title: HiC_NC_rep2

data_processing:
Hi-C data was processed by HiC-Pro (Servant et al., 2015). Briefly, reads were first aligned on the hg19 reference genome. Uniquely mapped reads were normalized using Iterative Correction and Eigenvector decomposition (ICE) and library size. For, compartment A/B analysis, HiTC (Servant et al., 2012) was used to visualize the interaction matrix and calculate the PC1 (at 150-kb resolution). And defining compartment switches by comparing the PC1 values between wildtype and NuMA depleted HCT116 cell.
Assembly: hg19
Supplementary files format and content: Hi-C interaction matrix

extract_protocol: The in situ Hi-C libraries was performed as previously described (Rao et al., 2014). Briefly, cells were grown to about 70%-80 % confluence, washed with PBS, fixed in 1% formaldehyde were suspended in Hi-C lysis buffer, to which 100 U MobI restriction enzyme (NEB, R0147) was added for overnight chromatin digestion. Free ends were labeled with biotin and then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500 bp and then biotinylated ligation junctions were recovered with streptavidin beads. Hi-C libraries were amplified using PCR and constructed according to the NEBnext library preparation protocol (NEB, E7335) and sequenced on the Illumina HiSeq X Ten platform.

value: colon cancer

value: human colon cancer cell line

value: wild type


title: JN_L12_1

status: Public on Mar 01 2024

type: SRA

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd

country: USA

institute: Children's Hospital of Philadelphia

description: RNA

library_source: transcriptomic

data_processing:
RNA sequencing reads were aligned to hg38 using STAR (v2.7.0f)
The index was prepared using default parameters except for ‐‐sjdbGTFfile, where the Gencode v23 annotations were used
Default parameters were used for alignment with the following modifications: ‐‐readFilesCommand zcat ‐‐outReadsUnmapped Fastx ‐‐quantMode GeneCounts ‐‐outSAMtype BAM SortedByCoordinate.
Gene‐level transcript quantification was performed using STAR's built‐in quantification algorithm
After filtering for low abundance transcripts differential expression analysis was carried out using DESeq2 (v1.28.1)
Significant genes were determined using a cutoff of adjusted p < 0.01
GSEA was performed with the fgsea (1.14.0) package
Kegg pathway enrichment analysis was performed with the clusterProfiler (v3.16.1) package
A hypergeometric test was used to calculate overlap significance of differentially expressed gene sets.
Genome_build: hg38
Supplementary_files_format_and_content: FGC2198_featureCounts.txt. TXT file of raw gene counts for washout samples.
Supplementary_files_format_and_content: STAR_raw_counts_with_ext_gene_lurb.txt. TXT file of raw gene counts for continuous samples.

molecule: total RNA

organism: Homo sapiens

source_name: JN-DSRCT-1 cells

growth_protocol: Cells were grown at 37_C with 5% CO2. RPMI1640 was supplemented with 10% FBS, 2 mmol/L L-glutamine, and 100 U/mL and 100 mg/mL penicillin and streptomycin, respectively.

extract_protocol:
RNA was extracted using the Qiagen RNEasy Mini kit.
Libraries prepared with Illumina's stranded poly-A selection kit

treatment_protocol: Continuous samples had media aspirated and replaced with 5nM lurbinectedin. Washout samples were treated with 25nM lurbinectedin for 1 hr followed by replacement with drug free medium

tag: cell line

value: JN-DSRCT-1 cells

tag: treatment

value: lurbinectedin

tag: time point

value: 12 hours washout


title: JN_L6_2

description: RNA

value: 6 hours washout


title: JN_L6_3

description: RNA


title: HiC_NC_rep1

city: Beijing

first: Wenxue

last: Zhao

address: Yiheyuan Road

country: China

institute: Peking University

library_source: genomic

molecule: genomic DNA

source_name: colon cancer

tag: tissue

tag: cell type

tag: genotype


title: JN_L6_1

description: RNA


title: B_M3

description: RNA

source_name: BER cells

value: BER cells

value: media

value: 16 hours washout


title: HiC_AID_rep2

value: NuMA depletion


title: 167: WT mice, 20 weeks NASH diet

city: Ann Arbor

first: Sujuan

last: Wang

state: MI

address: 2800 Plymouth Road

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
RNA-seq
Sequencing data Filtering: remove the reads mapped to rRNA and get raw data, and then processed and removed the sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads
Genome Mapping: mapped clean reads to reference genome using HISAT2
Gene Expression Analysis
Assembly: HISAT2(http://daehwankimlab.github.io/hisat2/)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Liver

growth_protocol: All mice are housed on a 12 hours:12 hours light/dark cycle at 25℃ with free access to water and regular chow (26.8% kcal from protein, 16.6% kcal from fat, and 56.4% kcal from starch).

extract_protocol:
RNA was harvested using Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription:Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The  synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Two-month old WT mice and E4bp4 liver specific knockout (E4bp4-LKO) mice to NASH diet for 20 weeks.

value: Liver

value: WT

value: NASH diet, 20 weeks


title: BM mRNA-Seq DbhVLM-mCherry replicate 3

city: Hefei

first: Liang

state: Anhui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

molecule: polyA RNA

source_name: bone marrow CD45+ cells

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 7 am to 7 pm), and ad libitum access to water and a standard chow diet.

extract_protocol:
Total RNA of CD45+ cells was extracted using a Takara MiniBest Universal RNA Extraction kit (code no. 9767) according to the manufacturer’s instructions. Poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).
poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).First-strand cDNA was synthesized with the SuperScript II Reverse Transcriptase (Invitrogen,18064014) and Second Strand cDNA was synthesized using Second Strand cDNA Synthesis Kit (Invitrogen,A48570). Libraries were subsequently constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB,E7645L).

treatment_protocol: AAV-DIO-hM3Dq-mCherry or the same volume of AAV-DIO-mCherry was bilaterally injected into the VLM of Dbh-Cre mice. CD45+ cells were obtained from the spleen and bone marrow 4 hour after CNO injections.

value: bone marrow CD45+ cells

tag: strain

value: DbhVLM-mCherry

tag: growth phase

value: 12 week

value: CNO injections


title: HiC_AID_rep1

value: colon cancer

value: human colon cancer cell line


title: SP mRNA-Seq DbhVLM-hM3Dq replicate 5

source_name: spleen CD45+ cells

value: spleen CD45+ cells


title: 166: WT mice, 20 weeks NASH diet


title: B_M2

description: RNA


title: 165: WT mice, 20 weeks NASH diet


title: BM mRNA-Seq DbhVLM-mCherry replicate 2


title: 179: E4bp4-LKO mice, 20 weeks NASH diet


title: A_#5 scTCR-Seq

city: Seoul

first: Su-Young

last: Kim

address: 81, Irwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description:
A_#5
10x Genomics

data_processing:
We used Cell Ranger v5.0.0 (10x Genomics) pipeline for FASTQ file generation from raw sequencing data, gene expression analysis of 5’ gene expression library data, and immune profiling analysis of V(D)J enriched library data.
Raw count matrices of 10x Genomics resulting by Cell Ranger ‘aggr’ were imported to Seurat 3.1.3.
Assembly: GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: 10x Genomics output files: clonotypes.csv, consensus_annotations.csv, filtered_contig_annotations.csv / clonotypes.csv : high-level descriptions of each clonotype / consensus_annotations.csv : high-level and detailed annotations of each clonotype consensus sequence / filtered_contig_annotations.csv : high-level annotations of each high-confidence contig from cell-associated barcodes.

