title: HIRA_CNT_1

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: DAXX_CNT_2

status: Public on Nov 02 2023

type: SRA

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

country: USA

institute: University of Florida

description: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, rep2

library_source: genomic

data_processing:
Reads were mapped to the GRCh38 human genome reference using Bowtie2.
ATAC peak calling was performed with MACS v2.2.7.1. with parameters appropriate for ATAC-Seq data.
Assembly: GRCh38
Supplementary files format and content: MACS output file containing peak locations and fold enrichment.

molecule: genomic DNA

organism: Homo sapiens

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO

growth_protocol: Cells were propogated in RPMI-1640 medium suplemented with 10% FBS, 1X penicillin/streptomycin at  5% CO2, 37C . Cells were plated in RPMI-1640 without phenol-red, suplemented with 10%CSS, 72 h before the experiment.

extract_protocol:
Samples were prepared using ATAC-seq kit from Active Motif (Active Motif, CA, #53150) according to the manual.
Samples were prepared using ATAC-seq kit from Active Motif (Active Motif, CA, #53150) according to the manual.

treatment_protocol: Cells were treated with 1 nM R1881 for 4 or 12 h

tag: cell line

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

tag: cell type

value: Prostate cancer

tag: genotype

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

tag: treatment

value: EtOH


title: Mouse, Ctrl 5 (ATAC-seq)

city: Shanghai

first: Anxiang

last: Cai

state: None Selected

address: No.1630 dongfang road, pudong new district

country: China

institute: Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China

data_processing:
Library quality was checked using the High Sensitivity DNA Analysis Kit (Agilent, 5067-4626). Last, 2 X 150 paired-end sequencing was performed on an Illumina Nova seq (Illumina, San Diego, CA).
Alignment and peak-calling of ATAC sequencing data were performed using the ENCODE-DCC ATAC-Seq pipeline. Briefly, data were aligned to the mouse reference genome (mm10) using Bowtie2. Aligned data were filtered for PCR duplicates, blacklisted regions, and shifted +4bp for the + strand and -5bp for the - strand. Peaks were called using MACS2. Differential peak calling was performed using Diffbind. Motif enrichment was performed using Hypergeometric Optimization of the Motif EnRichment program (HOMER) version 4.1.
Assembly: mm10
Supplementary files format and content: bed, MACS calling peaks

organism: Mus musculus

source_name: Kidney

extract_protocol:
Briefly, a total of 20,000 cells per sample was washed twice with 50 µL of cold Dulbecco's Phosphate-Buffered Saline and re-suspended in 50 µL of lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 µL of transposition reaction mix of TruePrep DNA Library Prep Kit V2 for Illumina. Samples were then incubated at 37°C for 30 min. DNA was isolated using the QIAquick PCR Purification Kit (QIAGEN, 28106).
ATAC-seq libraries were first subjected to five cycles of pre-amplification using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, M0541S). To determine the suitable number of cycles required for the second round of PCR, the library was assessed by qPCR using NEBNext High-Fidelity 2X PCR Master Mix with SYBR Green I Nucleic Acid Gel Stain (Thermo Fisher Scientific, S7563) and then PCR amplified for the appropriate number of cycles. Libraries were purified with the QIAquick PCR Purification Kit.

tag: tissue

value: Kidney

value: WT

value: Normal


title: AR_CNT_2

description: R1-AD1 FLAGHA-H3F3A cells, AR KO, rep2

source_name: R1-AD1 FLAGHA-H3F3A, AR KO

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: DAXX_CNT_1

description: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, rep1


title: Mouse, Db 1 (ATAC-seq)

value: db/db


title: AR_CNT_1

description: R1-AD1 FLAGHA-H3F3A cells, AR KO, rep1


title: Mouse, Ctrl 4 (ATAC-seq)


title: IC4_CNT_2

description: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 2

source_name: R1-AD1 FLAGHA-H3F3A

value: R1-AD1 FLAGHA-H3F3A

value: Prostate cancer cells

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: Mouse, Ctrl 1 (ATAC-seq)


title: IC4_CNT_1

description: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 1


title: Mouse, Ctrl 3 (ATAC-seq)


title: Mouse, Ctrl 2 (ATAC-seq)


title: Mouse, Db 12

library_source: transcriptomic

data_processing:
Purified libraries were quantified by Qubit 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. The clusters were generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
For each sample, 33-95M RNA-sequencing (RNA-seq) clean reads were obtained that mapped to the mouse reference genome (mm10) using hierarchical indexing for spliced alignment of transcripts (HISAT2) v2.0.477. Sequencing read counts were calculated using Stringtie78,79 (v.1.3.0). Then, expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method.
Assembly: mm10
Supplementary files format and content: Excel for all expressed RNA includes all counts and FPKM value

molecule: total RNA

extract_protocol:
Total RNA was isolated using an RNeasy mini kit (Qiagen, Germany).
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA), following the manufacturer's instructions. Briefly, mRNA was enriched with oligo(dT) beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first-strand cDNA using reverse transcriptase and random primers. This is followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, adding a single'A'base, and then ligating the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

value: Dapagliflozin


title: Mouse, Db 10


title: Mouse, Db 8


title: NL3_SM_TGF

city: GRAND RAPIDS

first: Xiaopeng

last: Li

state: MI

address: 400 Monroe Ave NW

department: Pediatrics & Human Development

institute: Michigan State University

data_processing:
RNA-Seq reads were mapped on Hg38 transcriptome using the ENSEMBL GRCh38.p3 annotation with the STAR aligner
Normalized count was obtained from the STAR aligner
Assembly: UCSC human reference genome (hg38)
Supplementary files format and content: CSV file includes human ensembl_gene_id and normalized counts (TPM) for each gene in individual samples. Combatseq was used for batch correction.

source_name: Small Airways

growth_protocol: The small airways were micro-dissected from all  lung explant and digested in a buffer containing protease from Streptomyces griseus, (P5147, Millipore-Sigma), 1X Gentamicin, (15750060, Gibco), 1X penicillin/streptomycin, (15140122, Gibco), and DNase I (10104159001, Millipore-Sigma). Epithelial cells were isolated and expanded by culturing with PneumaCult™-Ex Plus Medium, (05040, STEMCELL Technologies), at 37°C, 5% CO2, for approximately 1 week of expansion.

extract_protocol:
RNA was extracted using the RNeasy plus mini kit (Qiagen).
cDNA libraries for RNA-seq were prepared  by the Genomics Core at the Van Andel Institute. cDNA was synthesized from the isolated RNA samples using the SuperScript™ IV VILO™ Master Mix (11756050, Invitrogen) with ezDNase enzyme treatment according to the manufacturer’s protocol. cDNA concentration was quantified and diluted to 1 µg/µL. Individual master mixes for each gene of interest were prepared using the TB Green® Premix Ex Taq II (TLi RNaseH Plus) reagent kit (RR820A, Takara Bio) and primer sets ordered from Sigma-Aldrich. Each master mix contained a 1X concentration of TB Green® Premix Ex Taq II (TLi RNaseH Plus), 0.4µM of forward and reverse primers, and nuclease-free water. To each well of a 96-well PCR plate (AB-0600-L, Thermo Scientific), 18 µL of the prepared master mix was added, followed by 2 µL of template cDNA. The reaction was carried out using the CFX96™ Real-Time System (Bio-Rad) using the following settings: a holding stage of 30 seconds at 95°C, followed by 40 cycles of 95°C for 5 seconds and 60°C for 30 seconds, and ending with the melt curve stage. The instrument software from Bio-Rad was used to quantify the results.
Sequencing was performed by 2 × 150 bp paired-end read format.

treatment_protocol: The cells were cultured at the air-liquid interface (ALI), with or without TGF-beta, for 2-3 weeks before being collected for experimentation.

tag: disease state

value: Healthy Donor Lung

value: Small Airways

value: TGFB

tag: time

value: 2-3 weeks

tag: replicates


title: NL2_SM_TGF


title: Mouse, Db 7


title: NL1_SM_CTL

description: Batch 1

value: Control


title: NL2_SM_CTL

description: Batch 1


title: Mouse, Db 6


title: COV3_SM_TGF

description: Batch 2

value: post COVID19 Fibrosis Lung


title: Mouse, Db 5


title: COV2_SM_TGF

description: Batch 2


title: Mouse, Db 4


title: COV1_SM_TGF

description: Batch 2


title: COV3_SM_CTL

description: Batch 2


title: Mouse, Db 2


title: Mouse, Db 1


title: Mouse, Ctrl 5


title: Mouse, Db 11


title: COV1_SM_CTL

description: Batch 2


title: IPF2_SM_TGF

description: Batch 1

value: IPF Lung


title: IPF1_SM_TGF

description: Batch 1


title: IPF3_SM_TGF

description: Batch 1


title: Mouse, Ctrl 2

value: Kidney


title: Mouse, Db 9


title: NL3_SM_CTL

description: Batch 1


title: COV2_SM_CTL

description: Batch 2


title: Mouse, Ctrl 1

value: WT


title: IPF1_SM_CTL

description: Batch 1


title: NL1_SM_TGF

description: Batch 1


title: IPF3_SM_CTL

description: Batch 1


title: Mouse, Db 3

value: Normal


title: Adult48-Hipp-H4, Female, GH

city: Galway

first: Aodan

last: Laighneach

address: University Rd.

country: Ireland

institute: University of Galway

data_processing:
Raw reads were trimmed using trimmomatic v0.39 (parameters: LEADING:3, TRAILING:3, MINLEN:36)
Trimmed reads were quasi-mapped to the GRCm39/mm39 transcriptome and quantified using salmon v1.8.0
DESeq2 v1.24.0 was used to perform normalisation and differential expression
Assembly: mm39
Supplementary files format and content: Tab-deliminated text (.txt) file with raw counts for each sample

source_name: brain

extract_protocol:
Total RNA was extracted from frozen hippocampus using the Absolutely RNA Miniprep kit (Agilent; product code: #400800) following appropriate standard procedure for quantity of tissue.
Library preparation was performed by Genewiz Germany GmbH (Leipzig, Germany) using Illumina kits selecting for mRNA with PolyA selection

value: brain

tag: brain region

value: hippocampus

tag: Sex

value: Female

value: Group Housed


title: IPF2_SM_CTL

description: Batch 1


title: H1299 12 h 5 uM BRM014 rep 1

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
Reads were trimmed for a minimum quality score of 20 Using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE) reads were trimmed for a minimum quality score of 20 prior to trimming adapater sequences using cutadapt (v1.14). Reads were then first mapped to ERCC92 spike-ins using bowtie (v1.2.2), before aligning to hg38 using STAR (v2.7.3a). Mapped reads were deduplicated using STAR.
GetGeneAnnotations (GGA) scripts (https://github.com/AdelmanLab/GetGeneAnnotation_GGA) were used to annotate dominant active TSS and TES positions from RNA-seq data in H1299 and A549 cells. Gene counts were generated using featurecounts function of the Rsubread package (v2.0.1), and log2 fold change following  BRM011 treatment calculated with DESeq2 version (v1.26.0). As the ERCC92 spike-ins did not show a statistically significant difference between DMSO and BRM014 conditions, RNA-seq was normalized using the DESeq2 generated size factors.
Assembly: hg38
Supplementary files format and content: A549_RNAseq_raw_gene_counts.tsv - A549 RNA-seq raw gene counts generated by featureCounts
Supplementary files format and content: H1299_RNAseq_raw_gene_counts.tsv - H1299 RNA-seq raw gene counts generated by featureCounts

growth_protocol: Cells were grown in RPMI + glutamine (Corning #10-040-CV) with 10% Fetal Bovine Serum (Thermo Fisher #1600044) and 1X Penicillin-Streptomycin (Thermo Fisher #10378016)

extract_protocol:
Cells were collected in Trizol and ERCC92 spike-ins were added by cell number. Total RNA was extracted with chloroform precipitation and Dnase treated. Samples were run on the tapestation to confirm RNA integrity scores > 8.5
Sequencing libraries were prepared from 500 ng of RNA using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion using 8 cycles of PCR amplification.

