_patient_sample_90

description: Library name: sample_90


title: LR_patient_sample_88

description: Library name: sample_88


title: LR_patient_sample_92

description: Library name: sample_92


title: LR_patient_sample_87

description: Library name: sample_87


title: LR_patient_sample_82

description: Library name: sample_82


title: LR_patient_sample_83

description: Library name: sample_83


title: LR_patient_sample_67

description: Library name: sample_67


title: LR_patient_sample_84

description: Library name: sample_84


title: LR_patient_sample_59

description: Library name: sample_59


title: LR_patient_sample_65

description: Library name: sample_65


title: LR_patient_sample_58

description: Library name: sample_58


title: LR_patient_sample_56

description: Library name: sample_56


title: E14_mESC_Rep48_Seq1

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

description: Library name: Sample 162

data_processing:
Reads were demultiplexed using lima to produce a .bam file for subreads for each sample.
Circular consensus sequences (CCS) were generated for each sample using ccs to produce a corresponding .bam file per sample.
Alignment was done using pbmm2 on each CCS .bam file to mm10 genome.
Assembly: mm10
Supplementary files format and content: _full.pickle files contain IPD measurements for each base in forward and reverse strands per CCS read. _zmwinfo.pickle files contain additional information per CCS read.
Supplementary files format and content: .bam files contain alignment information (to mm10 genome) and requisite tags for visualization of single-molecule accessibility patterns on IGV (Ml and Mm) from the default t-value used in our NN-HMM (t = 1 / 1,000). Included are additional corresponding tags for t = 31 / 1,000 (Mn and Mo), t = 51 / 1,000 (Mp and Mq), t = 71 / 1,000 (Mr and Ms), and t = 101 / 1,000 (Mt and Mu).

source_name: Cultured mESCs

extract_protocol:
Nuclei were isolated by incubating 1e6 cells in 1 mL ice-cold NE1 Buffer (20 mM HEPES, 10 mM KCl, 1 mM MgCl2, 0.1% Triton X-100, 20% glycerol, 1x Protease Inhibitor (Roche 4693132001)) for 5 min on ice. Nuclei were pelleted by centrifuging at 500 g for 5 min at 4C, and rinsed in 1 mL Buffer M (15 mM Tris-HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 0.5 mM spermidine). Nuclei were re-pelleted by centrifuging at 500 g for 5 min at 4C, and were resuspended in 200 µL Buffer M with 1 mM SAM (NEB B9003S) and 10 µL high-concentration EcoGII (custom order from NEB). For footprinting, nuclei were incubated at 37C for a total of 30 min, with 1 µL 32 mM SAM stock spike-in after 15 min to supplement the reaction. Footprinted nuclei were pelleted by centrifuging at 500 g for 5 min at 4C, resuspended in 200 µL Buffer M with 1 mM CaCl2 and 0.02 U MNase (Sigma N3755), and incubated on ice for 30 min for MNase digest. 2 mM EGTA was added to stop the MNase reaction. For purifying DNA, samples were treated with 10 µL RNaseA (ThermoFisher AM2270) for 10 min at 37C, followed by the addition of 2 µL 10% SDS and 2 µL 20 mg/mL Proteinase K (ThermoFisher AM2548) and incubation >2 hr (up to overnight) at 65C. To extract DNA, an equal volume (~250 µL) phenol-chloroform-isoamyl alcohol was added, samples were mixed by brief vortexing, and samples were centrifuged at max speed for 2 min. The aqueous phase was transferred to a fresh tube, and 0.1x volumes 3M NaOAc, 2x volumes ice-cold 100% ethanol, and 1 µL GlycoBlue co-precipitant (Thermo AM9516) were added. Samples were mixed by inverting tubes and incubated overnight at -20C, centrifuged at max speed for 30 min at 4C, washed with 500 µL ice-cold 70% ethanol, air dried, and resuspended in 30 µL Buffer EB. DNA concentrations were measured by Qubit dsDNA High Sensitivity Quantification Kit (ThermoFisher Q32851).
Up to 1 µg DNA was prepared into PacBio SMRT libraries with the SMRTbell Express Template Prep Kit 2.0 / 3.0 per manufacturer’s directions. Briefly, this includes DNA damage repair, end repair, A-tailing, ligation of barcoded SMRTbell adapters, exonuclease clean-up, and 1x AMPure PB bead clean-up. DNA concentrations were measured by Qubit dsDNA High Sensitivity Quantification Kit and fragment size distributions were estimated with the Femto Pulse.

