title: Spleen,Pdcd1^low CD4 T cells,rep3

first: Jaehyun

last: Choi

address: 50, Yonsei-ro, Seodaemun-gu

department: systembiology

institute: Yonsei university

description: Library name: Spleen_sample6

data_processing:
The raw read sequences were obtained from mRNA-sequencing as fastq format. Adaptor trimming was performed using Trim-Galore (v0.6.6 , https://github.com/FelixKrueger/TrimGalore) to consistently remove low quality reads and sequencing adaptors by FastQC(v0.11.5) and cutadapt (v2.3). After trimming, reads were aligned to mouse reference genome (GRCm38) with STAR (v ersionGenome: 2.6.0c) aligner [PMID: 23104886] using GTF and FASTA file from GENCODE (GRCm38 vM23) with default parameters. Read counts of each gene were counted using HTSeq (v2.0.2) [PMID: 25260700].
Assembly: GRCm 38
Supplementary files format and content: Raw sequencing reads were generated in FASTQ format from mRNA-seq libraries. Adapters and low-quality bases were trimmed using Trim Galore (v0.6.6), which utilizes FastQC (v0.11.5) and cutadapt (v2.3). Trimmed reads were aligned to the mouse reference genome (GRCm38) using STAR (v2.6.0c) with default parameters. Gene-level read counts were quantified using HTSeq (v2.0.2) with the GENCODE GRCm38 vM23 annotations.

source_name: Spleen

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, Germany) following the manufacturer's instruction. RNA quality and quantity were assesed with the 4150 TapeStation Instrument (Agilent Technologies).
cDNA libraries were generated from low-input total RNA using the NEBNext Low Input RNA Library Prep Kit for Illumina (#E6420S/L), according to the manufacturer’s protocol, and sequencing was performed on an Illumina NovaSeq X Plus platform.

value: Spleen

value: Pdcd1 low CD4 T cells

tag: Sex

value: female


title: er XVE:ER, 3h induction, rep 4

status: Public on Nov 19 2025

type: SRA

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Library name: ER_15_3h_4

library_source: transcriptomic

data_processing:
Paired-end reads were mapped to the Arabidopsis TAIR10 genome (EnsemblePlants, release 58) sequence with corresponding gtf file to obtain reads per gene using STAR aligner (v 2.7.11a )
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count per gene, one file per sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings

growth_protocol: Seeds were surface-sterilized with absolute ethyl alcohol for 5 min and 75% ethanol for 15 min, then washed three-four times with sterilized distilled water under aseptic conditions. Surface-sterilized seeds were germinated on half-strength Murashige and Skoog (MS) medium in an incubator (22 °C on a 16 h/8 h light/dark cycle).

extract_protocol:
RNA was extracted from 7-day-old Arabidopsis seedlings using ReliaPrep™ RNA Miniprep.
RNA library for RNA-Seq were prepared using SMARTER mRNA-Seq library prep kit following manufacturers' protocol.

treatment_protocol: For estradiol induction, seeds of wild type, er mutant and XVE:ER transformed er mutant were first germinated on ½MS plates for seven days, and then the 7-day-old seedlings were transferred to mock-plates for 0h induction, or 5 mM 17-β estradiol plates for 3h or 8h induction.

tag: tissue

value: 7-day-old seedlings

tag: genotype

value: XVE:ER transformed er mutant

tag: treatment

value: Estradiol induction

tag: estradiol induction_time

value: 3 hours


title: Spleen,Pdcd1^high CD4 T cells,rep3

city: Seoul

country: South Korea

description: Library name: Spleen_sample5

organism: Mus musculus

tag: strain

tag: cell type

value: Pdcd1 high CD4 T cells

tag: age


title: er XVE:ER, 3h induction, rep 2

description: Library name: ER_15_3h_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040183

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

institute: Yonsei University

description: Library name: OP23YS040388

data_processing:
Raw sequencing reads were quality-checked using FastQC. Adapter trimming was performed using Trimmomatic.
Trimmed reads were aligned to the human reference genome (GRCh38) using STAR aligner with default parameters.
Gene-level quantification was performed using featureCounts based on GENCODE annotations.
Expression values were normalized to TPM, log2-transformed, and compiled into a processed expression matrix.
All processed data are provided in a matrix format where rows represent genes and columns represent samples.
Assembly: GRCh38 (GENCODE v38 annotation)
Supplementary files format and content: Processed data files are in CSV format and contain TPM-log2 normalized expression values. Each row represents a gene, and each column represents a sample. File name: YUHS_TPM_EXPR_Biopsy_processed.csv
Supplementary files format and content: Gene symbols are used as row names; expression values are log2(TPM + 1) transformed.

organism: Homo sapiens

source_name: prostate

extract_protocol:
Total RNA was extracted from frozen biopsy tissues using the Qiagen RNeasy Mini Kit, following the manufacturer's protocol. On-column DNase I treatment was included to remove genomic DNA contamination.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Poly-A selection was used to enrich for mRNA. Libraries were quantified using Qubit and Bioanalyzer.

treatment_protocol: Fresh prostate adenocarcinoma biopsy samples were collected from patients at Yonsei University Health System. Samples were immediately stabilized in RNAlater and stored at −80°C until RNA extraction.

value: prostate


title: Spleen,Pdcd1^low CD4 T cells,rep2

description: Library name: Spleen_sample4


title: NLV-specific T cells from HF donors , VDJ_GEM3

city: Hannover

first: Ahmed

last: Hassan

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

description:
Library name: VDJ_GEM3
GEX_HTO_ADT_VDJ_multiout_GEM3.tar.gz
single_cell_processed_seu_obj.tar.gz

library_source: other

data_processing:
Cellranger-7.0.1, Kallisto (v0.46.2), MIXCR(v4.7.0)
Assembly: GRCh38
Supplementary files format and content: Cellranger output file: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger output file: airr_rearrangement.tsv
Supplementary files format and content: Kallisto output files: abundance.h5, abundance.tsv
Supplementary files format and content: MIXCR output files: clones_TRA.tsv, clones_TRB.tsv

molecule: other

source_name: Blood

extract_protocol:
Following the recommendation of 10x genomics :: single cell Using RNeasy Plus Mini Kit from Qiagen
Following the recommendation of 10x genomics :: single cell Following NEBNext Ultra II RNA Library Prep Kit protocol :: BulkRNAseq Following SMART-Seq Human TCR (with UMIs) protocol from Takara Bio :: BulkTCR

value: Blood

value: NLV-specific T cells


title: NLV-specific T cells from HF donors , GEX_GEM3

description:
Library name: GEX_GEM3
GEX_HTO_ADT_VDJ_multiout_GEM3.tar.gz
single_cell_processed_seu_obj.tar.gz

library_source: transcriptomic single cell

molecule: polyA RNA


title: Spleen,Pdcd1^high CD4 T cells,rep2

description: Library name: Spleen_sample3


title: er XVE:ER, 3h induction, rep 1

description: Library name: ER_15_3h_1


title: WT, 3h induction, rep 4

description: Library name: WT_3h_4

value: Wild type


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040181

description: Library name: OP23YS040298


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040186

description: Library name: OP24YS040099


title: NLV-specific T cells from HF donors , GEX_GEM2

description:
Library name: GEX_GEM2
GEX_HTO_ADT_VDJ_multiout_GEM2.tar.gz
single_cell_processed_seu_obj.tar.gz


title: Spleen,Pdcd1^low CD4 T cells,rep1

description: Library name: Spleen_sample2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040180

description: Library name: OP23YS040295


title: NLV-specific T cells from HF donors , GEX_GEM1

description:
Library name: GEX_GEM1
GEX_HTO_ADT_VDJ_multiout_GEM1.tar.gz
single_cell_processed_seu_obj.tar.gz


title: WT, 3h induction, rep 3

description: Library name: WT_3h_3


title: Spleen,Pdcd1^high CD4 T cells,rep1

description: Library name: Spleen_sample1


title: WT, 3h induction, rep 2

description: Library name: WT_3h_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040179

description: Library name: OP23YS040292


title: NLV-specific T cells from HF donors , HTO_ADT_GEM2

description:
Library name: HTO_ADT_GEM2
GEX_HTO_ADT_VDJ_multiout_GEM2.tar.gz
single_cell_processed_seu_obj.tar.gz

molecule: protein


title: Rh16,Naive,antiIL15,Day7,FC

city: Iowa City

first: Chen

middle: Sabrina

last: Tan

state: IA

address: 200 Hawkins Dr.

department: Medicine

country: USA

institute: University of Iowa

description:
Library name: p22131.s013_Rh16.Infect14d.FC_S13_L001
p22131.s013_Rh16.Infect14d.FC_S13_L001

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.5.2b.(Dobin et al.)
Transcripts were annotated using the UNMC rhesus annotation v 7.6.8
Transcript abundance was estimated in STAR during alignment using the algorithm or htseq-count
Assembly: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf available at https://www.unmc.edu/rhesusgenechip/index.htm)
Supplementary files format and content: comma delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: frontal cortex

extract_protocol:
RNA was isolated from the frontal cortex tissue preserved in RNAlater using the RNeasy Mini kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer and 10 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina HiSeq3000 at 100SR

treatment_protocol: Macaques were infected intrarectally with a single high dose challenge of SIVmac239X as described previously [Del Prete et al., J Virol 2014]

value: frontal cortex

tag: infection

value: anti-IL-15 mAb

tag: timepoint

value: day 7


title: NLV-specific T cells from HF donors , HTO_ADT_GEM1

description:
Library name: HTO_ADT_GEM1
GEX_HTO_ADT_VDJ_multiout_GEM1.tar.gz
single_cell_processed_seu_obj.tar.gz