source_name: Blood

extract_protocol:
PBMCs were isolated from peripheral venous blood via standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation, frozen in freezing media, and stored in liquid nitrogen until use. All samples showed a high viability of about 94% on average after thawing. LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) was used to consult the 10x Genomics Single Cell Protocols Cell Preparation Guide with the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126 respectively) for more information on preparing cells.
Libraries were prepared using the Chromium controller according to the 10x Chromium Next GEM Single Cell V(D)J User Guide (10x Genomics). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and enriched with PCR. For V(D)J Enriched Library, the enriched cDNA pool was first amplified using T Cell Mix1 primer and second amplified using T Cell Mix2 primer. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). And then the libraries were sequenced using HiSeq platform (Illumina) according to the read length in the user guide.
scTCR-seq

value: Blood

value: PBMC

tag: disease stage

value: Spontaneous culture conversion 5


title: B_M1

description: RNA

value: BER cells


title: BM mRNA-Seq DbhVLM-mCherry replicate 1


title: A_#4 scTCR-Seq

description:
A_#4
10x Genomics

value: Spontaneous culture conversion 4


title: B_S16_3

description: RNA

value: solvent

value: 16 hours washout


title: BM mRNA-Seq DbhVLM-hM3Dq replicate 8


title: AcrIIA5 pre-sort single-mutant library replicate 2 [AcrDMS_v2_26-2]

city: Heidelberg

first: Dominik

last: Niopek

state: Baden-Württemberg

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences

country: Germany

institute: Heidelberg University

library_source: other

data_processing:
*library strategy: Amplicon sequencing
combine paired-end reads with exact matches in overlapping sequence
discard reads without an exact match in the overlapping sequence
translate Acr ORF in combined reads, discarding reads with more than one non-silent mutation relative to the wildtype
count remaining reads for each variant in each fraction and replicate
Assembly: not applicable
Supplementary files format and content: files named "count_matrix_(a4|a5)_rep_(1|2|3).csv" contain read counts for the wildtype and all single mutants of AcrIIA4 (a4) and AcrIIA5 (a5) across three replicates (rep_1, rep_2, rep_3). Columns are comma-separated. The first row contains a brief description of the columns. Column 1 contains the name of each single-mutant: wt for the wild type, and single-mutants named <wt amino acid><1-based position><mutated amino acid>, e.g. E9P for the variant with the position 9 glutamic acid mutated to a proline. Columns 2-5 contain the read counts for each variant in the sorted fractions 1-4.
Supplementary files format and content: files named "count_matrix_library_replicates_(a4|a5).csv" contain read counts for the wildtype and all single mutants of AcrIIA4 (a4) and AcrIIA5 (a5) across two sequencing replicates of the initial AcrIIA4 and AcrIIA5 libraries. Columns are comma-separated. The first row contains a brief description of each column. Column 1 contains the name of the variant (wt or <wt-aa><position><mutant-aa>, e.g. E9P, for the variant with the E at position 9 mutated to P). Columns 2 and 3 contain the read-count for that variant in replicate 1 and 2, respectively.

molecule: other

organism: Escherichia coli DH5[alpha]

source_name: DH5-alpha, genotpye: E. coli DH5a fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17

extract_protocol:
Plasmid purification from E. coli
Amplikon sequencing library. Acr region was amplified from purified plasmids using primers with partial Illumina adapter overhang followed by gel purification of DNA fragments. Library preparation was performed by PCR barcoding of DNA fragments using the Nextera XT Index Kit v2 (Illumina).

value: E. coli plasmid harboring Acr DMS library


title: 164: WT mice, 20 weeks NASH diet

value: Liver

value: WT


title: 143: E4bp4-LKO mice, 20 weeks NASH diet

value: NASH diet, 20 weeks


title: B_S16_2

description: RNA


title: BM mRNA-Seq DbhVLM-mCherry replicate 4

value: bone marrow CD45+ cells

value: DbhVLM-mCherry


title: B_S16_1

description: RNA


title: C-2_#3 scTCR-Seq

description:
C-2_#3
10x Genomics

value: Progressive disease_unfavorable 3


title: BM mRNA-Seq DbhVLM-hM3Dq replicate 6

value: 12 week

value: CNO injections


title: AcrIIA5 pre-sort single-mutant library replicate 1 [AcrDMS_v2_26]


title: B_#7 scTCR-Seq

description:
B_#7
10x Genomics

value: Stable disease 7


title: BM mRNA-Seq DbhVLM-hM3Dq replicate 7


title: B_#6 scTCR-Seq

description:
B_#6
10x Genomics

value: Blood

value: Stable disease 6


title: B_L16_2

description: RNA

value: lurbinectedin


title: AcrIIA4 pre-sort single-mutant library replicate 2 [AcrDMS_v2_25-2]


title: A_#2 scTCR-Seq

description:
A_#2
10x Genomics

value: PBMC

value: Spontaneous culture conversion 2


title: BM mRNA-Seq DbhVLM-hM3Dq replicate 5


title: AcrIIA5 single-mutant library fraction 4 replicate 3 [AcrDMS_v2_24]


title: AcrIIA4 pre-sort single-mutant library replicate 1 [AcrDMS_v2_25]


title: B_L16_1

description: RNA

value: BER cells


title: A_#3 scTCR-Seq

description:
A_#3
10x Genomics

value: Spontaneous culture conversion 3


title: AcrIIA5 single-mutant library fraction 3 replicate 3 [AcrDMS_v2_23]

value: E. coli plasmid harboring Acr DMS library


title: C3: SfB-ABCFPfA_mfLon-rep3

city: Tianjin

first: Hao

last: Qi

address: No. 135 Yaguan Road, Haihe Educaton Park

institute: Tianjin University

data_processing:
Bcl2fastq (v2.17.1.14) software for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli BL21(DE3) whole genome using Bowtie v2.2.6.
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi et al., Nature methods, 2008
Genome_build: E.coli BL21(DE3) （GenBank: CP001509.3）
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM values for every gene and every sample

organism: Escherichia coli

source_name: Ecoli cells

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SfB-ABCFPfA

tag: abbreviations in data


title: B_S12_3

description: RNA

value: solvent

value: 12 hours washout


title: C2: SfB-ABCFPfA_mfLon-rep2


title: B_#4 scTCR-Seq

description:
B_#4
10x Genomics

value: Stable disease 4


title: B_#5 scTCR-Seq

description:
B_#5
10x Genomics

value: Stable disease 5


title: C1: SfB-ABCFPfA_mfLon-rep1


title: B_S12_2

description: RNA


title: B_S12_1

description: RNA


title: A3: S-AB_mfLon-rep3

value: S-AB


title: AcrIIA5 single-mutant library fraction 1 replicate 3 [AcrDMS_v2_21]


title: B_#3 scTCR-Seq

description:
B_#3
10x Genomics

value: Stable disease 3


title: B_L16_3

description: RNA

value: 16 hours washout


title: A2: S-AB_mfLon-rep2


title: AcrIIA5 single-mutant library fraction 2 replicate 3 [AcrDMS_v2_22]


title: C-1_#3 scTCR-Seq

description:
C-1_#3
10x Genomics

value: Progressive disease_favorable 3


title: B_L12_3

description: RNA


title: A_#1 scTCR-Seq

description:
A_#1
10x Genomics

value: Blood

value: Spontaneous culture conversion 1


title: A1: S-AB_mfLon-rep1


title: AcrIIA4 single-mutant library fraction 3 replicate 3 [AcrDMS_v2_19]


title: AcrIIA4 single-mutant library fraction 4 replicate 3 [AcrDMS_v2_20]


title: B_L12_2

description: RNA

value: lurbinectedin


title: W3: BL21(DE3) Star_mfLon-rep3


title: AcrIIA4 single-mutant library fraction 2 replicate 3 [AcrDMS_v2_18]


title: B_L12_1

description: RNA


title: W2: BL21(DE3) Star_mfLon-rep2


title: B_S6_3

description: RNA

value: 6 hours washout


title: AcrIIA4 single-mutant library fraction 1 replicate 3 [AcrDMS_v2_17]


title: W1: BL21(DE3) Star_mfLon-rep1


title: B_#1 scTCR-Seq

description:
B_#1
10x Genomics

value: PBMC

value: Stable disease 1


title: AcrIIA5 single-mutant library fraction 4 replicate 2 [AcrDMS_v2_16]


title: B_S6_2

description: RNA

value: BER cells


title: AcrIIA5 single-mutant library fraction 3 replicate 2 [AcrDMS_v2_15]

value: E. coli plasmid harboring Acr DMS library


title: C-x_#3 scTCR-Seq

description:
C-x_#3
10x Genomics

value: Progressive disease_refusing treatment


title: AcrIIA5 single-mutant library fraction 2 replicate 2 [AcrDMS_v2_14]


title: C-1_#1 scTCR-Seq

description:
C-1_#1
10x Genomics

value: Progressive disease_favorable 1


title: C-x_#2 scTCR-Seq

description:
C-x_#2
10x Genomics


title: B_S6_1

description: RNA

value: solvent


title: B_#2 scTCR-Seq

description:
B_#2
10x Genomics

value: Stable disease 2


title: B_L6_2

description: RNA


title: B_L6_1

description: RNA


title: AcrIIA4 single-mutant library fraction 4 replicate 2 [AcrDMS_v2_12]