treatment_protocol: Cells were treated with 5uM BRM014 or 0.05% DMSO for 12 hours

value: non small cell lung cancer cell line

value: wt


title: Adult45-Hipp-E4, Female, SI

value: Social Isolation


title: H1299 12 h 5 uM BRM014 rep 2


title: Mouse, Ctrl 4


title: Adult71-Hipp-G4, Female, GH


title: Mouse, Ctrl 3


title: H1299 12 h 0.05% DMSO rep 3


title: Adult24-Hipp-B4, Male, GH

value: Male


title: Adult68-Hipp-A4, Female, SI


title: H1299 12 h 0.05% DMSO rep 1


title: Adult63-Hipp-H3, Female, SI


title: H1299 12 h 0.05% DMSO rep 2


title: Adult39-Hipp-G3, Male, SI


title: Adult16-Hipp-F3, Male, GH


title: Adult15-Hipp-E3, Male, GH


title: A549 12 h 5 uM BRM014 rep 2

growth_protocol: Cell were grown in F12-K + L-glutamine (Gibco 21127-022, lot 2517130) with 10% Fetal Bovine Serum (Thermo Fisher #1600044) and 1X Penicillin-Streptomycin (Thermo Fisher #10378016)

extract_protocol:
Cells were collected in Trizol and ERCC92 spike-ins were added by cell number. Total RNA was extracted with chloroform precipitation and Dnase treated. Samples were run on the tapestation to confirm RNA integrity scores > 8.5
Sequencing libraries were prepared from 500 ng of RNA using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion using 9 cycles of PCR amplification.


title: Adult2-Hipp-D3, Male, GH


title: Adult52-Hipp-C3, Female, SI


title: Adult79-Hipp-D4, Female, GH


title: A549 12 h 0.05% DMSO rep 3


title: Adult27-Hipp-B3, Male, SI


title: A549 12 h 5 uM BRM014 rep 1


title: A549 12 h 5 uM BRM014 rep 3


title: A549 12 h 0.05% DMSOrep 1


title: A549 12 h 0.05% DMSO rep 2


title: CART-20-2, scRNA-seq

city: La Jolla

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Use Cell ranger to perform alignment, filtering, barcode counting, and UMI counting
Genome_build: hg38
Supplementary_files_format_and_content: all the zip files contain Features (Genes).tsv, Barcodes.tsv, and Matrix.mtx (set of 3 files)

source_name: PBMC from ALL patients

extract_protocol:
PBMCs were isolated from patient blood and processed for library generation for scRNA-Seq
[PBMC and BMMC extract protocol] PBMC or BMMC from the patients' blood or bone marrow were isloated by EasySep™ Direct Human PBMC Isolation Kit following the manufacturer’s instructions.
PBMC or BMMC were used for library construction using Chromium™ Single Cell 3’ Reagent Kits v2/v3
Libraries were generated by Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2/v3 (10X Genomics)

treatment_protocol: ALL patients treated with CAR T cells at various time points

value: Human PBMC

tag: patient id

tag: age

tag: diagnosis

value: B-ALL

value: CAR T treatment Relapse

value: Relapse CD19

tag: therapy

value: CAR T


title: Adult41-Hipp-G2, Female, SI


title: Adult73-Hipp-H2, Female, SI


title: Adult78-Hipp-F2, Female, GH


title: CART-15-2, scRNA-seq

value: 360 days of CAR T treatment

value: Day 360


title: Adult38-Hipp-E2, Male, SI


title: CART-17-2, scRNA-seq

value: Relapse

value: Others


title: CART-16-2, scRNA-seq


title: Adult22-Hipp-D2, Male, GH

value: brain


title: CART-14-2, scRNA-seq


title: Adult54-Hipp-C2, Female, GH

value: hippocampus


title: Adult23-Hipp-B2, Male, GH


title: CART-13-2, scRNA-seq

value: 60 days of CAR T treatment

value: Day 60


title: Input

city: Montreal

first: HaEun

last: Kim

state: Quebec

address: 3999 ch de la Cote-Sainte-Catherine

country: Canada

institute: McGill

data_processing:
Quality control of reads and sequencing was assessed by FastQC (Babraham Bioinformatics).
Adapters and low-quality reads were removed by Trimmomatics using the following parameters: ILLUMINACLIP:$Adapters:2:30:10 SLIDINGWINDOW:4:30 LEADING:30 TRAILING:30.
Alignment on hg19 human genome was performed using bowtie2 using “-end-to-end --phred33” parameters, and reads were directly sorted and converted to bam format by samtools. As sequencing was performed on different lanes to increase the depth, related reads on separate lanes were merged by samtools, and the quality of mapping was checked by samstat. Multiple filtering steps – including removal of low-quality aligned reads and reads aligned to mitochondria chromosome or any chromosome other than chr1-22, X, Y – were performed. Multi-mapped reads were also excluded.
As the broad signal of H3K27me3 is inaccurately represented by most peakcallers, we defined our peaksets by binning the genome at 1kb resolution and thresholding the top bins (as explained in Ashot S. Harutyunyan et al., 2019), with an normalized read density above or equal to 100.
Gained or lost signal were measured as the Log2FoldChange of the ratio between the average of the triplicate in each sample, two-tailed t-tests were used to establish significance.
Genome binning and BigWig files used for visualization were generated by deepTools, bamCoverage function, excluded blacklisted regions and normalized using RPKM.
Assembly: hg19 human reference genome
Supplementary files format and content: bigwig

growth_protocol: MCF7 cells were maintained in RPMI1640 (Wisent Inc.) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Cells were fixed with 4% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a probe sonicator (Fisher Scientific Sonic Dismembrator Model 500) with 5 cycles at 20% power, 5 cycles at 25% power, and 5 cycles at 30% power for 10 sec each.
ChIPed DNA was sent to the Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) for ChIP-seq library prepatation using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: MCF7 cells were treated for 48 hours after overnight serum starvation - [Ink128] = 100 nM; [Rapamycin] = 50 nM.

value: Breast cancer

tag: chip antibody


title: H3K27me3 - Starvation - N3


title: Adult3-Hipp-A3, Male, GH

value: Group Housed


title: H3K27me3 - Starvation - N2


title: Adult8-Hipp-A2, Male, SI

value: Social Isolation


title: Adult25-Hipp-H1, Male, SI

value: Male


title: Adult7-Hipp-G1, Male, SI


title: Adult46-Hipp-E1, Female, GH

value: Female


title: H3K27me3 - Starvation - N1


title: Adult1-Hipp-F1, Male, GH


title: CART-19-2, scRNA-seq

value: Human PBMC

value: B-ALL


title: H3K27me3 - Rapamycin - N1


title: Adult49-Hipp-C1, Female, SI


title: H3K27me3 - Rapamycin - N3


title: H3K27me3 - Ink128 - N3


title: Adult47-Hipp-B1, Female, GH


title: H3K27me3 - Ink128 - N2


title: Plasma S4

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
The gene count matrix was generated by aligning raw reads to the mouse genome (GRCm38) using STARsolo 2.7.10a and requiring a simple overlap with a gene region (Genefull).
BCR reconstruction was performed using TRUST4
Assembly: GRCm38
Supplementary files format and content: singlecell count matrix and TRUST4 reports

source_name: lymph node

extract_protocol:
FACS sorting followed by single-cell RNA-seq (SMARTSeq2)
Template-switched cDNA was generated and pre-amplified. Tagmentation was performed with an Illumina DNA Prep kit and indexed using IDT for Illumina Index Sets.

treatment_protocol: NP-Ova in alhydrogel immunization 14 days prior to cell sorting into 96-well plates

value: lymph node

value: Plasma Cells


title: H3K27me3 - Stimul. (veh) - N3


title: Plasma S3


title: H3K27me3 - Ink128 - N1


title: H3K27me3 - Stimul. (veh) - N2


title: Plasma S1


title: Plasma S2


title: H3K27me3 - Stimul. (veh) - N1


title: Plasma M8

value: c-Myc-GFP


title: Adult33-Hipp-D1, Male, SI


title: MCF7 cells - Starvation - N3-2

data_processing:
The quality of reads and sequencing was assessed both before and after trimming using the FastQC package (Babraham Bioinformatics).
Before mapping, the reads were subjected to trimming using Trimmomatics 85 under the following conditions: ILLUMINACLIP:$Adapters:2:30:10:8:true, HEADCROP:4, SLIDINGWINDOW:4:30, LEADING:3, TRAILING:3, MINLEN:30.
Sequence alignment was performed with STAR 2.5.4b and compared with hg19 human reference genome using default parameters (Dobin et al., 2013) and converted into bam format using Samtools 1.9 (Li et al., 2009).
Differential expression analysis was generated using the featureCounts matrix (Liao et al., 2014).
Comparison across samples was performed with DESeq2 analysis using default parameters (Love et al., 2014).
Assembly: hg19 human reference genome
Supplementary files format and content: tab-delimited text file containing raw counts for each samples

molecule: polyA RNA

extract_protocol:
Total RNA was extracted according to the Sigma RNA Extraction Kit (#RTN350-1KT, Sigma) protocol.
RNA was sent to the Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) for poly(A) RNA library preparation, using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Serum starvation


title: MCF7 cells - Starvation - N3-1


title: H3K27me3 - Rapamycin - N2


title: Plasma M6


title: MCF7 cells - Starvation - N1-2


title: Plasma M5


title: MCF7 cells - Starvation - N2-2


title: Plasma M4


title: MCF7 cells - Starvation - N2-1


title: MCF7 cells - Rapamycin - N3-2

value: Rapamycin


title: Plasma M1


title: Plasma M2


title: MCF7 cells - Starvation - N1-1


title: LZ myc+ M8

value: Germinal Center LZ B cells


title: Adult53-Hipp-A1, Female, SI

value: brain


title: Plasma M3


title: MCF7 cells - Rapamycin - N2-1


title: LZ myc+ M5


title: LZ myc+ M6


title: LZ myc+ M4


title: MCF7 cells - Rapamycin - N1-2


title: LZ myc+ M2


title: MCF7 cells - Rapamycin - N3-1


title: MCF7 cells - Rapamycin - N2-2


title: MCF7 cells - Ink128 - N2-2


title: MCF7 cells - Ink128 - N3-2


title: LZ myc+ M1


title: LZ myc+ M3


title: MCF7 cells - Ink128 - N1-1


title: LZ IgL- S2


title: MCF7 cells - Rapamycin - N1-1


title: LZ IgL- S4


title: MCF7 cells - Ink128 - N1-2


title: MCF7 cells - Stimul. (veh) - N3-1

value: Serum stimulation with vehicle (DMSO)


title: H1299 12 h 5 uM BRM014 rep 3

value: non small cell lung cancer cell line

value: wt


title: MCF7 cells - Ink128 - N2-1

value: Breast cancer


title: MCF7 cells - Ink128 - N3-1


title: LZ IgL- S1


title: LZ IgL+ S4


title: LZ IgL- S3


title: MCF7 cells - Stimul. (veh) - N2-2


title: MCF7 cells - Stimul. (veh) - N3-2


title: MCF7 cells - Stimul. (veh) - N2-1


title: LZ IgL- M6


title: MCF7 cells - Stimul. (veh) - N1-1


title: LZ IgL+ S2


title: MCF7 cells - Stimul. (veh) - N1-2


title: LZ IgL- M1


title: LZ IgL+ S1


title: LZ IgL+ M6


title: LZ IgL+ M2


title: D5_CTL_3

first: Ling

last: Zhang

address: 1111 XianXia Road

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

description:
treatment without 100 μM IA
D5_CTL_3

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCh38.p13 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human primary visceral preadipocytes

growth_protocol: Human primary visceral preadipocytes (HPA-v) were cultured in preadipocyte medium (Sciencell) with 5% fetal bovine serum (FBS), 1% penicillin-streptomycin solution (PS) and 1% preadipocyte growth supplement in 5% CO2 incubator at 37°C. For adipose precursor cell differentiation, the HPA-v maintained for 2 day’s after post-confluence in preadipocyte medium (Day0), then the HPA-v were cultured in DMEM/F12 medium (Gibco), with 1 mM dexamethasone, 100 nM insulin, 1 mM rosiglitazone, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), and supplemented with 1% PS for 4 days (Day4). After that, the HPA-v were cultured with DMEM/F12 medium supplemented with 10nM insulin for 3 days (Day7).