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040178

description: Library name: OP23YS040290


title: Lung,Pdcd1^low CD4 T cells,rep3

description: Library name: Lung_sample6

source_name: Lung

value: Lung


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040177

description: Library name: OP23YS040289


title: Rh17,Naive,antiIL15,Day7,FC

description:
Library name: p22131.s012_Rh17.Infect7d.FC_S12_L001
p22131.s012_Rh17.Infect7d.FC_S12_L001


title: Rh3,Naive,Control,Day7,FC

description:
Library name: p22131.s011_Rh3.control.FC_S11_L001
p22131.s011_Rh3.control.FC_S11_L001

value: Control


title: WT, 3h induction, rep 1

description: Library name: WT_3h_1


title: XVE:EPFL4, uninduced, rep 3

description: Library name: EPFL4_0h_3

value: XVE:EPFL4 transformed wild type

value: mock

value: 0 hours


title: Lung,Pdcd1^high CD4 T cells,rep3

description: Library name: Lung_sample5

value: female


title: XVE:EPFL4, uninduced, rep 4

description: Library name: EPFL4_0h_4

value: 7-day-old seedlings


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040182

description: Library name: OP23YS040300


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040176

description: Library name: OP23YS040285


title: Lung,Pdcd1^low CD4 T cells,rep2

description: Library name: Lung_sample4

value: Pdcd1 low CD4 T cells


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040175

description: Library name: OP23YS040137


title: Rh2,Naïve,Control,Day7,FC

description:
Library name: p22131.s010_Rh2.control.FC_S10_L001
p22131.s010_Rh2.control.FC_S10_L001


title: Lung,Pdcd1^low CD4 T cells,rep1

description: Library name: Lung_sample2


title: Lung,Pdcd1^high CD4 T cells,rep2

description: Library name: Lung_sample3


title: XVE:EPFL4, uninduced, rep 2

description: Library name: EPFL4_0h_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040174

description: Library name: OP23YS040136


title: Rh1,Naïve,Control,Day7,FC

description:
Library name: p22131.s009_Rh1.control.FC_S9_L001
p22131.s009_Rh1.control.FC_S9_L001


title: XVE:EPFL4, uninduced, rep 1

description: Library name: EPFL4_0h_1


title: er XVE:ER uninduced, rep 4

description: Library name: ER_15_0h_4

value: XVE:ER transformed er mutant


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040173

description: Library name: OP23YS040129


title: Rh23,SIV,antiIL15,Day14,FC

description:
Library name: p22131.s007_Rh23.Infect14d.FC_S7_L001
p22131.s007_Rh23.Infect14d.FC_S7_L001

value: day 14


title: Lung,Pdcd1^high CD4 T cells,rep1

description: Library name: Lung_sample1

value: Pdcd1 high CD4 T cells


title: er XVE:ER uninduced, rep 3

description: Library name: ER_15_0h_3


title: Rh24,SIV,antiIL15,Day14,FC

description:
Library name: p22131.s008_Rh24.Infect14d.FC_S8_L001
p22131.s008_Rh24.Infect14d.FC_S8_L001


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040172

description: Library name: OP23YS040102

value: prostate


title: D21 8F mini-oocyte rep2

city: Kofu

first: Mizuki

last: Sakamoto

country: Japan

institute: University of Yamanashi

description:
Library name: Sample 7
RNA-seq

data_processing:
The first three bases of read 2 derived from the SMART-seq stranded adaptor were removed using Trim Galore! with a ‘–clip_R2 3’ option. After the reads were aligned to the mouse genome (mm10) using Hisat2, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts and Gencode annotation of the mm10 mouse genome (vM25) were used to analyze transcription level with options ‘-p -O --fraction’. TPM was calculated by counting reads mapped to the exon.
Assembly: mm10
Supplementary files format and content: text file indicating TPM values

source_name: Embryonic stem cell

growth_protocol: Female mouse embryonic stem cells were cultured in 2i+LIF condition without feeders, as described previously (Ying et al., 2008). BVSC H18 mESCs (Hayashi et al., 2012) were used as parental cells for 4F- and 8F-mESCs.

extract_protocol:
4F- or 8F-mESCs routinely cultured were detached from culture plates by 1× TrypLE solution (Thermo), and the detached cells were thoroughly dissociated into single cells by pipetting. The cell suspension was then transferred to tubes containing Wash medium [DMEM/F12 (Nacalai) supplemented with 7.5% BSA (Thermo)]. The cell suspension was centrifuged at 200 × g for 3 min at room temperature, and the supernatant was discarded. The cell pellet was resuspended in an appropriate volume of S10 medium supplemented with SCF, Y-27632, and Shield1. The cell suspension was added to the pre-coated culture plates in the desired amount, ensuring even distribution of cells (regarded as day 0). 3 × 104 cells were typically plated per well in a 24-well plate. The medium was replaced every 72 hours, with half of the medium exchanged for freshly prepared S10 medium containing SCF, Y-27632, and Shield. Starting from day 12, Shield1 was omitted from the fresh medium.
SMART-seq stranded kit (TAKARA) was used.

treatment_protocol: 0.01 % poly-L-ornithine solution was added to each well of a plate and incubated at room temperature for 1 h. Subsequently, poly-L-ornithine solution was removed, 300 ng/mL laminin solution was added to the same wells, and the plate was incubated overnight in a 5 % CO2 incubator. The wells were washed once with PBS, and S10 medium [StemPro-34 SFM (Thermo) supplemented with 10% FBS (Thermo), 150 μM 2-O-a-D-Glucopyranosyl-L-ascorbic Acid (TCI chemicals), 1 × Glutamax (Thermo), 1 × penicillin/streptomycin (Thermo) and 55 μM 2-mercaptoethanol (Thermo)] supplemented with 150 ng/mL SCF (R&D), 10 μM Y-27632 (FujiFilm), and 0.5 μM Shield1 (Selleck) was added to the plate to prepare it for cell seeding.

value: hybrid 129/C57BL6

tag: cell line

value: Embryonic stem cell

value: Forced expression of 8 TFs

tag: time

value: Day 21


title: D21 8F mini-oocyte rep1

description:
Library name: Sample 6
RNA-seq


title: er XVE:ER uninduced, rep 2

description: Library name: ER_15_0h_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040171

description: Library name: OP23YS040100


title: D7 4F mini-oocyte rep2

description:
Library name: Sample 2
RNA-seq

value: Forced expression of 4 TFs

value: Day 7


title: Rh22,SIV,antiIL15,Day14,FC

description:
Library name: p22131.s006_Rh22.Infect14d.FC_S6_L001
p22131.s006_Rh22.Infect14d.FC_S6_L001

value: frontal cortex

value: anti-IL-15 mAb


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040170

description: Library name: OP23YS040099


title: Rh21,SIV,antiIL15,Day14,FC

description:
Library name: p22131.s005_Rh21.Infect14d.FC_S5_L001
p22131.s005_Rh21.Infect14d.FC_S5_L001


title: D7 4F mini-oocyte rep1

description:
Library name: Sample 1
RNA-seq


title: Rh20,SIV,antiIL15,Day14,FC

description:
Library name: p22131.s004_Rh20.Infect14d.FC_S4_L001
p22131.s004_Rh20.Infect14d.FC_S4_L001


title: WT, uninduced, rep 4

description: Library name: WT_0h_4

value: Wild type

value: mock


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040169

description: Library name: OP23YS040095


title: Rh19,SIV,antiIL15,Day7,FC

description:
Library name: p22131.s003_Rh19.Infect7d.FC_S3_L001
p22131.s003_Rh19.Infect7d.FC_S3_L001

value: day 7


title: Ctlr3

city: Wuhan

first: Han

last: Wang

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Gastroenterology,

country: China

institute: Tongji Hospital, Tongji Medical College,

description: Library name: Sample6

data_processing:
Quality Control: Raw sequencing reads were evaluated for quality using FastQC. Read Alignment: Cleaned reads were aligned to the mouse reference genome using STAR aligner. Quantification: Gene expression levels were quantified using featureCounts.
Assembly: The mouse reference genome used for alignment was GRCm39 (mm39).
Supplementary files format and content: gene expression and rna expression text files includes raw counts

source_name: Liver

extract_protocol:
eGFP+ Treg cells were isolated from the liver of control and AIH mouse models using fluorescence-activated cell sorting (FACS). Single cells were lysed, and total RNA was reverse transcribed into cDNA using the SMART-SeqII protocol. The process included cDNA synthesis and pre-amplification to enable downstream library construction and sequencing.
cDNA libraries were constructed following the SMART-SeqII protocol, utilizing a transposon-based method for fragmentation and adapter ligation. After cDNA quality control, the libraries were prepared for sequencing by generating DNA nanoballs (DNBs) through denaturation, circularization of single-stranded PCR products, and subsequent amplification. The final libraries were sequenced using combinatorial Probe-Anchor Synthesis (cPAS) technology, ensuring high precision and sensitivity for single-cell RNA quantification.

value: Liver

value: Primary cell

value: T cell


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040168

description: Library name: OP23YS040056


title: Rh15,Naive,antiIL15,Day7,FC

description:
Library name: p22131.s002_Rh15.Infect7d.FC_S2_L001
p22131.s002_Rh15.Infect7d.FC_S2_L001


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040167

description: Library name: OP23YS040049


title: Ctrl2

description: Library name: Sample5


title: WT, uninduced, rep 2

description: Library name: WT_0h_2

value: 7-day-old seedlings

value: 0 hours


title: Rh18,SIV,antiIL15,Day7,FC

description:
Library name: p22131.s001_Rh18.Infect7d.FC_S1_L001
p22131.s001_Rh18.Infect7d.FC_S1_L001


title: Ctrl1

description: Library name: Sample4


title: WT, uninduced, rep 1

description: Library name: WT_0h_1


title: WT, uninduced, rep 3

description: Library name: WT_0h_3


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040165

description: Library name: OP23YS040014

value: prostate


title: AIH3

description: Library name: Sample3


title: AIH2

description: Library name: Sample2


title: il22koCoH4

city: Paris

first: Pedro

middle: P

last: Hernandez

address: 11-13 rue Pierre et Marie Curie, BDD building

department: Genetics and Developmental Biology

country: France

institute: Institut Curie

description: Library name: D1491T90

data_processing:
Institut Curie - Nextflow raw-qc analysis pipeline
Assembly: danRer11
Supplementary files format and content: A csv file containing raw read counts, with each column representing a sample

organism: Danio rerio

source_name: Gut

extract_protocol:
10-15 guts per replicate were dissected and RNA was extracted using the Single Cell RNA Purification Kit (Norgen, #51800) following the manufacturer’s instructions. RNA integrity and concentration were analyzed on the Agilent 4200 Tapestation system using the High Sensitivity RNA ScreenTape Analysis kit (Agilent, #5067-5579). cDNA quality was checked on the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit (Agilent #5067-4626). After quality control, libraries were sequenced with 100-bp paired-end (PE100) reads on the NovaSeq 6000 (Illumina) sequencer. Raw data were checked for quality using FastQC (v0.11.8) and aligned to the reference genome for Danio rerio danRer11 from the Genome Reference Consortium.
RNA sequencing libraries were prepared from 500 ng to 1 μg of total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit

value: Gut


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040164

description: Library name: OP24YS040112


title: il22koCoH3

description: Library name: D1491T89


title: er XVE:ER uninduced, rep 1

description: Library name: ER_15_0h_1

value: XVE:ER transformed er mutant


title: HiChIP_T3M4_Rep1

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

description: Library name: Sample042

library_source: genomic

data_processing:
HiChIP data were analyzed using the HiC-Pro pipeline. Briefly, sequencing reads were mapped with HiC-Pro v3.1.0 and FitHiChIP v11.0 was utilized to generate bedpe file format. For HiC-Pro, we used MIN_CIS_DIST = 10000 and BIN_SIZE = 2500. We generated an in-house script (https://github.com/bhc-rbct/Filter-A2A-loops-for-active-genes.git) which extracts the active TSS of target genes using a cell line specific H3K4me3 bed file (anchor 1) which interacts with (enhancer) regions of interest (anchor 2). Resulting bedpe files and .hic files (generated from hicpro2juicebox.sh) were used to generate aggregate peak analysis (APA) plots and contact maps utilizing the Tinker Box platform (https://docs.axiotl.com/). Counts per million were used to normalize samples.
Assembly: hg38
Supplementary files format and content: Merged all-to-all bedpe file
Library strategy: HiChIP

molecule: genomic DNA

growth_protocol: BxPC3, TCCPAN2, T3M4 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII (phenol red free MEM, 10% FBS, 1% Pen-Strep) and CFPAC1 (DMEM 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
H3K4me3 HiChIP was performed as previously described with a few modifications (PMID: 32051612, PMID: 33658703). Briefly, cells were trypsinized, counted, and 10 million cells were used for each condition. Pertinent modifications are digestion was carried out by incubating with 200 U each of MboI, DpnII, and HinfI (NEB) at 37°C for 2 hr and samples were sonicated for 8 cycles 30 sec on/off. 6 µg of H3K4me3 and Protein A beads were added to the samples. DNA was purified as described above for ChIP-seq and on-bead libraries were prepped using MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001).
Libraries were prepped using MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001).

