title: 17V

city: Shanghai

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. 3' adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis.
Supplementary_files_format_and_content: junction read counts of each sample
Supplementary_files_format_and_content: circRNA Expression Profiling.xlsx

source_name: TACE2 case5

extract_protocol:
hepatic artery blood were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA)

tag: case

value: hepatic artery blood

value: TACE

tag: time


title: 15V

status: Public on Jan 21 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: TACE2 case4

tag: tissue

tag: treatment


title: 24A

source_name: TACE1 case4


title: 25A

source_name: TACE1 case5


title: 12V

source_name: TACE2 case2


title: 23A

source_name: TACE1 case3


title: 22A

source_name: TACE1 case2


title: 17A

source_name: Pre-TACE case5

value: Pre-TACE


title: 53-6_P2 GUT

city: Davis

first: Smita

last: Iyer

state: CA

address: county rd 98 & hutchison, ccm room 2075

department: Center for Immunology and Infectious Disease

country: USA

institute: University of California-Davis

data_processing:
The raw read data was filtered using HTStream (version 1.3.1) which included screening for contaminants (such as PhiX and rRNA), quality-based trimming, and adapter trimming. (https://github.com/s4hts/HTStream)
STAR (version 2.7.3a) was used to align the processed data to the rhesus genome (Mmul_10). Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29.1 (2013): 15-21.
MultiQC (custom version) was then used for read and alignment quality assessment. https://github.com/s4hts/MultiQC
Differential expression analyses were conducted using the limma-voom Bioconductor pipeline, using edgeR version 3.30.3 and limma version 3.44.3 in R 4.0.1  The model used in limma included effects for brain region, infection status, and their interaction, and standard errors of log fold changes were adjusted for within-animal correlations.
Supplementary_files_format_and_content: Tables of normalized counts per gene. Comparison between tissue types and characteristics.

source_name: GUT

extract_protocol:
2000 sorted cells were flash frozen in 300 ul of RLT buffer and extracted using the Qiagen mini lipid RNA isolation kit according to manufacturers instructions.
The libraries were constructed following the 3' TagSeq protocol using Lexogen kit (QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina). 500ng of total RNA was used as input.

tag: cell type code

tag: cell type

value: B7- CD4


title: 14A

source_name: Pre-TACE case3


title: 21A

source_name: TACE1 case1


title: 15A

source_name: Pre-TACE case4


title: 11V

source_name: TACE2 case1


title: WT Sample 3

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
RNA-seq raw reads  were mapped to the human reference genome GRCh38 using HISAT2 v2.1.0 with default parameters
Counts on genes were generated using subread-1.5.1 featureCounts and ensembl gene annotation GRCh38.92
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression counts in a tab delimmited text file

source_name: Human B cell

extract_protocol:
Human CLL cells were isolated from whole blood. Cell pellets were captured and washed in PBS on ice prior to resuspension in TRIzol reagent and stored at -80°. Total RNA was isolated from TRIzol suspensions using a chloroform/ethanol extraction method and quantified via Qubit RNA HS Assay kit (Invitrogen).
The Clontech SMARTer v4 kit (Takara Bio USA, Inc.) was used for global preamplification. Illumina sequencing libraries were derived from the resultant cDNA using the Illumina Nextera XT DNA Library Prep Kit following manufacturer’s instructions. RNA-sequencing libraries were prepared with the Illumina Tru-Seq stranded kit and sequenced on a Hiseq 4000 targeting 40x10E6 fragments per sample.

value: CLL B cell

tag: e571 status

value: wild type


title: E571K Sample 3

value: mutant


title: E571K Sample 1


title: WT Sample 1


title: WT Sample 4


title: 11A

source_name: Pre-TACE case1


title: H4K20me3_OV_OVCAR-8_rep2

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description:
Chromatin IP against H4K20me3
GAWSU718-OVCAR-8-H4K20me3-ChIP-rep2_ACAGTG_GAWSU718_CKDL200158688-1a-5_HC2WKBBXX_L2_1.fastq.gz

library_source: genomic

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

growth_protocol: NCI60 cancer cells were cultured in RPMI 1640 / 5% FBS media containing glutamine and pen/strep at 37oC with 5% CO2. Cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: cell line

value: cancer cell

tag: chip antibody

value: Anti-H4K20me3 antibody (Abcam; ab9053)


title: E571K Sample 2


title: H4K20me3_LE_MOLT-4_rep2

description:
Chromatin IP against H4K20me3
GAWSU714-MOLT-4-H4K20me3-ChIP-rep2_ATCACG_GAWSU714_CKDL200158688-1a-1_HC2WKBBXX_L2_1.fastq.gz


title: WT Sample 2


title: H4K20me3_LC_HOP-62_rep2

description:
Chromatin IP against H4K20me3
GAWSU715-HOP-62-H4K20me3-ChIP-rep2_CGATGT_GAWSU715_CKDL200158688-1a-2_HC2WKBBXX_L2_1.fastq.gz


title: 14V

source_name: TACE2 case3


title: H4K20me3_RE_TK-10_rep2

description:
Chromatin IP against H4K20me3
GAWSU717-TK-10-H4K20me3-ChIP-rep2_TGACCA_GAWSU717_CKDL200158688-1a-4_HC2WKBBXX_L2_1.fastq.gz


title: H4K20me3_LC_A549_rep2

description:
Chromatin IP against H4K20me3
GAWSU716-A549-H4K20me3-ChIP-rep2_TTAGGC_GAWSU716_CKDL200158688-1a-3_HC2WKBBXX_L2_1.fastq.gz


title: H4K20me3_RE_UO-31_rep2

description:
Chromatin IP against H4K20me3
GAWSU708-UO-31-H4K20me3-ChIP-rep2_GTGAAA_GAWSU708_CKDL200157358-1a-19_HC7WYBBXX_L3_1.fastq.gz


title: 12A

source_name: Pre-TACE case2


title: H4K20me3_RE_SN12C_rep2

description:
Chromatin IP against H4K20me3
GAWSU576-SN12C-H4K20me3-ChIP-rep2_CAGATC_GAWSU576_CKDL200157352-1a-7_HC3LFBBXX_L5_1.fastq.gz


title: H4K20me3_RE_RXF_393_rep2

description:
Chromatin IP against H4K20me3
GAWSU532-RXF-393-H4K20me3-ChIP-rep2_GGCTAC_GAWSU532_CKDL200157350-1a-11_HC3LFBBXX_L3_1.fastq.gz


title: H4K20me3_RE_ACHN_rep2

description:
Chromatin IP against H4K20me3
GAWSU709-ACHN-H4K20me3-ChIP-rep2_GTGGCC_GAWSU709_CKDL200157358-1a-20_HC7WYBBXX_L3_1.fastq.gz

source_name: ACHN

value: ACHN


title: H4K20me3_RE_786-0_rep2

description:
Chromatin IP against H4K20me3
GAWSU719-786-O-H4K20me3-ChIP-rep2_GTGAAA_GAWSU719_CKDL200158688-1a-19_HC2WKBBXX_L2_1.fastq.gz


title: H4K20me3_RE_A498_rep2

description:
Chromatin IP against H4K20me3
GAWSU687-A498-H4K20me3-ChIP-rep2_CGTACG_GAWSU687_CKDL200157357-1a-22_HC7WYBBXX_L2_1.fastq.gz


title: H4K20me3_PC-3_rep2

description:
Chromatin IP against H4K20me3
GAWSU712-PC-3-H4K20me3-ChIP-rep2_GAGTGG_GAWSU712_CKDL200157358-1a-23_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_OV_OVCAR-5_rep2

description:
Chromatin IP against H4K20me3
GAWSU556-OVCAR5-H4K20me3-ChIP-rep2_GGCTAC_GAWSU556_CKDL200157352-1a-11_HC3LFBBXX_L5_1.fastq.gz


title: H4K20me3_RE_CAKI-1_rep2

description:
Chromatin IP against H4K20me3
GAWSU628-CAKI1-H4K20me3-ChIP-rep2_GGCTAC_GAWSU628_CKDL200157354-1a-11_HC3LFBBXX_L7_1.fastq.gz


title: H4K20me3_ME_SK-MEL-2_rep2

description:
Chromatin IP against H4K20me3
GAWSU703-SK-MEL-2-H4K20me3-ChIP-rep2_AGTTCC_GAWSU703_CKDL200157358-1a-14_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_ME_SK-MEL-28_rep2