value: Cultured mESCs

value: EcoGII


title: E14_mESC_Rep47_Seq1

description: Library name: Sample 161


title: LR_patient_sample_52

description: Library name: sample_52


title: LR_patient_sample_51

description: Library name: sample_51


title: E14_mESC_Rep42_Seq1

description: Library name: Sample 156


title: LR_patient_sample_54

description: Library name: sample_54


title: E14_mESC_Rep44_Seq1

description: Library name: Sample 158


title: LR_patient_sample_47

description: Library name: sample_47


title: LR_patient_sample_50

description: Library name: sample_50


title: E14_mESC_Rep43_Seq1

description: Library name: Sample 157


title: LR_patient_sample_74

description: Library name: sample_74


title: LR_patient_sample_61

description: Library name: sample_61


title: H1_TKO_Rep2_Seq1

description: Library name: Sample 154


title: LR_patient_sample_55

description: Library name: sample_55


title: E14_mESC_Rep46_Seq1

description: Library name: Sample 160


title: LR_patient_sample_48

description: Library name: sample_48


title: H1_TKO_Rep1_Seq1

description: Library name: Sample 153


title: E14_mESC_Rep45_Seq1

description: Library name: Sample 159


title: H1_WT_Rep3_Seq1

description: Library name: Sample 152


title: H1_TKO_Rep3_Seq1

description: Library name: Sample 155


title: H1_WT_Rep2_Seq1

description: Library name: Sample 151


title: LR_patient_sample_46

description: Library name: sample_46


title: H1_WT_Rep1_Seq1

description: Library name: Sample 150


title: LR_patient_sample_32

description: Library name: sample_32


title: LR_patient_sample_25

description: Library name: sample_25


title: LR_patient_sample_31

description: Library name: sample_31


title: LR_patient_sample_24

description: Library name: sample_24


title: NIPBL_mESC_DMSO_Rep2_Seq2

description: Library name: Sample 143

value: NIPBL-dTAG


title: LR_patient_sample_26

description: Library name: sample_26


title: LR_patient_sample_15

description: Library name: sample_15


title: NIPBL_mESC_DMSO_Rep1_Seq2

description: Library name: Sample 142


title: LR_patient_sample_22

description: Library name: sample_22


title: NIPBL_mESC_dTAG_Rep3_Seq2

description: Library name: Sample 140


title: LR_patient_sample_17

description: Library name: sample_17


title: NIPBL_mESC_DMSO_Rep2_Seq1

description: Library name: Sample 137


title: LR_patient_sample_12

description: Library name: sample_12


title: NIPBL_mESC_dTAG_Rep2_Seq1

description: Library name: Sample 133


title: LR_patient_sample_30

description: Library name: sample_30


title: LR_patient_sample_13

description: Library name: sample_13


title: LR_patient_sample_18

description: Library name: sample_18


title: LR_patient_sample_9

description: Library name: sample_9


title: NIPBL_mESC_dTAG_Rep1_Seq2

description: Library name: Sample 138


title: Foxa2_dHx_mHep_Rep2_Seq1

description: Library name: Sample 131

source_name: Primary hepatocytes

value: Primary hepatocytes


title: NIPBL_mESC_dTAG_Rep2_Seq2

description: Library name: Sample 139


title: LR_patient_sample_23

description: Library name: sample_23


title: NIPBL_mESC_DMSO_Rep1_Seq1

description: Library name: Sample 136


title: NIPBL_mESC_dTAG_Rep1_Seq1

description: Library name: Sample 132


title: LR_patient_sample_10

description: Library name: sample_10


title: NIPBL_mESC_dTAG_Rep4_Seq2

description: Library name: Sample 141


title: NIPBL_mESC_dTAG_Rep4_Seq1

description: Library name: Sample 135


title: LR_patient_sample_3

description: Library name: sample_3


title: C57BL6J_mHep_Rep2_Seq1

description: Library name: Sample 127


title: LR_patient_sample_4

description: Library name: sample_4


title: LR_patient_sample_5

description: Library name: sample_5


title: LR_patient_sample_14

description: Library name: sample_14


title: C57BL6J_mHep_Rep3_Seq1

description: Library name: Sample 126


title: NIPBL_mESC_dTAG_Rep3_Seq1

description: Library name: Sample 134


title: SOX2_mESC_DMSO_Rep2_Seq1

description: Library name: Sample 124


title: C57BL6J_mHep_Rep1_Seq1

description: Library name: Sample 125


title: H3K27Ac_LR_patient_sample_82

description: Library name: Sample 82

data_processing:
Paired-end reads were processed using trimmomatic-v0.39 for base-quality check and adaptor removal.Sequences were mapped onto the human genome using Bowtie-2 with the following settings: -N 1 -p 4 --end-to-end --time -x <genome index> -1 <fastq.gz1> -2 <fastq.gz2> -U <unpaired fastq.gz> --un-conc-gz <unmapped fastq.gz> --al-conc-gz <mapped fastq.gz>. Uniquely mapped reads were retained using samtools view with options -b -q 10 -o <out.bam>. Properly mapped pairs were selected and duplicate reads were then removed using ‘markdup –r’ function from samtools. Peaks were called using Macs-v2  against a reference ChIP input with parameters --format BAMPE –broad –broad--cutoff 0.01. Peaks overlapping blacklisted regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz) was discarded using bedtools_v.2.30. For each sample, a fragment pile-up in ‘read per million’ was generated using Macs2-callpeak’ function with parameters --format BAMPE -B --SPMR. The resulting BedGraph file was then compared to that of the input to generate a signal profile in BigWig format for browser visualization with the Integrative Genomic Viewer.
Assembly: GRCh38 assembly version
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

extract_protocol:
Human bone marrow aspirates were obtained from in accordance with the Italian laws and the policies and practices of the Ethical Committee of Humanitas Research Hospital. Patients were classified following the updated WHO classification of tumors and lymphoid tissues guidelines 1 and stratified by risk of evolution following the IPSS-R parameters. Bone marrow mononuclear cells (BMNCs) were isolated by density gradient separation with Lympholyte®-H Cell Separation Media (Cedarlane corporation, Burlington, USA) according to manufacturer’s instructions, frozen in fetal bovine serum (FBS) (Lonza, Basel, Switzerland) containing 10% DimethylSulfoxide (DMSO) (Sigma Aldrich, St. Louis, Missouri, USA) and cryopreserved in liquid nitrogen.
Bone marrow HSPCs were isolated based on CD34+ surface marker using the MACS CD34 microbead kit on autoMACS (Miltenyi Biotech Inc, San Diego, CA). MDS-L cells were kindly provided by Dr. Daniel Starczynowski, Cincinnati Children's Hospital Medical Center and were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated FBS and 1% P/S and 10ng/mL of hrIL-3 (PeproTech, Paisley, UK). Cell lines were grown at 37°C and 5%CO2 and treated with DB2115 (Cat. No. HY-124676A Medchem, NJ, USA) for the specified time and concentrations
For CD34+ HSPCs and MDS-L cells, H3K27Ac and PU.1 ChIP-seq were carried out fixing 1x10⁵ cells with 1% formaldehyde (cat. no. 252549, Merck, NJ, USA) for 10 min at room temperature followed by quenching with 125 mM Tris-HCl pH 7.6. Fixed samples were lysed using SDS Shearing Buffer D3 (Covaris, MA, USA) supplemented by protease inhibitors to prepare total extracts. Chromatin shearing was performed by sonication using microtube-130 AFA Fiber Strip V2 (Cat no. 520217, Covaris, MA, USA) with Covaris ME220 Focused-Ultrasonicator. For H3K27Ac and PU.1 ChIP-seq, then lysates were diluted with ChIP Buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen, Paisley, UK) previously coupled with 3 μg of H3K27Ac antibody (cat. no. ab4729, Abcam, Cambridge, UK), or 1.5ug of PU.1 antibody (Cat no. 2258S, Cell Signaling, MA, USA). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate). Immunoprecipitated chromatin was eluted and crosslink-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen, Hilden, Germany) and then quantified with QuantiFluor (cat. no. E2670, Promega, WI, USA).
DNA libraries were prepared from 0.5ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat no.  NEB E7645S, New England Biolabs GmbH) and Unique Dual Index Primer Pairs (Cat no. NEB E6440S, New England Biolabs GmbH) following producer instructions. The purified DNA libraries were quantified with Quantifluor reagent (cat. no. E2670, Promega, WI, USA) and library quality size was controlled with 4200 TapeStation System (Agilent, CA, USA) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent, CA, USA).
All ChIPseq data sets were processed in paired-end.