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Indol-3-acrylic acid (IA) was purchased from Shanghai yuanye Bio-Technology Co Ltd, HPA-v were treatment with the concentration of 50 μM, 100 μM, 250 μM and 500 μM IA. During the HPA-v differentiation, the concentration of 100 μM IA were supplement with differentiation medium at day0, day2, day4 and day6.

value: Human primary visceral preadipocytes

value: human

value: During the HPA-v differentiation, only medium was used.


title: D5_CTL_1

description:
treatment without 100 μM IA
D5_CTL_1


title: D5_CTL_2

description:
treatment without 100 μM IA
D5_CTL_2


title: LZ IgL+ M1


title: D5_20_3

description:
treatment with 100 μM IA
D5_20_3

value: During the HPA-v differentiation, the concentration of 100 microM IA were supplement with differentiation medium at day0, day2, day4 and day6.


title: D5_20_2

description:
treatment with 100 μM IA
D5_20_2


title: DZ IgL- S4

value: Germinal Center DZ B cells


title: DZ IgL- S3


title: DZ IgL- M8


title: D5_20_1

description:
treatment with 100 μM IA
D5_20_1


title: DZ IgL- M4


title: HaCaTpLVX_Rep2

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

description: Non-tumorigenic Keratinocytes transduced with Empty-vector

data_processing:
The Quality Check was performed through the FastQC tool (v0.12.1)
All the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference
The BAM files, of which the number of reads was counted by the featureCounts tool (v2.0.3)
The differential gene expression measurements were normalized by DESeq2´s median of ratios (median of ratio of gene counts relative to geometric mean per gene) method.
Assembly: GRCh38.p14 v43
Supplementary files format and content: The tab-delimited text files include the FPKM and log2FC (Fold Change) values for each sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

growth_protocol: HaCaT E6/E7 HPV16, HaCaT E6/E7 HPV18, and HaCaT pLVX were cultured in Dulbecco’s Modified Eagle Medium (DMEM) + GlutaMAX™ supplemented with D-glucose (1 g/L) (Cat. No. 10567-014 Gibco, Thermo FisherScientific, Waltham, MA, USA), penicillin (100 U/mL), streptomycin (100 μg/mL), L-glutamine (584 mg/L), sodium pyruvate (110 mg/L) and 10% fetal bovine serum (FBS). The incubator (C170UL-120V-R, Binder, Tuttlingen, Germany) conditions were at 37 °C and a 5% CO2 atmosphere.

extract_protocol:
The total RNA extraction was collected with Quick-RNA miniprep plus kit (Cat. No. R1058, Zymo Research, Irvine, CA, USA) according to manufacturers’ instructions
mRNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model.

treatment_protocol: Cells were selected by adding puromicine (0.3 micrograms/mL) to culture medium during 2 weeks

value: Skin

value: HaCaT

value: Epithelial cell

value: Empty-vector


title: Ha_E6E7_18_Rep2

description: Non-tumorigenic Keratinocytes transduced with E6/E7 from HPV18


title: DZ IgL- M5

value: lymph node

value: c-Myc-GFP


title: HaCaTpLVX_Rep1


title: DZ IgL- M3


title: LZ IgL+ S3

value: Germinal Center LZ B cells


title: DZ IgL+ S3


title: Ha_E6E7_18_Rep1


title: Ha_E6E7_16_Rep2

description: Non-tumorigenic Keratinocytes transduced with E6/E7 from HPV16


title: DZ IgL+ S4


title: DZ IgL+ S1


title: HaCaT_Rep1

description: Non-tumorigenic keratinocytes


title: Ha_E6E7_16_Rep1


title: HaCaT_Rep2

description: Non-tumorigenic keratinocytes


title: DZ IgL+ M8


title: C33A_Rep1

description: Cervical Cancer derived cell line HPV negative

source_name: Uterus; Cervix

value: Uterus; Cervix


title: HeLa_Rep1

description: Cervical Cancer derived cell line HPV18 positive

value: HeLa


title: HeLa_Rep2


title: DZ IgL+ M3


title: GC-2 cells, MLN4924 1 μM, normoxia 24h, 3 [NM3]

city: Wuhan

first: Hongyan

last: Deng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
Fastp version 0.21.0 (https://github.com/OpenGene/fastp) was used to perform basic statistics on the quality of the raw reads. The data processing steps were as follows: discard a paired reads if either one read contains adapter contamination; discard a paired reads if more than 10% of bases are uncertain in either read; discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
The clean reads were mapped to the mouse reference genome (http://ftp.ensembl.org/pub/current_fasta/mus_musculus/) using Star version 2.7.9a (https://github.com/alexdobin/STAR).
RSEM version 1.3.3 (https://github.com/deweylab/RSEM) was used to calculate read counts of genes and transcripts.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: mouse type B spermatogonia

growth_protocol: GC-2 cells, originally from the National Collection of Authenticated Cell Cultures, China, were cultivated in Dulbeccos’ modified Eagle medium (DMEM) (VivaCell) with 10% fetal bovine serum (FBS) at 37℃ in an incubator containing 5% CO2.

extract_protocol:
Total RNAs were extracted using RNAiso Plus (TaKaRa Bio),and then purified using the RNeasy Mini Kit (QIAGEN, 74104).
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) according to the manufacturer’s protocol. Qualified libraries were pooled and sequenced on Illumina NovaSeq platforms using PE150 strategy at Wuhan Benagen Technology Co., Ltd. (Wuhan, China).

treatment_protocol: GC-2 cells were incubated with MLN4924 (1 μM) or DMSO as control, and then the cells were cultured under normoxia or hypoxia for 24 hours. GC-2 Cells were incubated under the hypoxic condition (1% O2, 5% CO2, and balanced with N2) in an NBS Galaxy 48R incubator.

value: mouse type B spermatogonia

value: GC-2 cells

value: mouse type B spermatogonia GC-13 cells

value: WT

value: MLN4924 1 μM, normoxia 24h


title: GC-2 cells, MLN4924 1 μM, normoxia 24h, 2 [NM2]

value: mouse type B spermatogonia GC-12 cells


title: GC-2 cells, MLN4924 1 μM, normoxia 24h, 1 [NM1]

value: mouse type B spermatogonia GC-11 cells


title: GC-2 cells, DMSO, normoxia 24h, 2 [ND2]

value: mouse type B spermatogonia GC-9 cells

value: DMSO, normoxia 24h


title: DZ IgL+ M5

value: Germinal Center DZ B cells


title: SSSavi_DKE_WGBS_B

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
WGBS data was processed by trimming the reads for read quality and adapters followed by merging read1 and read2 for better mappability using parameters -q 20,  --merge, --overlap_len_require 15, --overlap_diff_percent_limit 20 with fastp (Chen et al., 2018). Trimmed, single and merged reads were aligned against an in silico bisulfite converted hg38 genome using bwa-meth (Pederson et al., 2014). Read deduplication of single-end and merged reads was performed with paleomix (Schubert et al., 2014) rmdup_collapsed --remove-duplicates. Methylation was called on deduplicated WGBS mapped bam files with MethylDackel default options and symmetric CpG option --mergeContext.Targeted DNA methylation changes were examined at +/- 500 bp of the gRNA binding site which corresponds to the bedfile named "gRNA_SSSavi_6xHRBKET_+-500bp.bed".
Assembly: hg38

source_name: HEK293T stably expressing dCas9-SSSavi and 6xgRNA

growth_protocol: HEK293T cells were grown in a humidified cell culture incubator at 37˚C with 5% (v/v) CO₂. HEK293T cells were grown in DMEM (Dulbecco's Modified Eagle Medium) supplemented with 10% (v/v) FBS (Moregate BioTech, #23301121), 1X (v/v) Glutamax (Life Technologies, #35050061) and 1% MEM Non-essential amino acid solution (ThermoFisher, #11140050).

extract_protocol:
WGBS: gDNA was extracted using a Qiagen DNeasy Blood & Tissue Kit (#69504). From this, 200 ng of each sample and 2 ng of lambda DNA (Promega #D150A) was sheared (Covaris, M220) for 5 min, 20% duty cycle, 75 peak power, and 200 cycles per burst.
Sheared DNA fragments were then End-repaired and A-tailed using a NxSeq AmpFREE Low DNA Lib Kit (Lucigen, #14000-2), followed by ligation of Nextflex methylated adapters (Perkin Elmer, #NOVA-511913) and cleaned up and size selected for >300 bp using Agencourt AMPure XP beads. Samples were then bisulfite converted using a EZ DNA Methylation-Direct Kit (Zymogen, #D5021) following the manufacturer's protocol.  KAPA HiFi Uracil+ readymix (Roche, #KM2801) was then used for 6 cycles of library amplification using 25 µM mix of p5 and p7 primers (5’ AATGATACGGCGACCACCGAGATCTACAC and 5’ CAAGCAGAAGACGGCATACGAGAT, respectively) primrs from IDT, followed by a final bead clean-up.

treatment_protocol: HEK293T cells expressing dCas9-SSSavi, BirA and 6x sgRNA (HSB6G) were created using lentiviral transduction (gRNA) and PiggyBac (dCas9-SSSavi and BirA). These cells were transfected with either (1) D3A-K-E, (2) K-E-D3A or (3) the non-catalytic control, 𝛼GCN4-mCherry and crosslinked for 10 min in 1% formaldehyde and quenched in 125 mM glycine. 100,000 cells were then FACS sorted for GFP.

value: human embyonic kidney


title: GC-2 cells, DMSO, normoxia 24h, 1 [ND1]

value: mouse type B spermatogonia GC-8 cells


title: SiHa_Rep2

description: Cervical Cancer derived cell line HPV16 postive

value: SiHa

value: Epithelial cell


title: GC-2 cells, MLN4924 1 μM, hypoxia 24h, 2 [HM2]

value: mouse type B spermatogonia GC-6 cells

value: MLN4924 1 μM, hypoxia 24h


title: SSSavi_KED_ChIP_rep1_input

data_processing:
ChIP-seq data was processed by quality and adapter trimming of the reads with fastp (Chen et al., 2018), followed by mapping the reads with minimap2 against hg38 with parameters -I 8G -K 2G. Duplicate removal was performed using samtools’ markdup function followed by subsequent filtering of said duplicate reads (Li et al., 2009) through gnu-parallel (Tange, 2011). Aligned ChIPseq datasets were input normalised with deeptools bamCompare (Ramirez et al., 2016) using Signal extraction scaling (SES) (Diaz et al., 2012). Input normalised ChIP-seq signal for each replicate was summed up +/- 500 bp at the gRNA binding site and compared to dCas9-SSSavi-mCherry control. Peaks were called with macs2 (Zhang et al., 2008).
Assembly: hg38

extract_protocol:
ChIP-seq: Chromatin from FACS sorted samples were sheared (Covaris, M220) for 5 min (20% duty cycle, 75 peak power, and 200 cycles per burst at 4 ˚C). For dCas9 binding, cells were incubated with 10 µg of HA antibody (Biolegend, #901502), for histone modifications 2 µg of H3K4me3 (Abcam, #ab8580), H3K9me3 (Abcam, #ab8898), or H3K27me3 (Abcam, #ab6002) antibody was used. Each antibody was conjugated to 65 µLprotein G Dynabeads (Invitrogen, #10003D). After wash steps, DNA was eluted, crosslinks were reversed, and immunoprecipitated DNA was purified by Agencourt AMPure XP beads (Beckman Coulter, #A63880).
Libraries were prepared from the ChIP eluate containing 1-40 ng input material per replicate using the ThruPLEX DNA-seq 12S kit (Rubicon Genomics, #R400429). After limited PCR amplification (8-10 cycles), libraries were purified using 1x Agencourt AMPure XP beads, and eluted in a final volume of 20 μL.

value: HEK293T stably expressing dCas9-SSSavi and 6xgRNA


title: SSSavi_KED_ChIP_rep1

value: HA (Biolegend, #901502)


title: SSSavi_DKE_WGBS_C


title: SSSavi_DKE_ChIP_rep1


title: GC-2 cells, MLN4924 1 μM, hypoxia 24h, 1 [HM1]

value: mouse type B spermatogonia

value: GC-2 cells

value: mouse type B spermatogonia GC-5 cells


title: GC-2 cells, DMSO, normoxia 24h, 3 [ND3]

value: mouse type B spermatogonia GC-10 cells

value: WT


title: DZ IgL+ M4

value: lymph node

value: c-Myc-GFP


title: GC-2 cells, DMSO, hypoxia 24h, 3 [HD3]

value: mouse type B spermatogonia GC-4 cells

value: DMSO, hypoxia 24h


title: GC-2 cells, DMSO, hypoxia 24h, 2 [HD2]

value: mouse type B spermatogonia GC-3 cells


title: SSSavi_mCherry_rep3_input

value: human embyonic kidney


title: SSSavi_mCherry_H3K4me3_ChIP_rep3

value: H3K4me3, abcam, ab8580


title: GC-2 cells, DMSO, hypoxia 24h, 1 [HD1]

value: mouse type B spermatogonia GC-2 cells


title: SSSavi_mCherry_H3K9me3_ChIP_rep3

value: H3K9me3, abcam, ab8898


title: COHP_49274_513_TET_OFF_NIL_ON_D_10wks

city: Duarte

first: Denis

last: OMeally

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description: cml_mrna_processed_1tpm_in_5_samples.tsv.gz

data_processing:
nf-core RNASeq pipeline version 3.7
Trimmed reads were mapped using STAR to the GRCm39 reference (Genbank accession GCA_000001635.9) amended with the human BCR-ABL1 fusion gene sequence (Genbank accession EF158045.1) using GENCODE annotation Release m28
Each library was subjected to extensive quality control, including estimation of library complexity, gene body coverage, and duplication rates, among other metrics detailed in the pipeline repository
Transcript abundance was estimated across genomic features using Salmon and merged into a matrix of pseudocounts per million transcripts (TPM) per gene for each sample. BCR-ABL1 transcript abundance was measured by counting reads that spanned the fusion boundary
Assembly: GCA_000001635.9
Supplementary files format and content: tab delimited file includes Salmon pseudocounts for each sample (TPM)

source_name: PBMC

growth_protocol: Inducible transgenic SCLtTA/BCR-ABL mice of B6 background were maintained on tetracycline (tet) water at 0.5 g/L. Tet withdrawal (tet-off) results in expression of BCR-ABL and generation of a CML-like disease in these mice with a median survival of approximately 10 weeks after induction of BCR-ABL, which recapitulates human CP CML.