description:
Chromatin IP against H4K20me3
GAWSU681-SKMEL28-H4K20me3-ChIP-rep2_CCGTCC_GAWSU681_CKDL200157357-1a-16_HC7WYBBXX_L2_1.fastq.gz


title: H4K20me3_ME_MDA-MB-435_rep2

description:
Chromatin IP against H4K20me3
GAWSU588-MDA-MB-435-H4K20me3-ChIP-rep2_GTGAAA_GAWSU588_CKDL200157353-1a-19_HC3LFBBXX_L6_1.fastq.gz


title: H4K20me3_DU-145_rep2

description:
Chromatin IP against H4K20me3
GAWSU552-DU-145-H4K20me3-ChIP_CAGATC_GAWSU552_CKDL200157351-1a-7_HC3LFBBXX_L4_1.fastq.gz


title: H4K20me3_OV_SK-OV-3_rep2

description:
Chromatin IP against H4K20me3
GAWSU536-SK-OV-3-H4K20me3-ChIP-rep2_ATGTCA_GAWSU536_CKDL200157351-1a-15_HC3LFBBXX_L4_1.fastq.gz


title: H4K20me3_OV_OVCAR-4_rep2

description:
Chromatin IP against H4K20me3
GAWSU640-OVCAR4-H4K20me3-ChIP-rep2_GAGTGG_GAWSU640_CKDL200157355-1a-23_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_LE_K-562_rep2

description:
Chromatin IP against H4K20me3
GAWSU645-K562-H4K20me3-ChIP-rep2_TGACCA_GAWSU645_CKDL200157355-1a-4_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_ME_LOX_IMVI_rep2

description:
Chromatin IP against H4K20me3
GAWSU696-LOX-IMVI-H4K20me3-ChIP-rep2_CAGATC_GAWSU696_CKDL200157358-1a-7_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_ME_M14_rep2

description:
Chromatin IP against H4K20me3
GAWSU584-M14-H4K20me3-ChIP-rep2_ATGTCA_GAWSU584_CKDL200157353-1a-15_HC3LFBBXX_L6_1.fastq.gz


title: H4K20me3_LE_HL-60_rep2

description:
Chromatin IP against H4K20me3
GAWSU657-HL60-H4K20me3-ChIP-rep2_CCGTCC_GAWSU657_CKDL200157356-1a-16_HC7WYBBXX_L1_1.fastq.gz


title: H4K20me3_OV_OVCAR-3_rep2

description:
Chromatin IP against H4K20me3
GAWSU637-OVCAR3-H4K20me3-ChIP-rep2_GTGGCC_GAWSU637_CKDL200157355-1a-20_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_LE_CCRF-CEM_rep2

description:
Chromatin IP against H4K20me3
GAWSU672-CCRF-CEM-H4K20me3-ChIP-rep2_CAGATC_GAWSU672_CKDL200157357-1a-7_HC7WYBBXX_L2_1.fastq.gz

source_name: CCRF-CEM

value: CCRF-CEM


title: H4K20me3_LC_NCI-H23_rep2

description:
Chromatin IP against H4K20me3
GAWSU684-NCI-H23-H4K20me3-ChIP-rep2_GTGAAA_GAWSU684_CKDL200157357-1a-19_HC7WYBBXX_L2_1.fastq.gz


title: H4K20me3_LC_NCI-H460_rep2

description:
Chromatin IP against H4K20me3
GAWSU580-NCI-H460-H4K20me3-ChIP-rep2_GGCTAC_GAWSU580_CKDL200157353-1a-11_HC3LFBBXX_L6_1.fastq.gz


title: H4K20me3_ME_UACC-62_rep2

description:
Chromatin IP against H4K20me3
GAWSU651-UACC-62-H4K20me3-ChIP-rep2_TAGCTT_GAWSU651_CKDL200157355-1a-10_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_OV_IGROV1_rep2

description:
Chromatin IP against H4K20me3
GAWSU678-IGROV1-H4K20me3-ChIP-rep2_AGTCAA_GAWSU678_CKDL200157357-1a-13_HC7WYBBXX_L2_1.fastq.gz


title: H4K20me3_ME_UACC-257_rep2

description:
Chromatin IP against H4K20me3
GAWSU669-UACC-257-H4K20me3-ChIP-rep2_TGACCA_GAWSU669_CKDL200157356-1a-4_HC7WYBBXX_L1_1.fastq.gz


title: H4K20me3_ME_MALME-3M_rep2

description:
Chromatin IP against H4K20me3
GAWSU693-MALME-3M-H4K20me3-ChIP-rep2_TGACCA_GAWSU693_CKDL200157358-1a-4_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_LE_SR_rep2

description:
Chromatin IP against H4K20me3
GAWSU612-SR-H4K20me3-ChIP-rep2_GTGAAA_GAWSU612_CKDL200157354-1a-19_HC3LFBBXX_L7_1.fastq.gz

source_name: SR

value: SR


title: H4K20me3_LC_EKVX_rep2

description:
Chromatin IP against H4K20me3
GAWSU625-EKVX-H4K20me3-ChIP-rep2_ACTTGA_GAWSU625_CKDL200157355-1a-8_HC3LFBBXX_L8_1.fastq.gz

source_name: EKVX

value: EKVX


title: H4K20me3_CO_SW-620_rep2

description:
Chromatin IP against H4K20me3
GAWSU592-SW-620-H4K20me3-ChIP-rep2_GAGTGG_GAWSU592_CKDL200157353-1a-23_HC3LFBBXX_L6_1.fastq.gz


title: H4K20me3_CO_KM12_rep2

description:
Chromatin IP against H4K20me3
GAWSU548-KM12-H4K20me3-ChIP_TTAGGC_GAWSU548_CKDL200157351-1a-3_HC3LFBBXX_L4_1.fastq.gz


title: H4K20me3_LC_HOP-92_rep2

description:
Chromatin IP against H4K20me3
GAWSU666-HOP92-H4K20me3-ChIP-rep2_ATCACG_GAWSU666_CKDL200157356-1a-1_HC7WYBBXX_L1_1.fastq.gz


title: H4K20me3_LC_NCI-H226_rep2

description:
Chromatin IP against H4K20me3
GAWSU690-NCI-H226-H4K20me3-ChIP-rep2_ATCACG_GAWSU690_CKDL200157357-1a-1_HC7WYBBXX_L2_1.fastq.gz


title: H4K20me3_LE_RPMI-8226_rep2

description:
Chromatin IP against H4K20me3
GAWSU616-RPMI-8226-H4K20me3-ChIP-rep2_GAGTGG_GAWSU616_CKDL200157354-1a-23_HC3LFBBXX_L7_1.fastq.gz


title: H4K20me3_CO_HCC-2998_rep2

description:
Chromatin IP against H4K20me3
GAWSU560-HCT-2998-H4K20me3-ChIP-rep2_ATGTCA_GAWSU560_CKDL200157352-1a-15_HC3LFBBXX_L5_1.fastq.gz


title: H4K20me3_CNS_SNB-19_rep2

description:
Chromatin IP against H4K20me3
GAWSU704-SNB-19-H4K20me3-ChIP-rep2_ATGTCA_GAWSU704_CKDL200157358-1a-15_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_LC_NCI-H322M_rep2

description:
Chromatin IP against H4K20me3
GAWSU648-NCI-H322M-H4K20me3-ChIP-rep2_CAGATC_GAWSU648_CKDL200157355-1a-7_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_ME_SK-MEL-5_rep2

description:
Chromatin IP against H4K20me3
GAWSU622-SK-MEL-5-H4K20me3-ChIP-rep2_ACAGTG_GAWSU622_CKDL200157354-1a-5_HC3LFBBXX_L7_1.fastq.gz


title: H4K20me3_OV_NCI_ADR-RES_rep2

description:
Chromatin IP against H4K20me3
GAWSU711-ADR-RES-H4K20me3-ChIP-rep2_CGTACG_GAWSU711_CKDL200157358-1a-22_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_CO_HT29_rep2

description:
Chromatin IP against H4K20me3
GAWSU713-HT29-H4K20me3-ChIP-rep2_GGTAGC_GAWSU713_CKDL200157358-1a-24_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_CO_HCT-15_rep2

description:
Chromatin IP against H4K20me3
GAWSU721-HCT-15-H4K20me3-ChIP-rep2_GTTTCG_GAWSU721_CKDL200158688-1a-21_HC2WKBBXX_L2_1.fastq.gz