value: Pancreatic ductal adenocarcinoma


title: HiChIP_TCCPAN2_Rep2

description: Library name: Sample041


title: HiChIP_T3M4_Rep2

description: Library name: Sample043


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040163

description: Library name: OP23YS040406


title: AIH1

description: Library name: Sample1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040162

description: Library name: OP23YS040019


title: il22koCoH1

description: Library name: D1491T87


title: HiChIP_TCCPAN2_Rep1

description: Library name: Sample040


title: il22koGF3

description: Library name: D1491T85


title: il22koCoH2

description: Library name: D1491T88


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040160

description: Library name: OP23YS040408


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040166

description: Library name: OP23YS040038


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040159

description: Library name: OP23YS040398


title: il22koGF4

description: Library name: D1491T86


title: il22koGF2

description: Library name: D1491T84


title: HiChIP_CFPAC1_Rep2

description: Library name: Sample037


title: HiChIP_HPAFII_Rep1

description: Library name: Sample038

source_name: HPAFII

value: HPAFII


title: il22koGF1

description: Library name: D1491T83


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040158

description: Library name: OP23YS040287


title: HiChIP_BxPC3_Rep2

description: Library name: Sample035


title: il22koCV4

description: Library name: D1491T82


title: il22koCV3

description: Library name: D1491T81


title: HiChIP_BxPC3_Rep1

description: Library name: Sample034


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040157

description: Library name: OP23YS040048


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040156

description: Library name: OP23YS040030


title: il22koCV2

description: Library name: D1491T80


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040155

description: Library name: OP24YS040121


title: ChIPseq_BxPC3_H3K27ac_Rep2

description: Library name: Sample032

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge. Bigwig files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage . MACS3 callpeak was used to call the significant peaks with non-broad cutoff of 0.05 for while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: Normalized bigwig for each condition
Supplementary files format and content: Bed file for each condition

growth_protocol: BxPC3 and T3M4 (RPMI, 10% FBS, 1% Pen-Strep) and HPAFII (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.

tag: chip antibody


title: il22koCV1

description: Library name: D1491T79


title: ChIPseq_BxPC3_H3K27ac_Rep3

description: Library name: Sample033


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040154

description: Library name: OP24YS040136


title: HiChIP_HPAFII_Rep2

description: Library name: Sample039


title: WTGF4

description: Library name: D1491T78


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040153

description: Library name: OP24YS040114


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040161

description: Library name: OP24YS040107


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040152

description: Library name: OP23YS040071


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040150

description: Library name: OP23YS040018


title: WTGF2

description: Library name: D1491T76


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040151

description: Library name: OP23YS040060


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040149

description: Library name: OP24YS040144


title: ChIPseq_T3M4_CTCF_Rep3

description: Library name: Sample027

value: CTCF


title: ChIPseq_BxPC3_dNp63_Rep2

description: Library name: Sample029


title: WTGF1

description: Library name: D1491T75


title: WTGF3

description: Library name: D1491T77


title: ChIPseq_BxPC3_H3K27ac_Rep1

description: Library name: Sample031


title: ChIPseq_BxPC3_dNp63_Rep3

description: Library name: Sample030


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040148

description: Library name: OP24YS040122


title: ChIPseq_BxPC3_dNp63_Rep1

description: Library name: Sample028


title: ChIPseq_T3M4_CTCF_Rep1

description: Library name: Sample025


title: WTCV3

description: Library name: D1491T73


title: WTCV2

description: Library name: D1491T72


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040147

description: Library name: OP24YS040113


title: ChIPseq_HPAFII_CTCF_Rep3

description: Library name: Sample024


title: ChIPseq_T3M4_CTCF_Rep2

description: Library name: Sample026


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040146

description: Library name: OP24YS040096


title: WTCV1

description: Library name: D1491T71


title: G1E-ER4 cells, differentiating, siZIP10, DTPA, 24 hours,  biol rep 2

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu, Samsung Hall 611

description:
Library name: Sample 11
Low ZIP10+Low zinc

data_processing:
151bp paired-end reads for 6 samples (n=24.0 Million reads average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (mm10) as reference.
Gene quantification was done via Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: erythron

growth_protocol: G1E-ER4 mouse erythroid progenitor cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 15% fetal bovine serum, 100 U/mL penicillin-streptomycin, 1:10,000 monothioglycerol, 2 U/mL erythropoietin (Epogen, Amgen), and 1:200 diluted conditioned medium from Kit ligand-producing CHO. The cells were incubated in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Kit (Zymo Research)
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep kit following manufacturer's protocols.

treatment_protocol: Gene knockdown was accomplished via nucleofector-mediated delivery of siRNA into cells twice at a 24-h interval. At the second transfection, differentiation was induced by treatment of 100 nM β-estradiol. Zinc deficiency was achieved by addition of  25 µM DTPA at the beginning of the differentiation. Treated cells were harvested at 24-hour of post-treatment.

value: erythron

value: erythroid progenitors

value: siZIP10, 25 µM DTPA, 24 hours


title: G1E-ER4 cells, differentiating, siZIP10, DTPA, 24 hours,  biol rep 3

description:
Library name: Sample 12
Low ZIP10+Low zinc


title: ChIPseq_HPAFII_CTCF_Rep2

description: Library name: Sample023


title: HiChIP_CFPAC1_Rep1

description: Library name: Sample036


title: G1E-ER4 cells, differentiating, siZIP10, DTPA, 24 hours,  biol rep 1

description:
Library name: Sample 10
Low ZIP10+Low zinc


title: il22ko4

description: Library name: D580T08


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040145

description: Library name: OP24YS040093


title: WTCV4

description: Library name: D1491T74


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040144

description: Library name: OP23YS040297


title: G1E-ER4 cells, differentiating, siZIP10, 24 hours,  biol rep 3

description:
Library name: Sample 9
Low ZIP10

value: siZIP10, 24 hours


title: G1E-ER4 cells, differentiating, siZIP10, 24 hours,  biol rep 2

description:
Library name: Sample 8
Low ZIP10


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040142

description: Library name: OP23YS040152


title: ChIPseq_HPAFII_CTCF_Rep1

description: Library name: Sample022


title: G1E-ER4 cells, differentiating, siZIP10, 24 hours,  biol rep 1

description:
Library name: Sample 7
Low ZIP10


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040141

description: Library name: OP23YS040151


title: il22ko2

description: Library name: D580T06


title: RPB1degron_125nM_dTAGv1_Ser5plus2P_1

city: Copenhagen

first: Jesper

middle: Q

last: Svejstrup

address: Blegdamsvej 3B

department: ICMM

country: Denmark

institute: University of Copenhagen

description: Library name: 125nM_Ser5plus2P_1

data_processing:
Paired-end reads were aligned against the GRCh38 genome with hisat2 (v2.2.1) using the --no-spliced-alignment, --no-mixed and --no-discordant options. Afterwards, multi-mappers were removed using samtools (v1.15.1), followed by removal of PCR duplicates using the UMI-tools dedup function (v1.1.4). BAM files were then converted to bigwig files for visualization using the deeptools (v3.5.5) bamCoverage function with options --normalizeUsing CPM, --binSize 10, and --extendReads. Normalization of RNAPII coverage to IgG, as well as normalization of Ser5p+Ser2p RNAPII coverage to total RNAPII was performed using the deeptools function bigwigcompare.
Assembly: GRCh38
Supplementary files format and content: bigwig, CPM normalized
Library strategy: CUT&Run

growth_protocol: RPB1 degron cells were cultured in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 100U/mL penicillin, and 100µg/mL streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
CUT&RUN was performed essentially as per manufacturer's instructions (#86652, Cell Signaling). After 16 hours of dTAGV-1 treatment, cells were trypsinized and fixed for 2 minutes at room temperature with 0.1% formaldehyde. Fixing was stopped by addition of 250mM glycine for 5 minutes, and cells were washed once with 1X wash buffer supplemented with spermidine and protease inhibitor cocktail. Cells for each condition were then aliquoted into 100 thousand cells per Lo-bind microcentrifuge tube, and incubated with activated concanavalin A beads for 5 minutes at room temperate. After addition of antibody binding buffer, cells were incubated overnight at 4C with rabbit anti-HA (4uL per replicate, 3 replicates per dTAGv-1 condition), rabbit anti-Ser5+2P (4uL per replicate, 3 replicates per dTAGv-1 condition), and rabbit anti-IgG (5uL per replicate, 3 replicates per dTAGv-1 condition) antibody. Binding of pAG-MNase and DNA digestion was performed as per manufacturer's instructions, and included the addition of 50pg spike-in DNA. To reverse crosslinks, the eluted DNA was incubated with agitation overnight at 65C in the presence of 0.1% SDS and 133ng/ug proteinase K. Finally, the eluted DNA was purified using DNA Purification Buffers and Spin Columns (#14209 Cell Signaling)
40uL of DNA from each condition was used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina (#E7370L, NEB). Unique dual indices (#E7395S, NEB) were used to facilitate multiplexing and the detection of PCR duplicates. Finally, libraries were pooled and sequenced on an Illumina NextSeq 2000, yielding 50bp paired-end reads.

treatment_protocol: RPB1 degron cells were seeded at a density of 5 million cells in a 10cm plate and were either treated with DMSO or different concentrations of dTAGv-1 for 16 hours before harvest.

value: RPB1 degron D4

value: 125nM dTAGv1


title: G1E-ER4 cells, differentiating, siControl, DTPA, 24 hours,  biol rep 3

description:
Library name: Sample 6
Low zinc

value: siControl,25 µM DTPA, 24 hours


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040140

description: Library name: OP23YS040067


title: RPB1degron_62nM_dTAGv1_Ser5plus2P_3

description: Library name: 62nM_Ser5plus2P_3

value: 62nM dTAGv1


title: RPB1degron_125nM_dTAGv1_Ser5plus2P_2

description: Library name: 125nM_Ser5plus2P_2


title: G1E-ER4 cells, differentiating, siControl, DTPA, 24 hours,  biol rep 2

description:
Library name: Sample 5
Low zinc


title: WT3

description: Library name: D580T03


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040139

description: Library name: OP23YS040066


title: il22ko1

description: Library name: D580T05


title: il22ko3

description: Library name: D580T07


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040143

description: Library name: OP23YS040153


title: WT2

description: Library name: D580T02


title: RPB1degron_62nM_dTAGv1_Ser5plus2P_2

description: Library name: 62nM_Ser5plus2P_2


title: G1E-ER4 cells, differentiating, siControl, DTPA, 24 hours,  biol rep 1

description:
Library name: Sample 4
Low zinc


title: RPB1degron_62nM_dTAGv1_Ser5plus2P_1

description: Library name: 62nM_Ser5plus2P_1


title: WT1

description: Library name: D580T01


title: WT4

description: Library name: D580T04


title: G1E-ER4 cells, differentiating, siControl, 24 hours, biol rep 3

description:
Library name: Sample 3
Control

value: siControl, 24 hours


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040138

description: Library name: OP24YS040140


title: RPB1degron_32nM_dTAGv1_Ser5plus2P_3

description: Library name: 32nM_Ser5plus2P_3

value: 32nM dTAGv1


title: RPB1degron_125nM_dTAGv1_Ser5plus2P_3

description: Library name: 125nM_Ser5plus2P_3


title: G1E-ER4 cells, differentiating, siControl, 24 hours, biol rep 2

description:
Library name: Sample 2
Control


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040137

description: Library name: OP24YS040105


title: WT_mock_3

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 w 12th Ave.