extract_protocol:
Total RNA was extracted from whole blood using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany); quality and quantity were estimated using a BioAnalyser (Agilent, Santa Clara, CA). Samples with a RIN > 4.0 were included.
Sequencing libraries were constructed using the KapaHyper with RiboErase (Kapa Biosystems, Wilmington, MA) and are reverse stranded.

treatment_protocol: Six to eight weeks old male and female SCLtTA/BCR-ABL mice were randomly divided into 4 groups: control (Tet on, n=3 mice), CML (Tet off, n=6 mice), Tet Off-On (TOTO; Tet off 6 weeks then Tet on for 12 weeks, n=4 mice), TKI [Tet off 6 weeks then TKI (Nilotinib, 50mg/kg, oral gavage, daily) treatment 4 weeks, n=7 mice]. Blood was collected from these mice weekly, i.e., before BCR-ABL induction (t = 0) and weekly after induction up to 18 weeks (t = 1 to 18) or when the mouse developed leukemia and became moribund, whichever event occurred first.

tag: mouse id

tag: sample weeks

tag: batch

value: PBMC

tag: strain

value: M

value: tTA+/-, BCR-ABL+/-


title: COHP_49275_513_TET_OFF_NIL_ON_D_11wks

tag: genotype


title: SSSavi_mCherry_WGBS_B

tag: cell line

value: HEK293T stably expressing dCas9-SSSavi and 6xgRNA

tag: cell type

tag: treatment


title: SSSavi_DKE_rep3_input


title: SiHa_Rep1

tag: tissue

value: Uterus; Cervix

value: SiHa

value: Epithelial cell


title: GC-2 cells, MLN4924 1 μM, hypoxia 24h, 3 [HM3]

value: mouse type B spermatogonia

value: GC-2 cells

value: mouse type B spermatogonia GC-7 cells

value: WT

value: MLN4924 1 μM, hypoxia 24h


title: SSSavi_DKE_H3K4me3_ChIP_rep3


title: SSSavi_DKE_H3K9me3_ChIP_rep3

description:
RL4231 raw files correspond to SRR25735551
RL4349 raw files correspond to SRR25735552
RL4349 sequenced deeper
gRNA_SSSavi_6xHRBKET.bed


title: COHP_49273_513_TET_OFF_NIL_ON_D_9wks


title: SSSavi_DKE_H3K27me3_ChIP_rep3

value: H3K27me3, abcam, ab6002


title: SSSavi_DKE_ChIP_rep1_input

value: human embyonic kidney


title: COHP_49270_513_TET_OFF_NIL_ON_D_6wks


title: COHP_49272_513_TET_OFF_NIL_ON_D_8wks


title: COHP_49271_513_TET_OFF_NIL_ON_D_7wks


title: SSSavi_mCherry_H3K4me3_ChIP_rep1

value: H3K4me3, abcam, ab8580


title: SSSavi_DKE_rep1_input


title: SSSavi_mCherry_H3K9me3_ChIP_rep1


title: SSSavi_mCherry_H3K27me3_ChIP_rep1


title: COHP_49269_513_TET_OFF_NIL_ON_D_5wks


title: COHP_49267_513_TET_OFF_NIL_ON_D_3wks


title: COHP_49265_513_TET_OFF_NIL_ON_D_1wks


title: SSSavi_DKE_H3K4me3_ChIP_rep1


title: COHP_49268_513_TET_OFF_NIL_ON_D_4wks


title: COHP_49264_513_TET_OFF_NIL_ON_D_0wks


title: SSSavi_mCherry_H3K27me3_ChIP_rep3


title: SSSavi_DKE_H3K27me3_ChIP_rep1


title: SSSavi_DKE_H3K9me3_ChIP_rep1

description:
RL4211 raw files correspond to SRR25735560
RL4342 raw files correspond to SRR25735561
RL4342 sequenced deeper
gRNA_SSSavi_6xHRBKET.bed


title: R1-AD1 FLAGHA-H3F3A DAXX KO, Dex 4h, biol rep 3

data_processing:
Short reads were mapped to the human transcriptome using the STAR aligner v2.6.1d.
Alignment results were quantified to produce raw counts and FPKM values for every gene in each sample.
Differential analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: readcount_genename.txt: raw counts for every gene in each sample
Supplementary files format and content: fpkm_genename.txt: FPKM values for every gene in each sample
Supplementary files format and content: normcount_genename.txt: read counts for every gene in every sample normalized by DESeq2

extract_protocol: RNA was isolated using RNeasy Plus Kit (QIAGENE) according to the manual

treatment_protocol: Cells were treated with 100nM Dexamethasone for 4 hours

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: Prostate cancer cells

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

value: 100 nM Dexamethasone 4h


title: COHP_49261_511_TET_OFF_NIL_ON_D_9wks

value: PBMC

value: M

value: tTA+/-, BCR-ABL+/-


title: COHP_49260_511_TET_OFF_NIL_ON_D_8wks


title: R1-AD1 FLAGHA-H3F3A DAXX KO, Dex 4h, biol rep 2


title: R1-AD1 FLAGHA-H3F3A DAXX KO, Dex 4h, biol rep 1


title: COHP_49259_511_TET_OFF_NIL_ON_D_7wks


title: SSSavi_mCherry_rep1_input

value: HEK293T stably expressing dCas9-SSSavi and 6xgRNA


title: COHP_49266_513_TET_OFF_NIL_ON_D_2wks


title: COHP_49258_511_TET_OFF_NIL_ON_D_6wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO, Dex 4h, biol rep 1

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: COHP_49257_511_TET_OFF_NIL_ON_D_5wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO, Dex 4h, biol rep 3


title: R1-AD1 FLAGHA-H3F3A AR KO, Dex 4h, biol rep 3

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: COHP_49263_511_TET_OFF_NIL_ON_D_11wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO, Dex 4h, biol rep 2


title: R1-AD1 FLAGHA-H3F3A AR KO, Dex 4h, biol rep 1


title: R1-AD1 FLAGHA-H3F3A AR KO, Dex 4h, biol rep 2


title: R1-AD1 FLAGHA-H3F3A, Dex 4h, biol rep 2

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_49251_514_TET_OFF_NIL_ON_D_10wks

value: F


title: COHP_49252_511_TET_OFF_NIL_ON_D_0wks


title: COHP_49253_511_TET_OFF_NIL_ON_D_1wks


title: COHP_49250_514_TET_OFF_NIL_ON_D_9wks


title: R1-AD1 FLAGHA-H3F3A, Dex 4h, biol rep 3


title: R1-AD1 FLAGHA-H3F3A DAXX KO, biol rep 2

value: No treatment


title: COHP_49248_514_TET_OFF_NIL_ON_D_7wks


title: COHP_49262_511_TET_OFF_NIL_ON_D_10wks


title: COHP_49247_514_TET_OFF_NIL_ON_D_6wks


title: R1-AD1 FLAGHA-H3F3A DAXX KO, biol rep 1


title: COHP_49246_514_TET_OFF_NIL_ON_D_5wks


title: COHP_49254_511_TET_OFF_NIL_ON_D_2wks


title: COHP_49245_514_TET_OFF_NIL_ON_D_4wks


title: R1-AD1 FLAGHA-H3F3A DAXX KO, biol rep 3


title: COHP_49256_511_TET_OFF_NIL_ON_D_4wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO, biol rep 1


title: R1-AD1 FLAGHA-H3F3A HIRA KO, biol rep 2


title: R1-AD1 FLAGHA-H3F3A, Dex 4h, biol rep 1


title: COHP_49249_514_TET_OFF_NIL_ON_D_8wks


title: R1-AD1 FLAGHA-H3F3A AR KO, biol rep 3


title: R1-AD1 FLAGHA-H3F3A HIRA KO, biol rep 3


title: R1-AD1 FLAGHA-H3F3A AR KO, biol rep 2


title: COHP_49255_511_TET_OFF_NIL_ON_D_3wks


title: COHP_49243_514_TET_OFF_NIL_ON_D_2wks


title: COHP_49242_514_TET_OFF_NIL_ON_D_1wks


title: COHP_49241_514_TET_OFF_NIL_ON_D_0wks


title: R1-AD1 FLAGHA-H3F3A, biol rep 3


title: COHP_49239_542_TET_OFF_B_15wks


title: R1-AD1 FLAGHA-H3F3A, biol rep 2


title: R1-AD1 FLAGHA-H3F3A, biol rep 1


title: COHP_49238_542_TET_OFF_B_14wks


title: Torn rotator cuff tendon, DM-3

city: Beijing

first: Ziyang

last: Yuan

address: Yongan Road No.95

institute: Beijing Friendship Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two groups was performed using the DESeq2.
Assembly: hg38
Supplementary files format and content: TXT file includes FPKM values for each Sample

source_name: Torn rotator cuff tendon

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Torn rotator cuff tendon

tag: disease state

value: diabetic


title: COHP_49236_542_TET_OFF_B_12wks


title: COHP_49237_542_TET_OFF_B_13wks


title: Torn rotator cuff tendon, DM-2


title: Torn rotator cuff tendon, N-3

value: control


title: COHP_49244_514_TET_OFF_NIL_ON_D_3wks


title: COHP_49234_542_TET_OFF_B_10wks


title: Torn rotator cuff tendon, DM-1


title: COHP_49235_542_TET_OFF_B_11wks


title: COHP_49231_542_TET_OFF_B_7wks


title: R1-AD1 FLAGHA-H3F3A AR KO, biol rep 1

value: Prostate cancer cells


title: Torn rotator cuff tendon, N-1


title: Torn rotator cuff tendon, N-2


title: COHP_49230_542_TET_OFF_B_6wks


title: COHP_49240_542_TET_OFF_B_16wks


title: COHP_49232_542_TET_OFF_B_8wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 27, EtOH

data_processing:
Short reads were mapped to the human transcriptome using the STAR aligner v2.6.1d.
Alignment results were quantified to produce raw counts and FPKM values for every gene in each sample.
Differential analysis was performed with DESeq2.
Supplementary files format and content: readcount_genename.txt: raw counts for every gene in each sample
Supplementary files format and content: fpkm_genename.txt: FPKM values for every gene in each sample

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 27

treatment_protocol: Cells were treated with 1 nM R1881 for 4, 12 and 24 hours

value: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 27

value: EtOH


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 27, R1881 4 h


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 27, R1881 12 h


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 14, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 14

value: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 14


title: COHP_49227_542_TET_OFF_B_3wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: COHP_49229_542_TET_OFF_B_5wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 14, R1881 4 h


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 14, R1881 12 h


title: COHP_49228_542_TET_OFF_B_4wks


title: COHP_49226_542_TET_OFF_B_2wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 14, EtOH


title: COHP_49225_542_TET_OFF_B_1wks


title: COHP_49224_542_TET_OFF_B_0wks


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 3, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 4

value: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 4


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 3, R1881 12 h

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 3

value: R1-AD1 FLAGHA-H3F3A, HIRA KO clone 3

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: COHP_49233_542_TET_OFF_B_9wks


title: COHP_49223_487_TET_OFF_B_18wks


title: COHP_49222_487_TET_OFF_B_17wks


title: mESC_EP400_ChIPseq_4h_DMSO_rep2

data_processing:
Reads were trimmed for a minimum quality score of 20 using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE), adapter sequences were removed using cutadapt version 1.14.
Data was mapped to mm10 using bowtie 1.2.2
Bedgraphs were generated for frgament midpoints, in 50bp bins from using deduplicated reads
Assembly: mm10
Supplementary files format and content: All files with the .bw suffix are normalized BigWig files containing combined data from all replicates of the indicated treatment condition.