title: H4K20me3_CO_COLO_205_rep2

description:
Chromatin IP against H4K20me3
GAWSU544-COLO-205-H4K20me3-ChIP-rep2_GAGTGG_GAWSU544_CKDL200157351-1a-23_HC3LFBBXX_L4_1.fastq.gz


title: H4K20me3_CNS_SNB-75_rep2

description:
Chromatin IP against H4K20me3
GAWSU663-SNB75-H4K20me3-ChIP-rep2_CGTACG_GAWSU663_CKDL200157356-1a-22_HC7WYBBXX_L1_1.fastq.gz


title: H4K20me3_CNS_U251_rep2

description:
Chromatin IP against H4K20me3
GAWSU699-U251-H4K20me3-ChIP-rep2_TAGCTT_GAWSU699_CKDL200157358-1a-10_HC7WYBBXX_L3_1.fastq.gz


title: H3K9me3_RE_SN12C_rep2

description:
Chromatin IP against H3K9me3
GAWSU577-SN12C-H3K9me3-ChIP-rep2_ACTTGA_GAWSU577_CKDL200157352-1a-8_HC3LFBBXX_L5_1.fastq.gz

value: Anti-H3K9me3 antibody (Abcam; ab8898)


title: H3K9me3_RE_786-0_rep2

description:
Chromatin IP against H3K9me3
GAWSU573-786-O-H3K9me3-ChIP-rep2_TGACCA_GAWSU573_CKDL200157352-1a-4_HC3LFBBXX_L5_1.fastq.gz


title: H3K9me3_RE_RXF_393_rep2

description:
Chromatin IP against H3K9me3
GAWSU533-RXF-393-H3K9me3-ChIP-rep2_CTTGTA_GAWSU533_CKDL200157350-1a-12_HC3LFBBXX_L3_1.fastq.gz

source_name: RXF 393

value: RXF 393


title: H3K9me3_RE_CAKI-1_rep2

description:
Chromatin IP against H3K9me3
GAWSU629-CAKI1-H3K9me3-ChIP-rep2_CTTGTA_GAWSU629_CKDL200157354-1a-12_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_PC-3_rep2

description:
Chromatin IP against H3K9me3
GAWSU497-PC-3-H3K9me3-ChIP-rep2_GGTAGC_GAWSU497_CKDL200157350-1a-24_HC3LFBBXX_L3_1.fastq.gz


title: H4K20me3_CNS_SF-295_rep2

description:
Chromatin IP against H4K20me3
GAWSU710-SF-295-H4K20me3-ChIP-rep2_GTTTCG_GAWSU710_CKDL200157358-1a-21_HC7WYBBXX_L3_1.fastq.gz


title: H3K9me3_DU-145_rep2

description:
Chromatin IP against H3K9me3
GAWSU553-DU-145-H3K9me3-ChIP_ACTTGA_GAWSU553_CKDL200157351-1a-8_HC3LFBBXX_L4_1.fastq.gz


title: H4K20me3_CNS_SF-539_rep2

description:
Chromatin IP against H4K20me3
GAWSU631-SF539-H4K20me3-ChIP-rep2_AGTTCC_GAWSU631_CKDL200157355-1a-14_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_BR_T-47D_rep2

description:
Chromatin IP against H4K20me3
GAWSU619-T47D-H4K20me3-ChIP-rep2_CGATGT_GAWSU619_CKDL200157354-1a-2_HC3LFBBXX_L7_1.fastq.gz


title: H4K20me3_CNS_SF-268_rep2

description:
Chromatin IP against H4K20me3
GAWSU707-SF-268-H4K20me3-ChIP-rep2_GTCCGC_GAWSU707_CKDL200157358-1a-18_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_LC_NCI-H522_rep2

description:
Chromatin IP against H4K20me3
GAWSU634-NCI-H522-H4K20me3-ChIP-rep2_GTAGAG_GAWSU634_CKDL200157355-1a-17_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_BR_MDA-MB-468_rep2

description:
Chromatin IP against H4K20me3
GAWSU720-MDA-MB-468-H4K20me3-ChIP-rep2_GTGGCC_GAWSU720_CKDL200158688-1a-20_HC2WKBBXX_L2_1.fastq.gz


title: H4K20me3_BR_MDA-MB-231_rep2

description:
Chromatin IP against H4K20me3
GAWSU706-MDA-MB-231-H4K20me3-ChIP-rep2_GTAGAG_GAWSU706_CKDL200157358-1a-17_HC7WYBBXX_L3_1.fastq.gz


title: H3K9me3_OV_OVCAR-3_rep2

description:
Chromatin IP against H3K9me3
GAWSU638-OVCAR3-H3K9me3-ChIP-rep2_GTTTCG_GAWSU638_CKDL200157355-1a-21_HC3LFBBXX_L8_1.fastq.gz


title: H4K20me3_BR_MCF7_rep2

description:
Chromatin IP against H4K20me3
GAWSU654-MCF7-H4K20me3-ChIP-rep2_AGTCAA_GAWSU654_CKDL200157356-1a-13_HC7WYBBXX_L1_1.fastq.gz


title: H4K20me3_BR_HS_578T_rep2

description:
Chromatin IP against H4K20me3
GAWSU705-HS-578T-H4K20me3-ChIP-rep2_CCGTCC_GAWSU705_CKDL200157358-1a-16_HC7WYBBXX_L3_1.fastq.gz


title: H4K20me3_BR_BT-549_rep2

description:
Chromatin IP against H4K20me3
GAWSU660-BT549-H4K20me3-ChIP-rep2_GTGAAA_GAWSU660_CKDL200157356-1a-19_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_OV_IGROV1_rep2

description:
Chromatin IP against H3K9me3
GAWSU679-IGROV1-H3K9me3-ChIP-rep2_AGTTCC_GAWSU679_CKDL200157357-1a-14_HC7WYBBXX_L2_1.fastq.gz


title: H3K9me3_RE_UO-31_rep2

description:
Chromatin IP against H3K9me3
GAWSU473-UO-31-H3K9me3-ChIP-rep2_GGTAGC_GAWSU473_CKDL200157349-1a-24_HC3LFBBXX_L2_1.fastq.gz


title: H3K9me3_RE_TK-10_rep2

description:
Chromatin IP against H3K9me3
GAWSU517-TK-10-H3K9me3-ChIP-rep2_GTGGCC_GAWSU517_CKDL200157351-1a-20_HC3LFBBXX_L4_1.fastq.gz


title: H4K20me3_CO_HCT-116_rep2

description:
Chromatin IP against H4K20me3
GAWSU540-HCT-116-H4K20me3-ChIP-rep2_GTGAAA_GAWSU540_CKDL200157351-1a-19_HC3LFBBXX_L4_1.fastq.gz


title: H3K9me3_RE_A498_rep2

description:
Chromatin IP against H3K9me3
GAWSU688-A498-H3K9me3-ChIP-rep2_GAGTGG_GAWSU688_CKDL200157357-1a-23_HC7WYBBXX_L2_1.fastq.gz


title: H3K9me3_RE_ACHN_rep2

description:
Chromatin IP against H3K9me3
GAWSU477-ACHN-H3K9me3-ChIP-rep2_TGACCA_GAWSU477_CKDL200157349-1a-4_HC3LFBBXX_L2_1.fastq.gz


title: H3K9me3_OV_SK-OV-3_rep2

description:
Chromatin IP against H3K9me3
GAWSU537-SK-OV-3-H3K9me3-ChIP-rep2_CCGTCC_GAWSU537_CKDL200157351-1a-16_HC3LFBBXX_L4_1.fastq.gz


title: H3K9me3_OV_OVCAR-8_rep2

description:
Chromatin IP against H3K9me3
GAWSU521-OVCAR-8-H3K9me3-ChIP-rep2_GGTAGC_GAWSU521_CKDL200157351-1a-24_HC3LFBBXX_L4_1.fastq.gz


title: H3K9me3_OV_OVCAR-5_rep2

description:
Chromatin IP against H3K9me3
GAWSU557-OVCAR5-H3K9me3-ChIP-rep2_CTTGTA_GAWSU557_CKDL200157352-1a-12_HC3LFBBXX_L5_1.fastq.gz


title: H3K9me3_OV_OVCAR-4_rep2

description:
Chromatin IP against H3K9me3
GAWSU641-OVCAR4-H3K9me3-ChIP-rep2_GGTAGC_GAWSU641_CKDL200157355-1a-24_HC3LFBBXX_L8_1.fastq.gz