department: Department of Microbial Infection and Immunity

institute: The Ohio State University College of Medicine

description: Library name: Sample_12

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Assembly: GRCm39
Supplementary files format and content: GSDME_raw_counts: txt file with raw counts for each sample and each gene

extract_protocol:
TRIzol RNA extraction from lung tissue.
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: For in vivo infections, mice were anesthetized using 4% isoflurane, and 50 uL of diluted virus (50 TCID50) in sterile saline was delivered intranasally.

value: Lung

value: WT

value: Mock (Saline)


title: RPB1degron_32nM_dTAGv1_Ser5plus2P_2

description: Library name: 32nM_Ser5plus2P_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040136

description: Library name: OP24YS040104

value: prostate


title: WT_mock_2

description: Library name: Sample_11


title: G1E-ER4 cells, differentiating, siControl, 24 hours, biol rep 1

description:
Library name: Sample 1
Control


title: G1E-ER4 cells, differentiating, DTPA, 24 hours,  biol rep 3

description:
Library name: Sample 7
differentiation under low zinc

treatment_protocol: Differentiation was induced by treatment of 100 nM β-estradiol. Zinc deficiency was achieved by addition of  50 µM DTPA at the beginning of the differentiation. Treated cells were harvested at 24-hour of post-treatment.

value: 50 µM DTPA


title: RPB1degron_32nM_dTAGv1_Ser5plus2P_1

description: Library name: 32nM_Ser5plus2P_1


title: WT_mock_1

description: Library name: Sample_10


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040135

description: Library name: OP24YS040092


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040134

description: Library name: OP23YS040407


title: RPB1degron_DMSO_Ser5plus2P_3

description: Library name: DMSO_Ser5plus2P_3

value: DMSO


title: RPB1degron_DMSO_Ser5plus2P_2

description: Library name: DMSO_Ser5plus2P_2


title: GSDME_KO_mock_3

description: Library name: Sample_9


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040133

description: Library name: OP23YS040396


title: GSDME_KO_mock_2

description: Library name: Sample_8


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040132

description: Library name: OP23YS040389


title: G1E-ER4 cells, differentiating, DTPA, 24 hours,  biol rep 1

description:
Library name: Sample 5
differentiation under low zinc


title: G1E-ER4 cells, differentiating, Control, 24 hours, biol rep 3

description:
Library name: Sample 4
differentiation under normal zinc

value: Control


title: GSDME_KO_mock_1

description: Library name: Sample_7


title: G1E-ER4 cells, differentiating, Control, 24 hours, biol rep 2

description:
Library name: Sample 3
differentiation under normal zinc

value: erythron


title: RPB1degron_125nM_dTAGv1_IgG_3

description: Library name: 125nM_IgG_3


title: RPB1degron_DMSO_Ser5plus2P_1

description: Library name: DMSO_Ser5plus2P_1


title: WT_PR8_3

description: Library name: Sample_6


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040131

description: Library name: OP23YS040286


title: WT_PR8_2

description: Library name: Sample_5


title: G1E-ER4 cells, differentiating, Control, 24 hours, biol rep 1

description:
Library name: Sample 2
differentiation under normal zinc

value: erythroid progenitors


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040130

description: Library name: OP23YS040150


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040129

description: Library name: OP23YS040147


title: G1E-ER4 cells, differentiating, SA, 24 hours,  biol rep 3

description:
Library name: Sample 12
Low protoporphyrin IX

treatment_protocol: Differentiation was induced by treatment of 100 nM β-estradiol. Zinc deficiency was achieved by addition of  50 µM DTPA at the beginning of the differentiation. Iron deifieiciency was achieved by addition of 50 µM DFO at the beginning of the differentiation. Protoporphyrin deficiency via ALAD inhibition was achieved by addition of 50 µM DFO at the beginning of the differentiation.Treated cells were harvested at 24-hour of post-treatment.

value: 0.2 mM SA, 24 hours


title: RPB1degron_125nM_dTAGv1_IgG_1

description: Library name: 125nM_IgG_1


title: G1E-ER4 cells, non-differentiating, Control, 0 hours, biol rep 1

description:
Library name: Sample 1
no differentation

value: Control, non-differentiating


title: WT_PR8_1

description: Library name: Sample_4


title: GSDME_KO_PR8_2

description: Library name: Sample_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040128

description: Library name: OP23YS040135


title: GSDME_KO_PR8_3

description: Library name: Sample_3


title: RPB1degron_62nM_dTAGv1_IgG_3

description: Library name: 62nM_IgG_3

value: RPB1 degron D4


title: GSDME_KO_PR8_1

description: Library name: Sample_1


title: G1E-ER4 cells, differentiating, DTPA, 24 hours,  biol rep 2

description:
Library name: Sample 6
differentiation under low zinc


title: FMT-SP4

city: Beijing

first: Jing

last: Lan

address: No. 2 Yuanmingyuan West Road, Haidian District

institute: China Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using protocal
Data filtering steps. Prior to assembly, the low quality reads were removed.
Read alignment software, software HISAT, version 2.0.
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hippocampal tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis by Bioanalyzer 2100 and Agilent RNA 6000 Nano Kit
RNA library were prepared for sequencing using standard lllumina protocols

value: hippocampal tissue


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040126

description: Library name: OP23YS040093


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040127

description: Library name: OP23YS040098


title: G1E-ER4 cells, differentiating, SA, 24 hours,  biol rep 2

description:
Library name: Sample 11
Low protoporphyrin IX


title: RPB1degron_62nM_dTAGv1_IgG_2

description: Library name: 62nM_IgG_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040125

description: Library name: OP23YS040090


title: RPB1degron_32nM_dTAGv1_IgG_3

description: Library name: 32nM_IgG_3


title: RPB1degron_62nM_dTAGv1_IgG_1

description: Library name: 62nM_IgG_1


title: RPB1degron_125nM_dTAGv1_IgG_2

description: Library name: 125nM_IgG_2

value: 125nM dTAGv1


title: G1E-ER4 cells, differentiating, DFO, 24 hours,  biol rep 3

description:
Library name: Sample 9
Low iron

value: 50 µM DFO, 24 hours


title: RPB1degron_32nM_dTAGv1_IgG_1

description: Library name: 32nM_IgG_1


title: G1E-ER4 cells, differentiating, DFO, 24 hours,  biol rep 2

description:
Library name: Sample 8
Low iron


title: FMT-SP3


title: G1E-ER4 cells, differentiating, SA, 24 hours,  biol rep 1

description:
Library name: Sample 10
Low protoporphyrin IX


title: RPB1degron_32nM_dTAGv1_IgG_2

description: Library name: 32nM_IgG_2


title: FMT-SP2


title: G1E-ER4 cells, differentiating, DFO, 24 hours,  biol rep 1

description:
Library name: Sample 7
Low iron


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040123

description: Library name: OP23YS040062


title: RPB1degron_16nM_dTAGv1_IgG_3

description: Library name: 16nM_IgG_3

value: 16nM dTAGv1


title: G1E-ER4 cells, differentiating, DTPA, 24 hours,  biol rep 3

description:
Library name: Sample 6
Low zinc

value: 50 µM DTPA, 24 hours


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040124

description: Library name: OP23YS040077


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040122

description: Library name: OP23YS040057


description:
Library name: Sample 5
Low zinc


title: RPB1degron_16nM_dTAGv1_IgG_2

description: Library name: 16nM_IgG_2


title: FMT-DSS4


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040119

description: Library name: OP23YS040001


title: FMT-DSS2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040118

description: Library name: OP23YS040409


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040120

description: Library name: OP23YS040004


title: FMT-DSS3


title: RPB1degron_DMSO_IgG_3

description: Library name: DMSO_IgG_3


title: G1E-ER4 cells, differentiating, Control, 24 hours, biol rep 2

description:
Library name: Sample 2
Normal


title: RPB1degron_DMSO_IgG_1

description: Library name: DMSO_IgG_1


title: G1E-ER4 cells, differentiating, Control, 24 hours, biol rep 1

description:
Library name: Sample 1
Normal


title: FMT-CON4


title: RPB1degron_16nM_dTAGv1_IgG_1

description: Library name: 16nM_IgG_1


title: G1E-ER4 cells, differentiating, Control, 24 hours, biol rep 3

description:
Library name: Sample 3
Normal


title: FMT-CON3


title: RPB1degron_125nM_dTAGv1_HA_3

description: Library name: 125nM_HA_3


title: G1E-ER4 cells, differentiating, DTPA, 24 hours,  biol rep 1

description:
Library name: Sample 4
Low zinc


title: RPB1degron_DMSO_IgG_2

description: Library name: DMSO_IgG_2


title: FMT-DSS1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040117

description: Library name: OP23YS040404


title: RPB1degron_125nM_dTAGv1_HA_2

description: Library name: 125nM_HA_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040116

description: Library name: OP23YS040402


title: FMT-CON2


title: FMT-SP1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040121

description: Library name: OP23YS040055


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040115

description: Library name: OP23YS040061


title: RPB1degron_125nM_dTAGv1_HA_1

description: Library name: 125nM_HA_1


title: FMT-CON1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040114

description: Library name: OP23YS040053


title: RPB1degron_62nM_dTAGv1_HA_3

description: Library name: 62nM_HA_3

value: 62nM dTAGv1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040112

description: Library name: OP23YS040101


title: RPB1degron_62nM_dTAGv1_HA_2

description: Library name: 62nM_HA_2


title: RPB1degron_62nM_dTAGv1_HA_1

description: Library name: 62nM_HA_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040111

description: Library name: OP24YS040110


title: Stc1-CreERT2 Bax/Bak1 KO CMO

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

description:
Library name: Stc1-BB-KO-CML
Cell multiplexing oligo (CMO) label data from EPCAM-, CD31-, CD45- cells sorted by FACS from Stc1-BB KO mouse lungs (2 male, 1 female) collected at P30 after tamoxifen injection at P1. CMO305, CMO306, CMO307 were used to label each of the 3 mice, respectively.