growth_protocol: Cells were grown in serum-free ES media supplemented with glutamine (Gibco), monothioglycerol (Sigma), MEK inhibitor (Reprocell), GSK3 inhibitor (Reprocell) and LIF (Cell Guidance Systems). Cells were passaged onto new gelatin-coated plates every other day, and received fresh media on other days.

extract_protocol:
After the indicated treatment interval, cells were fixed for 1 h in 2 mM DSG with the addition of 1% formaldehyde for the final 12.5 min, as described in.86 Crosslinking was quenched by the addition of glycine to a final concentration of 0.125 M. Cells were collected and washed with ice-cold 1X PBS before being resuspended in Sonication Buffer (20 mM Tris, pH 8.0, 2 mM EDTA, 0.5 mM EGTA, 1X Complete Mini EDTA-free Protease Inhibitor Cocktail [Roche 11836170001], 0.5% SDS, and 0.5 mM PMSF) at a concentration of 1 x 108 cells per mL. Chromatin was sheared to an average fragment size of ∼200 bp using a QSonica sonicator, flash-frozen in liquid nitrogen, and stored at -80°C until use. ChIP material was diluted into IP buffer (20 mM Tris pH 8.0, 2 mM EDTA, 0.5% Triton X-100, 150 mM NaCl, 10% Glycerol, 5% BSA) and pre-cleared with 30 μL of Protein A agarose beads (Millipore Cat No. 16-125) for 1 h at 4°C. Cleared samples were collected and combined with primary antibody before overnight incubation at 4°C with rotation. Subsequently, 200 μL Protein A beads were added to each IP reaction, and samples were rotated for 2 h at 4°C. Samples were washed once with Low-Salt Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, 0.1% SDS), three times with High-Salt Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 500 mM NaCl, 0.1% SDS), once with Lithium Chloride Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate), and twice with TE Buffer (10 mM Tris-HCl, 1mM EDTA). Each wash was performed by rotating samples for 3 minutes with 1 mL volume of ice-cold wash solution. Two elutions were performed by resuspending beads in Elution Buffer (100 mM NaHCO3, 1% SDS) and rotating for 15 min at room temperature (22°C). The combined eluate was supplemented with 200 mM NaCl and incubated overnight in a 65°C water bath. Samples were treated with Proteinase K (New England Biolabs P8107), extracted with phenol:chloroform:isoamyl alcohol (25:24:1, Sigma P3803), and resuspended in 65 μl H2O. To enable accurate sample normalization, an equal amount of fragmented D. melanogaster DNA was added to the eluate of each sample.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

value: mESC

value: wt

value: EP400 (Bethyl Laboratories A300-541A, lot #2)


title: R1-AD1 FLAGHA-H3F3A HIRA KO clone 3, R1881 4 h


title: mESC_EP400_ChIPseq_4h_DMSO_rep3


title: mESC_EP400_ChIPseq_4h_DMSO_rep1


title: mESC_EP400_ChIPseq_4h_BRM014_rep3

value: 1µM BRM014, 4h


title: COHP_49221_487_TET_OFF_B_16wks

value: F


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 33, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 33

value: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 33

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: mESC_EP400_ChIPseq_4h_BRM014_rep2


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 33, R1881 4 h


title: mESC_EP400_ChIPseq_2h_DMSO_rep1


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 33, R1881 12 h


title: mESC_EP400_ChIPseq_4h_BRM014_rep1


title: mESC_EP400_ChIPseq_2h_DMSO_rep2


title: COHP_49219_487_TET_OFF_B_14wks


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 24, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 24

value: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 24


title: mESC_EP400_ChIPseq_2h_BRM014_rep2

value: 1µM BRM014, 2h


title: mESC_BRG1_ChIPseq_4h_DMSO_rep2


title: COHP_49218_487_TET_OFF_B_13wks


title: COHP_49220_487_TET_OFF_B_15wks


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 24, R1881 12 h

value: Prostate cancer cells


title: mESC_BRG1_ChIPseq_4h_DMSO_rep1


title: COHP_49217_487_TET_OFF_B_12wks


title: mESC_BRG1_ChIPseq_4h_BRM014_rep1


title: COHP_49216_487_TET_OFF_B_11wks


title: mESC_BRG1_ChIPseq_4h_BRM014_rep3


title: mESC_BRG1_ChIPseq_4h_DMSO_rep3


title: COHP_49215_487_TET_OFF_B_10wks


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 33, EtOH

value: EtOH


title: Tle6 -/- GV oocyte, biol rep 4, tech rep B [Tle6_KO4_S7_B]

city: Goettingen

first: Sarah Mae

last: Penir

address: Am Fassberg 11

department: Department of Meiosis

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

data_processing:
Basecalling with bcl2fastq v2.20.0.422
Adapter trimming with cutadapt v2.8 using the “-q 20 -m 35 -j 15” parameters
Read mapping with STAR v2.7.8a using the default settings
Read counting with HTSeq v2.0.2
Assembly: mm39
Supplementary files format and content: A table with counts for each feature

source_name: GV oocyte

extract_protocol:
Libraries and polyA mRNA was extracted from 15 oocytes using the QIAseq FX Single Cell RNA Library Kit
Libraries and polyA mRNA was extracted from 15 oocytes using the QIAseq FX Single Cell RNA Library Kit

value: GV oocyte

value: C57BL/6J strain background

value: Tle6 knockout


title: mESC_EP400_ChIPseq_2h_BRM014_rep1


title: Tle6 -/- GV oocyte, biol rep 3 [Tle6_KO3_S6_A]


title: COHP_49214_487_TET_OFF_B_9wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 13, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 13

value: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 13


title: Tle6 -/- GV oocyte, biol rep 1 [Tle6_KO1_S4_A]


title: COHP_49213_487_TET_OFF_B_8wks


title: COHP_49212_487_TET_OFF_B_7wks


title: Tle6 +/- GV oocyte, biol rep 1, tech rep B [Tle6_WT1_S1_B]

value: Tle6 heterozygote


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 13, R1881 12 h


title: Tle6 +/- GV oocyte, biol rep 1, tech rep A [Tle6_WT1_S1_A]


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 13, R1881 4 h


title: mESC_BRG1_ChIPseq_4h_BRM014_rep2

value: mESC

value: wt


title: Tle6 +/- GV oocyte, biol rep 2, tech rep B [Tle6_WT2_S2_B]


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 13, EtOH


title: Tle6 +/- GV oocyte, biol rep 2, tech rep A [Tle6_WT2_S2_A]


title: COHP_49210_487_TET_OFF_B_5wks


title: COHP_49211_487_TET_OFF_B_6wks


title: Padi6 -/- GV oocyte, biol rep 2 [Padi6_KO2_S5]

value: FVB/N strain background

value: Padi6 knockout


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 24, R1881 4 h


title: Tle6 -/- GV oocyte, biol rep 4, tech rep A [Tle6_KO4_S7_A]


title: R1-AD1 FLAGHA-H3F3A AR KO clone 35, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, AR KO clone 35

value: R1-AD1 FLAGHA-H3F3A, AR KO clone 35

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: Padi6 +/- GV oocyte, biol rep 3 [Padi6_WT3_S3]

value: Padi6 heterozygote


title: COHP_49209_487_TET_OFF_B_4wks

value: F


title: R1-AD1 FLAGHA-H3F3A AR KO clone 35, R1881 12 h

value: Prostate cancer cells


title: R1-AD1 FLAGHA-H3F3A DAXX KO clone 24, EtOH

value: R1-AD1 FLAGHA-H3F3A, DAXX KO clone 24

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO

value: EtOH


title: Padi6 +/- GV oocyte, biol rep 1 [Padi6_WT1_S1]

value: GV oocyte


title: Padi6 +/- GV oocyte, biol rep 2 [Padi6_WT2_S2]


title: Tle6 -/- GV oocyte, biol rep 2 [Tle6_KO2_S5_A]

value: C57BL/6J strain background

value: Tle6 knockout


title: 8C,rep2

first: Songpeng

last: Zu

state: CA

department: Department of Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Paired-end sequencing reads were demultiplexed and the cell index transferred to the read name. Sequencing reads were aligned to mm10 reference genome using bwa.
We combined the sequencing reads to fragments with the function make_fragment_file in SnapATAC2. , and for each fragment we followed the quality controls: 1) Keep only fragments with quality scores MAPQ > 30; 2) remove PCR duplicates. Reads were also sorted based on cell barcodes in read names, and shifted +4 bp for positive strand and -5 bp for negative strand to correct the 9-bp duplication induced from Tn5 transposase.
We used the function filter_cells in SnapATAC2 to calculate TSSenrichment (TSSe). Nuclei with >=1,000 uniquely mapped fragments and TSSe >= 10 were filtered for each of 234 samples by following the ENCODE ATAC-seq data standards and process pipeline(https://www.encodeproject.org/atac-seq/). We used the function filter_cells in SnapATAC2 to filter out cells.
We applied a modified version of Scrublet to remove potential doublets for every sample independently using SnapATAC2. Firstly, we used the function of add_tile_matrix to add the 500-bp genomic bin features, then used the function of select_features to filter out the features with the frequencies along the samples lower than 0.5% or higher than 99.5%. Then applied the function of scrublet in SnapATAC2 to get the doublet scores. The parameter expected_doublet_rate is set to 0.08, which is based on our previous experiment on the snATAC-seq pipeline. Barcodes with the scrublet scores larger than 0.5 will be treated as potential doublets, and then removed from our analysis.
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: SnapATAC2 HDF5 matrix files (cells with the raw fragments, 500bp bmat)

source_name: brain

extract_protocol:
Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56-63 day old mice and sectioned into 600 µm coronal sections along the anterior-posterior axis in ice-cold dissection media. Specific brain regions were dissected according to the Allen Brain Reference Atlas (Wang, Q. et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell (2020). https://doi.org:10.1016/j.cell.2020.04.007). For each region, dissected brain tissues were pooled from 2-31 male C57BL/6J mice  to obtain enough nuclei for single nucleus ATAC-seq for each biological replica, and two biological replicas were performed.
Brain nuclei were pelleted with a swinging bucket centrifuge (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei pellets were resuspended in 1 ml nuclei permeabilization buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT and cOmpleteTM, EDTA-free protease inhibitor cocktail (Roche) in PBS) and pelleted again (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei were resuspended in 500 μl high-salt tagmentation buffer (36.3 mM Tris-acetate (pH 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% dimethylformamide) and counted using a haemocytometer. Concentration was adjusted to 1,000–4,500 nuclei per 9 μl, and 1,000–4,500 nuclei were dispensed into each well of a 96-well plate. For tagmentation, 1 μl barcoded Tn5 transposomes26 were added using a BenchSmart 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 μl of 40 mM EDTA was added to each well with a BenchSmart 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 μl 2× sort buffer (2% BSA, 2 mM EDTA in PBS) were added using a BenchSmart 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 μM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 nuclei were sorted per well into eight 96-well plates (total of 768 wells, 30,720 nuclei total, 15,360 nuclei per sample) containing 10.5 μl EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). If processing two samples per day, tagmentation was performed with different sets of barcodes in separate 96 well plates. After tagmentation nuclei from individual plates were pooled together. Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After the addition of 1 μl 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). Then, 1 μl 12.5% Triton X-100 was added to each well to quench the SDS. Next, 12.5 μl NEBNext High-Fidelity 2 × PCR Master Mix (NEB) were added and samples were amplified by PCR (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72 °C 60 s) × 11 or 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life Technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries generated with indexing version 1 were sequenced on a HiSeq2500 sequencer (Illumina) using custom sequencing primers, 25% spike-in library and following read lengths: 50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). Libraries generated with indexing version 2 were sequenced on a Libraries were sequenced on a HiSeq 4000 (Illumina) or a NovaSeq 6000 (Illumina) with these settings:  50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

value: brain

tag: tissue region

value: Isocortex

tag: number of_animals_pooled

value: Male

value: 8-9 weeks old

tag: library type

value: ATAC-seq


title: R1-AD1 FLAGHA-H3F3A AR KO clone 35, R1881 4 h


title: COHP_49207_487_TET_OFF_B_2wks

value: PBMC

tag: Sex

value: tTA+/-, BCR-ABL+/-


title: 8C,rep1

tag: age


title: Padi6 -/- GV oocyte, biol rep 3 [Padi6_KO3_S6]