title: H3K9me3_OV_NCI_ADR-RES_rep2

description:
Chromatin IP against H3K9me3
GAWSU493-ADR-RES-H3K9me3-ChIP-rep2_GTGGCC_GAWSU493_CKDL200157350-1a-20_HC3LFBBXX_L3_1.fastq.gz

source_name: NCI/ADR-RES

value: NCI/ADR-RES


title: H3K9me3_ME_UACC-257_rep2

description:
Chromatin IP against H3K9me3
GAWSU670-UACC-257-H3K9me3-ChIP-rep2_ACAGTG_GAWSU670_CKDL200157356-1a-5_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_LE_RPMI-8226_rep2

description:
Chromatin IP against H3K9me3
GAWSU617-RPMI-8226-H3K9me3-ChIP-rep2_GGTAGC_GAWSU617_CKDL200157354-1a-24_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_ME_M14_rep2

description:
Chromatin IP against H3K9me3
GAWSU585-M14-H3K9me3-ChIP-rep2_CCGTCC_GAWSU585_CKDL200157353-1a-16_HC3LFBBXX_L6_1.fastq.gz


title: H3K9me3_ME_UACC-62_rep2

description:
Chromatin IP against H3K9me3
GAWSU652-UACC-62-H3K9me3-ChIP-rep2_GGCTAC_GAWSU652_CKDL200157356-1a-11_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_ME_SK-MEL-5_rep2

description:
Chromatin IP against H3K9me3
GAWSU623-SK-MEL-5-H3K9me3-ChIP-rep2_GCCAAT_GAWSU623_CKDL200157354-1a-6_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_LE_HL-60_rep2

description:
Chromatin IP against H3K9me3
GAWSU658-HL60-H3K9me3-ChIP-rep2_GTAGAG_GAWSU658_CKDL200157356-1a-17_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_LE_CCRF-CEM_rep2

description:
Chromatin IP against H3K9me3
GAWSU673-CCRF-CEM-H3K9me3-ChIP-rep2_ACTTGA_GAWSU673_CKDL200157357-1a-8_HC7WYBBXX_L2_1.fastq.gz


title: H3K9me3_ME_MDA-MB-435_rep2

description:
Chromatin IP against H3K9me3
GAWSU589-MDA-MB-435-H3K9me3-ChIP-rep2_GTGGCC_GAWSU589_CKDL200157353-1a-20_HC3LFBBXX_L6_1.fastq.gz


title: H3K9me3_LC_NCI-H522_rep2

description:
Chromatin IP against H3K9me3
GAWSU635-NCI-H522-H3K9me3-ChIP-rep2_GTCCGC_GAWSU635_CKDL200157355-1a-18_HC3LFBBXX_L8_1.fastq.gz


title: H3K9me3_ME_SK-MEL-2_rep2

description:
Chromatin IP against H3K9me3
GAWSU453-SK-MEL-2-H3K9me3-ChIP-rep2_TGACCA_CKDL200155697-1a-4_HC2WJBBXX_L5_1.fastq.gz


title: H3K9me3_LE_SR_rep2

description:
Chromatin IP against H3K9me3
GAWSU613-SR-H3K9me3-ChIP-rep2_GTGGCC_GAWSU613_CKDL200157354-1a-20_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_ME_LOX_IMVI_rep2

description:
Chromatin IP against H3K9me3
GAWSU697-LOX-IMVI-H3K9me3-ChIP-rep2_ACTTGA_GAWSU697_CKDL200157358-1a-8_HC7WYBBXX_L3_1.fastq.gz

source_name: LOX IMVI

value: LOX IMVI


title: H3K9me3_LC_NCI-H226_rep2

description:
Chromatin IP against H3K9me3
GAWSU691-NCI-H226-H3K9me3-ChIP-rep2_CGATGT_GAWSU691_CKDL200157357-1a-2_HC7WYBBXX_L2_1.fastq.gz


title: H3K9me3_LE_K-562_rep2

description:
Chromatin IP against H3K9me3
GAWSU646-K562-H3K9me3-ChIP-rep2_ACAGTG_GAWSU646_CKDL200157355-1a-5_HC3LFBBXX_L8_1.fastq.gz


title: H3K9me3_ME_MALME-3M_rep2

description:
Chromatin IP against H3K9me3
GAWSU694-MALME-3M-H3K9me3-ChIP-rep2_ACAGTG_GAWSU694_CKDL200157358-1a-5_HC7WYBBXX_L3_1.fastq.gz


title: H3K9me3_LC_HOP-92_rep2

description:
Chromatin IP against H3K9me3
GAWSU667-HOP92-H3K9me3-ChIP-rep2_CGATGT_GAWSU667_CKDL200157356-1a-2_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_LE_MOLT-4_rep2

description:
Chromatin IP against H3K9me3
GAWSU505-MOLT-4-H3K9me3-ChIP-rep2_ACTTGA_GAWSU505_CKDL200157350-1a-8_HC3LFBBXX_L3_1.fastq.gz


title: H3K9me3_LC_NCI-H23_rep2

description:
Chromatin IP against H3K9me3
GAWSU685-NCI-H23-H3K9me3-ChIP-rep2_GTGGCC_GAWSU685_CKDL200157357-1a-20_HC7WYBBXX_L2_1.fastq.gz


title: H3K9me3_LC_HOP-62_rep2

description:
Chromatin IP against H3K9me3
GAWSU509-HOP-62-H3K9me3-ChIP-rep2_CTTGTA_GAWSU509_CKDL200157349-1a-12_HC3LFBBXX_L2_1.fastq.gz


title: H3K9me3_LC_NCI-H460_rep2

description:
Chromatin IP against H3K9me3
GAWSU581-NCI-H460-H3K9me3-ChIP-rep2_CTTGTA_GAWSU581_CKDL200157353-1a-12_HC3LFBBXX_L6_1.fastq.gz


title: H3K9me3_LC_EKVX_rep2

description:
Chromatin IP against H3K9me3
GAWSU626-EKVX-H3K9me3-ChIP-rep2_GATCAG_GAWSU626_CKDL200157354-1a-9_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_LC_NCI-H322M_rep2

description:
Chromatin IP against H3K9me3
GAWSU649-NCI-H322M-H3K9me3-ChIP-rep2_ACTTGA_GAWSU649_CKDL200157356-1a-8_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_LC_A549_rep2

description:
Chromatin IP against H3K9me3
GAWSU513-A549-H3K9me3-ChIP-rep2_CCGTCC_GAWSU513_CKDL200157350-1a-16_HC3LFBBXX_L3_1.fastq.gz


title: H3K9me3_CO_KM12_rep2

description:
Chromatin IP against H3K9me3
GAWSU549-KM12-H3K9me3-ChIP_TGACCA_GAWSU549_CKDL200157351-1a-4_HC3LFBBXX_L4_1.fastq.gz


title: H3K9me3_CO_SW-620_rep2

description:
Chromatin IP against H3K9me3
GAWSU593-SW-620-H3K9me3-ChIP-rep2_GGTAGC_GAWSU593_CKDL200157353-1a-24_HC3LFBBXX_L6_1.fastq.gz


title: H3K9me3_CO_HCT-15_rep2

description:
Chromatin IP against H3K9me3
GAWSU601-HCT-15-H3K9me3-ChIP-rep2_ACTTGA_GAWSU601_CKDL200157354-1a-8_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_CO_HT29_rep2

description:
Chromatin IP against H3K9me3
GAWSU501-HT29-H3K9me3-ChIP-rep2_TGACCA_GAWSU501_CKDL200157350-1a-4_HC3LFBBXX_L3_1.fastq.gz


title: H3K9me3_CO_HCT-116_rep2

description:
Chromatin IP against H3K9me3
GAWSU541-HCT-116-H3K9me3-ChIP-rep2_GTGGCC_GAWSU541_CKDL200157352-1a-20_HC3LFBBXX_L5_1.fastq.gz


title: H3K9me3_CO_COLO_205_rep2

description:
Chromatin IP against H3K9me3
GAWSU545-COLO-205-H3K9me3-ChIP-rep2_GGTAGC_GAWSU545_CKDL200157352-1a-24_HC3LFBBXX_L5_1.fastq.gz

source_name: COLO 205

value: COLO 205


title: H3K9me3_CNS_SNB-75_rep2

description:
Chromatin IP against H3K9me3
GAWSU664-SNB75-H3K9me3-ChIP-rep2_GAGTGG_GAWSU664_CKDL200157356-1a-23_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_CNS_U251_rep2