title: AcrIIA5 single-mutant library fraction 1 replicate 2 [AcrDMS_v2_13]


title: C-x_#1 scTCR-Seq

description:
C-x_#1
10x Genomics

value: Progressive disease_follow-up loss


title: C-2_#1 scTCR-Seq

description:
C-2_#1
10x Genomics

value: Progressive disease_unfavorable 1


title: AcrIIA4 single-mutant library fraction 3 replicate 2 [AcrDMS_v2_11]


title: C-1_#2 scTCR-Seq

description:
C-1_#2
10x Genomics

value: Progressive disease_favorable 2


title: AcrIIA4 single-mutant library fraction 2 replicate 2 [AcrDMS_v2_10]


title: JM2

description: RNA

value: JN-DSRCT-1 cells

value: media

value: 12 hours continuous


title: JM3

description: RNA


title: JM1

description: RNA


title: B_L6_3

description: RNA


title: Seq02_Tfh_5

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

institute: University Hospital Bonn

data_processing:
Fastq files were demultiplexes with Multi Demultiplex (Galaxy Version 1.0) using Illumina Index file
All raw fastq data were mapped to the mouse genome (mm10) using STAR 2.7.2b (Dobin et al., 2013)
Count matrices were generated using FeatureCount 1.6.4 (Liao et al., 2014) with the gene annotation file for mm10
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts

source_name: activated murine CD4 T cells in vitro

growth_protocol: Isolated naive CD4 cells were cultured in cRPMI for 3.5 days

extract_protocol:
Cells were stained for flow cytometry and and sorted directly into Trizol LS. RNA was isolated using Maxwell RSC miRNA Tissue Kit (Promega) and purified using Agencourt RNAClean XP Beads (Beckman Coulter)
Libraries were generated with the SENSE mRNA-Seq Lib Prep Kit V2 (Lexogen) using 100 ng RNA as input and with half of the volume as described in the manual. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter)

treatment_protocol: The cell culture are activated with plate-bound anti-CD3 and anti-CD28 and differentiated in the indicated conditions

value: CD4 T cell

tag: condition

value: Tfh


title: Seq02_Tfh_4


title: A_#5

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We used Cell Ranger v5.0.0 (10x Genomics) pipeline for FASTQ file generation from raw sequencing data and gene expression analysis of 5’ gene expression library data.
Raw count matrices of 10x Genomics resulting by Cell Ranger ‘aggr’ were imported to Seurat 3.1.3.
Assembly: GRCh38-2020-A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
PBMCs were isolated from peripheral venous blood via standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation, frozen in freezing media, and stored in liquid nitrogen until use. All samples showed a high viability of about 94% on average after thawing. LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) was used to consult the 10x Genomics Single Cell Protocols Cell Preparation Guide with the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126 respectively) for more information on preparing cells.
Libraries were prepared using the Chromium controller according to the 10x Chromium Next GEM Single Cell User Guide (10x Genomics). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and enriched with PCR. For 5’ Gene Expression Library, the cDNA pool go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the 5’ Gene Expression Library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). And then the libraries were sequenced using HiSeq platform (Illumina) according to the read length in the user guide.

value: Blood

value: Spontaneous culture conversion 5


title: A_#4

description: 10x Genomics

value: PBMC

value: Spontaneous culture conversion 4


title: AcrIIA4 single-mutant library fraction 1 replicate 2 [AcrDMS_v2_09]

value: E. coli plasmid harboring Acr DMS library


title: Normal T24 cellls 3

type: RNA

city: su zhou shi

first: Jin

state: None Selected

address: 199 Renai road, Suzhou industrial park, Dushu Lake Campus of Soochow University

institute: Suzhou University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

source_name: Normal T24 cellls

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Human BC cell line T24 was purchased from the American Type Culture Collection (ATCC). All cells were cultured in DMEM (Thermo Fisher Scientific, Inc.) with 10% FBS (Thermo Fischer Scientific, Inc.) at 37°C in the presence of 5% CO2.

extract_protocol: Quantitative analysis of total RNA samples was performed using Agilent 2100, and then the GeneChip 3'IVT Express kit was used to prepare aRNA (amplified RNA) according to the instructions. cDNA is then synthesized to obtain a double-stranded DNA template, which is further transcribed in vitro to obtain aRNA, which has been labeled by biotin.

treatment_protocol: T24 cells were treated with MAP30 at a concentration of 10 μg/ml and collected at 48 hours.


title: T24 cells treated with MAP30 3

source_name: T24 cells treated with MAP30


title: T24 cells treated with MAP30 2


title: T24 cells treated with MAP30 1


title: Normal T24 cellls 2


title: Normal T24 cellls 1


title: AcrIIA5 single-mutant library fraction 4 replicate 1 [AcrDMS_v2_08]


title: Seq02_Tfh_3


title: C-2_#2 scTCR-Seq

description:
C-2_#2
10x Genomics

value: Progressive disease_unfavorable 2


title: J12S3

description: RNA


title: J12S2

description: RNA


title: AcrIIA5 single-mutant library fraction 3 replicate 1 [AcrDMS_v2_07]


title: A_#3

description: 10x Genomics

value: Spontaneous culture conversion 3


title: AcrIIA5 single-mutant library fraction 2 replicate 1 [AcrDMS_v2_06]


title: C-2_#3

description: 10x Genomics

value: Progressive disease_unfavorable 3


title: Seq02_Tfh_1


title: B_#7

description: 10x Genomics

value: Stable disease 7


title: AcrIIA5 single-mutant library fraction 1 replicate 1 [AcrDMS_v2_05]


title: J12S1

description: RNA

value: solvent


title: J12L2

description: RNA

value: lurbinectedin


title: AcrIIA4 single-mutant library fraction 4 replicate 1 [AcrDMS_v2_04]


title: Seq02_Tfh_2


title: J12L3

description: RNA


title: A_#2

description: 10x Genomics

value: Spontaneous culture conversion 2


title: Seq02_Th17_4


title: J12L1

description: RNA

value: JN-DSRCT-1 cells


title: AcrIIA4 single-mutant library fraction 3 replicate 1 [AcrDMS_v2_03]


title: B_#5

description: 10x Genomics

value: Stable disease 5


title: Seq02_Th17_3


title: AcrIIA4 single-mutant library fraction 2 replicate 1 [AcrDMS_v2_02]


title: B_#4

description: 10x Genomics

value: Stable disease 4


title: J6S3

description: RNA

value: 6 hours continous


title: Seq02_Th17_2

value: CD4 T cell


title: J6S2

description: RNA


title: B_#3

description: 10x Genomics

value: Blood

value: Stable disease 3


title: Seq02_Th17_5


title: Seq02_Th17_1


title: B_#6

description: 10x Genomics

value: PBMC

value: Stable disease 6


title: J6S1

description: RNA


title: C-1_#3

description: 10x Genomics

value: Progressive disease_favorable 3


title: Seq02_Th1_5


title: J6L3

description: RNA


title: J6L2

description: RNA


title: B_#2

description: 10x Genomics

value: Stable disease 2


title: A_#1

description: 10x Genomics

value: Spontaneous culture conversion 1


title: Seq02_Th1_4


title: Seq02_Th1_3


title: Seq02_Th1_2


title: B_#1

description: 10x Genomics

value: Stable disease 1


title: BM3

description: RNA

value: BER cells

value: media

value: 12 hours continuous


title: J6L1

description: RNA

value: lurbinectedin


title: Seq02_Th1_1


title: C-1_#2

description: 10x Genomics

value: Progressive disease_favorable 2


title: AcrIIA4 single-mutant library fraction 1 replicate 1 [AcrDMS_v2_01]

value: E. coli plasmid harboring Acr DMS library


title: BM2

description: RNA


title: C-x_#3

description: 10x Genomics

value: Progressive disease_refusing treatment


title: BM1

description: RNA


title: C-x_#2

description: 10x Genomics


title: B12S3

description: RNA

value: solvent


title: Seq01_Tfh5_4

value: CD4 T cell


title: KO_CHW_3

type: genomic

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: R studio (v. 4.2.0) via the Enmix package