title: H3K27Ac_LR_patient_sample_83

description: Library name: Sample 83


title: H3K27Ac_LR_patient_sample_88

description: Library name: Sample 85


title: SOX2_mESC_dTAG_30min_Rep1_Seq1

description: Library name: Sample 119


title: SOX2_mESC_dTAG_6hr_Rep2_Seq1

description: Library name: Sample 122


title: Foxa2_control_mHep_Rep1_Seq1

description: Library name: Sample 130


title: H3K27Ac_AML_patient_sample_77

description: Library name: Sample 77


title: H3K27Ac_HR_patient_sample_81

description: Library name: Sample 81


title: H3K27Ac_HR_patient_sample_224

description: Library name: Sample 75


title: H3K27Ac_LR_patient_sample_84

description: Library name: Sample 84


title: H3K27Ac_AML_patient_sample_260

description: Library name: Sample 86


title: Foxa2_dHx_mHep_Rep3_Seq1

description: Library name: Sample 129


title: CTCF_mESC_auxin_Rep4_Seq2

description: Library name: Sample 114

value: CTCF-AID


title: CTCF_mESC_auxin_Rep3_Seq2

description: Library name: Sample 113


title: H3K27Ac_AML_patient_sample_80

description: Library name: Sample 80


title: H3K27Ac_AML_patient_sample_78

description: Library name: Sample 78


title: SOX2_mESC_DMSO_Rep1_Seq1

description: Library name: Sample 123


title: H3K27Ac_AML_patient_sample_79

description: Library name: Sample 79


title: H3K27Ac_HR_patient_sample_225

description: Library name: Sample 76


title: SOX2_mESC_dTAG_6hr_Rep1_Seq1

description: Library name: Sample 121


title: H3K27Ac_HR_patient_sample_222

description: Library name: Sample 72


title: H3K27Ac_LR_patient_sample_74

description: Library name: Sample 74


title: CTCF_mESC_auxin_Rep6_Seq2

description: Library name: Sample 116


title: SOX2_mESC_dTAG_2hr_Rep2_Seq1

description: Library name: Sample 118


title: CTCF_mESC_auxin_Rep5_Seq2

description: Library name: Sample 115


title: H3K27Ac_HR_patient_sample_223

description: Library name: Sample 73


title: CTCF_mESC_auxin_Rep1_Seq2

description: Library name: Sample 111


title: H3K27Ac_HR_patient_sample_219

description: Library name: Sample 69


title: H3K27Ac_HR_patient_sample_220

description: Library name: Sample 70


title: SOX2_mESC_dTAG_30min_Rep2_Seq1

description: Library name: Sample 120


title: CTCF_mESC_auxin_Rep6_Seq1

description: Library name: Sample 110


title: H3K27Ac_HR_patient_sample_221

description: Library name: Sample 71


title: CTCF_mESC_auxin_Rep5_Seq1

description: Library name: Sample 109


title: CTCF_mESC_auxin_Rep3_Seq1

description: Library name: Sample 107


title: H3K27Ac_HR_patient_sample_66

description: Library name: Sample 66


title: Foxa2_dHx_mHep_Rep1_Seq1

description: Library name: Sample 128


title: CTCF_mESC_auxin_Rep2_Seq2

description: Library name: Sample 112


title: SOX2_mESC_dTAG_2hr_Rep1_Seq1

description: Library name: Sample 117


title: CTCF_mESC_auxin_Rep1_Seq1

description: Library name: Sample 105


title: CTCF_mESC_auxin_Rep4_Seq1

description: Library name: Sample 108


title: H3K27Ac_AML_patient_sample_68

description: Library name: Sample 68


title: H3K27Ac_LR_patient_sample_65

description: Library name: Sample 65


title: CTCF_mESC_auxin_Rep2_Seq1

description: Library name: Sample 106


title: H3K27Ac_LR_patient_sample_61

description: Library name: Sample 61


title: H3K27Ac_AML_patient_sample_63

description: Library name: Sample 63


title: H3K27Ac_AML_patient_sample_62

description: Library name: Sample 62


title: CTCF_mESC_DMSO_Rep4_Seq2

description: Library name: Sample 102


title: H3K27Ac_AML_patient_sample_64

description: Library name: Sample 64


title: CTCF_mESC_DMSO_Rep3_Seq2

description: Library name: Sample 101


title: H3K27Ac_HR_patient_sample_60

description: Library name: Sample 60


title: H3K27Ac_LR_patient_sample_58

description: Library name: Sample 58


title: H3K27Ac_LR_patient_sample_59

description: Library name: Sample 59


title: H3K27Ac_LR_patient_sample_67

description: Library name: Sample 67


title: CTCF_mESC_DMSO_Rep1_Seq2

description: Library name: Sample 99


title: CTCF_mESC_DMSO_Rep6_Seq2

description: Library name: Sample 104


title: CTCF_mESC_DMSO_Rep2_Seq2

description: Library name: Sample 100


title: H3K27Ac_AML_patient_sample_57

description: Library name: Sample 57


title: H3K27Ac_LR_patient_sample_56

description: Library name: Sample 56


title: CTCF_mESC_DMSO_Rep5_Seq2

description: Library name: Sample 103


title: H3K27Ac_LR_patient_sample_54

description: Library name: Sample 54


title: CTCF_mESC_DMSO_Rep5_Seq1

description: Library name: Sample 97


title: H3K27Ac_LR_patient_sample_52

description: Library name: Sample 52


title: CTCF_mESC_DMSO_Rep3_Seq1

description: Library name: Sample 95


title: H3K27Ac_LR_patient_sample_55

description: Library name: Sample 55


title: CTCF_mESC_DMSO_Rep2_Seq1

description: Library name: Sample 94


title: CTCF_mESC_DMSO_Rep1_Seq1

description: Library name: Sample 93


title: H3K27Ac_LR_patient_sample_50

description: Library name: Sample 50


title: H3K27Ac_LR_patient_sample_51

description: Library name: Sample 51


title: H3K27Ac_LR_patient_sample_48

description: Library name: Sample 48


title: H3K27Ac_LR_patient_sample_47

description: Library name: Sample 47


title: E14_mESC_Rep40_Seq4

description: Library name: Sample 87

value: E14 (wild type)