description:
Chromatin IP against H3K9me3
GAWSU700-U251-H3K9me3-ChIP-rep2_GGCTAC_GAWSU700_CKDL200157358-1a-11_HC7WYBBXX_L3_1.fastq.gz


title: H3K9me3_CNS_SF-268_rep2

description:
Chromatin IP against H3K9me3
GAWSU469-SF-268-H3K9me3-ChIP-rep2_GTGGCC_GAWSU469_CKDL200157349-1a-20_HC3LFBBXX_L2_1.fastq.gz


title: H3K9me3_CNS_SNB-19_rep2

description:
Chromatin IP against H3K9me3
GAWSU457-SNB-19-H3K9me3-ChIP-rep2_ACTTGA_CKDL200155697-1a-8_HC2WJBBXX_L5_1.fastq.gz


title: H3K9me3_ME_SK-MEL-28_rep2

description:
Chromatin IP against H3K9me3
GAWSU682-SKMEL28-H3K9me3-ChIP-rep2_GTAGAG_GAWSU682_CKDL200157357-1a-17_HC7WYBBXX_L2_1.fastq.gz


title: H3K9me3_CO_HCC-2998_rep2

description:
Chromatin IP against H3K9me3
GAWSU561-HCT-2998-H3K9me3-ChIP-rep2_CCGTCC_GAWSU561_CKDL200157352-1a-16_HC3LFBBXX_L5_1.fastq.gz


title: H3K9me3_CNS_SF-539_rep2

description:
Chromatin IP against H3K9me3
GAWSU632-SF539-H3K9me3-ChIP-rep2_ATGTCA_GAWSU632_CKDL200157355-1a-15_HC3LFBBXX_L8_1.fastq.gz


title: H3K9me3_CNS_SF-295_rep2

description:
Chromatin IP against H3K9me3
GAWSU481-SF-295-H3K9me3-ChIP-rep2_ACTTGA_GAWSU481_CKDL200157349-1a-8_HC3LFBBXX_L2_1.fastq.gz


title: H3K9me3_BR_T-47D_rep2

description:
Chromatin IP against H3K9me3
GAWSU620-T47D-H3K9me3-ChIP-rep2_TTAGGC_GAWSU620_CKDL200157354-1a-3_HC3LFBBXX_L7_1.fastq.gz


title: H3K9me3_BR_MDA-MB-231_rep2

description:
Chromatin IP against H3K9me3
GAWSU465-MDA-MB-231-H3K9me3-ChIP-rep2_CCGTCC_CKDL200155697-1a-16_HC2WJBBXX_L5_1.fastq.gz


title: H3K9me3_BR_MCF7_rep2

description:
Chromatin IP against H3K9me3
GAWSU655-MCF7-H3K9me3-ChIP-rep2_AGTTCC_GAWSU655_CKDL200157356-1a-14_HC7WYBBXX_L1_1.fastq.gz


title: H3K9me3_BR_HS_578T_rep2

description:
Chromatin IP against H3K9me3
GAWSU461-HS-578T-H3K9me3-ChIP-rep2_CTTGTA_CKDL200155697-1a-12_HC2WJBBXX_L5_1.fastq.gz

source_name: HS 578T

value: HS 578T


title: H3K27ac_RE_TK-10_rep2

description:
Chromatin IP against H3K27ac
GAWSU515-TK-10-H3K27ac-ChIP-rep2_GTCCGC_GAWSU515_CKDL200157350-1a-18_HC3LFBBXX_L3_1.fastq.gz

value: Anti-H3K27ac antibody (Abcam; ab4729)


title: H3K27ac_RE_SN12C_rep2

description:
Chromatin IP against H3K27ac
GAWSU575-SN12C-H3K27ac-ChIP-rep2_GCCAAT_GAWSU575_CKDL200157352-1a-6_HC3LFBBXX_L5_1.fastq.gz


title: H3K9me3_BR_BT-549_rep2

description:
Chromatin IP against H3K9me3
GAWSU661-BT549-H3K9me3-ChIP-rep2_GTGGCC_GAWSU661_CKDL200157356-1a-20_HC7WYBBXX_L1_1.fastq.gz


title: H3K27ac_RE_ACHN_rep2

description:
Chromatin IP against H3K27ac
GAWSU475-ACHN-H3K27ac-ChIP-rep2_CGATGT_GAWSU475_CKDL200157349-1a-2_HC3LFBBXX_L2_1.fastq.gz


title: H3K27ac_RE_UO-31_rep2

description:
Chromatin IP against H3K27ac
GAWSU471-UO-31-H3K27ac-ChIP-rep2_CGTACG_GAWSU471_CKDL200157349-1a-22_HC3LFBBXX_L2_1.fastq.gz


title: H3K27ac_RE_CAKI-1_rep2

description:
Chromatin IP against H3K27ac
GAWSU627-CAKI1-H3K27ac-ChIP-rep2_TAGCTT_GAWSU627_CKDL200157354-1a-10_HC3LFBBXX_L7_1.fastq.gz


title: H3K27ac_PR_PC-3_rep2

description:
Chromatin IP against H3K27ac
GAWSU495-PC-3-H3K27ac-ChIP-rep2_CGTACG_GAWSU495_CKDL200157350-1a-22_HC3LFBBXX_L3_1.fastq.gz


title: H3K27ac_RE_A498_rep2

description:
Chromatin IP against H3K27ac
GAWSU686-A498-H3K27ac-ChIP-rep2_GTTTCG_GAWSU686_CKDL200157357-1a-21_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_PR_DU-145_rep2

description:
Chromatin IP against H3K27ac
GAWSU551-DU-145-H3K27ac-ChIP_GCCAAT_GAWSU551_CKDL200157351-1a-6_HC3LFBBXX_L4_1.fastq.gz


title: H3K27ac_RE_786-0_rep2

description:
Chromatin IP against H3K27ac
GAWSU571-786-O-H3K27ac-ChIP-rep2_CGATGT_GAWSU571_CKDL200157352-1a-2_HC3LFBBXX_L5_1.fastq.gz


title: H3K27ac_OV_SK-OV-3_rep2

description:
Chromatin IP against H3K27ac
GAWSU535-SK-OV-3-H3K27ac-ChIP-rep2_AGTTCC_GAWSU535_CKDL200157351-1a-14_HC3LFBBXX_L4_1.fastq.gz


title: H3K27ac_ME_SK-MEL-5_rep2

description:
Chromatin IP against H3K27ac
GAWSU621-SK-MEL-5-H3K27ac-ChIP-rep2_TGACCA_GAWSU621_CKDL200157354-1a-4_HC3LFBBXX_L7_1.fastq.gz


title: H3K27ac_OV_OVCAR-3_rep2

description:
Chromatin IP against H3K27ac
GAWSU636-OVCAR3-H3K27ac-ChIP-rep2_GTGAAA_GAWSU636_CKDL200157355-1a-19_HC3LFBBXX_L8_1.fastq.gz


title: H3K27ac_OV_OVCAR-5_rep2

description:
Chromatin IP against H3K27ac
GAWSU555-OVCAR5-H3K27ac-ChIP-rep2_TAGCTT_GAWSU555_CKDL200157352-1a-10_HC3LFBBXX_L5_1.fastq.gz


title: H3K27ac_ME_M14_rep2

description:
Chromatin IP against H3K27ac
GAWSU583-M14-H3K27ac-ChIP-rep2_AGTTCC_GAWSU583_CKDL200157353-1a-14_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_ME_MALME-3M_rep2

description:
Chromatin IP against H3K27ac
GAWSU692-MALME-3M-H3K27ac-ChIP-rep2_TTAGGC_GAWSU692_CKDL200157357-1a-3_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_ME_UACC-257_rep2

description:
Chromatin IP against H3K27ac
GAWSU668-UACC-257-H3K27ac-ChIP-rep2_TTAGGC_GAWSU668_CKDL200157356-1a-3_HC7WYBBXX_L1_1.fastq.gz


title: H3K27ac_OV_NCI_ADR-RES_rep2

description:
Chromatin IP against H3K27ac
GAWSU491-ADR-RES-H3K27ac-ChIP-rep2_GTCCGC_GAWSU491_CKDL200157349-1a-18_HC3LFBBXX_L2_1.fastq.gz