data_processing:
Read alignment and cell calling using STAR-solo (velocyto output)
Ambient-RNA correction using scvi-tools scAR
h5ad file creation using anndata
Assembly: GRCm39
Supplementary files format and content: HDF5 format anndata objects (.h5ad) for these data alone and these data integrated with P7 lung mesenchyme data from Zepp 2021 (GSE149563). Files contain cell barcodes, feature names, annotations, and counts/normalized expression matrices. The log1p(scAR_CP10k) expression matrix is loaded in the `X` slot. The `layers` dictionary contains the log1p(scAR_CP10k), spliced, unspliced, counts_raw, and counts_scAR keys, corresponding to the ln(1+CP10k) expression, velocyto spliced/unspliced counts, the raw total (spliced + unspliced + ambiguous) counts, and the scAR ambient-RNA corrected total counts, respectively.

source_name: lung

extract_protocol:
Live, EPCAM-, CD31-, CD45- cells sorted by FACS from Stc1-BB HET/KO mouse lungs. 10X Chromium GEX v3 3’-biased scRNA-seq chemistry was used to extract mRNA from individual cells.
10X Genomics 3’-biased gene expression library construction (v3.1).

value: lung

value: PDGFRa-H2B-GFP, Stc1-CreERT2 x (Bax fl/fl, Bak1 -/-, R26-LSL-tdTomato)

value: Tamoxifen injection at P1

tag: batch


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040109

description: Library name: OP24YS040132

value: prostate


title: RPB1degron_32nM_dTAGv1_HA_2

description: Library name: 32nM_HA_2

value: 32nM dTAGv1


title: Stc1-CreERT2 Bax/Bak1 KO GEX

description:
Library name: Stc1-BB-KO-GEX
Gene expression data from EPCAM-, CD31-, CD45- cells sorted by FACS from Stc1-BB KO mouse lungs (2 male, 1 female) collected at P30 after tamoxifen injection at P1.


title: RPB1degron_32nM_dTAGv1_HA_3

description: Library name: 32nM_HA_3


title: Stc1-CreERT2 Bax/Bak1 HET CMO

description:
Library name: Stc1-BB-HET-CML
Cell multiplexing oligo (CMO) label data from EPCAM-, CD31-, CD45- cells sorted by FACS from Stc1-BB HET mouse lungs (2 male, 1 female) collected at P30 after tamoxifen injection at P1. CMO305, CMO306, CMO307 were used to label each of the 3 mice, respectively.

value: PDGFRa-H2B-GFP, Stc1-CreERT2 x (Bax fl/+, Bak1 -/-, R26-LSL-tdTomato)


title: Stc1-CreERT2 Bax/Bak1 HET GEX

description:
Library name: Stc1-BB-HET-GEX
Gene expression data from EPCAM-, CD31-, CD45- cells sorted by FACS from Stc1-BB HET mouse lungs (2 male, 1 female) collected at P30 after tamoxifen injection at P1.


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040110

description: Library name: OP23YS040131


title: RPB1degron_16nM_dTAGv1_HA_3

description: Library name: 16nM_HA_3


title: Sample7_GutWT

city: London

first: Daria

last: Gavriouchkina

state: London

address: UCL Cruciform Building, Gower Street

department: UK Dementia Research Institute at UCL

institute: University College London

description:
Library name: Sample7_GutWT
10x Genomics

data_processing:
Fastq files were mapped to mm10 using cellranger-7.1.0
Assembly: mm10 as provided by 10x Genomics website (refdata-gex-mm10-2020-A)
Supplementary files format and content: fastq files, matrix files generated by cellranger

extract_protocol:
To obtain single cell suspensions, peeled ME was cut in 1-2 mm pieces and digested with 2 mg/mL Collagenase type IV and 0.8 mg/mL dispase in RPMI (Gibco) supplemented with 2% HEPES (Gibco), 2% FBS (Gibco), and 50μg/mL DNase for 1h at 37°C with continuous agitation. The single cell suspensions were then homogenised with a potter grinder and strained through 70 μm cell strainers (BD Falcon).
Single-cell libraries were prepared using 10X Genomics Chromium Next GEM Single Cell 5′ kit v3.1, according to the manufacturer’s instructions. Libraries were sequenced using an S2 flowcell on an Illumina NovaSeq S6000 instrument, with sequencing parameters recommended by 10X Genomics, aiming for 40,000 reads per cell.

value: Gut

value: 4 mo

value: M

value: WT


title: Sample8_Gut3KL

description:
Library name: Sample8_Gut3KL
10x Genomics


title: RPB1degron_32nM_dTAGv1_HA_1

description: Library name: 32nM_HA_1

value: RPB1 degron D4


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040108

description: Library name: OP24YS040100


title: Sample1_GutWT

description:
Library name: Sample1_GutWT
10x Genomics


title: Sample2_Gut3KL

description:
Library name: Sample2_Gut3KL
10x Genomics


title: AB18257.txt

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample 187

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cell_metadata.csv

growth_protocol: hTREM2 mice were s.c. injected with 1M MC38 tumor cells (day 0). Mice were intravenously treated with 200 µg per dose of anti-RSV, anti-TREM2, anti-PD-1, anti-TREM2 + anti-PD1, anti-CTLA-4, anti-TREM2 + anti-CTLA-4, MiTE-144, MiTE-144 + anti-PD1, or MiTE-144 + anti-CTLA-4 on days 8 and 10 (n = 5). Immune cells were isolated on day 11, FACS sorted (total CD45+ and T/NK cell enrichment) and underwent scRNAseq employing SPID-seq resulting in a total of 45,505 high-quality cells from 45 mice.

extract_protocol:
Tumors were minced into small pieces on ice and digested using RPMI supplemented with 1mg/ml Collagenase IV (LS004188, Enco) and 0.05mg/ml DnaseI (DnaseI, Sigma Aldrich) at 37 degrees for three times 8 min. In between the incubation steps, the tissue was further dissociated using a gentleMACS dissociator (130-093-235, Miltenyi Biotec). After digestion, the cells were filtered trough a 100um cell strainer and washed with ice cold PBS.  Cells were stained with FACS antibodies and viability dye for 30min on ice. After washing them again with ice cold PBS, cells were sorted and acquired on a BD FACS Symphony 6 flow cytometer. After excluding doublets and dead cells, two 384-well plates of CD45+ cells and CD90.2+ and/or NK1.1+ (=T/NKT/NK/ILCs) were sorted per sample The 384-well plates contained a lysis solution, mineral oil and barcoded poly(T) reverse transciption primers enabeling scRNA sequencing.
SPID-seq92, an adapted version of the MARS-seq pipeline93, was used to generate scRNA-seq libraries. In short, polyadenylated mRNA from individual cells that had been sorted into 384-well plates was captured, followed by a barcoding step of the mRNA during reverse transcription into cDNA. cDNA of each plate was pooled into a single tube, and was fragmented and amplified to generate sequencing-ready libraries for NovaSeq X plus (Illumina) sequencing. Quality control was performed on each library created from a plate.

tag: mouse id


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040107

description: Library name: OP23YS040400


title: RPB1degron_16nM_dTAGv1_HA_2

description: Library name: 16nM_HA_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040113

description: Library name: OP23YS040288


title: RPB1degron_16nM_dTAGv1_HA_1

description: Library name: 16nM_HA_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040106

description: Library name: OP24YS040125


title: AB18256.txt

description: Library name: Sample 186

treatment_protocol: hTREM2 mice were s.c. injected with 1M MC38 tumor cells (day 0). Mice were intravenously treated with 200 µg per dose of anti-RSV, anti-TREM2, anti-PD-1, anti-TREM2 + anti-PD1, anti-CTLA-4, anti-TREM2 + anti-CTLA-4, MiTE-144, MiTE-144 + anti-PD1, or MiTE-144 + anti-CTLA-4 on days 8 and 10 (n = 5). Immune cells were isolated on day 11, FACS sorted (total CD45+ and T/NK cell enrichment) and underwent scRNAseq employing SPID-seq resulting in a total of 45,505 high-quality cells from 45 mice.


title: mESC, ChiP Input, rep2

city: Shanghai

first: jiaying

last: xie

address: Dongfang Road

institute: Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Wdr5_Input_Rep2
none

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality.
Alignment was done by using Bowtie2
Reads that mapped to multiple locations in the genome were discarded
Annotation was done by using the script annotatePeaks.pl of HOMER.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: mouse embryonic stem cells

growth_protocol: The ESC medium was prepared as follows: 85% Dulbecco’s Modified Eagle Media (DMEM) (Gibco, Waltham, Massachusetts, USA), 15% fetal bovine serum (HyClone, Logan, Utah, USA), 2 mM L-glutamine (Invitrogen, Carlsbad, CA, USA), 100 units/ml penicillin and 100 µg/ml streptomycin (Invitrogen), 0.1 mM nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, United States), and 1000 units/mL LIF. Mouse ESCs were plated on tissue culture dishes which were pre-coated with 0.2% gelatin (Sigma-Aldrich) for at least 20 min and grown in humidified 5% CO2 at 37°C incubator. The medium was changed every day and ESCs were passaged every 2-3 days.

extract_protocol:
Chromatin fragmentation by Mnase and immunoprecipitation were carried out following the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocols.
Purified ChIP DNA was used for library construction following the Illumina ChIP–seq library generation protocol (NEB)

treatment_protocol: Under normal culture

value: mouse embryonic stem cells

value: mESC

value: Wild type


title: mESC, ChIP Input, rep1

description:
Library name: Wdr5_Input_Rep1
none


title: AB18255.txt

description: Library name: Sample 185


title: mESC, R153A, Wdr5 ChIP-seq, rep2

description:
Library name: Wdr5_R153A_Rep2
ChIP antibody Wdr5

value: Nanog R153A

value: In vitro culture


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040104

description: Library name: OP24YS040103


title: AB18254.txt

description: Library name: Sample 184


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040103

description: Library name: OP23YS040401


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040102

description: Library name: OP23YS040367


title: mESC, R153A, Wdr5 ChIP-seq, rep1

description:
Library name: Wdr5_R153A_Rep1
ChIP antibody Wdr5


title: RPB1degron_DMSO_HA_1

description: Library name: DMSO_HA_1

value: DMSO


title: RPB1degron_DMSO_HA_2

description: Library name: DMSO_HA_2


title: RPB1degron_125nM_45min_DRB_release_3

description: Library name: 125nM_45min_DRB_release_3

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.20.0.422) and resultant FASTQ files were quality checked using MultiQC (v1.11). Reads were aligned to the GRCh38 genome using hisat2 (v2.2.1) with default options, followed by identification of PCR duplicates using picard Markduplicates (v2.27.3). Further analysis was conducted as in Gregersen et al. (2020). Briefly, bp-resolution read-depth coverage was calculated over intervals representing non-overlapping, protein-coding genes at least 60kb in width, extended -2kb:+120kb around the TSS region. Counts were normalized for sequencing depth (RPM) and meta-profiles were created by taking a trimmed mean across genes at each bp location. A smoothing spline was fitted to each meta-profile using R’s smooth.spline function (spar=0.3). Wave peaks were subsequently calculated as the maximum point on the spline for each sample, ensuring that wave peaks advanced with time. Elongation rates in kb/min were estimated by fitting a linear model to the wave peak positions of all samples (i.e. 15, 30, and 45 minutes post release) as a function of time.
Assembly: GRCh38
Supplementary files format and content: bigwig, CPM normalized