title: H3K27Ac_HR_patient_sample_49

description: Library name: Sample 49

value: Bone marrow-CD34+


title: CTCF_mESC_auxin_Rep8_Seq1

description: Library name: Sample 90


title: CTCF_mESC_auxin_Rep7_Seq1

description: Library name: Sample 89


title: CTCF_mESC_auxin_Rep10_Seq1

description: Library name: Sample 92


title: E14_mESC_Rep41_Seq4

description: Library name: Sample 88


title: CTCF_mESC_DMSO_Rep4_Seq1

description: Library name: Sample 96


title: H3K27Ac_HR_patient_sample_43

description: Library name: Sample 43


title: CTCF_mESC_DMSO_Rep6_Seq1

description: Library name: Sample 98


title: H3K27Ac_AML_patient_sample_44

description: Library name: Sample 44

value: AML


title: H3K27Ac_LR_patient_sample_114

description: Library name: Sample 53


title: E14_mESC_Rep37_Seq4

description: Library name: Sample 84


title: H3K27Ac_AML_patient_sample_45

description: Library name: Sample 45


title: E14_mESC_Rep39_Seq4

description: Library name: Sample 86


title: H3K27Ac_AML_patient_sample_42

description: Library name: Sample 42


title: E14_mESC_Rep36_Seq4

description: Library name: Sample 83


title: H3K27Ac_AML_patient_sample_251

description: Library name: Sample 41


title: H3K27Ac_AML_patient_sample_38

description: Library name: Sample 38


title: E14_mESC_Rep33_Seq4

description: Library name: Sample 80


title: E14_mESC_Rep35_Seq4

description: Library name: Sample 82


title: H3K27Ac_AML_patient_sample_39

description: Library name: Sample 39


title: H3K27Ac_AML_patient_sample_36

description: Library name: Sample 36


title: CTCF_mESC_auxin_Rep9_Seq1

description: Library name: Sample 91


title: E14_mESC_Rep38_Seq4

description: Library name: Sample 85


title: E14_mESC_Rep32_Seq4

description: Library name: Sample 79


title: H3K27Ac_AML_patient_sample_37

description: Library name: Sample 37


title: H3K27Ac_AML_patient_sample_34

description: Library name: Sample 34


title: E14_mESC_Rep34_Seq4

description: Library name: Sample 81


title: E14_mESC_Rep30_Seq4

description: Library name: Sample 77


title: H3K27Ac_AML_patient_sample_35

description: Library name: Sample 35


title: E14_mESC_Rep31_Seq4

description: Library name: Sample 78


title: H3K27Ac_LR_patient_sample_32

description: Library name: Sample 32


title: E14_mESC_Rep40_Seq3

description: Library name: Sample 75


title: H3K27Ac_AML_patient_sample_33

description: Library name: Sample 33


title: E14_mESC_Rep38_Seq3

description: Library name: Sample 73


title: E14_mESC_Rep41_Seq3

description: Library name: Sample 76


title: E14_mESC_Rep36_Seq3

description: Library name: Sample 71


title: H3K27Ac_LR_patient_sample_31

description: Library name: Sample 31


title: E14_mESC_Rep37_Seq3

description: Library name: Sample 72


title: H3K27Ac_LR_patient_sample_30

description: Library name: Sample 30


title: H3K27Ac_HR_patient_sample_29

description: Library name: Sample 29


title: E14_mESC_Rep35_Seq3

description: Library name: Sample 70


title: E14_mESC_Rep39_Seq3

description: Library name: Sample 74


title: E14_mESC_Rep34_Seq3

description: Library name: Sample 69


title: H3K27Ac_AML_patient_sample_28

description: Library name: Sample 28


title: H3K27Ac_AML_patient_sample_27

description: Library name: Sample 27


title: E14_mESC_Rep31_Seq3

description: Library name: Sample 66


title: H3K27Ac_LR_patient_sample_26

description: Library name: Sample 26


title: E14_mESC_Rep41_Seq2

description: Library name: Sample 64


title: H3K27Ac_LR_patient_sample_25

description: Library name: Sample 25


title: H3K27Ac_LR_patient_sample_24

description: Library name: Sample 24


title: E14_mESC_Rep40_Seq2

description: Library name: Sample 63


title: H3K27Ac_LR_patient_sample_23

description: Library name: Sample 23


title: E14_mESC_Rep39_Seq2

description: Library name: Sample 62


title: E14_mESC_Rep30_Seq3

description: Library name: Sample 65


title: H3K27Ac_AML_patient_sample_20

description: Library name: Sample 20


title: H3K27Ac_LR_patient_sample_22

description: Library name: Sample 22


title: H3K27Ac_LR_patient_sample_197

description: Library name: Sample 21


title: E14_mESC_Rep32_Seq3

description: Library name: Sample 67


title: E14_mESC_Rep37_Seq2

description: Library name: Sample 60


title: E14_mESC_Rep38_Seq2

description: Library name: Sample 61


title: H3K27Ac_HR_patient_sample_19

description: Library name: Sample 19


title: E14_mESC_Rep36_Seq2

description: Library name: Sample 59


title: E14_mESC_Rep33_Seq2

description: Library name: Sample 56


title: H3K27Ac_LR_patient_sample_17

description: Library name: Sample 17


title: E14_mESC_Rep35_Seq2

description: Library name: Sample 58


title: H3K27Ac_AML_patient_sample_16

description: Library name: Sample 16


title: E14_mESC_Rep34_Seq2

description: Library name: Sample 57


title: E14_mESC_Rep32_Seq2

description: Library name: Sample 55


title: H3K27Ac_LR_patient_sample_121

description: Library name: Sample 40


title: H3K27Ac_LR_patient_sample_18

description: Library name: Sample 18


title: H3K27Ac_LR_patient_sample_14

description: Library name: Sample 14


title: H3K27Ac_LR_patient_sample_15

description: Library name: Sample 15


title: E14_mESC_Rep31_Seq2

description: Library name: Sample 54


title: H3K27Ac_LR_patient_sample_13

description: Library name: Sample 13


title: H3K27Ac_LR_patient_sample_12

description: Library name: Sample 12


title: H3K27Ac_HR_patient_sample_11

description: Library name: Sample 11


title: E14_mESC_Rep33_Seq3

description: Library name: Sample 68


title: E14_mESC_Rep39_Seq1

description: Library name: Sample 50


title: E14_mESC_Rep40_Seq1

description: Library name: Sample 51


title: H3K27Ac_LR_patient_sample_46

description: Library name: Sample 46


title: H3K27Ac_LR_patient_sample_10

description: Library name: Sample 10


title: E14_mESC_Rep30_Seq2

description: Library name: Sample 53


title: E14_mESC_Rep36_Seq1

description: Library name: Sample 47


title: E14_mESC_Rep41_Seq1

description: Library name: Sample 52


title: H3K27Ac_AML_patient_sample_6

description: Library name: Sample 6


title: E14_mESC_Rep34_Seq1

description: Library name: Sample 45


title: H3K27Ac_AML_patient_sample_7

description: Library name: Sample 7


title: E14_mESC_Rep31_Seq1

description: Library name: Sample 42


title: H3K27Ac_LR_patient_sample_9

description: Library name: Sample 9


title: E14_mESC_Rep32_Seq1

description: Library name: Sample 43


title: H3K27Ac_HR_patient_sample_8

description: Library name: Sample 8


title: E14_mESC_Rep25_Seq2

description: Library name: Sample 37


title: E14_mESC_Rep37_Seq1

description: Library name: Sample 48


title: H3K27Ac_LR_patient_sample_4

description: Library name: Sample 4


title: H3K27Ac_HR_patient_sample_218

description: Library name: Sample 2


title: SLE, Donor 00168, NoTx

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

description:
Library name: Sample 28
10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10x Cellranger software v6.0.1 was used to process data including gene quantification, quality control, and read alignment (via refdata-cellranger-GRCh38-3.0.0 curated by 10X based on hg38).
Assembly: Human reference genome (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Upper-thigh Skin

extract_protocol:
Skin biopsies were transported to the laboratory on ice in Hanks Balanced Salt Solution (HBSS) buffer (Gibco) and processed immediately. Biopsies were incubated in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) overnight at 4 degrees Celsius to separate epidermis from dermis. Digestion of the epidermis was performed in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNaseI (Thermo Scientific) for 1 hour at 37°C. Simultaneously, dermal samples were dissociated mechanically and then digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) with 10U/mL DNaseI in plain medium for 1.5 hours at 37 degrees Celsius. Following their respective incubation times, epidermal and dermal samples were strained through a 40uM mesh filter and centrifuged. Cells were subsequently mixed at a ratio of 1:1 before being submitted for single cell RNA sequencing.
The 10x Chromium system with chemistry v3 was used by the University of Michigan Advanced Genomics Core to generate libraries, which were subsequently sequenced on the Illumina NovaSeq 6000 platform, generating 150-base pair paired-end reads.

treatment_protocol: All patients were treated according to the declaration of Helsinki. Following signing of written informed consent, subjects were exposed to varying doses of UVB light via a Kodacel lamp ranging from 10mJ/cm2 to 80mJ/cm2. 24 hours after UV exposure, 6mm punch skin biopsies were taken from UV-unexposed skin as well as the portion of skin corresponding with the minimal erythema dose (MED). Patients who didn’t achieve MED were biopsied at the 80 mJ/cm2 site.

value: Upper-thigh Skin

value: systemic lupus erythematosus (SLE)