label: Cy3 and Cy5

source_name: liver

label_protocol: Standard Illumina Protocol

extract_protocol: At 13 weeks, the mice were sacrificed by cervical dislocation after anaesthesia with ketamine and xylazine diluted in phosphate-buffered saline (PBS) (2:2:6). Liver samples were immediately snap frozen and genomic DNA was extracted and purified from liver biopsies  using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: 7-week old male hepatocyte-specific PPARα KO and WT mice were fed either a chow diet (normal standard diet, containing 9% energy from fat, 58% from carbohydrates, and 33% from protein) or a CDAHFD (choline-deficient L-amino acid defined high-fat diet, A06071302, New Brunswick, NJ USA, containing 62% energy from fat, 20% from carbohydrates, and 18% from protein) for 6 weeks ad libitum

tag: Sex

value: male

value: liver

value: CHOW

value: Hepatocyte-specific PPARa KO


title: C-1_#1

description: 10x Genomics

value: Blood

value: PBMC

value: Progressive disease_favorable 1


title: B12S2

description: RNA


title: B12S1

description: RNA


title: C-x_#1

description: 10x Genomics

value: Progressive disease_follow-up loss


title: Seq01_Tfh5_2


title: Seq01_Tfh5_5


title: B12L3

description: RNA

value: BER cells


title: Seq01_Tfh5_3


title: C-2_#1

description: 10x Genomics

value: Progressive disease_unfavorable 1


title: B12L2

description: RNA

value: 12 hours continuous


title: Seq01_Tfh5_1


title: K562 PABPC1-IP rep2

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

description:
eCLIP-seq of PABPC1 in K562 cell line
PABPC1.peaks_merge.txt
PABPC1_ip_pos.bw
PABPC1_ip_neg.bw

data_processing:
(Sample 1-4) For RNA-seq: Reads were aligned to human genome using STAR with parameters " --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 " to retain uniquely mapped reads. FeatureCounts were used for calculating gene counts, and then normalized for transcript per million (TPM) using in-house scripts.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
(Sample 5-8) For eCLIP-seq: Raw reads with distinct inline barcodes were demultiplexed and the 10-mer random sequence was appended to the reads name in bam file. Cutadapt was used to trimming low quality reads and adapter sequence. Reads were aligned with the sequence of human repetitive elements in the RepBase database by STAR to remove the repetitive reads and obtain the cleaned reads. Cleaned reads were then mapped to human genome using STAR. Removing PCR duplicate reads based on sharing identical random sequence. Two biological replicates were merged by SAMtools. Peaks calling and downstream data analysis were performed by clipper. Peaks normalization by “Peak_input_normalization_wrapper.pl” tools. The eCLIP-seq peaks were filtered by P-value < 10e-6 and fold change > 2.5.
Assembly: GRCh38
Supplementary files format and content: peak text file, bw file

source_name: K562 cell line

growth_protocol: Human blast crisis CML cell line K562 was maintained in RPMI1640 supplemented with 10% FBS and 100 IU ml-1 penicillin and 100 μg ml-1 streptomycin

extract_protocol:
The RNA binded by PABPC1 was purified by RNA Clean & Concentrator-5 kit (ZYMO).
Libraries were prepared for high-throughput sequencing using standard Illumina protocols.

treatment_protocol: About 108 K562 cells were  UV crosslinked. RNA-PABPC1 complexes were captured with RNase A digestion and anti-PABPC1 antibody immunopricipitation.

value: untreated

tag: antibody


title: KO_CDAHFD_3

value: CDAHFD


title: C-2_#2

description: 10x Genomics

value: Progressive disease_unfavorable 2


title: B12L1

description: RNA

value: lurbinectedin


title: Seq01_TfhA_4

value: TfhA


title: Liver, frozen, RSP_1011

city: Canberra

first: Erin

middle: Elizabeth

last: Hahn

state: ACT

address: Clunies Ross

department: National Research Collections Australia

country: Australia

institute: CSIRO

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: For deduplication with the IDT library unique molecular identifiers (UMIs), we converted the Fastq files to BAM format using FastqToSam (PICARD v 2.9.2), extracted the UMIs with ExtractUmisFromBam (FGBio v. 1.3.0) and restored the files to FastQ format with SamToFastq (PICARD). We aligned raw reads using kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE and utilising UMIs. We computed and corrected for GC-bias with deepTools version 3.5.1 using an effective genome size of 1,716,675,060 bp.
Peak analysis: We analysed regional occupancy after quantile normalisation of sequencing depth differences between treatment and input control to calculate differential occupancy values with the dtriple function in DANPOS3. For differential peak analyses, we analysed all archival alignments as individual samples against a pool of the three fresh tissue alignments.
Assembly: Pogona vitticeps pvi1.1 RefSeq assembly
Supplementary files format and content: WIG files are provided for all individual samples and DANPOS3 comparions with input controls

organism: Intellagama lesueurii lesueurii

extract_protocol:
With archival specimens, we cryopulverised liver tissue applied an optimised Mnase digest to recover differentially accessible gDNA fragments. With fresh specimens, we cryopulverised liver tissue and extracted gDNA with a Qiagen AllPrep kit.
xGen cfDNA & FFPE DNA Library Prep Kit (IDT)

tag: specimen id

tag: preservation

value: fresh frozen

value: M

tag: collection year


title: K562 PABPC1-IP rep1


title: Liver, frozen, RSP_537

value: liver


title: Seq01_TfhA_2

value: CD4 T cell


title: B6S3

description: RNA

value: solvent

value: 6 hours continous


title: Liver, frozen, RSP_535


title: Seq01_TfhA_5


title: B6S2

description: RNA


title: Seq01_TfhA_1


title: K562 input rep2

description:
eCLIP-seq input in K562 cell line
PABPC1.peaks_merge.txt
PABPC1_input_pos.bw
PABPC1_input_neg.bw


title: B6S1

description: RNA


title: K562 input rep1


title: K562 PABPC1-KD rep2

description:
Poly(A)+ RNA-seq after PABPC1 knockdown in K562 cell line
RNA-seq_Raw_gene_counts_matrix.txt

extract_protocol:
The cells were collected and total RNA was harvested at third day after treatment using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: K562 cells were maintaied in complete medium with the addition of 8 µg/ml (working concentration) polybrene and concentrated viral particles (shCtrl, shPABPC1) for 24 hours. Lentivirus infection medium system of K562 cells were replaced with fresh complete medium, and K562 cells were subjected to the following experiments after 48-72 hours of transfection.

value: PABPC1 knockdown


title: Seq01_Th1_5


title: KO_CHW_2

value: male

value: CHOW

value: Hepatocyte-specific PPARa KO


title: WT_CHOW_3

value: WT


title: WT_CDAHFD_2


title: Liver, archival, J76769

value: archival formalin

value: F


title: WT_CDAHFD_1

value: CDAHFD


title: Seq01_Th1_4


title: KO_CDAHFD_2


title: Liver, archival, J91140


title: B6L3

description: RNA

value: BER cells


title: KO_CDAHFD_1


title: Liver, archival, J76089


title: K562 PABPC1-KD rep1


title: B6L2

description: RNA

value: lurbinectedin


title: WT_CHOW_1


title: K562 WT rep2

description:
control Poly(A)+ RNA-seq in K562 cell line
RNA-seq_Raw_gene_counts_matrix.txt

value: untreated


title: Seq01_Th1_3


title: Seq01_Th1_2


title: Liver, archival, J54438


title: K562 WT rep1


title: WT_CHOW_2


title: B6L1

description: RNA


title: Liver, archival, J51722


title: Seq01_Th1_1


title: B35, Sepsis SB1 stage, bulkRNA-seq

status: Public on Feb 29 2024

first: Haihan

last: Xiao

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute Of Microbiology, Chinese Academy Of Sciences

data_processing:
The pooling sequencing data from one lane was demultiplexed into FASTQ files of each sample according to index sequence in cellranger software package (10X genomics).
Clean raw data was generated after the reads with polluted adapter, Ns and low-quality were filtered out in fastp package.
The extraction of ATCAATC barcode and UMIs, that of reads mapping to human genome GRCh38.p13, and the generation of gene counts were processed in the combined workflow of UMI-tools, STAR, Subread and Samtools.
Assembly: GRCh38.p13
Supplementary files format and content: Gene counts for every gene and every sample.