title: H3K27ac_ME_LOX_IMVI_rep2

description:
Chromatin IP against H3K27ac
GAWSU695-LOX-IMVI-H3K27ac-ChIP-rep2_GCCAAT_GAWSU695_CKDL200157358-1a-6_HC7WYBBXX_L3_1.fastq.gz


title: H3K27ac_ME_SK-MEL-28_rep2

description:
Chromatin IP against H3K27ac
GAWSU680-SKMEL28-H3K27ac-ChIP-rep2_ATGTCA_GAWSU680_CKDL200157357-1a-15_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_LE_RPMI-8226_rep2

description:
Chromatin IP against H3K27ac
GAWSU615-RPMI-8226-H3K27ac-ChIP-rep2_CGTACG_GAWSU615_CKDL200157354-1a-22_HC3LFBBXX_L7_1.fastq.gz


title: H3K27ac_OV_OVCAR-8_rep2

description:
Chromatin IP against H3K27ac
GAWSU519-OVCAR-8-H3K27ac-ChIP-rep2_CGTACG_GAWSU519_CKDL200157351-1a-22_HC3LFBBXX_L4_1.fastq.gz


title: H3K9me3_BR_MDA-MB-468_rep2

description:
Chromatin IP against H3K9me3
GAWSU597-MDA-MB-468-H3K9me3-ChIP-rep2_TGACCA_GAWSU597_CKDL200157353-1a-4_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_OV_IGROV1_rep2

description:
Chromatin IP against H3K27ac
GAWSU677-IGROV1-H3K27ac-ChIP-rep2_CTTGTA_GAWSU677_CKDL200157357-1a-12_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_ME_UACC-62_rep2

description:
Chromatin IP against H3K27ac
GAWSU650-UACC-62-H3K27ac-ChIP-rep2_GATCAG_GAWSU650_CKDL200157355-1a-9_HC3LFBBXX_L8_1.fastq.gz


title: H3K27ac_OV_OVCAR-4_rep2

description:
Chromatin IP against H3K27ac
GAWSU639-OVCAR4-H3K27ac-ChIP-rep2_CGTACG_GAWSU639_CKDL200157355-1a-22_HC3LFBBXX_L8_1.fastq.gz


title: H3K27ac_RE_RXF_393_rep2

description:
Chromatin IP against H3K27ac
GAWSU531-RXF-393-H3K27ac-ChIP-rep2_TAGCTT_GAWSU531_CKDL200157350-1a-10_HC3LFBBXX_L3_1.fastq.gz


title: H3K27ac_LC_NCI-H522_rep2

description:
Chromatin IP against H3K27ac
GAWSU633-NCI-H522-H3K27ac-ChIP-rep2_CCGTCC_GAWSU633_CKDL200157355-1a-16_HC3LFBBXX_L8_1.fastq.gz


title: H3K27ac_LE_CCRF-CEM_rep2

description:
Chromatin IP against H3K27ac
GAWSU671-CCRF-CEM-H3K27ac-ChIP-rep2_GCCAAT_GAWSU671_CKDL200157357-1a-6_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_LE_MOLT-4_rep2

description:
Chromatin IP against H3K27ac
GAWSU503-MOLT-4-H3K27ac-ChIP-rep2_GCCAAT_GAWSU503_CKDL200157350-1a-6_HC3LFBBXX_L3_1.fastq.gz


title: H3K27ac_LC_NCI-H460_rep2

description:
Chromatin IP against H3K27ac
GAWSU579-NCI-H460-H3K27ac-ChIP-rep2_TAGCTT_GAWSU579_CKDL200157353-1a-10_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_LC_NCI-H23_rep2

description:
Chromatin IP against H3K27ac
GAWSU683-NCI-H23-H3K27ac-ChIP-rep2_GTCCGC_GAWSU683_CKDL200157357-1a-18_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_LE_K-562_rep2

description:
Chromatin IP against H3K27ac
GAWSU644-K562-H3K27ac-ChIP-rep2_TTAGGC_GAWSU644_CKDL200157355-1a-3_HC3LFBBXX_L8_1.fastq.gz


title: H3K27ac_LE_HL-60_rep2

description:
Chromatin IP against H3K27ac
GAWSU656-HL60-H3K27ac-ChIP-rep2_ATGTCA_GAWSU656_CKDL200157356-1a-15_HC7WYBBXX_L1_1.fastq.gz


title: H3K27ac_LC_NCI-H226_rep2

description:
Chromatin IP against H3K27ac
GAWSU689-NCI-H226-H3K27ac-ChIP-rep2_GGTAGC_GAWSU689_CKDL200157357-1a-24_HC7WYBBXX_L2_1.fastq.gz


title: H3K27ac_LC_HOP-92_rep2

description:
Chromatin IP against H3K27ac
GAWSU665-HOP92-H3K27ac-ChIP-rep2_GGTAGC_GAWSU665_CKDL200157356-1a-24_HC7WYBBXX_L1_1.fastq.gz


title: H3K27ac_LC_HOP-62_rep2

description:
Chromatin IP against H3K27ac
GAWSU507-HOP-62-H3K27ac-ChIP-rep2_TAGCTT_GAWSU507_CKDL200157349-1a-10_HC3LFBBXX_L2_1.fastq.gz


title: H3K27ac_LE_SR_rep2

description:
Chromatin IP against H3K27ac
GAWSU611-SR-H3K27ac-ChIP-rep2_GTCCGC_GAWSU611_CKDL200157354-1a-18_HC3LFBBXX_L7_1.fastq.gz


title: H3K27ac_ME_MDA-MB-435_rep2

description:
Chromatin IP against H3K27ac
GAWSU587-MDA-MB-435-H3K27ac-ChIP-rep2_GTCCGC_GAWSU587_CKDL200157353-1a-18_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_ME_SK-MEL-2_rep2

description:
Chromatin IP against H3K27ac
GAWSU451-SK-MEL-2-H3K27ac-ChIP-rep2_CGATGT_CKDL200155697-1a-2_HC2WJBBXX_L5_1.fastq.gz


title: H3K27ac_LC_A549_rep2

description:
Chromatin IP against H3K27ac
GAWSU511-A549-H3K27ac-ChIP-rep2_AGTTCC_GAWSU511_CKDL200157350-1a-14_HC3LFBBXX_L3_1.fastq.gz


title: H3K27ac_CO_SW-620_rep2

description:
Chromatin IP against H3K27ac
GAWSU591-SW-620-H3K27ac-ChIP-rep2_CGTACG_GAWSU591_CKDL200157353-1a-22_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_CO_KM12_rep2

description:
Chromatin IP against H3K27ac
GAWSU547-KM12-H3K27ac-ChIP_CGATGT_GAWSU547_CKDL200157351-1a-2_HC3LFBBXX_L4_1.fastq.gz


title: H3K27ac_CO_HCT-116_rep2

description:
Chromatin IP against H3K27ac
GAWSU539-HCT-116-H3K27ac-ChIP-rep2_GTCCGC_GAWSU539_CKDL200157351-1a-18_HC3LFBBXX_L4_1.fastq.gz


title: H3K27ac_CO_COLO_205_rep2

description:
Chromatin IP against H3K27ac
GAWSU543-COLO-205-H3K27ac-ChIP-rep2_CGTACG_GAWSU543_CKDL200157352-1a-22_HC3LFBBXX_L5_1.fastq.gz


title: H3K27ac_CO_HCC-2998_rep2

description:
Chromatin IP against H3K27ac
GAWSU559-HCT-2998-H3K27ac-ChIP-rep2_AGTTCC_GAWSU559_CKDL200157352-1a-14_HC3LFBBXX_L5_1.fastq.gz


title: H3K27ac_LC_EKVX_rep2

description:
Chromatin IP against H3K27ac
GAWSU624-EKVX-H3K27ac-ChIP-rep2_CAGATC_GAWSU624_CKDL200157354-1a-7_HC3LFBBXX_L7_1.fastq.gz


title: H3K27ac_BR_T-47D_rep2

description:
Chromatin IP against H3K27ac
GAWSU618-T47D-H3K27ac-ChIP-rep2_ATCACG_GAWSU618_CKDL200157354-1a-1_HC3LFBBXX_L7_1.fastq.gz


title: H3K27ac_BR_MDA-MB-231_rep2

description:
Chromatin IP against H3K27ac
GAWSU463-MDA-MB-231-H3K27ac-ChIP-rep2_AGTTCC_CKDL200155697-1a-14_HC2WJBBXX_L5_1.fastq.gz