value: NoTx


title: H3K27Ac_LR_patient_sample_5

description: Library name: Sample 5


title: H3K27Ac_LR_patient_sample_214

description: Library name: Sample 1


title: SLE, Donor 00171, NoTx

description:
Library name: Sample 30
10x Genomics


title: E14_mESC_Rep28_Seq2

description: Library name: Sample 39


title: E14_mESC_Rep23_Seq2

description: Library name: Sample 35


title: SLE, Donor 00171, UVTx

description:
Library name: Sample 29
10x Genomics

value: UVTx


title: SLE, Donor 00162, UVTx

description:
Library name: Sample 23
10x Genomics


title: SLE, Donor 00162, NoTx

description:
Library name: Sample 24
10x Genomics


title: E14_mESC_Rep30_Seq1

description: Library name: Sample 41


title: E14_mESC_Rep29_Seq2

description: Library name: Sample 40


title: E14_mESC_Rep35_Seq1

description: Library name: Sample 46


title: SLE, Donor 00155, UVTx

description:
Library name: Sample 21
10x Genomics


title: E14_mESC_Rep26_Seq2

description: Library name: Sample 38


title: E14_mESC_Rep24_Seq2

description: Library name: Sample 36


title: H3K27Ac_LR_patient_sample_3

description: Library name: Sample 3


title: E14_mESC_Rep24_Seq1

description: Library name: Sample 29


title: E14_mESC_Rep38_Seq1

description: Library name: Sample 49


title: SLE, Donor 00155, NoTx

description:
Library name: Sample 22
10x Genomics


title: SLE, Donor 00164, UVTx

description:
Library name: Sample 25
10x Genomics


title: E14_mESC_Rep29_Seq1

description: Library name: Sample 34


title: E14_mESC_Rep23_Seq1

description: Library name: Sample 28


title: SLE, Donor 00074, UVTx

description:
Library name: Sample 17
10x Genomics


title: SLE, Donor 00164, NoTx

description:
Library name: Sample 26
10x Genomics


title: SLE, Donor 00071, NoTx

description:
Library name: Sample 16
10x Genomics


title: E14_mESC_Rep28_Seq1

description: Library name: Sample 33


title: SLE, Donor 00071, UVTx

description:
Library name: Sample 15
10x Genomics


title: E14_mESC_Rep33_Seq1

description: Library name: Sample 44


title: E14_mESC_Rep26_Seq1

description: Library name: Sample 31


title: SLE, Donor 00104, UVTx

description:
Library name: Sample 19
10x Genomics


title: E14_mESC_Rep18_Seq1

description: Library name: Sample 23


title: CTL, Donor 00184, NoTx

description:
Library name: Sample 12
10x Genomics


title: E14_mESC_Rep27_Seq1

description: Library name: Sample 32


title: CTL, Donor 00184, UVTx

description:
Library name: Sample 11
10x Genomics


title: E14_mESC_Rep16_Seq1

description: Library name: Sample 21


title: SLE, Donor 00104, NoTx

description:
Library name: Sample 20
10x Genomics


title: E14_mESC_Rep17_Seq1

description: Library name: Sample 22


title: CTL, Donor 00150, UVTx

description:
Library name: Sample 9
10x Genomics


title: SLE, Donor 00168, UVTx

description:
Library name: Sample 27
10x Genomics


title: E14_mESC_Rep19_Seq1

description: Library name: Sample 24


title: E14_mESC_Rep22_Seq1

description: Library name: Sample 27


title: CTL, Donor 00147, NoTx

description:
Library name: Sample 8
10x Genomics


title: CTL, Donor 00139, NoTx

description:
Library name: Sample 6
10x Genomics


title: CTL, Donor 00147, UVTx

description:
Library name: Sample 7
10x Genomics


title: E14_mESC_Rep10_Seq2

description: Library name: Sample 15


title: E14_mESC_Rep21_Seq1

description: Library name: Sample 26


title: E14_mESC_Rep20_Seq1

description: Library name: Sample 25


title: CTL, Donor 00139, UVTx

description:
Library name: Sample 5
10x Genomics


title: E14_mESC_Rep14_Seq2

description: Library name: Sample 19


title: CTL, Donor 00136, NoTx

description:
Library name: Sample 4
10x Genomics


title: CTL, Donor 00188, UVTx

description:
Library name: Sample 13
10x Genomics


title: E14_mESC_Rep25_Seq1

description: Library name: Sample 30


title: E14_mESC_Rep13_Seq2

description: Library name: Sample 18


title: E14_mESC_Rep15_Seq1

description: Library name: Sample 20


title: CTL, Donor 00150, NoTx

description:
Library name: Sample 10
10x Genomics


title: CTL, Donor 00188, NoTx

description:
Library name: Sample 14
10x Genomics


title: SLE, Donor 00074, NoTx

description:
Library name: Sample 18
10x Genomics


title: E14_mESC_Rep11_Seq2

description: Library name: Sample 16


title: E14_mESC_Rep14_Seq1

description: Library name: Sample 14


title: CTL, Donor 00133, UVTx

description:
Library name: Sample 1
10x Genomics


title: CTL, Donor 00136, UVTx

description:
Library name: Sample 3
10x Genomics


title: E14_mESC_Rep9_Seq1

description: Library name: Sample 9


title: E14_mESC_Rep7_Seq1

description: Library name: Sample 7


title: E14_mESC_Rep8_Seq1

description: Library name: Sample 8


title: E14_mESC_Rep13_Seq1

description: Library name: Sample 13


title: E14_mESC_Rep12_Seq1

description: Library name: Sample 12


title: E14_mESC_Rep11_Seq1

description: Library name: Sample 11


title: hBM-MSC, patient 15

city: Hong Kong

first: Hyun Woo

last: Kim

address: Pokfulam Road

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: Sample5
column name in raw_counts.csv: P15_BMSC

data_processing:
Raw sequencing reads were trimmed using trimmomatic. Processed reads were aligned to the genome using STAR with GENCODE v35 as the reference annotation. Gene-level quantification was performed using featureCounts.
Assembly: GENCODE v35
Supplementary files format and content: single csv file with counts of mapped reads

source_name: bone marrow

extract_protocol:
RNA was extracted using NucleoSpin RNA Plus. 500ng of total RNA was used for library preparation for each sample
KAPA RNA HyperPrep Kit (KR1350)

value: bone marrow

value: mesenchymal stem cells

value: neurosphere induction


title: E14_mESC_Rep12_Seq2

description: Library name: Sample 17


title: E14_mESC_Rep4_Seq1

description: Library name: Sample 4


title: E14_mESC_Rep10_Seq1

description: Library name: Sample 10


title: Nasquent-seq SRSF5 KO Replicate 2

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

description:
Library name: Nascent-seq_HeLa_SRSF5_KO_rep2.fq.gz
RNA-seq

data_processing:
RNA-seq: Reads were mapped to the human genome hg38 using STAR (v2.6.1d) with default parameters. Mapped reads were counted with htSeq-count.
Mapped reads were analysed with DESeq2 for differential expression and IRFinder for intron retention.
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: Count tables in .txt format.

source_name: cell line

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and 1% penicilin at 37˚C with 5% CO2.

extract_protocol:
The reaction was stopped by applying TRIzol™RI reagent to the culture dishes. RNA extraction and pulldown of newly transcribed RNA was performed according to (Gressel et al., 2019, PMID: 31399571) without fractionation of the RNA by sonification. Nascent RNA was purified using RNA Clean and Concentrate Kit (ZymoResearch).
cDNA libraries for RNA-seq were prepared with universal Plus™ Total RNA-Seq Library Preparation Kit (Tecan) according to manufacturer's instructions. Ribosomal RNA fragments were removed and the library was sequenced on an Illumina NovaSeq6000 instrument

treatment_protocol: One hour before harvesting, cells were incubated with 400 µM 4-sU for exactly 1 hour to label newly transcribed RNAs.

value: cell line

value: HeLa

value: SRSF5 KO


title: hBM-neurosphere, patient 9

description:
Library name: Sample2
column name in raw_counts.csv.csv: P9_NS

value: MSC medium


title: Nasquent-seq Control Replicate 2

description:
Library name: Nascent-seq_HeLa_WT_rep2.fq.gz
RNA-seq

value: WT


title: hBM-MSC, patient 9

description:
Library name: Sample1
column name in raw_counts.csv: P9_BMSC


title: CTL, Donor 00133, NoTx

description:
Library name: Sample 2
10x Genomics


title: hBM-MSC, patient 12

description:
Library name: Sample3
column name in raw_counts.csv: P12_BMSC


title: Nasquent-seq SRSF5 KO Replicate 1

description:
Library name: Nascent-seq_HeLa_SRSF5_KO_rep1.fq.gz
RNA-seq


title: E14_mESC_Rep1_Seq1

description: Library name: Sample 1

value: Cultured mESCs

value: EcoGII


title: E14_mESC_Rep5_Seq1

description: Library name: Sample 5

value: E14 (wild type)


title: 8d 3

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
HISAT 2.2.1
Read count extraction and normalization were performed using HtseqCount 2.0.3 and z-score, respectively.
Assembly: hg19/grch37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Human iPSC

growth_protocol: Cardiac organoids were maintained in Cardiac Manteinance Media until 54 days.

extract_protocol:
total RNA was isolated using TRIZOL reagent.  total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep it following manufacturer's protocols.

treatment_protocol:
On days 22 of cardiac differentiation, hCOs were treated for 2 consecutive days with Doxorubicin (0,5 uM)
Senolytic (Dasatinib and Quercetin (D+Q)) were administered at the dose of 0.25 umol/l and 10uM respectively. Six hours later, D+Q conditioned medium was replaced with cardiomyocytes maintenance medium. D+Q treatment was repeated every two days for a total of three pulse. D+Q-treated hCOs were collected at days 54

value: Human iPSC

value: cardiac organoids

value: Wild-type

value: cardiac organoid differentiation

tag: time

value: Day 8


title: hBM-neurosphere, patient 12

description:
Library name: Sample4
column name in raw_counts.csv: P12_NS


title: E14_mESC_Rep3_Seq1

description: Library name: Sample 3


title: Nasquent-seq Control Replicate 1

description:
Library name: Nascent-seq_HeLa_WT_rep1.fq.gz
RNA-seq


title: E14_mESC_Rep6_Seq1

description: Library name: Sample 6


title: KO2

city: Wuhan

first: Xincheng

last: Gao

state: Hubei

address: 1277 Jiefang Avenue

department: Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a P value less than 0.05 and an absolute value of Δψ greater than 0.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes all junction event records for each Sample

growth_protocol: T24 cells were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10% FBS (Gibco, USA), 1% penicillin/streptomycin (Gibco, USA). Cells were cultured in an incubator at 37°C with humidifified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated from CUL5 knockout T24 cells and the corresponding control cells using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: bladder cancer cells

value: CUL5 Knockout


title: 8d 1


title: KO3


title: 8d 2


title: E14_mESC_Rep2_Seq1

description: Library name: Sample 2


title: KO1


title: WT3


title: SgT5-2_ACL_iNSCs_PN5

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description: Library name: IonCode_01151

data_processing:
Bulk RNAseq: we used the DESeq2 method for normalization and for differential gene expression analysis
Assembly: hg38
Supplementary files format and content: Bulk RNAseq: tab-delimited csv files include normalized data count

source_name: hindbrain

extract_protocol:
RNA samples were extracted using the RNeasy® Mini kit (Qiagen)
Bulk RNAseq: Libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (A31446),and Ion Torrent Ion Chef Instrument (4484177) (Thermo Fisher Scientific, Tokyo, Japan)