source_name: peripheral blood leukocytes

extract_protocol:
RNAprep pure Cell kit (DP430, TIANGEN) were used for extracting cellular total RNA of PBLs, according to the manual. Fifty nanograms of total RNA were reverse transcribed into complementary DNA (cDNA) using a unique primer containing ATCAATC barcode and 16bp UMI sequence. Second-strand cDNA synthesis and whole transcript amplification were then implemented based on poly-A tagging.
For conversion from amplified cDNA to sequence library DNA, 100 nanograms of amplified second-strand cDNA was fragmented into 400 bp sequences. After purification, fragmented cDNA was end-repaired and ligated with a truncated sequence adaptor, which had a pool barcode sequence. The resulting sequence library DNA was further enriched by PCR amplification.
The library DNA was sequenced by paired-end strategy using a HiSeq X Ten sequencing system (Illumina). The sequence specifications were as follows: Read1, 151 cycles; Index1, 8 cycles; Read2, 151 cycles. It sequenced the ATCAATC barcode site and the UMI site at Read1, the pool barcode site at Index1, and the transcript sequence at Read2.

treatment_protocol: Fresh blood were obtained via vein puncture. PBLs were collected after being treated with ACK Lysis Buffer to remove red blood cells.

value: peripheral blood leukocytes

tag: patient

value: Female

tag: age at_the_time_of_sampling

value: 36 DAY


title: KO_CHW_1

value: liver

tag: treatment


title: WT_CDAHFD_3


title: B33, Sepsis SB2 stage, bulkRNA-seq

value: Male

value: 52 DAY


title: B31, Sepsis SB1 stage, bulkRNA-seq

value: 41 DAY


title: B30, Sepsis SB2 stage, bulkRNA-seq

value: 110 DAY


title: B29, Sepsis SB2 stage, bulkRNA-seq

value: 90 DAY


title: B27, Sepsis SB1 stage, bulkRNA-seq

value: 67 DAY


title: B25, Sepsis SB2 stage, bulkRNA-seq

value: 94 DAY


title: B26, Sepsis SB1 stage, bulkRNA-seq

value: 59 DAY


title: B24, Sepsis SB2 stage, bulkRNA-seq


title: B32, Sepsis SB1 stage, bulkRNA-seq

value: 45 DAY


title: B34, Sepsis SB1 stage, bulkRNA-seq

value: 287 DAY


title: C106, BM S3 stage, bulkRNA-seq

source_name: CSF cells

extract_protocol:
The total RNA of the prepared cells was extracted using an RNAprep Pure Cell Kit (DP430, TIANGEN) if the CSF total cell count (TCC) was over 100 × 106/L or an RNAprep Pure Micro Kit (DP420, TIANGEN) if the TCC was below 100 × 106/L, according to the manual. Fifty nanograms of total RNA were reverse transcribed into complementary DNA (cDNA) using a unique primer containing ATCAATC barcode and 16bp UMI sequence. Second-strand cDNA synthesis and whole transcript amplification were then implemented based on poly-A tagging.
For conversion from amplified cDNA to sequence library DNA, 100 nanograms of amplified second-strand cDNA was fragmented into 400 bp sequences. After purification, fragmented cDNA was end-repaired and ligated with a truncated sequence adaptor, which had a pool barcode sequence. The resulting sequence library DNA was further enriched by PCR amplification.
The library DNA was sequenced by paired-end strategy using a HiSeq X Ten sequencing system (Illumina). The sequence specifications were as follows: Read1, 151 cycles; Index1, 8 cycles; Read2, 151 cycles. It sequenced the ATCAATC barcode site and the UMI site at Read1, the pool barcode site at Index1, and the transcript sequence at Read2.

treatment_protocol: CSF cells were were separated by direct centrifugation at 1800 rpm for 5 min.

value: CSF cells

value: 34 DAY

tag: clinical csf_total_cell_count_/×106/l


title: B23, Sepsis SB2 stage, bulkRNA-seq

value: 116 DAY


title: C104, BM S5 stage, bulkRNA-seq

value: 0 (Lower than the detection limit)


title: C101, BM S3 stage, bulkRNA-seq


title: C100, BM S1 stage, bulkRNA-seq

value: 39 DAY


title: C102, BM S4 stage, bulkRNA-seq


title: C94, BM S8 stage, bulkRNA-seq


title: C95, BM S1 stage, bulkRNA-seq


title: C96, BM S3 stage, bulkRNA-seq

value: 68 DAY


title: C98, BM S7 stage, bulkRNA-seq

value: 88 DAY


title: C99, BM S7 stage, bulkRNA-seq

value: Male

value: 102 DAY


title: C139, BM S4 stage, scRNA-seq

data_processing:
The pooled raw data from one lane were demultiplexed into FASTQ files of each sample according to the index sequence in the Cell Ranger software package.
Clean data were generated after reads containing polluted adapters or Ns and low-quality reads were removed using the fastp package.
The extraction of cell barcodes and unique molecular identifiers (UMIs), that of reads mapping to human genome GRCh38.p13, and the generation of a cell-count matrix were processed in the combined workflow of UMI-tools, STAR, Subread and Samtools.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

extract_protocol:
This part, including reverse transcription and whole-transcript amplification, was carried out in accordance with the protocols for the QUARTZ-SEQ2.
100 nanograms of amplified second-strand cDNA was fragmented into 400 bp sequences. After purification, fragmented cDNA was end-repaired and ligated with truncated sequence adaptors. The library was further amplified and purified under the conditions described in the QUARTZ-SEQ2 protocols.
The library DNA was sequenced using a HiSeq X Ten sequencing system. The sequence specifications were as follows: Read1, 151 cycles; Index1, 8 cycles; Read2, 151 cycles.

treatment_protocol: CSF cells were stained with 2 μM calcein-AM and sorted using a MoFol XDP cell sorter. Single cells with positive green fluorescence were sorted into two pre-prepared 384-well plates with cell lysis buffer, in which each well contained a unique cell barcoding primer.

value: 336 Day

tag: clinical csf_cell_counts_/×106/l


title: C89, BM S7 stage, bulkRNA-seq

tag: cell type

value: Female


title: C131, replicate 2, BM S1 stage, scRNA-seq

value: 65 DAY


title: C129, BM S8 stage, scRNA-seq


title: C131, replicate 1, BM S1 stage, scRNA-seq


title: C126, BM S3 stage, scRNA-seq

value: 302 Day


title: C91, BM S6 stage, bulkRNA-seq


title: C121, replicate 4, BM S1 stage, scRNA-seq

value: 40 DAY


title: C121, replicate 3, BM S1 stage, scRNA-seq


title: C122, BM S3 stage, scRNA-seq

value: 46 DAY


title: C106, BM S3 stage, scRNA-seq


title: C121, replicate 2, BM S1 stage, scRNA-seq


title: C114, replicate 1, BM S7 stage, scRNA-seq

value: 132 DAY


title: C121, replicate 1, BM S1 stage, scRNA-seq


title: C119, BM S4 stage, scRNA-seq

value: 73 DAY


title: C107, BM S3 stage, scRNA-seq

value: CSF cells

value: 41 DAY


title: C100, BM S1 stage, scRNA-seq


title: C101, BM S3 stage, scRNA-seq

value: 45 DAY


title: C102, BM S4 stage, scRNA-seq

value: 52 DAY


title: C114, replicate 2, BM S7 stage, scRNA-seq


title: C96, BM S3 stage, scRNA-seq

value: 68 Day


title: C103, BM S1 stage, scRNA-seq

value: 280 Day


title: C80, BM S8 stage, scRNA-seq

value: 179 DAY


title: C73, BM S8 stage, scRNA-seq

value: Male

value: 208 DAY


title: C77, BM S4 stage, scRNA-seq

value: 155 DAY


title: C69, BM S8 stage, scRNA-seq

value: 818 DAY


title: C71, BM S7 stage, scRNA-seq

value: 194 DAY


title: C66, BM S7 stage, scRNA-seq

value: 790 DAY


title: C60, BM S7 stage, scRNA-seq

value: 86 DAY


title: C67, BM S7 stage, scRNA-seq

value: 797 DAY


title: C61, BM S7 stage, scRNA-seq

value: 96 DAY


title: C62, BM S8 stage, scRNA-seq

value: 111 DAY


title: C65, BM S3 stage, scRNA-seq

value: CSF cells

value: 783 DAY


title: C56, BM S6 stage, scRNA-seq

value: 48 DAY


title: K27 p300 KD-3

status: Public on Feb 28 2024

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The raw sequences are aligned to the GRCm38 reference genome, then duplicates are removed using Picard. After removing duplicates, the reads that are mapped to the blacklist region from UCSC are filtered. Then bedGraph was generated using the deepTools.
Assembly: GRCm38
Supplementary files format and content: gzipped bedGraph file from deepTools