value: FVB/N strain background

value: Padi6 knockout


title: COHP_49208_487_TET_OFF_B_3wks

value: F


title: 7C,rep2


title: R1-AD1 FLAGHA-H3F3A AR KO clone 30, R1881 24 h

source_name: R1-AD1 FLAGHA-H3F3A, AR KO clone 30

value: R1-AD1 FLAGHA-H3F3A, AR KO clone 30

value: Prostate cancer cells

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: 11A,rep1


title: R1-AD1 FLAGHA-H3F3A AR KO clone 35, EtOH

value: R1-AD1 FLAGHA-H3F3A, AR KO clone 35

value: EtOH


title: 11A,rep2


title: COHP_49206_487_TET_OFF_B_1wks


title: R1-AD1 FLAGHA-H3F3A AR KO clone 30, R1881 12 h


title: 7A,rep2


title: Padi6 -/- GV oocyte, biol rep 1 [Padi6_KO1_S4]

value: GV oocyte


title: COHP_49205_487_TET_OFF_B_0wks


title: 12A,rep2


title: 12A,rep1


title: 11C,rep2


title: R1-AD1 FLAGHA-H3F3A AR KO clone 30, EtOH


title: 11C,rep1


title: COHP_47027_508_TET_OFF_NIL_ON_D_10wks


title: R1-AD1 FLAGHA-H3F3A, R1881 24 h, biol rep 3

source_name: R1-AD1 FLAGHA-H3F3A

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_47028_508_TET_OFF_NIL_ON_D_11wks


title: 11D,rep1

value: brain

value: HPF


title: COHP_47029_508_TET_OFF_NIL_ON_D_12wks


title: 7A,rep1

value: Isocortex

value: Male

value: 8-9 weeks old


title: COHP_47026_508_TET_OFF_NIL_ON_D_9wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: 7C,rep1

value: ATAC-seq


title: R1-AD1 FLAGHA-H3F3A AR KO clone 30, R1881 4 h


title: 8A,rep2


title: 10G,rep2

value: TH


title: R1-AD1 FLAGHA-H3F3A,R1881 12 h, biol rep 3


title: R1-AD1 FLAGHA-H3F3A,R1881 4 h, biol rep 3


title: 10G,rep1


title: COHP_47024_508_TET_OFF_NIL_ON_D_7wks

value: F


title: 8A,rep1


title: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 3

value: Prostate cancer cells


title: COHP_47025_508_TET_OFF_NIL_ON_D_8wks


title: 10F,rep2


title: 10F,rep1


title: 9C,rep1


title: R1-AD1 FLAGHA-H3F3A, R1881 24 h, biol rep 2


title: 9C,rep2


title: COHP_47023_508_TET_OFF_NIL_ON_D_6wks


title: 10A,rep2


title: 11D,rep2


title: 10A,rep1


title: R1-AD1 FLAGHA-H3F3A,R1881 4 h, biol rep 2


title: 10E,rep1


title: Ependymal zone, short photoperiod > intermediate photoperiod, rep5

city: Tromsoe

first: Shona

last: Wood

address: Hansine Hansens veg 18

country: Norway

institute: UiT

description: Samples were sequenced by BGI using illumina hisq 4000. Note the count files use ensembl Ids for the mouse. This was produced by performing a liftoff annotation from the mouse on to our new phodopus sungorous genome.

data_processing:
QC checks and barcode removal according to BGI protocol
Both nanopore and illumina sequecing to produce a new assembly for the sibernian hamster. Then a liftoff annotation using: liftoff -g Mus_musculus.GRCm39.104.gff3 -o sib-ham-annotation.GFF3 sib-ham-assembly.fasta Mus_musculus.GRCm39.dna.toplevel.fa -polish. Subsequent genome assembly and annotation was used to map and count the reads.
Mapping of FASTQ files using bowtie2 using these parameters: bowtie2 -q --phred33 --fr -t -p 8 -x
Feature counts to count the mapped reads using these parameters: featureCounts -p -t exon -g gene_id
Assembly: SAMN28537735 : Siberian hamster liver DNA, BIOproject PRJNA839344, submission SUB11495380
Supplementary files format and content: Text files containing mouse ensembl Ids from the liftoff annotation and the number of counts per gene

organism: Phodopus sungorus

source_name: laser captured ependymal zone from 3rd ventricle of hypothalamus

growth_protocol: Animals were gestated on either short (8L:16D) or long photoperiods (16L:8D) and maintained on the indicated photoperiod or transfered to an intermediate photoperiod (14L:10D)

extract_protocol:
LCM method in the qiagen RNAeasy mini extraction kit
Library construction was performed by BGI: 1)mRNA enrichment and purification: rRNA depletion or Oligo dT Selection to enrich the mRNA  2)RNA fragment and reverse transcription  3)End repair, add A and adaptor ligation  4)RCR amplification  5)Single strand separation and cyclization  6)DNA nanoball synthesis  7)Sequencing on BGISEQ platform

treatment_protocol: Samples were collected immediately after sacrifice and snap frozen. A cyrostat was used to make slices and a laser capture microdissection mircoscope was used to microdissect the cells lining the 3rd ventricle of the hypothalamus, to ensure a tanycte enriched sample. Extraction was performed according to the qiagen RNAeasy mini protocol for laser captured material.

value: gestated on short photoperiod transfered to intermediate photoperiod


title: Ependymal zone, short photoperiod > intermediate photoperiod, rep4

value: laser captured ependymal zone from 3rd ventricle of hypothalamus


title: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 2

institute: University of Florida

value: EtOH


title: COHP_47020_508_TET_OFF_NIL_ON_D_3wks


title: 10E,rep2


title: COHP_47019_508_TET_OFF_NIL_ON_D_2wks


title: COHP_47018_508_TET_OFF_NIL_ON_D_1wks


title: Ependymal zone, short photoperiod > intermediate photoperiod, rep3


title: R1-AD1 FLAGHA-H3F3A, R1881 24 h, biol rep 1


title: COHP_47017_508_TET_OFF_NIL_ON_D_0wks


title: R1-AD1 FLAGHA-H3F3A,R1881 12 h, biol rep 2


title: Ependymal zone, short photoperiod > intermediate photoperiod, rep1


title: R1-AD1 FLAGHA-H3F3A,R1881 12 h, biol rep 1


title: 10C,rep1


title: R1-AD1 FLAGHA-H3F3A,R1881 4 h, biol rep 1


title: COHP_47016_507_TET_OFF_NIL_ON_D_16wks


title: Ependymal zone, short photoperiod, rep5

value: Short photoperiod


title: 9B,rep1


title: COHP_47022_508_TET_OFF_NIL_ON_D_5wks


title: 10C,rep2


title: Ependymal zone, short photoperiod, rep4


title: COHP_47015_507_TET_OFF_NIL_ON_D_15wks


title: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 1

value: R1-AD1 FLAGHA-H3F3A


title: R1-D567 FLAGHA-H3F3A, HIRA shRNA, biol rep 3

source_name: R1-D567 FLAGHA-H3F3A, HIRA shRNA

value: R1-D567 FLAGHA-H3F3A, HIRA shRNA

value: AR deltaLBD, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA shRNA


title: COHP_47021_508_TET_OFF_NIL_ON_D_4wks

source_name: PBMC


title: COHP_47014_507_TET_OFF_NIL_ON_D_14wks


title: 9B,rep2

value: brain


title: R1-D567 FLAGHA-H3F3A, HIRA shRNA, biol rep 2


title: R1-D567 FLAGHA-H3F3A, HIRA shRNA, biol rep 1


title: Ependymal zone, short photoperiod, rep3


title: Ependymal zone, short photoperiod, rep2


title: COHP_47012_507_TET_OFF_NIL_ON_D_12wks


title: Ependymal zone, short photoperiod > intermediate photoperiod, rep2


title: Ependymal zone, short photoperiod, rep1


title: COHP_47013_507_TET_OFF_NIL_ON_D_13wks


title: COHP_47011_507_TET_OFF_NIL_ON_D_11wks


title: R1-D567 FLAGHA-H3F3A, DAXX KO clone 39

source_name: R1-D567 FLAGHA-H3F3A, DAXX KO clone 39

value: R1-D567 FLAGHA-H3F3A, DAXX KO clone 39

value: AR deltaLBDFLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: Ependymal zone, long photoperiod > intermediate photoperiod, rep5

value: gestated on long photoperiod transfered to intermediate photoperiod


title: 12B,rep2

value: Isocortex

value: Male

value: 8-9 weeks old


title: COHP_47010_507_TET_OFF_NIL_ON_D_10wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: 12B,rep1

value: ATAC-seq


title: R1-D567 FLAGHA-H3F3A, DAXX KO clone 7

source_name: R1-D567 FLAGHA-H3F3A, DAXX KO clone 7

value: R1-D567 FLAGHA-H3F3A, DAXX KO clone 7

value: Prostate cancer cells

value: AR deltaLBD, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: Ependymal zone, long photoperiod > intermediate photoperiod, rep4

value: laser captured ependymal zone from 3rd ventricle of hypothalamus


title: COHP_47008_507_TET_OFF_NIL_ON_D_8wks

value: F


title: Ependymal zone, long photoperiod > intermediate photoperiod, rep2


title: COHP_47009_507_TET_OFF_NIL_ON_D_9wks


title: Ependymal zone, long photoperiod > intermediate photoperiod, rep3


title: 6B,rep2


title: COHP_47007_507_TET_OFF_NIL_ON_D_7wks


title: R1-D567 FLAGHA-H3F3A, AR KO clone 69

source_name: R1-D567 FLAGHA-H3F3A, AR KO clone 69

value: R1-D567 FLAGHA-H3F3A, AR KO clone 69

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO

value: EtOH


title: Ependymal zone, long photoperiod > intermediate photoperiod, rep1


title: R1-D567 FLAGHA-H3F3A, R1881 24 h, biol rep 3

source_name: R1-D567 FLAGHA-H3F3A

value: R1-D567 FLAGHA-H3F3A

value: AR deltaLBD, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_47006_507_TET_OFF_NIL_ON_D_6wks


title: COHP_47005_507_TET_OFF_NIL_ON_D_5wks


title: Ependymal zone, long photoperiod, rep6

value: long photoperiod


title: Ependymal zone, long photoperiod, rep5


title: 9A,rep2

value: brain

value: Isocortex


title: R1-D567 FLAGHA-H3F3A, DAXX KO clone 21

source_name: R1-D567 FLAGHA-H3F3A, DAXX KO clone 21

value: R1-D567 FLAGHA-H3F3A, DAXX KO clone 21


title: 7B,rep2

value: Male

value: 8-9 weeks old


title: R1-D567 FLAGHA-H3F3A, AR KO clone 15

source_name: R1-D567 FLAGHA-H3F3A, AR KO clone 15

value: R1-D567 FLAGHA-H3F3A, AR KO clone 15


title: Ependymal zone, long photoperiod, rep4


title: COHP_47004_507_TET_OFF_NIL_ON_D_4wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: Ependymal zone, long photoperiod, rep3


title: R1-D567 FLAGHA-H3F3A, AR KO clone 74

source_name: R1-D567 FLAGHA-H3F3A, AR KO clone 74

value: R1-D567 FLAGHA-H3F3A, AR KO clone 74

value: Prostate cancer cells


title: COHP_47003_507_TET_OFF_NIL_ON_D_3wks

value: F


title: R1-D567 FLAGHA-H3F3A, R1881 24 h, biol rep 2


title: 6A,rep1

value: ATAC-seq


title: R1-D567 FLAGHA-H3F3A, R1881 24 h, biol rep 1


title: R1-D567 FLAGHA-H3F3A, EtOH, biol rep 3


title: 7B,rep1


title: COHP_47002_507_TET_OFF_NIL_ON_D_2wks


title: Ependymal zone, long photoperiod, rep2

value: laser captured ependymal zone from 3rd ventricle of hypothalamus


title: R1-D567 FLAGHA-H3F3A, EtOH, biol rep 2

value: EtOH


title: 6A,rep2


title: COHP_47001_507_TET_OFF_NIL_ON_D_1wks


title: 9A,rep1


title: R1-D567 FLAGHA-H3F3A, EtOH, biol rep 1

value: R1-D567 FLAGHA-H3F3A


title: R1-D567 FLAGHA-H3F3A, HIRA shRNA, HA Ab, rep2

data_processing:
Reads were mapped to the GRCh38 human genome reference using Bowtie2.
ChIP-Seq peak calling was performed with MACS v2.2.7.1. with default parameters.
Assembly: GRCh38
Supplementary files format and content: MACS output file containing peak locations and fold enrichment.