value: hindbrain

value: Stem cells

tag: timepoint

value: Week 5


title: WT2


title: HiPSCs 3

value: Control


title: D+Q aged-hCOs 2

value: Aged cardiac organoid

value: Doxorubicin + Dasatinib and Quercetin

value: Day 54


title: WT1

value: WT


title: HiPSCs 1


title: HiPSCs 2


title: iNSCs_PN55

description: Library name: IonCode_0116

value: Week 55


title: D+Q aged-hCOs 3


title: iNSCs_PN45

description: Library name: IonCode_0114

value: Week 45


title: D+Q aged-hCOs 1

value: Human iPSC


title: iNSCs_PN50

description: Library name: IonCode_0115

value: Week 50


title: aged-hCOs 2

value: Wild-type

value: Doxorubicin


title: aged-hCOs 1


title: iNSCs_PN35

description: Library name: IonCode_01121

value: Week 35


title: iNSCs_PN40

description: Library name: IonCode_01131

value: Week 40


title: iNSCs_PN30

description: Library name: IonCode_01111

value: Week 30


title: hCOs 2

value: cardiac organoids


title: hCOs 3


title: iNSCs_PN20

description: Library name: IonCode_0109

value: hindbrain

value: Stem cells

value: Week 20


title: iNSCs_PN25

description: Library name: IonCode_0110

value: Week 25


title: hCOs 1

value: Control


title: CD4+ T cells, HIV-1 delVPR, donor #3, rep 3

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

institute: University of Tuebingen

data_processing:
Raw data analysis was performed with the Nextflow-based nf-core/rnaseq (version 1.3, https://github.com/nf-core/rnaseq) pipeline. In short, quality control of the FASTQ files was performed using FastQC (version 0.11.8). Adapter trimming was conducted with Trim Galore (version 0.5.0). Reads that passed the quality control were mapped to the reference genome using the STAR aligner (version 2.6.1d). The RNA-seq data quality control was performed with RSeQC (version 3.0.0). Quantification of raw gene expression was performed with featureCounts (version 1.6.4).
Differential expression analysis was performed using the featureCounts raw read count table as input for the R package DESeq2 (version 1.22.2), used in the R language (version 3.5.1). DESeq2 utilized normalized counts to calculate the log2 fold change and assess its statistical significance using the Wald test, reported as a p-value. Adjusted p-values (padj) were calculated using the Benjamini-Hochberg correction for multiple testing. Genes with a padj ≤0.05 were considered differentially expressed.
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Buffy coat

growth_protocol: CD4+ T cells were isolated by negative selection using the RosetteSep CD4+ T cell isolation kit (StemCell Technologies, Grenoble, France) and cultured in RPMI-1640 supplemented with 10% heat-inactivated fetal calf serum (Gibco), 1% Penicillin/Streptomycin (Life Technologies), 2mM L-glutamine (Merck Millipore), and 10ng/ml IL-2 (StemCell Technologies). Cells were pre-stimulated for three days with 1µg/ml Phytohemagglutinin (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
RNA Extraction was carried out using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions, additionally employing QIAshredder (QIAGEN) spin columns for improved homogenization. To prevent DNA contaminations, on-column DNase (QIAGEN) digestion was performed. RNA was eluted from the column twice, each time adding 35μl RNase-free water (QIAGEN) to the column membrane, incubating for 1 min, and centrifuging as indicated by the protocol. RNA concentration and purity were assessed with a NanoDrop (Thermo Fisher Scientific) spectrophotometer. RNA was handled at 4°C and stored either at -20°C (short-term) or -80°C (long-term).
RNA libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following the manufacturer’s protocol.

treatment_protocol: Primary CD4+ T cells were seeded into 24-well plates and infected with highly-concentrated VSV-G-pseudotyped HIV-1 NL4-3 viral stocks (HIV-1 / HIV-1 ΔVpr). At 48 hours post-infection, cells were washed with PBS and underwent RNA extraction as described below.

value: Buffy coat

value: CD4+ T cells

value: HIV-1 delVPR

tag: blood type

value: A negative

tag: Sex

value: M


title: CD4+ T cells, MOCK, donor #3, rep 3

value: MOCK


title: iNSCs_PN10

description: Library name: IonCode_0107

value: Week 10


title: CD4+ T cells, MOCK, donor #2, rep 2

value: O positive


title: HLA_ACL_iNSCs_PN5

description: Library name: IonCode_0111

value: Week 5


title: ACL_PN60

description: Library name: IonCode_0119

value: Week 60


title: aged-hCOs 3

value: Human iPSC

value: Aged cardiac organoid

value: Wild-type

value: Doxorubicin

value: Day 54


title: CD4+ T cells, HIV-1 WT, donor #2, rep 2

value: HIV-1 WT


title: ACL_PN60_3

description: Library name: IonCode_0120

value: hindbrain

value: Stem cells


title: ACL_PN5_3

description: Library name: IonCode_0118


title: ACL_PN5_2

description: Library name: IonCode_0117


title: CD4+ T cells, HIV-1 WT, donor #1, rep 1

value: Buffy coat

value: CD4+ T cells

value: F


title: CD4+ T cells, MOCK, donor #1, rep 1


title: CD4+ T cells, HIV-1 WT, donor #3, rep 3

value: A negative

value: M


title: ACL_P0D7_1

description: Library name: IonCode_0122

value: Week 1


title: ATACseq_Ctrl_3

first: Yihao

last: Wang

state: State

address: Zhizaoju Road 833, Shanghai

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: ATAC-seq

data_processing:
Paired-end reads were trimmed for Illumina adapter sequences and then mapped to hg38 using bowtie2 (v 2.4.2).
Duplicate reads were discarded with Picard (v 1.79).
Peaks were identified using macs2 (v 2.2.7.1) with parameters callpeak -nomodel -q 0.01 -shift 0. Problematic regions were removed according to the ENCODE Blacklist. Peak sets called in individual replicates were combined.
Differentially expressed regions were detected using DESeq2 (v 1.26.0) based on absolute log2 transformed fold-change values >1.5 and adjusted values of p < 0.1 after applying the Benjamini–Hochberg correction.
Homer 2 was used for motif finding.
Assembly: hg38
Supplementary files format and content: Format: bigWig files.
Supplementary files format and content: Content:  ATAC-seq signals of control (shCtrl; n=3) and ARID1A-loss (shARID1A; n=3) HCT116 cells.

extract_protocol:
Sequencing library was generated using Omni-ATAC-seq protocol following recommendations and index codes were added to each sample for chromatin accessibility profiling. Briefly, the single cell nucleus suspension obtained above was incubated in 50 ul labeled Tn5 transposase mixture (25 ul 2×TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) for transposition reaction of each sample. Incubate reaction at 37ºC for 30 minutes. Cleanup reaction with a Zymo DNA Clean and Concentrator-5 Kit (cat #D4014). Pre-amplified transposed fragments were subjected to qPCR amplification. Purify the final PCR reaction using a Zymo DNA Clean and Concentrator-5 Kit (cat #D4014). Quantify library concentration using the KAPA Library Quantification Kit (cat #KK4854).
Use 10× Geomics Chromium™ system to capture and mark each nucleus for the ATAC library construction. After ATAC library construction, Illumina high-throughput sequencing instrument was used to sequence samples and obtain sequencing data.
ATAC libraries were sequenced using the Illumina NovaSeq 6000 platform, paired-end 150.

value: human colorectal carcinoma cell line

value: WT


title: ACL_P0D7_2

description: Library name: IonCode_0123


title: iNSCs_PN15

description: Library name: IonCode_0108

value: Week 15


title: CD4+ T cells, HIV-1 delVPR, donor #1, rep 1

value: HIV-1 delVPR

value: O positive


title: hBM-neurosphere, patient 15

description:
Library name: Sample6
column name in raw_counts.csv: P15_NS

value: bone marrow

value: mesenchymal stem cells

value: neurosphere induction


title: ACL_iNSCs_PN60

description: Library name: IonCode_0132

value: Week 60


title: ATACseq_Ctrl_1

description: ATAC-seq


title: CD4+ T cells, HIV-1 delVPR, donor #2, rep 2


title: ACL_P0D7_3

description: Library name: IonCode_0124

value: hindbrain


title: ACLiNSCs_PN5_Diff2D

description: Library name: IonCode_0112

value: Stem cells

value: Week 5


title: Ped B30 H1 only additional 1 ADT

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Pediatrics

institute: Weill Cornell Medicine

description:
Library name: H1 only add totB1 ADT
count
b_h1only_add_feature_reference.csv