extract_protocol:
Following a 10 minute pulse with 1mM 4sU, media was aspirated and cells were harvested by the addition of 1mL Trizol to stop the reaction. To isolate total RNA, one-fifth of chloroform was added to lysates and shaken well, followed by centrifugation (12000g, 5 minutes at 4C). The upper aqueous phase was transferred to MaXtract high-density phase-lock tubes, that were previously prepared according to manufacturer’s instructions, and an equal volume of chloroform/isoamyl alcohol (24:1) was added. Lysates were then centrifuged again (12000g, 5 minutes at 4C) and the upper aqueous phase was transferred to a new tube. The RNA was then precipitated through the addition of 1.1X volumes of 100% isopropanol, incubation at room temperature for 20 minutes and centrifugation (12000g, 20 minutes at 4C). RNA pellets were washed once with 85% (v/v) ethanol, and air dried at room temperature before resuspension in Ultrapure DNase/RNase-free distilled water. As an external reference control, 500ng S.cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) nascent RNA was spiked-in to 100µg of H.sapiens total RNA. The RNA was then fragmented by the addition of 20µL 1M NaOH and incubation on ice for 20 minutes. Fragmentation was stopped by the addition of 80µL 1M Tris HCl pH 6.8 and material was purified twice using the Micro Bio-Spin P-30 Gel Columns according to manufacturer’s instructions. Thiol-specific biotinylation of RNA was performed using 10 mM Tris-HCl pH 7.4, 1 mM EDTA and 5 mg MTSEA biotin-XX linker in a final volume of 250µL and incubation at room temperature for 30 minutes in the dark. Biotinylated RNA was then purified by addition of 250μL of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol)), followed by shaking and addition to MaXtract high-density phase-lock tubes that were previously prepared according to manufacturers instructions. Following centrifugation (12000g, 5minutes at 4C), the upper aqueous phase was transferred to a new tube and biotinylated RNA was precipitated using one-tenth the volume 5M NaCl and 1.1X volume 100% isopropanol, followed by incubation at room temperature for 10 minutes and centrifugation (20000g, 20 minutes at 4C). RNA pellets were washed once in 85% (v/v) ethanol, air dried at room temperature, and resuspended in 50µL Ultrapure DNase/RNase-free distilled water. The RNA was then denatured by incubating for 10 minutes at 65°C in the dark. Biotinylated RNA was separated from the total RNA pool by addition of 100 μL μMACS Streptavidin MicroBeads and incubation for 15 minutes at room temperature with constant rotation. Beads were then applied to a μColumn pre-equilibrated with 100 µL nucleic acid equilibration buffer and immobilised on a magnetic stand, washed twice with pre-warmed (55°C) wash buffer (100 mM Tris HCl pH 7.4 10mM EDTA, 1M NaCl and 0.1% (v/v) Tween 20) and biotinylated RNA was eluted by two additions of 100μL 100 mM DTT, 5 minutes apart. Purification of biotinylated RNA was performed using the RNeasy MinElute kit according to manufacturer’s instructions, where 1050 μL 100% ethanol and 750 μL RLT buffer was added per 200μL reaction to precipitate RNA < 200 nt.
Sequencing libraries were prepared from biotinylated RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (without additional fragmentation) and NEBNextMultiplex Oligos for Illumina (Unique Dual Index UMI adapters RNA Set 1) and were sequenced on the NextSeq 2000 (P3 50 kit).

treatment_protocol: RPB1 degron cells were seeded at a density of 4 million cells in a 10cm plate and were either treated with DMSO or different concentrations of dTAGv-1 for 16 hours before harvest. After 12.5 hours, transcription was synchronized by the addition of 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hours, followed by a release from DRB inhibition for 15, 30, or 45 minutes prior to harvest. During the final 10 minutes prior to harvest, cells were pulsed for 1mM 4-thiouridine, to metabolically label nascently transcribed RNA.

value: 125nM dTAGv1; 100uM DRB for 3.5hr


title: AB18251.txt

description: Library name: Sample 181


title: mESC, WT, Wdr5 ChIP-seq, rep1

description:
Library name: Wdr5_WT_Rep1
ChIP antibody Wdr5


title: Full-length human ETS1 W356C

type: protein

first: Yuval

last: Bayer

address: Herzl St 234

description: Measurements were done in chamber 1

hyb_protocol: Microarray was double-stranded using Thermo Sequenase polymerase and primers.

scan_protocol: GenePix 4400A array scanner uses 450, 600, and 800 gain for multiple scans.

data_processing: For each probe area, calculate the median of pixels as intensity. Apply linear regression to combine different gain scans and then use a moving window to remove spatial correlation. Finally, we standardized the normalized values by subtracting the mean and dividing by the standard deviation.

source_name: E coli

label_protocol: GST-tag mouse mAb Alexa Fluor.

extract_protocol: Expressed in E coli.

tag: tag

value: GST-tagged protein


title: AB18252.txt

description: Library name: Sample 182


title: RPB1degron_125nM_45min_DRB_release_2

description: Library name: 125nM_45min_DRB_release_2


title: mESC, HD, Wdr5 ChIP-seq, rep2

description:
Library name: Wdr5_HD_Rep2
ChIP antibody Wdr5

value: 1,6 HD treatment


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040100

description: Library name: OP23YS040399

data_processing:
Raw sequencing reads were quality-checked using FastQC. Adapter trimming was performed using Trimmomatic.
Trimmed reads were aligned to the human reference genome (GRCh38) using STAR aligner with default parameters.
Gene-level quantification was performed using featureCounts based on GENCODE annotations.
Expression values were normalized to TPM, log2-transformed, and compiled into a processed expression matrix.
All processed data are provided in a matrix format where rows represent genes and columns represent samples.
Assembly: GRCh38 (GENCODE v38 annotation)
Supplementary files format and content: Processed data files are in CSV format and contain TPM-log2 normalized expression values. Each row represents a gene, and each column represents a sample. File name: YUHS_TPM_EXPR_Biopsy_processed.csv
Supplementary files format and content: Gene symbols are used as row names; expression values are log2(TPM + 1) transformed.

extract_protocol:
Total RNA was extracted from frozen biopsy tissues using the Qiagen RNeasy Mini Kit, following the manufacturer's protocol. On-column DNase I treatment was included to remove genomic DNA contamination.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Poly-A selection was used to enrich for mRNA. Libraries were quantified using Qubit and Bioanalyzer.

value: prostate


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040105

description: Library name: OP23YS040028


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040099

description: Library name: OP24YS040094


title: RPB1degron_DMSO_HA_3

description: Library name: DMSO_HA_3


title: AB18250.txt

description: Library name: Sample 180


title: RPB1degron_125nM_45min_DRB_release_1

description: Library name: 125nM_45min_DRB_release_1


title: mESC, HD, Wdr5 ChIP-seq, rep1

description:
Library name: Wdr5_HD_Rep1
ChIP antibody Wdr5


title: AB18249.txt

description: Library name: Sample 179


title: AB18253.txt

description: Library name: Sample 183


title: mESC, Ctrl, Wdr5 ChIP-seq, rep2

description:
Library name: Wdr5_Ctrl_Rep2
ChIP antibody Wdr5

value: Control


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040098

description: Library name: OP23YS040394


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040101

description: Library name: OP23YS040070


title: mESC, Ctrl, Wdr5 ChIP-seq, rep1

description:
Library name: Wdr5_Ctrl_Rep1
ChIP antibody Wdr5


title: RPB1degron_125nM_30min_DRB_release_2

description: Library name: 125nM_30min_DRB_release_2


title: AB18248.txt

description: Library name: Sample 178


title: mESC, WT, Wdr5 ChIP-seq, rep2

description:
Library name: Wdr5_WT_Rep2
ChIP antibody Wdr5


title: AB18247.txt

description: Library name: Sample 177


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040097

description: Library name: OP23YS040037


title: RPB1degron_125nM_30min_DRB_release_1

description: Library name: 125nM_30min_DRB_release_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040096