extract_protocol:
Cells were fixed with 1% formaldehyde in PBS for 10 min at RT, quenched with glycine (f.c. 0.125 M) for 5 min. After cell lysis chromatin was sheared by Diagenode Bioraptor Pico with peak enrichment at 200 bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Cells were treated with 1 nM R1881 for 4, 12 or 24 hours

value: R1-D567 FLAGHA-H3F3A, HIRA shRNA

value: Prostate cancer

value: AR deltaLBD, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO

value: HA (BioLegend, # 901502)


title: Ependymal zone, long photoperiod, rep1

value: long photoperiod


title: COHP_46999_512_TET_OFF_NIL_ON_D_16wks

value: M


title: 6C,rep1

value: brain

value: Isocortex

value: Male

value: 8-9 weeks old


title: COHP_47000_507_TET_OFF_NIL_ON_D_0wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: R1-D567 FLAGHA-H3F3A, DAXX KO, HA Ab, rep2

source_name: R1-D567 FLAGHA-H3F3A, DAXX KO

value: R1-D567 FLAGHA-H3F3A, DAXX KO

value: AR deltaLBD, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: R1-D567 FLAGHA-H3F3A, HIRA shRNA, HA Ab, rep1


title: R1-D567 FLAGHA-H3F3A, DAXX KO, HA Ab, rep1


title: 9D,rep1

value: ATAC-seq


title: 6C,rep2


title: COHP_46998_512_TET_OFF_NIL_ON_D_15wks


title: COHP_46997_512_TET_OFF_NIL_ON_D_14wks


title: COHP_46996_512_TET_OFF_NIL_ON_D_13wks


title: 9D,rep2


title: COHP_46995_512_TET_OFF_NIL_ON_D_12wks


title: R1-D567 FLAGHA-H3F3A, AR KO, HA Ab, rep2

source_name: R1-D567 FLAGHA-H3F3A, AR KO

value: R1-D567 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: R1-D567 FLAGHA-H3F3A, HA Ab, rep2

value: R1-D567 FLAGHA-H3F3A

value: AR deltaLBD, FLAG-HA knock-in 5' ORF of H3F3A gene


title: R1-D567 FLAGHA-H3F3A, HA Ab, rep1

value: Prostate cancer


title: COHP_46993_512_TET_OFF_NIL_ON_D_10wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, H33S31Ph Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, H33S31Ph Ab, rep1


title: COHP_46989_512_TET_OFF_NIL_ON_D_6wks

value: M


title: COHP_46990_512_TET_OFF_NIL_ON_D_7wks


title: 6D,rep1

value: brain

value: OLF


title: 6D,rep2

value: Male


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, H33S31Ph Ab, rep 2


title: COHP_46988_512_TET_OFF_NIL_ON_D_5wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, H33S31Ph Ab, rep 1


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, H33S31Ph Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: COHP_46986_512_TET_OFF_NIL_ON_D_3wks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, H33S31Ph Ab, rep1


title: COHP_46984_512_TET_OFF_NIL_ON_D_1wks


title: COHP_46987_512_TET_OFF_NIL_ON_D_4wks


title: 11B,rep2

source_name: brain

value: Isocortex

value: 8-9 weeks old


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, H33S31Ph Ab, rep1

value: EtOH


title: COHP_46985_512_TET_OFF_NIL_ON_D_2wks


title: 11B,rep1

value: ATAC-seq


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, H33S31Ph Ab, rep 1


title: COHP_46991_512_TET_OFF_NIL_ON_D_8wks


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, H33S31Ph Ab, rep 2


title: COHP_46994_512_TET_OFF_NIL_ON_D_11wks


title: R1-D567 FLAGHA-H3F3A, AR KO, HA Ab, rep1

value: R1-D567 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO

value: HA (BioLegend, # 901502)


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, H33S31Ph Ab, rep1

value: Prostate cancer


title: COHP_46982_502_TET_OFF_NIL_ON_D_16wks


title: 7G,rep2

value: TH


title: COHP_46980_502_TET_OFF_NIL_ON_D_14wks

value: M


title: 2E,rep2

value: brain


title: COHP_46983_512_TET_OFF_NIL_ON_D_0wks


title: 13A,rep1


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, H33S31Ph Ab, rep1

source_name: R1-AD1 FLAGHA-H3F3A, AR KO

value: R1-AD1 FLAGHA-H3F3A, AR KO


title: R1-AD1 FLAGHAH3F3A cells, DAXX KO, H33S31Ph Ab, rep2


title: R1-AD1 FLAGHAH3F3A cells, HIRA KO, H33S31Ph Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, H33S31Ph Ab, rep2


title: 7G,rep1

value: Male


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, H33S31Ph Ab, rep 1


title: 13A,rep2


title: COHP_46977_502_TET_OFF_NIL_ON_D_11wks

value: PBMC


title: COHP_46975_502_TET_OFF_NIL_ON_D_9wks

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHAH3F3A cells, AR KO, H33S31Ph Ab, rep2


title: COHP_46976_502_TET_OFF_NIL_ON_D_10wks


title: COHP_46981_502_TET_OFF_NIL_ON_D_15wks


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, H33S31Ph Ab, rep1


title: COHP_46974_502_TET_OFF_NIL_ON_D_8wks


title: 8F,rep1


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, H33S31Ph Ab, rep2

source_name: R1-AD1 FLAGHA-H3F3A

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: 8F,rep2

value: 8-9 weeks old


title: Xenopus laevis egg extract, high pressure, time 2, rep2

city: Princeton

first: Martin

middle: H

last: Wühr

state: NJ

address: 246 Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton Univeristy

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to X. laevis v10.1 using STAR
Count normalization and differential expression analysis was performed with DESeq2
Assembly: X. laevis v10.1
Supplementary files format and content: rawCounts_allsamples.txt tab-delimited text file with raw counts for each sample
Supplementary files format and content: DESeq2.counts_normalized.txt tab-delimited text file with normalised DESeq2 counts for each sample

organism: Xenopus laevis

source_name: egg extract

extract_protocol:
TRIzol-based RNA extraction followed by isopropanol precipitation and RNA Clean & Concentrator kit (Zymo)
The RiboCop rRNA depletion Kit was used to deplete ribosomal RNA, followed by the PrepX RNA-Seq protocol (stranded - firststrand) to prepare the libraries according to the manufacturer's instructions.

value: egg extract

value: high pressure - time 2

tag: time

value: time 2


title: Xenopus laevis egg extract, high pressure, time 2, rep1


title: COHP_46979_502_TET_OFF_NIL_ON_D_13wks


title: 10B,rep2

value: Isocortex

value: ATAC-seq


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, H33S31Ph Ab, rep1

first: Alberto

last: Riva

address: 2033 Mowry Rd

value: Prostate cancer

tag: chip antibody


title: COHP_46973_502_TET_OFF_NIL_ON_D_7wks

tag: mouse id

value: M


title: Xenopus laevis egg extract, low pressure, time 1, rep3

value: low pressure - time 1

value: time 1


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, H33S31Ph Ab, rep 2

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: 10B,rep1

value: brain

value: Male


title: COHP_46971_502_TET_OFF_NIL_ON_D_5wks

tag: sample weeks

value: PBMC

value: tTA+/-, BCR-ABL+/-


title: 6B,rep1


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, H33S31Ph Ab, rep 2

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, H33S31Ph Ab, rep 1


title: COHP_46970_502_TET_OFF_NIL_ON_D_4wks

tag: batch


title: OVAtetramer_low

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

data_processing:
TCRseq data was assembled and aligned to reference V, D, J, and C genes of T-cell receptors using MiXCR v2.19 and built-in reference database. Specifically, a two-round assembly, including a first-round partial assembly and a second-round full assembly, was conducted to capture more clonotypes, referred to a specific CDR3 sequence. High-quality reads were firstly assembled into core clonotypes, which were then extended based on unique V and J genes against germline sequences. The final assembly was performed with error correction algorithms to merge similar clonotypes and their abundance.
Supplementary files format and content:  clonotypes and their abundance
Library strategy: TCR-seq

source_name: Spleen

growth_protocol: For B16OVA library, B16OVA cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues day 11 and analyzed by RNA-seq. For YUMM library, YUMM1.7 cells were subcutaneously injected into C57BL/6J mice. Total RNA was extracted from melanoma tissues day 12 and analyzed by RNA-seq. For dLN_KO library, C57BL/6J mice were subcutaneously injected with 50,000 Ctrl or NGF sgRNA B16-OVA cells. All mice in the Ctrl sgRNA group were sacrificed when tumor growth limits were exceeded. Tumor-free mice in the NGF sgRNA group were rechallenged with B16-OVA cells on day 78. 9 days later, OVA-tetramer+ CD8+ T cells were sorted from tumor draining lymph nodes and submitted for TCRb-seq. For dLN_NT_aPD-1 and dLN_KO_aPD-1 library, C57BL/6J mice were subcutaneously injected with 50,000 Ctrl or NGF sgRNA B16-OVA cells. 250 ug/mouse anti-PD-1 antibody was given twice. Tumor-free mice in both groups were rechallenged with B16-OVA cells on day 78. 9 days later, OVA-tetramer+ CD8+ T cells were sorted from tumor draining lymph nodes and submitted for TCRb-seq. For OVAtetramer_high and  OVAtetramer_low library, C57BL/6 mice were vaccinated i.v. with 0.1 LD50 of attenuated recombinant Listeria-OVA strain. OVA-tetramer-high and –low CD8 T cells were FACS-sorted from spleen on day 7 after a single vaccination, and then submitted for TCRb-seq.

extract_protocol:
Total RNA was extracted from OVA-tetramer+ CD8+ T cells using an RNeasy Mini Kit (Invitrogen) or from bulk tumor tissues using a Direct-zol RNA kit (ZYMO Research).
1 μg or lower amounts of RNA were converted into cDNA using a cDNA Synthesis Kit (Quantabio) with a constant region-specific primer. A multiplex PCR system was introduced to amplify the CDR3 region of rearranged TCRB loci. A set of forward primers, each specific to one or a set of functional TCR Vb segments, and a reverse primer specific to the constant region of TCRB, were used to generate amplicons covering the entire CDR3 region. PCR products were loaded onto 2.5% agarose gels, and bands centered at 250–400 bp were excised and purified using a QIAquick Gel Extraction kit (QIAGEN).

treatment_protocol: CRISPR/Cas9 technology was used to generate NGF knockout stable cell lines. C57BL/6 mice were vaccinated i.v. with 0.1 LD50 of attenuated recombinant Listeria-OVA strain.