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the ChIP-Seq protocol as described (Trombetta et al 2014).

value: Female

tag: disease

value: induced EAE


title: K27 Scramble-3

tag: strain


title: K27 p300 KD-2


title: K27 Scramble-2


title: C55, BM S7 stage, scRNA-seq

value: 41 DAY


title: C59, BM S6 stage, scRNA-seq

value: 72 DAY


title: C47, BM S6 stage, scRNA-seq

value: Male

value: 137 Day


title: IgG p300 KD-3


title: K27 Scramble-1


title: C72, BM S7 stage, scRNA-seq

value: 201 DAY


title: IgG Scramble-3


title: IgG p300 KD-1


title: IgG p300 KD-2


title: C58, BM S6 stage, scRNA-seq

value: 63 DAY


title: IgG Scramble-2


title: C57, BM S7 stage, scRNA-seq

value: 53 DAY


title: IgG Scramble-1


title: Histone ChIP-seq from Patski (ENCLB465ACM)

status: Public on Feb 27 2024

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR942RCG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR942RCG
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR776VHJ
encode release date: 2021-07-01
lab: Christine Disteche, UW
library encode accession: ENCLB465ACM
size range: 371-371

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain Patski Patski cell line

extract_protocol: not provided

tag: line

value: Patski

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

value: not collected

tag: dev stage

value: unknown

tag: age

tag: lab

value: Christine Disteche, UW

tag: source

value: Christine Disteche

tag: link

value: ENCBS632MSA at ENCODE; https://www.encodeproject.org/ENCBS632MSA/


title: TF ChIP-seq from Patski (ENCLB376UPR)

description:
https://www.encodeproject.org/experiments/ENCSR419OOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR419OOD
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR343HAH
encode release date: 2021-07-01
lab: Christine Disteche, UW
library encode accession: ENCLB376UPR
size range: 100-300

tag: antibody

value: CTCF

tag: Sex

value: ENCBS076RUH at ENCODE; https://www.encodeproject.org/ENCBS076RUH/


title: Histone ChIP-seq from BLaER1 (ENCLB656QAL)

description:
https://www.encodeproject.org/experiments/ENCSR999HNE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR999HNE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB656QAL
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 48 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: female

value: Roderic Guigo, CRG

value: Thomas Graf

tag: treatments

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS777PXO at ENCODE; https://www.encodeproject.org/ENCBS777PXO/


title: Histone ChIP-seq from BLaER1 (ENCLB865QYP)

description:
https://www.encodeproject.org/experiments/ENCSR837LWL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR837LWL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB865QYP
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 3 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS348QCD at ENCODE; https://www.encodeproject.org/ENCBS348QCD/


title: Histone ChIP-seq from BLaER1 (ENCLB842MWZ)

description:
https://www.encodeproject.org/experiments/ENCSR524VDR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR524VDR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB842MWZ
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line

value: ENCBS137KWE at ENCODE; https://www.encodeproject.org/ENCBS137KWE/


title: Histone ChIP-seq from BLaER1 (ENCLB580FXE)

description:
https://www.encodeproject.org/experiments/ENCSR524VDR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR524VDR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB580FXE
fragmentation methods: shearing (Covaris generic)

value: ENCBS017NGB at ENCODE; https://www.encodeproject.org/ENCBS017NGB/


title: Histone ChIP-seq from BLaER1 (ENCLB986ZYO)

description:
https://www.encodeproject.org/experiments/ENCSR839YFS/
***************
biological replicate number: 1
technical replicate number: 1
description: H4K20me1 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR839YFS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB986ZYO
fragmentation methods: shearing (Covaris generic)

value: cell line


title: Histone ChIP-seq from BLaER1 (ENCLB642FFX)

description:
https://www.encodeproject.org/experiments/ENCSR837LWL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR837LWL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB642FFX
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: ENCBS242WXP at ENCODE; https://www.encodeproject.org/ENCBS242WXP/


title: Histone ChIP-seq from BLaER1 (ENCLB824TVF)

description:
https://www.encodeproject.org/experiments/ENCSR506IRD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR506IRD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB824TVF
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 6 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: unknown

value: ENCBS584ALJ at ENCODE; https://www.encodeproject.org/ENCBS584ALJ/


title: Histone ChIP-seq from BLaER1 (ENCLB076BAZ)

description:
https://www.encodeproject.org/experiments/ENCSR506IRD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR506IRD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB076BAZ
fragmentation methods: shearing (Covaris generic)

value: ENCBS411JBC at ENCODE; https://www.encodeproject.org/ENCBS411JBC/


title: Histone ChIP-seq from BLaER1 (ENCLB039XRN)

description:
https://www.encodeproject.org/experiments/ENCSR506FPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR506FPQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB039XRN
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 24 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS528BRE at ENCODE; https://www.encodeproject.org/ENCBS528BRE/


title: Histone ChIP-seq from BLaER1 (ENCLB898WFP)

description:
https://www.encodeproject.org/experiments/ENCSR506FPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR506FPQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB898WFP
fragmentation methods: shearing (Covaris generic)

value: ENCBS564GVM at ENCODE; https://www.encodeproject.org/ENCBS564GVM/


title: Histone ChIP-seq from BLaER1 (ENCLB312ROH)

description:
https://www.encodeproject.org/experiments/ENCSR992WXP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR992WXP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB312ROH
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB019UOW)

description:
https://www.encodeproject.org/experiments/ENCSR822ZAQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR822ZAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB019UOW
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 12 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS932XAE at ENCODE; https://www.encodeproject.org/ENCBS932XAE/


title: Histone ChIP-seq from BLaER1 (ENCLB776QXK)

description:
https://www.encodeproject.org/experiments/ENCSR820DOR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR820DOR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR452GUC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB776QXK
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 120 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: female

value: ENCBS019UMZ at ENCODE; https://www.encodeproject.org/ENCBS019UMZ/


title: Histone ChIP-seq from BLaER1 (ENCLB805EUM)

description:
https://www.encodeproject.org/experiments/ENCSR820DOR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR820DOR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR452GUC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB805EUM
fragmentation methods: shearing (Covaris generic)

value: Roderic Guigo, CRG

value: Thomas Graf

value: ENCBS040UGC at ENCODE; https://www.encodeproject.org/ENCBS040UGC/


title: Histone ChIP-seq from BLaER1 (ENCLB365QHG)

description:
https://www.encodeproject.org/experiments/ENCSR822ZAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR822ZAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB365QHG
fragmentation methods: shearing (Covaris generic)

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS900NVU at ENCODE; https://www.encodeproject.org/ENCBS900NVU/


title: Histone ChIP-seq from brain (ENCLB029SAO)

description:
https://www.encodeproject.org/experiments/ENCSR817LUF/
***************
biological replicate number: 1
technical replicate number: 8
description:
experiment encode accession: ENCSR817LUF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR603VTC
encode release date: 2023-02-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB029SAO

source_name: Homo sapiens female embryo (120 days) brain tissue

value: brain

value: tissue

tag: note

value: Brain tissue from a healthy 120 day old female human fetus. Tissue provided by Ian Glass of University of Washington, Congenital Defects Lab.