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.0.1, v7.1.0, v9.0.0) functions (mkfastq, count, vdj, multi)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

source_name: Peripheral Blood Mononuclear Cell

extract_protocol:
HA-specific B cells (CD19+Probe+) and total CD19+ B cells were sorted and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) to achieve single cell resolution using the 10x Genomics Chromium Controller and according to the manufacturer’s instruction
The sorted single cells were processed according to 10x Genomics 5’ single cell gene expression (GEX), B cell Immunoglobulin (Ig) enrichment (VDJ), and cell surface feature barcode (ADT) protocol to prepare the libraries for Illumina sequencing.

value: Peripheral Blood Mononuclear Cell

value: B cells

value: H1N1 Influenza infection


title: Ped B30 H1 only additional 1 GEX

description:
Library name: H1 only add totB1 GEX
count
b_h1only_add_feature_reference.csv


title: G7_6hrs_THZ531_repl3

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
All processing was done on the Galaxy server, using the SlamDunk pipeline (http://github.com/t-neumann/slamdunk). Prior to mapping, the quality of the sequencing of the reads was inspected using FastQC (v.0.72+galaxy1) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters were trimmed from raw reads using cutadapt through the trim_galore (v.0.4.3.2) wrapper tool with adapter overlaps set to 3bp.
The reads were then processed using SlamDunk (v.0.4.1+galaxy2). Settings were adjusted to alignment against the human genome (GRCh38), 12bp trimming from the 5’ end, with multi-mapper retention strategy for 100 alignments, filtering for variants with a 0.2 variant fraction, filtering for base-quality cutoff of ≥27, and filtering for ≥1 T>C conversions.
Genome_build: hg38
Supplementary_files_format_and_content: TSV separated count tables from SLAMdunk

source_name: Primary GBM cell line

growth_protocol: Primary G7 cells were cultured in neural stem cell (NSC) medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β-mercaptoethanol, nonessential amino acids, bovine serum albumin, heparin, 100 U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors). They were kept in adherent culture, on dishes precoated with PDL and laminin.

extract_protocol:
SLAM-seq was performed according to the protocol by reference. Briefly, cells were seeded at approximately 70% confluency, and treated with THZ531 or vehicle control. 1 hour before harvest, 4sU was added to the medium at a final concentration of 500 μM. The samples were kept in the dark as RNA was extracted with Qiagen’s RNeasy Plus Mini Kit. 3 μg RNA was alkylated with iodoacetamide (Sigma, 10 mM) for 15 minutes, and the RNA was repurified by ethanol precipitation.
250 ng RNA was used to make libraries with Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and PCR Add-on Kit for Illumina. Deep sequencing was performed using the NovaSeq platform (Illumina).

treatment_protocol: G7 glioblastoma cells were treated with 500 nM THZ531 for 1 hr or 6 hrs or DMSO for 6 hrs.

value: glioblastoma

value: THZ531, 6hrs


title: Ped B30 H1 only additional 2 GEX

description:
Library name: H1 only add totB2 GEX
count
b_h1only_add_feature_reference.csv


title: ACL_iNSCs_PN5

description: Library name: IonCode_0131


title: G7_6hrs_THZ531_repl1


title: ATACseq_ARID1A_KD_3

description: ATAC-seq

value: human colorectal carcinoma cell line

value: ARID3A knockdown


title: ATACseq_ARID1A_KD_2

description: ATAC-seq

value: ARID2A knockdown


title: G7_6hrs_THZ531_repl2


title: ACLiNSCs_PN61_Diff2D

description: Library name: IonCode_0113

value: Week 61


title: Ped Ag30 H1 only additional VDJ

description:
Library name: H1 only add d30 VDJ
multi


title: G7_RNAPolIIS5P_6hrs_THZ531

data_processing:
Library strategy: Cut&Run
Reads were mapped to hg38 using Bowtie2 (v. 2.2.9, PMID: 22388286) and the settings "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700".
Mapped reads were filtered for an insert size between 20 and 120 base pairs using samtools (v. 1.10,  PMID: 19505943) in accordance with instructions (PMID: 29651053) in the following pipe: “samtools view -h -f 66 | awk -F'\t' 'function abs(x){return ((x < 0.0) ? -x : x)} {if ((abs($9) >= 20 && abs($9) <= 120) || $1 ~ /^@/) print $0}' | samtools view -Sb – “.
Filtered mapped reads were deduplicated and imported into EaSeq v. 1.2 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: hg38
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

extract_protocol:
Cells were harvested, washed and bound to Concanavalin A-coated magnetic beads. The cells were then permeabilized with wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine and a Roche complete tablet per 50 ml) containing 0.02% Digitonin. The cell-bead suspension was incubated with 1 μg antibody in a total volume of 50 μL overnight at 4oC on a nutator. After 3 washes with 1 mL Digitonin buffer, cells were resuspended in 50 μL volume with pAG-MNase and nutated for 10 minutes at RT. Cells were given two washes with Digitonin buffer, chilled on ice, and ice-cold CaCl2 was added, before nutating for 2 hours at 4oC. STOP buffer was added (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 50 μg/mL RNAse A, 50 μg/ml glycogen), and tubes were incubated at 37oC for 10 minutes in a ThermoMixer, to release fragments into solution. After centrifugation at 16,000 x g for 5 minutes at 4oC, tubes were placed on a magnet stand and the liquid transferred to new tubes. DNA was extracted using Qiagen’s MinElute PCR Purification Kit, according to manufacturer’s instructions.
Quantification was done by Qubit analysis, and libraries were made with 2 ng DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina” (New England Biolabs, E7645), according to manufacturer’s instructions. Deep sequencing was performed using the NovaSeq platform (Illumina).

tag: antibody used in cut&run


title: G7_DMSO_repl2

value: DMSO, 6hrs


title: G7_DMSO_repl1


title: ATACseq_ARID1A_KD_1

description: ATAC-seq

value: ARID1A knockdown


title: G7_RNAPolIIS2P_6hrs_DMSO


title: G7_RNAPolIIS5P_6hrs_DMSO


title: G7_RNAPolIIS5P_1hr_THZ531

value: THZ531, 1hr


title: ATACseq_Ctrl_2

description: ATAC-seq

value: WT


title: Ped Ag30 H1 only VDJ

description:
Library name: Ag30 H1 only VDJ
multi

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.0.1 and v7.1.0) functions (mkfastq, count, vdj, multi)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes


title: Ped Ag30 H1 only additional ADT

description:
Library name: H1 only add d30 ADT
multi
ag_h1only_add_feature_reference.csv


title: G7_DMSO_repl3


title: Ped Ag30 H1 only GEX

description:
Library name: Ag30 H1 only GEX
multi
ag_h1only_feature_reference.csv


title: Ped Ag1 H1 only additional GEX

description:
Library name: H1 only add d1 GEX
multi
ag_h1only_add_feature_reference.csv


title: G7_RNAPolII_6hrs_DMSO


title: Ped Ag30 H1 only additional GEX

description:
Library name: H1 only add d30 GEX
multi
ag_h1only_add_feature_reference.csv


title: Ped Ag1 H1 only additional ADT

description:
Library name: H1 only add d1 ADT
multi
ag_h1only_add_feature_reference.csv


title: Ped B30 H1 only additional 2 ADT

description:
Library name: H1 only add totB2 ADT
count
b_h1only_add_feature_reference.csv


title: G7_RNAPolIIS2P_6hrs_THZ531


title: G7_RNAPolIIS2P_1hr_THZ531


title: Ped Ag1 H1 only ADT

description:
Library name: Ag1 H1 only ADT
multi
ag_h1only_feature_reference.csv

library_source: other

molecule: protein


title: Ped Ag1 H1 only additional VDJ

description:
Library name: H1 only add d1 VDJ
multi


title: Ped Ag1 H1 only GEX

description:
Library name: Ag1 H1 only GEX
multi
ag_h1only_feature_reference.csv


title: G7_RNAPolII_1hr_THZ531


title: Ped Ag30 reverse VDJ

description:
Library name: Ag30 rev VDJ
multi

value: H1N1-H3N2 Influenza infection


title: Ped Ag30 H1 only ADT

description:
Library name: Ag30 H1 only ADT
multi
ag_h1only_feature_reference.csv