title: H3K27ac_CNS_SNB-19_rep2

description:
Chromatin IP against H3K27ac
GAWSU455-SNB-19-H3K27ac-ChIP-rep2_GCCAAT_CKDL200155697-1a-6_HC2WJBBXX_L5_1.fastq.gz


title: H3K27ac_LC_NCI-H322M_rep2

description:
Chromatin IP against H3K27ac
GAWSU647-NCI-H322M-H3K27ac-ChIP-rep2_GCCAAT_GAWSU647_CKDL200157355-1a-6_HC3LFBBXX_L8_1.fastq.gz


title: H3K27ac_CNS_SNB-75_rep2

description:
Chromatin IP against H3K27ac
GAWSU662-SNB75-H3K27ac-ChIP-rep2_GTTTCG_GAWSU662_CKDL200157356-1a-21_HC7WYBBXX_L1_1.fastq.gz


title: H3K27ac_CNS_SF-539_rep2

description:
Chromatin IP against H3K27ac
GAWSU630-SF539-H3K27ac-ChIP-rep2_AGTCAA_GAWSU630_CKDL200157355-1a-13_HC3LFBBXX_L8_1.fastq.gz


title: H3K4me3_RE_TK-10_rep2

description:
Chromatin IP against H3K4me3
GAWSU514-TK-10-H3K4me3-ChIP-rep2_GTAGAG_GAWSU514_CKDL200157350-1a-17_HC3LFBBXX_L3_1.fastq.gz

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: H3K27ac_CNS_SF-268_rep2

description:
Chromatin IP against H3K27ac
GAWSU467-SF-268-H3K27ac-ChIP-rep2_GTCCGC_CKDL200155697-1a-18_HC2WJBBXX_L5_1.fastq.gz


title: H3K27ac_BR_HS_578T_rep2

description:
Chromatin IP against H3K27ac
GAWSU459-HS-578T-H3K27ac-ChIP-rep2_TAGCTT_CKDL200155697-1a-10_HC2WJBBXX_L5_1.fastq.gz


title: H3K27ac_BR_BT-549_rep2

description:
Chromatin IP against H3K27ac
GAWSU659-BT549-H3K27ac-ChIP-rep2_GTCCGC_GAWSU659_CKDL200157356-1a-18_HC7WYBBXX_L1_1.fastq.gz


title: H3K4me3_RE_CAKI-1_rep2

description:
Chromatin IP against H3K4me3
GAWSU192-CAKI1-H3K4me3-ChIP-rep2-99298_TTAGGC_S3_L006


title: H3K4me3_RE_RXF_393_rep2

description:
Chromatin IP against H3K4me3
GAWSU530-RXF-393-H3K4me3-ChIP-rep2_GATCAG_GAWSU530_CKDL200157350-1a-9_HC3LFBBXX_L3_1.fastq.gz


title: H3K4me3_RE_ACHN_rep2

description:
Chromatin IP against H3K4me3
GAWSU474-ACHN-H3K4me3-ChIP-rep2_ATCACG_GAWSU474_CKDL200157349-1a-1_HC3LFBBXX_L2_1.fastq.gz


title: H3K27ac_BR_MDA-MB-468_rep2

description:
Chromatin IP against H3K27ac
GAWSU595-MDA-MB-468-H3K27ac-ChIP-rep2_CGATGT_GAWSU595_CKDL200157353-1a-2_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_CNS_SF-295_rep2

description:
Chromatin IP against H3K27ac
GAWSU479-SF-295-H3K27ac-ChIP-rep2_GCCAAT_GAWSU479_CKDL200157349-1a-6_HC3LFBBXX_L2_1.fastq.gz


title: H3K4me3_RE_A498_rep2

description:
Chromatin IP against H3K4me3
GAWSU336-A498-H3K4me3-ChIP-rep2-101940_TTAGGC_S51_L008


title: H3K4me3_RE_786-0_rep2

description:
Chromatin IP against H3K4me3
GAWSU570-786-O-H3K4me3-ChIP-rep2_ATCACG_GAWSU570_CKDL200157352-1a-1_HC3LFBBXX_L5_1.fastq.gz


title: H3K27ac_CO_HCT-15_rep2

description:
Chromatin IP against H3K27ac
GAWSU599-HCT-15-H3K27ac-ChIP-rep2_GCCAAT_GAWSU599_CKDL200157353-1a-6_HC3LFBBXX_L6_1.fastq.gz


title: H3K27ac_CO_HT29_rep2

description:
Chromatin IP against H3K27ac
GAWSU499-HT29-H3K27ac-ChIP-rep2_CGATGT_GAWSU499_CKDL200157350-1a-2_HC3LFBBXX_L3_1.fastq.gz


title: H3K27ac_CNS_U251_rep2

description:
Chromatin IP against H3K27ac
GAWSU698-U251-H3K27ac-ChIP-rep2_GATCAG_GAWSU698_CKDL200157358-1a-9_HC7WYBBXX_L3_1.fastq.gz


title: H3K4me3_PR_PC-3_rep2

description:
Chromatin IP against H3K4me3
GAWSU494-PC-3-H3K4me3-ChIP-rep2_GTTTCG_GAWSU494_CKDL200157350-1a-21_HC3LFBBXX_L3_1.fastq.gz


title: H3K4me3_RE_UO-31_rep2

description:
Chromatin IP against H3K4me3
GAWSU470-UO-31-H3K4me3-ChIP-rep2_GTTTCG_GAWSU470_CKDL200157349-1a-21_HC3LFBBXX_L2_1.fastq.gz


title: H3K27ac_BR_MCF7_rep2

description:
Chromatin IP against H3K27ac
GAWSU653-MCF7-H3K27ac-ChIP-rep2_CTTGTA_GAWSU653_CKDL200157356-1a-12_HC7WYBBXX_L1_1.fastq.gz


title: H3K4me3_OV_OVCAR-5_rep2

description:
Chromatin IP against H3K4me3
GAWSU554-OVCAR5-H3K4me3-ChIP_GATCAG_GAWSU554_CKDL200157351-1a-9_HC3LFBBXX_L4_1.fastq.gz


title: H3K4me3_OV_OVCAR-4_rep2

description:
Chromatin IP against H3K4me3
GAWSU228-OVCAR4-H3K4me3-ChIP-rep2-100146_GATCAG_S19_L007


title: H3K4me3_PR_DU-145_rep2

description:
Chromatin IP against H3K4me3
GAWSU550-DU-145-H3K4me3-ChIP_ACAGTG_GAWSU550_CKDL200157351-1a-5_HC3LFBBXX_L4_1.fastq.gz


title: H3K4me3_ME_SK-MEL-5_rep2

description:
Chromatin IP against H3K4me3
GAWSU250-SK-MEL-5-H3K4me3-ChIP-rep2-101405_ATCACG_S11_L008


title: H3K4me3_OV_OVCAR-8_rep2

description:
Chromatin IP against H3K4me3
GAWSU518-OVCAR-8-H3K4me3-ChIP-rep2_GTTTCG_GAWSU518_CKDL200157351-1a-21_HC3LFBBXX_L4_1.fastq.gz


title: H3K4me3_OV_OVCAR-3_rep2

description:
Chromatin IP against H3K4me3
GAWSU226-OVCAR3-H3K4me3-ChIP-rep2-100144_CAGATC_S17_L007


title: H3K4me3_RE_SN12C_rep2

description:
Chromatin IP against H3K4me3
GAWSU574-SN12C-H3K4me3-ChIP-rep2_ACAGTG_GAWSU574_CKDL200157352-1a-5_HC3LFBBXX_L5_1.fastq.gz


title: H3K4me3_ME_UACC-62_rep2

description:
Chromatin IP against H3K4me3
GAWSU252-UACC-62-H3K4me3-ChIP-rep2-101407_TTAGGC_S13_L008


title: H3K4me3_OV_NCI_ADR-RES_rep2

description:
Chromatin IP against H3K4me3
GAWSU490-ADR-RES-H3K4me3-ChIP-rep2_GTAGAG_GAWSU490_CKDL200157349-1a-17_HC3LFBBXX_L2_1.fastq.gz


title: H3K4me3_OV_IGROV1_rep2

description:
Chromatin IP against H3K4me3
GAWSU194-IGROV1-H3K4me3-ChIP-rep2-99300_ACAGTG_S5_L006


title: H3K4me3_ME_MALME-3M_rep2

description:
Chromatin IP against H3K4me3
GAWSU256-MALME-3M-H3K4me3-ChIP-rep2-101411_CAGATC_S17_L008