value: embryonic

value: 120 day

value: Bradley Bernstein, Broad

value: Unknown Source

value: ENCBS604GZI at ENCODE; https://www.encodeproject.org/ENCBS604GZI/


title: Histone ChIP-seq from BLaER1 (ENCLB726ZYD)

description:
https://www.encodeproject.org/experiments/ENCSR987EKG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR987EKG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB726ZYD
fragmentation methods: shearing (Covaris generic)

value: cell line

value: not applicable

value: unknown

value: ENCBS137KWE at ENCODE; https://www.encodeproject.org/ENCBS137KWE/


title: Histone ChIP-seq from BLaER1 (ENCLB901EKN)

description:
https://www.encodeproject.org/experiments/ENCSR980ZJN/
***************
biological replicate number: 1
technical replicate number: 1
description: H4K20me1 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR980ZJN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB901EKN
fragmentation methods: shearing (Covaris generic)

value: female

value: Roderic Guigo, CRG

value: ENCBS528BRE at ENCODE; https://www.encodeproject.org/ENCBS528BRE/


title: Histone ChIP-seq from BLaER1 (ENCLB661PNV)

description:
https://www.encodeproject.org/experiments/ENCSR987EKG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR987EKG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB661PNV
fragmentation methods: shearing (Covaris generic)

value: Thomas Graf

value: ENCBS017NGB at ENCODE; https://www.encodeproject.org/ENCBS017NGB/


title: Histone ChIP-seq from BLaER1 (ENCLB223COR)

description:
https://www.encodeproject.org/experiments/ENCSR980ZJN/
***************
biological replicate number: 2
technical replicate number: 1
description: H4K20me1 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR980ZJN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB223COR
fragmentation methods: shearing (Covaris generic)

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS564GVM at ENCODE; https://www.encodeproject.org/ENCBS564GVM/


title: Histone ChIP-seq from BLaER1 (ENCLB558SEN)

description:
https://www.encodeproject.org/experiments/ENCSR477ATR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR477ATR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB558SEN
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB630ELG)

description:
https://www.encodeproject.org/experiments/ENCSR999HNE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR999HNE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB630ELG
fragmentation methods: shearing (Covaris generic)

value: ENCBS766HUL at ENCODE; https://www.encodeproject.org/ENCBS766HUL/


title: Histone ChIP-seq from BLaER1 (ENCLB485YPX)

description:
https://www.encodeproject.org/experiments/ENCSR839YFS/
***************
biological replicate number: 2
technical replicate number: 1
description: H4K20me1 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR839YFS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB485YPX
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB370POH)

description:
https://www.encodeproject.org/experiments/ENCSR477ATR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR477ATR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB370POH
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB760YJU)

description:
https://www.encodeproject.org/experiments/ENCSR808DPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR808DPZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB760YJU
fragmentation methods: shearing (Covaris generic)

value: ENCBS411JBC at ENCODE; https://www.encodeproject.org/ENCBS411JBC/


title: Histone ChIP-seq from BLaER1 (ENCLB299TBE)

description:
https://www.encodeproject.org/experiments/ENCSR992WXP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR992WXP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB299TBE
fragmentation methods: shearing (Covaris generic)

value: ENCBS584ALJ at ENCODE; https://www.encodeproject.org/ENCBS584ALJ/


title: TF ChIP-seq from BLaER1 (ENCLB569HAH)

description:
https://www.encodeproject.org/experiments/ENCSR490DXW/
***************
biological replicate number: 2
technical replicate number: 1
description: CEBPA ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR490DXW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB569HAH
fragmentation methods: shearing (Covaris generic)

value: Cebpa

value: ENCBS113JQL at ENCODE; https://www.encodeproject.org/ENCBS113JQL/


title: Histone ChIP-seq from BLaER1 (ENCLB717RJG)

description:
https://www.encodeproject.org/experiments/ENCSR472CMR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR472CMR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR958BKG
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB717RJG
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 9 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS214PGM at ENCODE; https://www.encodeproject.org/ENCBS214PGM/


title: Histone ChIP-seq from BLaER1 (ENCLB207FYJ)

description:
https://www.encodeproject.org/experiments/ENCSR972GGW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR972GGW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB207FYJ
fragmentation methods: shearing (Covaris generic)

value: cell line

value: ENCBS348QCD at ENCODE; https://www.encodeproject.org/ENCBS348QCD/


title: Histone ChIP-seq from BLaER1 (ENCLB651EPH)

description:
https://www.encodeproject.org/experiments/ENCSR472CMR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR472CMR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR958BKG
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB651EPH
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: unknown

value: ENCBS902TME at ENCODE; https://www.encodeproject.org/ENCBS902TME/


title: TF ChIP-seq from BLaER1 (ENCLB864AXW)

description:
https://www.encodeproject.org/experiments/ENCSR490DXW/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPA ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR490DXW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB864AXW
fragmentation methods: shearing (Covaris generic)

value: female

value: Roderic Guigo, CRG

value: ENCBS554PIB at ENCODE; https://www.encodeproject.org/ENCBS554PIB/


title: Histone ChIP-seq from BLaER1 (ENCLB655AKK)

description:
https://www.encodeproject.org/experiments/ENCSR660WMS/
***************
biological replicate number: 2
technical replicate number: 1
description: H4K20me1 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR660WMS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB655AKK
fragmentation methods: shearing (Covaris generic)

value: Thomas Graf


title: Histone ChIP-seq from BLaER1 (ENCLB332HUD)

description:
https://www.encodeproject.org/experiments/ENCSR660WMS/
***************
biological replicate number: 1
technical replicate number: 1
description: H4K20me1 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR660WMS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB332HUD
fragmentation methods: shearing (Covaris generic)

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS777PXO at ENCODE; https://www.encodeproject.org/ENCBS777PXO/


title: Histone ChIP-seq from BLaER1 (ENCLB105KBL)

description:
https://www.encodeproject.org/experiments/ENCSR797ELD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR797ELD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB105KBL
fragmentation methods: shearing (Covaris generic)

value: ENCBS766HUL at ENCODE; https://www.encodeproject.org/ENCBS766HUL/


title: Histone ChIP-seq from BLaER1 (ENCLB231KAQ)

description:
https://www.encodeproject.org/experiments/ENCSR659KFN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR659KFN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB231KAQ
fragmentation methods: shearing (Covaris generic)

value: ENCBS932XAE at ENCODE; https://www.encodeproject.org/ENCBS932XAE/


title: Histone ChIP-seq from BLaER1 (ENCLB149ZFS)

description:
https://www.encodeproject.org/experiments/ENCSR660TLD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR660TLD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR452GUC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB149ZFS
fragmentation methods: shearing (Covaris generic)

value: ENCBS019UMZ at ENCODE; https://www.encodeproject.org/ENCBS019UMZ/


title: Histone ChIP-seq from BLaER1 (ENCLB675IZV)

description:
https://www.encodeproject.org/experiments/ENCSR797ELD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR797ELD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB675IZV
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB362FZP)

description:
https://www.encodeproject.org/experiments/ENCSR660TLD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR660TLD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR452GUC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB362FZP
fragmentation methods: shearing (Covaris generic)

value: ENCBS040UGC at ENCODE; https://www.encodeproject.org/ENCBS040UGC/


title: Histone ChIP-seq from BLaER1 (ENCLB963NVI)

description:
https://www.encodeproject.org/experiments/ENCSR808DPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR808DPZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB963NVI
fragmentation methods: shearing (Covaris generic)

value: ENCBS584ALJ at ENCODE; https://www.encodeproject.org/ENCBS584ALJ/


title: Histone ChIP-seq from BLaER1 (ENCLB395VYG)

description:
https://www.encodeproject.org/experiments/ENCSR451WXC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 168 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR451WXC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR354HOM
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB395VYG
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 168 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS428LHJ at ENCODE; https://www.encodeproject.org/ENCBS428LHJ/


title: Histone ChIP-seq from BLaER1 (ENCLB107AYD)

description:
https://www.encodeproject.org/experiments/ENCSR451WXC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 168 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR451WXC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR354HOM
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB107AYD
fragmentation methods: shearing (Covaris generic)

value: cell line

value: ENCBS421XOH at ENCODE; https://www.encodeproject.org/ENCBS421XOH/


title: Histone ChIP-seq from BLaER1 (ENCLB071DSK)

description:
https://www.encodeproject.org/experiments/ENCSR653NOJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR653NOJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB071DSK
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: ENCBS017NGB at ENCODE; https://www.encodeproject.org/ENCBS017NGB/


title: Histone ChIP-seq from BLaER1 (ENCLB350OEX)

description:
https://www.encodeproject.org/experiments/ENCSR653NOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR653NOJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB350OEX
fragmentation methods: shearing (Covaris generic)

value: unknown

value: ENCBS137KWE at ENCODE; https://www.encodeproject.org/ENCBS137KWE/


title: Histone ChIP-seq from BLaER1 (ENCLB948XJL)

description:
https://www.encodeproject.org/experiments/ENCSR452JBP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR452JBP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB948XJL
fragmentation methods: shearing (Covaris generic)