description: Library name: OP23YS040410


title: RPB1degron_125nM_30min_DRB_release_3

description: Library name: 125nM_30min_DRB_release_3


title: RPB1degron_125nM_15min_DRB_release_3

description: Library name: 125nM_15min_DRB_release_3


title: AB18246.txt

description: Library name: Sample 176


title: EGR1 DBD

description: Measurements were done in chamber 2


title: mESC, input, rep1

description:
Library name: Nanog_Input_Rep1
none


title: AB18245.txt

description: Library name: Sample 175


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040095

description: Library name: OP23YS040291


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040094

description: Library name: OP24YS040088


title: AB18244.txt

description: Library name: Sample 174


title: RPB1degron_125nM_15min_DRB_release_1

description: Library name: 125nM_15min_DRB_release_1


title: mESC, input, rep2

description:
Library name: Nanog_Input_Rep2
none


title: mESC, R153A, Nanog ChIP-seq, rep1

description:
Library name: Nanog_R153A_Rep1
ChIP antibody Nanog


title: AB18242.txt

description: Library name: Sample 172


title: mESC, WT, Nanog ChIP-seq, rep2

description:
Library name: Nanog_WT_Rep2
ChIP antibody Nanog


title: RPB1degron_62nM_45min_DRB_release_3

description: Library name: 62nM_45min_DRB_release_3

value: 62nM dTAGv1; 100uM DRB for 3.5hr


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040091

description: Library name: OP23YS040032


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040093

description: Library name: OP23YS040390


title: AB18243.txt

description: Library name: Sample 173


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040092

description: Library name: OP23YS040128


title: AB18241.txt

description: Library name: Sample 171


title: mESC, HD, Nanog ChIP-seq, rep2

description:
Library name: Nanog_HD_Rep2
ChIP antibody Nanog


title: RPB1degron_62nM_45min_DRB_release_1

description: Library name: 62nM_45min_DRB_release_1


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040090

description: Library name: OP23YS040284


title: AB18240.txt

description: Library name: Sample 170


title: RPB1degron_62nM_45min_DRB_release_2

description: Library name: 62nM_45min_DRB_release_2


title: mESC, WT, Nanog ChIP-seq, rep1

description:
Library name: Nanog_WT_Rep1
ChIP antibody Nanog


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040089

description: Library name: OP23YS040094


title: AB18239.txt

description: Library name: Sample 169


title: mESC, HD, Nanog ChIP-seq, rep1

description:
Library name: Nanog_HD_Rep1
ChIP antibody Nanog


title: RPB1degron_62nM_30min_DRB_release_3

description: Library name: 62nM_30min_DRB_release_3


title: mESC, Ctrl, Nanog ChIP-seq, rep2

description:
Library name: Nanog_Ctrl_Rep2
ChIP antibody Nanog


title: AB18238.txt

description: Library name: Sample 168


title: RPB1degron_62nM_30min_DRB_release_2

description: Library name: 62nM_30min_DRB_release_2


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040088

description: Library name: OP23YS040296


title: RPB1degron_125nM_15min_DRB_release_2

description: Library name: 125nM_15min_DRB_release_2


title: mESC, R153A, Nanog ChIP-seq, rep2

description:
Library name: Nanog_R153A_Rep2
ChIP antibody Nanog


title: RPB1degron_62nM_30min_DRB_release_1

description: Library name: 62nM_30min_DRB_release_1


title: mESC, Ctrl, Nanog ChIP-seq, rep1

description:
Library name: Nanog_Ctrl_Rep1
ChIP antibody Nanog


title: AB18237.txt

description: Library name: Sample 167


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040087

description: Library name: OP23YS040294


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040086

description: Library name: OP23YS040405


title: RPB1degron_62nM_15min_DRB_release_3

description: Library name: 62nM_15min_DRB_release_3


title: Bulk RNA-seq of prostate adenocarcinoma biopsy sample OP24YS040085

description: Library name: OP24YS040085


title: AB18236.txt

description: Library name: Sample 166


title: mESC, R153A, H4K16ac ChIP-seq, rep2

description:
Library name: H4K16ac_R153A_Rep2
ChIP antibody H4K16ac


title: mESC, R153A, H4K16ac ChIP-seq, rep1

description:
Library name: H4K16ac_R153A_Rep1
ChIP antibody H4K16ac


title: RPB1degron_62nM_15min_DRB_release_2

description: Library name: 62nM_15min_DRB_release_2


title: Single-cell RNA-seq of metastatic prostate cancer sample M5

description:
Library name: M5
Single-cell RNA-seq from metastatic prostate cancer biopsy sample M5 using 10x Genomics 3??v3 kit.

data_processing:
Raw BCL files were demultiplexed and converted to FASTQ using Cell Ranger mkfastq.
FASTQ files were aligned to the GRCh38 human reference genome and gene-barcode matrices were generated using Cell Ranger count.
Gene expression matrices were loaded into Seurat. Cells with <500 or >7500 detected genes or >15% mitochondrial content were filtered out.
Gene expression data were log-normalized, and dimensionality reduction (PCA, UMAP), clustering, and batch correction were performed using Seurat v5.
Cell type annotation was performed using canonical marker genes and SingleR referencing HumanPrimaryCellAtlasData and DICE.
Assembly: GRCh38
Supplementary files format and content: expression_matrix_data1.csv: log-normalized gene expression matrix (rows = genes, columns = cells).
Supplementary files format and content: cell_metadata.csv: cell-level metadata including sample ID, cluster, cell type, QC metrics.

source_name: metastatic prostate tumor

growth_protocol: Not applicable. Biopsy samples were processed immediately after collection without in vitro culturing.

extract_protocol:
Fresh metastatic prostate cancer biopsy tissues were enzymatically dissociated into single-cell suspensions using a tissue dissociation kit (e.g., Miltenyi). Cells were filtered, counted, and loaded onto the 10x Genomics Chromium controller.
Single-cell RNA libraries were generated using the 10x Genomics Chromium Single Cell 3’ v3 kit according to the manufacturer’s protocol. Libraries were sequenced on the Illumina NovaSeq 6000 platform with 2×101 bp paired-end reads.

treatment_protocol: None. Patients did not receive treatment prior to metastatic lesion biopsy.

value: metastatic prostate tumor

value: multiple


title: AB18235.txt

description: Library name: Sample 165


title: Single-cell RNA-seq of metastatic prostate cancer sample M4

description:
Library name: M4
Single-cell RNA-seq from metastatic prostate cancer biopsy sample M4 using 10x Genomics 3??v3 kit.


title: mESC, WT, H4K16ac ChIP-seq, rep2

description:
Library name: H4K16ac_WT_Rep2
ChIP antibody H4K16ac


title: mESC, WT, H4K16ac ChIP-seq, rep1

description:
Library name: H4K16ac_WT_Rep1
ChIP antibody H4K16ac


title: AB18234.txt

description: Library name: Sample 164


title: AB18233.txt

description: Library name: Sample 163


title: RPB1degron_32nM_45min_DRB_release_3

description: Library name: 32nM_45min_DRB_release_3

value: 32nM dTAGv1; 100uM DRB for 3.5hr


title: AB18232.txt

description: Library name: Sample 162


title: RPB1degron_32nM_45min_DRB_release_2

description: Library name: 32nM_45min_DRB_release_2


title: Single-cell RNA-seq of metastatic prostate cancer sample M3

description:
Library name: M3
Single-cell RNA-seq from metastatic prostate cancer biopsy sample M3 using 10x Genomics 3??v3 kit.


title: AB18231.txt

description: Library name: Sample 161


title: RPB1degron_32nM_45min_DRB_release_1

description: Library name: 32nM_45min_DRB_release_1


title: mESC, R153A, H3K4me3 ChIP-seq, rep2

description:
Library name: H3K4me3_R153A_Rep2
ChIP antibody H3K4me3


title: mESC, WT, H3K4me3 ChIP-seq, rep2

description:
Library name: H3K4me3_WT_Rep2
ChIP antibody H3K4me3


title: RPB1degron_32nM_30min_DRB_release_3

description: Library name: 32nM_30min_DRB_release_3


title: mESC, R153A, H3K4me3 ChIP-seq, rep1

description:
Library name: H3K4me3_R153A_Rep1
ChIP antibody H3K4me3


title: AB18230.txt

description: Library name: Sample 160


title: Single-cell RNA-seq of metastatic prostate cancer sample M1

description:
Library name: M1
Single-cell RNA-seq from metastatic prostate cancer biopsy sample M1 using 10x Genomics 3??v3 kit.


title: RPB1degron_32nM_30min_DRB_release_2

description: Library name: 32nM_30min_DRB_release_2


title: mESC, WT, H3K4me3 ChIP-seq, rep1

description:
Library name: H3K4me3_WT_Rep1
ChIP antibody H3K4me3


title: RPB1degron_62nM_15min_DRB_release_1

description: Library name: 62nM_15min_DRB_release_1


title: AB18229.txt

description: Library name: Sample 159


title: UT2105,sEOAD, snMultiome [GEX]

city: Houston

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St.

institute: The University of Texas Health Science Center at Houston

description: 10x Genomics

data_processing:
Cell Ranger ARC (v2.0.2) pipeline was used for aligning the snRNA-seq and snATAC-seq reads from each sample to the GRCh38 genome and quantifying them with ‘cellranger-arc count’.
Assembly: GRCh38
Supplementary files format and content: CellRanger-arc output files: raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: Prefrontal cortex

extract_protocol:
Samples were stored at -80 °C. The nuclei isolation protocol was modified based on a 10x Genomics protocol (CG000375). Briefly, 30 mg of frozen tissue was finely minced on dry ice to the smallest possible size, and then it was homogenized in homogenization buffer on ice within 20 minutes. The homogenized tissue was filtered through a 35 μm cell strainer. Small cell debris were removed by centrifuging at 300g for 3 minutes at 4 °C. The large cell debris was removed by gradient centrifugation using OptiPrep density gradient medium (Sigma, cat#D1556-250ML) at 7200g for 15 minutes at 4 °C. The nuclei pellet was resuspended in a 0.1x lysis buffer. After washing the isolated nuclei in the wash buffer, the nuclei were resuspended in 1x nuclei buffer before single-nuclei Multiome library construction. (UTHealth Cancer Genomic Core)
single-nuclei Multiome sequencing; Single-nuclei libraries were constructed following the 10x Chromium Single Cell Multiome ATAC + Gene Expression protocol (CG000338).

value: Prefrontal cortex

tag: disease state

value: sEOAD

value: M

tag: age on_death

tag: pmi (hours)


title: mESC, R153A, RNA-seq, rep-3

description: Library name: Nanog_R153A_3

data_processing:
Alignment was done by Bowtie2 (v2.3.4.3).
Sorting was done by name using Samtools (v1.9)
Count was done by Htseq (v0.11.2)
Normalization was done by using edgeR (v3.26.8)
Differentially expressed genes (DEGs) were identified based on a or |fold change| ≥2, p< 0.05
Assembly: mm9
Supplementary files format and content: FPKM values for transcripts
Supplementary files format and content: Matrix table with normalized expression levels for every gene and every sample

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Library construction and sequencing were performed by BGI Tech (Shenzhen, China)

value: mouse embryonic stem cells

tag: genotype


title: RPB1degron_32nM_30min_DRB_release_1

description: Library name: 32nM_30min_DRB_release_1

value: RPB1 degron D4

tag: treatment


title: AB18228.txt

description: Library name: Sample 158

tag: tissue


title: UT09,sEOAD, snMultiome [GEX]

description: 10x Genomics

tag: Sex


title: mESC, R153A, RNA-seq, rep-2

description: Library name: Nanog_R153A_2

tag: cell type


title: mESC, R153A, RNA-seq, rep-1

description: Library name: Nanog_R153A_1


title: UT04,sEOAD, snMultiome [GEX]

description: 10x Genomics


title: Single-cell RNA-seq of metastatic prostate cancer sample M2

first: Baek Gil

last: Kim

description:
Library name: M2
Single-cell RNA-seq from metastatic prostate cancer biopsy sample M2 using 10x Genomics 3??v3 kit.


title: RPB1degron_32nM_15min_DRB_release_2

description: Library name: 32nM_15min_DRB_release_2


title: AB18227.txt

description: Library name: Sample 157


title: AB18226.txt

description: Library name: Sample 156


title: RPB1degron_32nM_15min_DRB_release_1

description: Library name: 32nM_15min_DRB_release_1


title: UT2105,sEOAD, snMultiome [ATAC]

description: 10x Genomics

library_source: genomic single cell


title: mESC, WT, RNA-seq, rep-2

description: Library name: Nanog_WT_2

value: Wild type

value: WT


title: RPB1degron_DMSO_45min_DRB_release_3

description: Library name: DMSO_45min_DRB_release_3

value: DMSO; 100uM DRB for 3.5hr


title: mESC, WT, RNA-seq, rep-3

description: Library name: Nanog_WT_3


title: AB18225.txt

description: Library name: Sample 155


title: UT04,sEOAD, snMultiome [ATAC]