value: Spleen

value: primary T cell

value: CD8+ T cells (OVA-tetramer-low)

value: WT

value: Listeria infection


title: COHP_46978_502_TET_OFF_NIL_ON_D_12wks

source_name: PBMC

tag: strain


title: Xenopus laevis egg extract, high pressure, time 2, rep3

value: egg extract

value: high pressure - time 2

value: time 2


title: COHP_46992_512_TET_OFF_NIL_ON_D_9wks

value: M

tag: genotype


title: COHP_46969_502_TET_OFF_NIL_ON_D_3wks


title: OVAtetramer_high

tag: cell line

value: CD8+ T cells (OVA-tetramer-high)


title: Xenopus laevis egg extract, low pressure, time 1, rep1

tag: cell type

value: low pressure - time 1

value: time 1


title: Xenopus laevis egg extract, input, time 0, rep3

tag: treatment

value: input

value: time 0


title: dLN_NT_aPD1

source_name: Lymph node

tag: tissue

value: Lymph node

value: CD8+ T cells

value: WT (melanoma cell)

value: control plus anti-PD-1


title: Xenopus laevis egg extract, input, time 0, rep2


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, BRD4 Ab, rep2

city: Gainesville

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO

value: BRD4 (Fortis Life Science, # A301-985A100)


title: dLN_KO

value: primary T cell

value: NGF-/- (melanoma cell)

value: Knockout


title: COHP_46967_502_TET_OFF_NIL_ON_D_1wks

value: PBMC

value: M

value: tTA+/-, BCR-ABL+/-


title: Xenopus laevis egg extract, input, time 0, rep1

value: egg extract


title: COHP_46972_502_TET_OFF_NIL_ON_D_6wks


title: COHP_46968_502_TET_OFF_NIL_ON_D_2wks


title: dLN_KO_aPD1

value: Knockout plus anti-PD-1


title: COHP_46966_502_TET_OFF_NIL_ON_D_0wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, BRD4 Ab, rep1


title: Xenopus laevis egg extract, low pressure, time 1, rep2

value: low pressure - time 1

value: time 1


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, BRD4 Ab, rep 2


title: Germ cell samples 21-40

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

description:
Germ_24h_BGJ500_M1, Germ_24h_BGJ500_M3, Germ_24h_BGJ500_M4, Germ_24h_BGJ500_M5, Germ_72h_BGJ500_M2, Germ_72h_BGJ500_M4, Germ_72h_BGJ500_M5, Germ_72h_BGJ500_M6, Germ_72h_DMSO_F11, Germ_72h_DMSO_F4, Germ_72h_DMSO_F7, Germ_72h_DMSO_F8, Germ_72h_DMSO_M2, Germ_72h_DMSO_M4, Germ_72h_DMSO_M5, Germ_72h_DMSO_M6, Germ_72h_PD500_M2, Germ_72h_PD500_M3, Germ_72h_PD500_M4, Germ_72h_PD500_M5
germ_gene_counts.tsv
germ_sample_barcodes.tsv

data_processing:
FASTQ files were processed and mapped using scPipe (Tian et al., 2018) and Rsubread (Liao et al., 2019) (Bioconductor) packages in R studio. Briefly, FASTQ files were reformatted with sc_trim_barcode to incorporate barcode information from read 1 into read 2 into the header. Reads were aligned to a reference mouse genome (GENECODE GRCm39) using Rsubread. Reads were assigned to annotated exons with sc_exon_mapping, data were demultiplexed using sc_demultiplex and a gene count matrix was generated with UMI deduplication using sc_gene_counting. Gene count matrices from each set  were combined into a DGEList object for analysis.
Differential gene expression was assessed using the limma (Ritchie et al., 2015), Glimma (Su et al., 2017) and edgeR (Robinson et al., 2009) Bioconductor packages following a previously established workflow (Law et al., 2016).

source_name: Germ cells

growth_protocol: Gonad-mesonephros samples were cultured on 30mm Millicell Biopore membranes with 0.4μM pores in media containing 15mM Hepes, 0.1mM non-essential amino acids, 1mg/mL N-acetylcysteine, 1X penicillin/streptomycin, 55nM beta-mercaptoethanol and 10% fetal calf serum in DMEM/F12 with Glutamax supplemented with DMSO or inhibitor. Mesonephros was removed and cells sorted using FACS. Oct4-eGFP transgene was used to isolate GFP+ germ cells.

extract_protocol:
RNA was extracted using Macherey-Nagel NucleoSpin® RNA XS extraction kit (Scientifix, 740902.50). Libraries were prepared with 30ng of RNA.
Novel RNA-Seq pipeline. Briefly, index is added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by PCR and P7 by Nextera transposase. I7 indexes were added to the final libraries to enable parsing of sample sets. Sequencing was performed on NextSeq2000 (Illumina) following Illumina protocol 1000000109376 v3.

value: Germ cells

value: ASMU Swiss by Oct4(Pou5fl)-eGFP on 129svJT2 background

value: WT

value: mixed sample (non-demultiplexed)


title: COHP_46965_488_TET_ON_C_18wks

value: F


title: YUMM_NT_2 (biol rep 2)

source_name: Tumor

value: Tumor

value: melanoma

value: WT (melanoma cell)

value: Control


title: R1-AD1 FLAGHAH3F3A cells, H33S31Ph Ab, rep2

value: R1-AD1 FLAGHA-H3F3A

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene

value: EtOH


title: YUMM_NT_1 (biol rep 1)


title: 5G,rep2

value: brain

value: OLF

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: R1-AD1 FLAGHAH3F3A cells, HIRA KO, BRD4 Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO

value: BRD4 (Fortis Life Science, # A301-985A100)


title: COHP_46964_488_TET_ON_C_17wks

value: PBMC

value: F

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHA-H3F3A cells, H33S31Ph Ab, rep1


title: 5G,rep1


title: COHP_46963_488_TET_ON_C_16wks


title: COHP_46962_488_TET_ON_C_15wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, BRD4 Ab, rep1


title: YUMM_KO_3 (biol rep 3)

value: Tumor

value: melanoma

value: NGF-/- (melanoma cell)

value: Knockout


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, BRD4 Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: 1B,rep1

value: brain

value: OLF


title: YUMM_KO_2 (biol rep 2)


title: COHP_46961_488_TET_ON_C_14wks


title: YUMM_KO_1 (biol rep 1)


title: 1B,rep2

value: Male

value: 8-9 weeks old


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 12 h, BRD4 Ab, rep1


title: 3C,rep2

value: Isocortex

value: ATAC-seq


title: COHP_46959_488_TET_ON_C_12wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, BRD4 Ab, rep 1

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO

value: BRD4 (Fortis Life Science, # A301-985A100)


title: Germ cell samples 1-20

description:
Germ_0h_F2, Germ_0h_F3, Germ_0h_F4, Germ_0h_F5, Germ_0h_M2, Germ_0h_M3, Germ_0h_M5, Germ_0h_M6, Germ_24h_DMSO_F4, Germ_24h_DMSO_F5, Germ_24h_DMSO_F6, Germ_24h_DMSO_F9, Germ_24h_DMSO_M2, Germ_24h_DMSO_M3, Germ_24h_DMSO_M4, Germ_24h_DMSO_M5, Germ_24h_PD500_M1, Germ_24h_PD500_M2, Germ_24h_PD500_M4, Germ_24h_PD500_M6
germ_gene_counts.tsv
germ_sample_barcodes.tsv

value: Germ cells

value: ASMU Swiss by Oct4(Pou5fl)-eGFP on 129svJT2 background

value: WT

value: mixed sample (non-demultiplexed)


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, BRD4 Ab, rep 2


title: B16OVA_NT_4 (biol rep 4)

value: Tumor

value: melanoma

value: WT (melanoma cell)

value: Control


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 4 h, BRD4 Ab, rep 1

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: COHP_46960_488_TET_ON_C_13wks

value: PBMC

value: F

value: tTA+/-, BCR-ABL+/-


title: 3C,rep1

value: brain

value: Isocortex

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: YUMM_NT_3 (biol rep 3)


title: B16OVA_NT_3 (biol rep 3)


title: COHP_46958_488_TET_ON_C_11wks


title: B16OVA_NT_2 (biol rep 2)


title: COHP_46957_488_TET_ON_C_10wks


title: 4D,rep2

value: STR


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, BRD4 Ab, rep1

value: BRD4 (Fortis Life Science, # A301-985A100)

value: EtOH


title: 4D,rep1


title: R1-AD1 FLAGHAH3F3A cells, DAXX KO, BRD4 Ab, rep2


title: COHP_46956_488_TET_ON_C_9wks


title: B16OVA_NT_1 (biol rep 1)

value: Tumor

value: melanoma


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, BRD4 Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: B16OVA_KO_4 (biol rep 4)

value: NGF-/- (melanoma cell)

value: Knockout


title: 4C,rep2


title: COHP_46955_488_TET_ON_C_8wks

value: PBMC


title: 4C,rep1


title: B16OVA_KO_3 (biol rep 3)


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 12 h, BRD4 Ab, rep1

value: Prostate cancer


title: COHP_46954_488_TET_ON_C_7wks

value: F

value: tTA+/-, BCR-ABL+/-


title: 3D,rep2

value: brain

value: Isocortex


title: 3D,rep1

value: Male

value: 8-9 weeks old


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, BRD4 Ab, rep 1


title: COHP_46953_488_TET_ON_C_6wks


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, R1881, 4 h, BRD4 Ab, rep 2


title: R1-AD1 FLAGHAH3F3A cells, AR KO, BRD4 Ab, rep2


title: COHP_46952_488_TET_ON_C_5wks


title: 5J,rep2

value: STR

value: ATAC-seq


title: COHP_46951_488_TET_ON_C_4wks


title: MiE-24

city: Jacksonville

first: Yingxue

last: Ren

address: 4500 San Pablo Rd S

institute: Mayo Clinic

library_source: transcriptomic single cell

data_processing:
The single cell sequence preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite (v3.0.0).
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering and differential expression analyses were performed using Seurat v.4.0.
Assembly: mm10
Supplementary files format and content: matix files

source_name: cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P) (Cat#130-092-628, Myltenyi Biotec) at 37˚C in the gentleMACS™ Octo Dissociator with Heaters (Myltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat#130-096-733, Myltenyi Biotec). After myelin removal, samples were subjected to red blood cell removal (Cat.# 130-094-183, Miltenyi Biotec), followed by dead cell removal  (Cat. #130-090-101, Miltenyi Biotec) according to the manufacturer’s instructions. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
Libraries were prepared using the Chromium platform (10x Genomics) with the 3′ gene expression (3′ GEX) V3 kit with a targeted input of ~ 6,000 cells per sample following the manufacturer’s instructions.

tag: group


title: 5J,rep1

tag: tissue region


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, BRD4 Ab, rep1

value: BRD4 (Fortis Life Science, # A301-985A100)

value: EtOH


title: 5D,rep2

tag: number of_animals_pooled


title: MiE-23


title: COHP_46950_488_TET_ON_C_3wks


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, BRD4 Ab, rep2

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: COHP_46949_488_TET_ON_C_2wks


title: 5D,rep1

tag: library type


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, BRD4 Ab, rep1


title: MiE-22


title: 2C,rep2

tag: Sex


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, BRD4 Ab, rep 2


title: MiE-20


title: COHP_46947_488_TET_ON_C_0wks


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, BRD4 Ab, rep 1


title: B16OVA_KO_1 (biol rep 1)

value: Tumor

value: melanoma


title: B16OVA_KO_2 (biol rep 2)

value: NGF-/- (melanoma cell)

value: Knockout


title: MiE-19


title: 8B,rep1

tag: age


title: 8B,rep2


title: MiE-18


title: COHP_46946_477_TET_OFF_B_7wks

value: PBMC


title: COHP_46944_477_TET_OFF_B_5wks

value: F


title: R1-AD1 FLAGHA-H3F3A cells, BRD4 Ab, rep1

value: Prostate cancer


title: R1-AD1 FLAGHAH3F3A cells, BRD4 Ab, rep2


title: 4G,rep2

value: brain


title: COHP_46945_477_TET_OFF_B_6wks

value: tTA+/-, BCR-ABL+/-


title: R1-AD1 FLAGHAH3F3A cells, AR KO, AR Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO

value: AR (Santa Cruz, # sc-816)


title: MiE-17


title: MiE-21


title: COHP_46948_488_TET_ON_C_1wks


title: MiE-16


title: R1-AD1 FLAGHA-H3F3A cells, AR KO, AR Ab, rep1


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 24 h, AR Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: MiE-15


title: COHP_46942_477_TET_OFF_B_3wks


title: COHP_46943_477_TET_OFF_B_4wks


title: 2C,rep1

value: Isocortex

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: MiE-14


title: COHP_46941_477_TET_OFF_B_2wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 24 h, AR Ab, rep1


title: MiE-13


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, AR Ab, rep2


title: COHP_46940_477_TET_OFF_B_1wks


title: 5C,rep1


title: COHP_46939_477_TET_OFF_B_0wks


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 12 h, AR Ab, rep1


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, AR Ab, rep 2


title: MiE-11


title: 5A,rep2


title: MiE-12


title: MiE-10


title: 5C,rep2


title: COHP_46938_484_TET_OFF_B_11wks

value: M


title: 4G,rep1

value: STR


title: 2D,rep2

value: OLF


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, R1881, 4 h, AR Ab, rep 1


title: COHP_46936_484_TET_OFF_B_9wks

value: PBMC


title: COHP_46937_484_TET_OFF_B_10wks


title: 3E,rep2


title: MiE-9


title: COHP_46935_484_TET_OFF_B_8wks


title: 5A,rep1


title: MiE-8


title: R1-AD1 FLAGHAH3F3A cells, HIRA KO, AR Ab, rep2

value: EtOH


title: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, AR Ab, rep1

value: Prostate cancer


title: MiE-7


title: 2D,rep1

value: brain


title: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, R1881, 24 h, AR Ab, rep2

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: 4B,rep1


title: COHP_46934_484_TET_OFF_B_7wks

value: tTA+/-, BCR-ABL+/-


title: COHP_46933_484_TET_OFF_B_6wks


title: 4B,rep2