value: female

value: Roderic Guigo, CRG

value: ENCBS564GVM at ENCODE; https://www.encodeproject.org/ENCBS564GVM/


title: Histone ChIP-seq from BLaER1 (ENCLB732EZP)

description:
https://www.encodeproject.org/experiments/ENCSR649DTM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR649DTM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB732EZP
fragmentation methods: shearing (Covaris generic)

value: Thomas Graf

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;


title: Histone ChIP-seq from BLaER1 (ENCLB937PRV)

description:
https://www.encodeproject.org/experiments/ENCSR972GGW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR972GGW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB937PRV
fragmentation methods: shearing (Covaris generic)

value: ENCBS242WXP at ENCODE; https://www.encodeproject.org/ENCBS242WXP/


title: Histone ChIP-seq from BLaER1 (ENCLB750LDU)

description:
https://www.encodeproject.org/experiments/ENCSR440PPG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR440PPG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB750LDU
fragmentation methods: shearing (Covaris generic)

value: ENCBS900NVU at ENCODE; https://www.encodeproject.org/ENCBS900NVU/


title: Histone ChIP-seq from BLaER1 (ENCLB335VCA)

description:
https://www.encodeproject.org/experiments/ENCSR452JBP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR452JBP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB335VCA
fragmentation methods: shearing (Covaris generic)

value: ENCBS528BRE at ENCODE; https://www.encodeproject.org/ENCBS528BRE/


title: Histone ChIP-seq from BLaER1 (ENCLB090XTH)

description:
https://www.encodeproject.org/experiments/ENCSR440PPG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR440PPG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB090XTH
fragmentation methods: shearing (Covaris generic)

value: ENCBS932XAE at ENCODE; https://www.encodeproject.org/ENCBS932XAE/


title: Histone ChIP-seq from BLaER1 (ENCLB616CWZ)

description:
https://www.encodeproject.org/experiments/ENCSR642PBI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR642PBI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR958BKG
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB616CWZ
fragmentation methods: shearing (Covaris generic)

value: ENCBS902TME at ENCODE; https://www.encodeproject.org/ENCBS902TME/


title: Histone ChIP-seq from BLaER1 (ENCLB256HDM)

description:
https://www.encodeproject.org/experiments/ENCSR649DTM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR649DTM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB256HDM
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB503QJR)

description:
https://www.encodeproject.org/experiments/ENCSR763VEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR763VEJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB503QJR
fragmentation methods: shearing (Covaris generic)

value: ENCBS777PXO at ENCODE; https://www.encodeproject.org/ENCBS777PXO/


title: Histone ChIP-seq from BLaER1 (ENCLB229GMZ)

description:
https://www.encodeproject.org/experiments/ENCSR763VEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR763VEJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB229GMZ
fragmentation methods: shearing (Covaris generic)

value: cell line

value: ENCBS766HUL at ENCODE; https://www.encodeproject.org/ENCBS766HUL/


title: Histone ChIP-seq from BLaER1 (ENCLB421FST)

description:
https://www.encodeproject.org/experiments/ENCSR642PBI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR642PBI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR958BKG
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB421FST
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: ENCBS214PGM at ENCODE; https://www.encodeproject.org/ENCBS214PGM/


title: Histone ChIP-seq from BLaER1 (ENCLB914AAU)

description:
https://www.encodeproject.org/experiments/ENCSR939VQF/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR939VQF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB914AAU
fragmentation methods: shearing (Covaris generic)

value: unknown

value: ENCBS411JBC at ENCODE; https://www.encodeproject.org/ENCBS411JBC/


title: Histone ChIP-seq from BLaER1 (ENCLB174CCU)

description:
https://www.encodeproject.org/experiments/ENCSR433GMU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR433GMU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB174CCU
fragmentation methods: shearing (Covaris generic)

value: female


title: Histone ChIP-seq from BLaER1 (ENCLB835ZBB)

description:
https://www.encodeproject.org/experiments/ENCSR939VQF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR939VQF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB835ZBB
fragmentation methods: shearing (Covaris generic)

value: Roderic Guigo, CRG

value: ENCBS584ALJ at ENCODE; https://www.encodeproject.org/ENCBS584ALJ/


title: Histone ChIP-seq from BLaER1 (ENCLB451HZG)

description:
https://www.encodeproject.org/experiments/ENCSR659KFN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR659KFN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB451HZG
fragmentation methods: shearing (Covaris generic)

value: Thomas Graf


title: Histone ChIP-seq from BLaER1 (ENCLB982FVM)

description:
https://www.encodeproject.org/experiments/ENCSR638YPP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 18 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR638YPP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255SDP
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB982FVM
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 18 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS366SYI at ENCODE; https://www.encodeproject.org/ENCBS366SYI/


title: Histone ChIP-seq from BLaER1 (ENCLB362KXA)

description:
https://www.encodeproject.org/experiments/ENCSR638YPP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 18 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR638YPP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255SDP
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB362KXA
fragmentation methods: shearing (Covaris generic)

value: ENCBS172BJM at ENCODE; https://www.encodeproject.org/ENCBS172BJM/


title: Histone ChIP-seq from BLaER1 (ENCLB297SCT)

description:
https://www.encodeproject.org/experiments/ENCSR938FQG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR938FQG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR958BKG
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB297SCT
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB102ZQP)

description:
https://www.encodeproject.org/experiments/ENCSR433GMU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR433GMU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB102ZQP
fragmentation methods: shearing (Covaris generic)

value: ENCBS564GVM at ENCODE; https://www.encodeproject.org/ENCBS564GVM/


title: Histone ChIP-seq from BLaER1 (ENCLB184XBS)

description:
https://www.encodeproject.org/experiments/ENCSR938FQG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 9 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR938FQG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR958BKG
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB184XBS
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB313VEM)

description:
https://www.encodeproject.org/experiments/ENCSR754WUX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR754WUX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB313VEM
fragmentation methods: shearing (Covaris generic)

value: ENCBS900NVU at ENCODE; https://www.encodeproject.org/ENCBS900NVU/


title: Histone ChIP-seq from BLaER1 (ENCLB048OPU)

description:
https://www.encodeproject.org/experiments/ENCSR634UTP/
***************
biological replicate number: 1
technical replicate number: 1
description: H4K20me1 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR634UTP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB048OPU
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB288RYO)

description:
https://www.encodeproject.org/experiments/ENCSR632VNI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR632VNI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB288RYO
fragmentation methods: shearing (Covaris generic)

value: ENCBS348QCD at ENCODE; https://www.encodeproject.org/ENCBS348QCD/


title: Histone ChIP-seq from BLaER1 (ENCLB624JWV)

description:
https://www.encodeproject.org/experiments/ENCSR632VNI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR632VNI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB624JWV
fragmentation methods: shearing (Covaris generic)

value: ENCBS242WXP at ENCODE; https://www.encodeproject.org/ENCBS242WXP/


title: Histone ChIP-seq from BLaER1 (ENCLB515EQL)

description:
https://www.encodeproject.org/experiments/ENCSR422YCP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR422YCP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB515EQL
fragmentation methods: shearing (Covaris generic)

value: cell line


title: Histone ChIP-seq from BLaER1 (ENCLB190WIZ)

description:
https://www.encodeproject.org/experiments/ENCSR927XFE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR927XFE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR452GUC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB190WIZ
fragmentation methods: shearing (Covaris generic)

value: ENCBS040UGC at ENCODE; https://www.encodeproject.org/ENCBS040UGC/


title: Histone ChIP-seq from BLaER1 (ENCLB409EFJ)

description:
https://www.encodeproject.org/experiments/ENCSR634UTP/
***************
biological replicate number: 2
technical replicate number: 1
description: H4K20me1 ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR634UTP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB409EFJ
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: ENCBS932XAE at ENCODE; https://www.encodeproject.org/ENCBS932XAE/


title: Histone ChIP-seq from BLaER1 (ENCLB861HXB)

description:
https://www.encodeproject.org/experiments/ENCSR422YCP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR422YCP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB861HXB
fragmentation methods: shearing (Covaris generic)

value: unknown


title: Histone ChIP-seq from BLaER1 (ENCLB721HXZ)

description:
https://www.encodeproject.org/experiments/ENCSR927XFE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 120 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR927XFE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR452GUC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB721HXZ
fragmentation methods: shearing (Covaris generic)

value: ENCBS019UMZ at ENCODE; https://www.encodeproject.org/ENCBS019UMZ/