title: Ped Ag1 H1 only VDJ

description:
Library name: Ag1 H1 only VDJ
multi


title: G7_H3K27me3_6hrs_DMSO

value: Cell Signaling (C36B11)


title: Ped Ag30 reverse GEX

description:
Library name: Ag30 rev GEX
multi
ag_rev_feature_reference.csv


title: G7_H3K27ac_6hrs_DMSO

value: Cell Signaling (D5E4)


title: G7_Input_6hrs_DMSO


title: Ped Ag30 reverse ADT

description:
Library name: Ag30 rev ADT
multi
ag_rev_feature_reference.csv


title: Ped Ag1 reverse VDJ

description:
Library name: Ag1 rev VDJ
multi


title: Ped Ag1 reverse GEX

description:
Library name: Ag1 rev GEX
multi
ag_rev_feature_reference.csv


title: G7_Input_6hrs_THZ531


title: G7_RNAPolII_6hrs_THZ531


title: U2OS_ID3KO_moce_rep2

city: Heidelberg

first: Ali

last: Bakr

address: Im Neuenheimer Feld 280

department: Cancer Epigenomics

institute: Deutsches Krebsforschungszentrum

description: Library name: DivA_U2OS_ID3KO_moce_rep2_library

data_processing:
Data was processed by the Omics IT and Data Management Core Facility (DKFZ, Heidelberg), using the Roddy RNA-seq Workflow. Default parameters were used unless mentioned otherwise. Sequences were aligned to the human reference genome (hg19/GRCh37) by applying the software STAR (22). Gene counts were generated with featureCounts (23) and the gene annotation v.29 lift 37.
Assembly: hg19/GRCh37
Supplementary files format and content: *.tsv file with raw and normalised reads for each transcript

source_name: bone

extract_protocol:
RNA extraction was performed as described previously (see references in the paper)
Sequencing libraries were prepared by the Genomics and Proteomics Core Facility (DKFZ, Heidelberg) from total RNA using the Illumina TrueSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions. Samples were sequenced in a paired-end setting (100 bp) on an Illumina NovaSeq 6000 machine for sequencing.

value: bone

value: osteosarcoma

value: mocetinostat-treated


title: Ped Ag1 reverse ADT

description:
Library name: Ag1 rev ADT
multi
ag_rev_feature_reference.csv

value: Peripheral Blood Mononuclear Cell

value: B cells


title: Ped Ag30 additional VDJ

description:
Library name: Ag30 add VDJ
vdj

value: H3N2-H1N1 Influenza infection


title: U2OS_ID3KO_moce_rep1

description: Library name: DivA_U2OS_ID3KO_moce_rep1_library


title: U2OS_ID3KO_UT_rep2

description: Library name: DivA_U2OS_ID3KO_UT_rep2_library

value: untreated


title: U2OS_ID3KO_UT_rep1

description: Library name: DivA_U2OS_ID3KO_UT_rep1_library


title: Ped Ag30 additional ADT

description:
Library name: Ag30 add ADT
count
ag_add_feature_reference.csv


title: U2OS_WT_moce_rep3

description: Library name: DivA_U2OS_WT_moce_rep3_library

value: wt


title: U2OS_ID3KO_UT_rep3

description: Library name: DivA_U2OS_ID3KO_UT_rep3_library


title: Ped Ag1 additional GEX

description:
Library name: Ag1 add GEX
multi
ag_add_feature_reference.csv


title: Ped Ag1 additional VDJ

description:
Library name: Ag1 add VDJ
multi


title: U2OS_ID3KO_moce_rep3

description: Library name: DivA_U2OS_ID3KO_moce_rep3_library


title: U2OS_WT_UT_rep2

description: Library name: DivA_U2OS_WT_UT_rep2_library


title: Adults B1 GEX

description:
Library name: Adults B1 GEX
count
adults_b_feature_reference.csv

value: H1N1 Influenza infection


title: U2OS_WT_moce_rep2

description: Library name: DivA_U2OS_WT_moce_rep2_library


title: Adults B30 GEX

description:
Library name: Adults B30 GEX
count
adults_b_feature_reference.csv


title: U2OS_WT_moce_rep1

description: Library name: DivA_U2OS_WT_moce_rep1_library


title: Ped Ag30 additional GEX

description:
Library name: Ag30 add GEX
count
ag_add_feature_reference.csv


title: Adults Ag30 VDJ

description:
Library name: Adults Ag30 VDJ
multi


title: Adults Ag30 GEX

description:
Library name: Adults Ag30 GEX
multi
adults_ag_feature_reference.csv


title: Adults B1 ADT

description:
Library name: Adults B1 ADT
count
adults_b_feature_reference.csv


title: Human_gonad_14

city: Campinas

first: Helena

last: Fabbri-Scallet

state: São Paulo

address: Av. Cândido Rondon, 400

department: Center for Molecular Biology and Genetic Engineering

country: Brazil

institute: State University of Campinas

description: Library name: OT-P6B

data_processing:
Raw sequencing reads were quality-checked using FastQC.
Adapter sequences and low-quality reads were removed during preprocessing.
Cleaned reads were aligned to the human reference genome using STAR.
Gene-level read counts were generated using STAR ReadsPerGene.
Count matrices were used for downstream differential expression and pathway analyses.
Assembly: GRCh38
Supplementary files format and content: Processed data consist of tab-delimited text files containing gene-level read counts generated with STAR (ReadsPerGene) using Ensembl gene identifiers.

source_name: Gonad

extract_protocol:
Total RNA was extracted from FFPE or fresh gonadal tissue using protocols recommended by the library preparation kits, following the manufacturers’ instructions.
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero (Illumina, San Diego, CA, USA) for the FFPE samples and the SMARTer® Total RNA-Seq Kit v3 (Qiagen, CA, USA) for the RNA obtained from fresh tissue, following the manufacturer's recommendations.

value: Gonad

value: 3 years

value: Differences of Sex Development


title: G7_Input_1hr_THZ531

value: glioblastoma

value: THZ531, 1hr


title: Ped Ag1 additional ADT

description:
Library name: Ag1 add ADT
multi
ag_add_feature_reference.csv


title: Human_gonad_12

description: Library name: OT-P5B

value: 9 months


title: Adults Ag30 ADT

description:
Library name: Adults Ag30 ADT
multi
adults_ag_feature_reference.csv


title: U2OS_WT_UT_rep1

description: Library name: DivA_U2OS_WT_UT_rep1_library


title: Adults Ag1 GEX

description:
Library name: Adults Ag1 GEX
multi
adults_ag_feature_reference.csv


title: Ped B30 control GEX

description:
Library name: B30 ctrl GEX
count
d30_ctrl_feature_reference.csv


title: Adults Ag1 ADT

description:
Library name: Adults Ag1 ADT
multi
adults_ag_feature_reference.csv


title: Human_gonad_13

description: Library name: OT-P6A


title: U2OS_WT_UT_rep3

description: Library name: DivA_U2OS_WT_UT_rep3_library


title: Adults Ag1 VDJ

description:
Library name: Adults Ag1 VDJ
multi


title: Human_gonad_11

description: Library name: OT-P5A


title: Ped Ag30 control VDJ

description:
Library name: Ag30 ctrl VDJ
vdj


title: Human_gonad_5

description: Library name: CAIS-P1

value: 19 years


title: Human_gonad_3

description: Library name: PGD-P3

value: 18 years


title: Human_gonad_10

description: Library name: OT-P4B

value: 19 months


title: Human_gonad_2

description: Library name: PGD-P2

value: 6 years


title: Human_gonad_9

description: Library name: OT-P4A


title: Adults B30 ADT

description:
Library name: Adults B30 ADT
count
adults_b_feature_reference.csv


title: Ped B30 control ADT

description:
Library name: B30 ctrl ADT
count
d30_ctrl_feature_reference.csv


title: Ped Ag30 GEX

description:
Library name: Ag30 GEX
count
ag30_feature_reference.csv