description: 10x Genomics


title: mESC, WT, RNA-seq, rep-1

description: Library name: Nanog_WT_1


title: RPB1degron_DMSO_45min_DRB_release_2

description: Library name: DMSO_45min_DRB_release_2


title: AB18223.txt

description: Library name: Sample 153


title: AB18224.txt

description: Library name: Sample 154


title: NAMALWA_1k_1D_B_rep3

first: Zejia

last: Cui

address: Yiheyuan Road

institute: Peking University

data_processing:
*library strategy: SCOPTE-C
The preprocessing of SCOPE-C reads was similar to the Hi-C data. Firstly, the raw reads of the SCOPE-C two libraries, 150-200 bp short fragments (marked as B) and 200-700 bp long fragments (marked as A), were filtered by Cutadapt v2.6 and pre-processed using HiC-Pro v2.11.4. In brief, clean reads were mapped to the reference genomes (hg19 for human, rheMac10 for macaque, and mm10 for mouse) with bowtie2 v2.3.5. If a read pair locates in the same restriction fragment (DpnII), it was classified as dangling ends (inward), dumped pairs (same strand), or self-cycled (outward). We only retained dangling ends of two libraries combined which were less than 100 bp, they represented the openness of chromatin. Then, the uniquely aligned dangling ends were used to call peak by MACS2 v2.2.5 with “macs2 callpeak --keep-dup all -q 0.01 --extsize 200 --shift 100 --nomodel” options. If read pairs that mapped to two different restriction fragments, they were considered valid pairs and generated interaction heatmaps. Similarly, we merged the valid pairs of two libraries to generate 500 kb, 50 kb, and 25 kb bin size interaction matrixes. The 500 kb matrix was used to define AB compartments by R package HiTC (https://code.bioconductor.org/browse/HiTC/). The 50 kb matrix was used to identify TAD boundaries by matrix2insulation.pl (https://github.com/blajoie/crane-nature-2015). Finally, we used the model in Fit-Hi-C to calculate the statistical significance interactions with the 25 kb matrix. Significant loops were then selected by Fit-Hi-C reported Q value (Q < 0.00001).
Assembly: hg19,mm10,rheMac10
Supplementary files format and content: bigwig,narrowPeak
Supplementary files format and content: bedpe,hic

source_name: lymphoma

growth_protocol: Human B lymphoid cells (GM12878), human chronic myeloid leukemia cells (K562) and human Burkitt’s lymphoma cells (NAMALWA) were cultured in the medium (RPMI 1640; Thermo Fisher, 11875093) containing 10% fetal bovine serum, 100 units/mL penicillium and 100 μg/mL streptomycin.Human HeLa-S3 cell line (HeLa) were cultured in the medium (DMEM; Thermo, C11995500BT) containing 10% fetal bovine serum (FBS; Gibco, 10099141), 100 units/mL penicillium and 100 μg/mL streptomycin (Thermo Fisher, 15140122).Mouse ES cells (mESCs) were cultured on 0.1% gelatin (BD, 214340) pre-coated dishes in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, 11995065) containing 15% fetal bovine serum, 100 units/mL penicillium and 100 μg/mL streptomycin, leukemia-inhibiting factor (LIF) (Millipore, ESG1107), GlutaMAX (Thermo Fisher, 35050061), nucleoside mix (Adenosine, Sigma, A4036; Guanosine, Sigma, G6264;Uridine, Sigma, U3003; Cytidine, Sigma, C4654; Thymidine, Sigma, T1895), β-mercaptoethanol (β-ME; Sigma, M6250), and non-essential amino acids (NEAA; 100X, Gibco, 11140050).Mouse Neural Stem Cells (mNSCs) was performed as previously described (Dongchang Xiao et al., 2018). mNSCs were cultured in the NSC medium containing the N3 medium supplemented with 10 ng/ml recombinant mouse EGF (R&D systems) and 10 ng/ml recombinant human bFGF (R&D Systems), with or without 2 ng/ml Dox (Sigma). The N3 medium contains DMEM/F12 (Life Technologies) with 1x Pen/Strep, 25 μg/ml insulin (Sigma), 50 μg/ml Apo-transferrin (Sigma), 1.28 ng/ml progesterone (Sigma), 16 ng/ml putrescine (Sigma), and 0.52 μg/ml sodium selenite (Sigma). The SCR029 cells were cultured in the Neural Stem Cell Expansion Medium (Chemicon, SCM003) supplemented with 20 ng/ml mouse EGF, 20 ng/ml human bFGF, and 2 μg/ml heparin (Sigma).

extract_protocol:
DNA purification by Phenol-chloroform extraction assay, and biotin Pull-down by Dynabeads Streptavidin T1 beads (Life technologies, 65602) with 100 μL of 1X Tween Washing Buffer twice (1X TWB: 5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20). Separate on a magnet and discard the solution. Resuspend the beads in 25 μL of 2X Binding Buffer (2X BB: 10 mM Tris-HCl (pH 7.5); 1 mM EDTA; 2 M NaCl) and add to the DNA elution. Incubate at room temperature for 15 min. Separate on a magnet and discard the solution. Wash the beads by adding 100 μL of 1X TWB and transferring the mixture to a new tube. Heat the tubes on a Thermomixer at 55℃for 2 min with mixing. Reclaim the beads using a magnet. Discard supernatants.
Construction of the SCOPE-C library for sequencing includes crosslinking and lysis, restriction and digestion, biotin–dATP labeling, proximity ligation, open chromatin fragmentation, DNA purification and biotin pull-down, library construction. Subsequent Biotin Pull-down by Dynabeads Streptavidin T1 beads, SCOPE-C DNA was resuspended in 19 μL of ddH2O. Add 33 μL PCR mix, 25 μL 2X NEB Q5 HiFi Hot Start PCR Master Mix, 2.5 μL universal primer, 2.5 μL indexed primer. PCR-amplifies the libraries for 16 cycles. Run the PCR product directly on a 1.5% long gel. Cut the band from the gel, isolating the size of 150-200 bp and 200-500 bp and extract DNA with MinElute Gel Extraction Kit (Qiagen, 28604), respectively. Quantify the concentration with qubit 4.0.

value: lymphoma

value: NAMALWA

value: human Burkitt lymphoma cell line

value: wild type


title: RPB1degron_DMSO_45min_DRB_release_1

description: Library name: DMSO_45min_DRB_release_1


title: NAMALWA_1k_3D_A_rep3

description: allNAM_intraOnly.spline_pass1.res25000.significances.loop.bedpe


title: RPB1degron_32nM_15min_DRB_release_3

description: Library name: 32nM_15min_DRB_release_3


title: AB18222.txt

description: Library name: Sample 152


title: RPB1degron_DMSO_30min_DRB_release_3

description: Library name: DMSO_30min_DRB_release_3


title: D21 4F mini-oocyte rep2

description:
Library name: Sample 4
RNA-seq

data_processing:
The first three bases of read 2 derived from the SMART-seq stranded adaptor were removed using Trim Galore! with a ‘–clip_R2 3’ option. After the reads were aligned to the mouse genome (mm10) using Hisat2, the reads correspond to rRNA were removed by using Bedtools intersectBed function. The uniquely mapped reads were isolated by using the tag NH:i:1. featureCounts and Gencode annotation of the mm10 mouse genome (vM25) were used to analyze transcription level with options ‘-p -O --fraction’. TPM was calculated by counting reads mapped to the exon.
Assembly: mm10
Supplementary files format and content: text file indicating TPM values

extract_protocol:
4F- or 8F-mESCs routinely cultured were detached from culture plates by 1× TrypLE solution (Thermo), and the detached cells were thoroughly dissociated into single cells by pipetting. The cell suspension was then transferred to tubes containing Wash medium [DMEM/F12 (Nacalai) supplemented with 7.5% BSA (Thermo)]. The cell suspension was centrifuged at 200 × g for 3 min at room temperature, and the supernatant was discarded. The cell pellet was resuspended in an appropriate volume of S10 medium supplemented with SCF, Y-27632, and Shield1. The cell suspension was added to the pre-coated culture plates in the desired amount, ensuring even distribution of cells (regarded as day 0). 3 × 104 cells were typically plated per well in a 24-well plate. The medium was replaced every 72 hours, with half of the medium exchanged for freshly prepared S10 medium containing SCF, Y-27632, and Shield. Starting from day 12, Shield1 was omitted from the fresh medium.
SMART-seq stranded kit (TAKARA) was used.

tag: strain

value: hybrid 129/C57BL6

value: Embryonic stem cell

value: Forced expression of 4 TFs

value: Day 21


title: NAMALWA_1k_1D_B_rep2


title: AB18221.txt

description: Library name: Sample 151


title: RPB1degron_DMSO_30min_DRB_release_2

description: Library name: DMSO_30min_DRB_release_2


title: D21 4F mini-oocyte rep1

description:
Library name: Sample 3
RNA-seq


title: UT09,sEOAD, snMultiome [ATAC]

description: 10x Genomics

value: Control


title: NAMALWA_1k_3D_A_rep2


title: AB18219.txt

description: Library name: Sample 149


title: FID-D3 trt3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina NovaSeq 6000-S4 was used to sequence the libraries for 2 x 150 cycles
The genome of Mus musculus (version GRC38, mm10) from the Ensembl database was used as the reference sequences for RNA-seq analysis
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis
The cleaned reads of each sample were mapped to the reference sequences using the read mapper of the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a). The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2)70 samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates and count uniquely mapped reads for gene expression analysis
PCA analysis (for detecting outlier samples) and volcano plot analysis based on all identified genes in each analysis were performed with the R-package (v4.1.3). The gene expressions were analyzed by a DESeq2-based R pipeline. Genes were considered differentially expressed if the log2 fold change was > |1| and if the adjusted P-value was < 0.01. Bowtie2 (version 2.5.4) was used for searching gene and exon for each sample
Assembly: Mus musculus (version GRC38, mm10)
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

source_name: skeletal muscle

growth_protocol: Mice were housed under a 12hrs/12hrs day/night cycle and had ad libitum access to food and water

extract_protocol:
total RNA was isolated using Trizol Reagent (15596026, Thermo Fisher) according to the manufacturer’s protocol. RNA from primary FAPs was extracted with Qiagen RNeasy Micro Kit (74004, Qiagen) following manufacturer’s protocol.
RNA-seq libraries were constructed at the ICBR Gene Expression and Genotyping Core Lab using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, United States) following the manufacturer’s recommendations. A total of 1000 ng samples of RNA with RNA integrity numbers (RIN) greater than 5.6 were used

treatment_protocol: Tamoxifen (TAM) dissolved in corn oil was delivered via intraperitoneal (IP) injection to mice at 12-13 weeks of age for 5 consecutive days (100ug/g body weight). five times the amount of body weight (g) in microliters of tamoxifen (TAM) mixed in corn oil (20mg/mL). At least 1 week between the final TAM injection and subsequent experiments was done to allow washout of TAM. Both male and female mice were used as indicated in each experiment.

value: skeletal muscle

value: muscles were embedded in OCT and then frozen in melting 2-methylbutane cooled by liquid nitrogen


title: RPB1degron_DMSO_30min_DRB_release_1

description: Library name: DMSO_30min_DRB_release_1


title: NAMALWA_1k_1D_B_rep1


title: AB18218.txt

description: Library name: Sample 148


title: FID-D3 trt1


title: AB18217.txt

description: Library name: Sample 147


title: K562_1k_1D_B_rep3

source_name: bone marrow

value: bone marrow

value: lymphoblast cell line


title: RPB1degron_DMSO_15min_DRB_release_1

description: Library name: DMSO_15min_DRB_release_1

value: RPB1 degron D4


title: Control-D3 ctr3


title: D21 4F mini-oocyte rep3

first: Mizuki

last: Sakamoto

description:
Library name: Sample 5
RNA-seq


title: AB18216.txt

description: Library name: Sample 146


title: K562_1k_3D_A_rep3

description: allK562_intraOnly.spline_pass1.res25000.significances.loop.bedpe