title: H3K4me3_ME_M14_rep2

description:
Chromatin IP against H3K4me3
GAWSU582-M14-H3K4me3-ChIP-rep2_AGTCAA_GAWSU582_CKDL200157353-1a-13_HC3LFBBXX_L6_1.fastq.gz


title: H3K4me3_ME_UACC-257_rep2

description:
Chromatin IP against H3K4me3
GAWSU254-UACC-257-H3K4me3-ChIP-rep2-101409_ACAGTG_S15_L008


title: H3K4me3_ME_SK-MEL-28_rep2

description:
Chromatin IP against H3K4me3
GAWSU196-SKMEL28-H3K4me3-ChIP-rep2-99302_CAGATC_S7_L006


title: H3K4me3_LE_RPMI-8226_rep2

description:
Chromatin IP against H3K4me3
GAWSU614-RPMI-8226-H3K4me3-ChIP-rep2_GTTTCG_GAWSU614_CKDL200157354-1a-21_HC3LFBBXX_L7_1.fastq.gz


title: H3K4me3_LE_MOLT-4_rep2

description:
Chromatin IP against H3K4me3
GAWSU502-MOLT-4-H3K4me3-ChIP-rep2_ACAGTG_GAWSU502_CKDL200157350-1a-5_HC3LFBBXX_L3_1.fastq.gz


title: H3K4me3_ME_SK-MEL-2_rep2

description:
Chromatin IP against H3K4me3
GAWSU450-SK-MEL-2-H3K4me3-ChIP-rep2_ATCACG_CKDL200155697-1a-1_HC2WJBBXX_L5_1.fastq.gz


title: H3K4me3_LE_K-562_rep2

description:
Chromatin IP against H3K4me3
GAWSU220-K562-H3K4me3-ChIP-rep2-100138_ATCACG_S11_L007


title: H3K4me3_ME_LOX_IMVI_rep2

description:
Chromatin IP against H3K4me3
GAWSU258-LOX-IMVI-H3K4me3-ChIP-rep2-101413_GATCAG_S19_L008


title: H3K4me3_OV_SK-OV-3_rep2

description:
Chromatin IP against H3K4me3
GAWSU534-SK-OV-3-H3K4me3-ChIP-rep2_AGTCAA_GAWSU534_CKDL200157350-1a-13_HC3LFBBXX_L3_1.fastq.gz


title: H3K4me3_LE_SR_rep2

description:
Chromatin IP against H3K4me3
GAWSU610-SR-H3K4me3-ChIP-rep2_GTAGAG_GAWSU610_CKDL200157354-1a-17_HC3LFBBXX_L7_1.fastq.gz


title: H3K4me3_LC_NCI-H226_rep2

description:
Chromatin IP against H3K4me3
GAWSU302-NCI-H226-H3K4me3-ChIP-rep2-101598_ATCACG_S17_L006


title: H3K4me3_LC_NCI-H23_rep2

description:
Chromatin IP against H3K4me3
GAWSU298-NCI-H23-H3K4me3-ChIP-rep2-101593_AGTCAA_S13_L005


title: H3K4me3_LC_A549_rep2

description:
Chromatin IP against H3K4me3
GAWSU510-A549-H3K4me3-ChIP-rep2_AGTCAA_GAWSU510_CKDL200157349-1a-13_HC3LFBBXX_L2_1.fastq.gz


title: H3K4me3_LC_HOP-92_rep2

description:
Chromatin IP against H3K4me3
GAWSU294-HOP92-H3K4me3-ChIP-rep2-101589_GATCAG_S9_L005


title: H3K4me3_LE_CCRF-CEM_rep2

description:
Chromatin IP against H3K4me3
GAWSU224-CCRF-CEM-H3K4me3-ChIP-rep2-100142_ACAGTG_S15_L007


title: H3K4me3_LE_HL-60_rep2

description:
Chromatin IP against H3K4me3
GAWSU222-HL60-H3K4me3-ChIP-rep2-100140_TTAGGC_S13_L007


title: H3K4me3_LC_NCI-H460_rep2

description:
Chromatin IP against H3K4me3
GAWSU578-NCI-H460-H3K4me3-ChIP-rep2_GATCAG_GAWSU578_CKDL200157352-1a-9_HC3LFBBXX_L5_1.fastq.gz


title: H3K4me3_LC_NCI-H522_rep2

description:
Chromatin IP against H3K4me3
GAWSU286-NCI-H522-H3K4me3-ChIP-rep2-101581_ATCACG_S1_L005


title: H3K4me3_CO_HCT-15_rep2

description:
Chromatin IP against H3K4me3
GAWSU598-HCT-15-H3K4me3-ChIP-rep2_ACAGTG_GAWSU598_CKDL200157353-1a-5_HC3LFBBXX_L6_1.fastq.gz


title: H3K4me3_CO_HCT-116_rep2

description:
Chromatin IP against H3K4me3
GAWSU538-HCT-116-H3K4me3-ChIP-rep2_GTAGAG_GAWSU538_CKDL200157351-1a-17_HC3LFBBXX_L4_1.fastq.gz


title: H3K4me3_LC_NCI-H322M_rep2

description:
Chromatin IP against H3K4me3
GAWSU290-H322M-H3K4me3-ChIP-rep2-101585_ACAGTG_S5_L005


title: H3K4me3_CO_HCC-2998_rep2

description:
Chromatin IP against H3K4me3
GAWSU558-HCT-2998-H3K4me3-ChIP-rep2_AGTCAA_GAWSU558_CKDL200157352-1a-13_HC3LFBBXX_L5_1.fastq.gz


title: H3K4me3_CO_COLO_205_rep2

description:
Chromatin IP against H3K4me3
GAWSU542-COLO-205-H3K4me3-ChIP-rep2_GTTTCG_GAWSU542_CKDL200157352-1a-21_HC3LFBBXX_L5_1.fastq.gz


title: H3K4me3_LC_HOP-62_rep2

description:
Chromatin IP against H3K4me3
GAWSU506-HOP-62-H3K4me3-ChIP-rep2_GATCAG_GAWSU506_CKDL200157349-1a-9_HC3LFBBXX_L2_1.fastq.gz


title: H3K4me3_CO_SW-620_rep2

description:
Chromatin IP against H3K4me3
GAWSU590-SW-620-H3K4me3-ChIP-rep2_GTTTCG_GAWSU590_CKDL200157353-1a-21_HC3LFBBXX_L6_1.fastq.gz


title: H3K4me3_CO_KM12_rep2

description:
Chromatin IP against H3K4me3
GAWSU546-KM12-H3K4me3-ChIP_ATCACG_GAWSU546_CKDL200157351-1a-1_HC3LFBBXX_L4_1.fastq.gz


title: H3K4me3_BR_T-47D_rep2

description:
Chromatin IP against H3K4me3
GAWSU328-T47D-H3K4me3-ChIP-rep2-101931_AGTCAA_S43_L007


title: H3K4me3_CNS_SF-539_rep2

description:
Chromatin IP against H3K4me3
GAWSU316-SF539-H3K4me3-ChIP-rep2-101919_ATCACG_S31_L007


title: H3K4me3_CNS_SNB-75_rep2

description:
Chromatin IP against H3K4me3
GAWSU320-SNB75-H3K4me3-ChIP-rep2-101923_ACAGTG_S35_L007


title: H3K4me3_ME_MDA-MB-435_rep2

description:
Chromatin IP against H3K4me3
GAWSU586-MDA-MB-435-H3K4me3-ChIP-rep2_GTAGAG_GAWSU586_CKDL200157353-1a-17_HC3LFBBXX_L6_1.fastq.gz


title: H3K4me3_CNS_SF-295_rep2

description:
Chromatin IP against H3K4me3
GAWSU478-SF-295-H3K4me3-ChIP-rep2_ACAGTG_GAWSU478_CKDL200157349-1a-5_HC3LFBBXX_L2_1.fastq.gz


title: H3K4me3_CNS_SF-268_rep2

description:
Chromatin IP against H3K4me3
GAWSU466-SF-268-H3K4me3-ChIP-rep2_GTAGAG_CKDL200155697-1a-17_HC2WJBBXX_L5_1.fastq.gz


title: H3K4me3_CNS_SNB-19_rep2

description:
Chromatin IP against H3K4me3
GAWSU454-SNB-19-H3K4me3-ChIP-rep2_ACAGTG_CKDL200155697-1a-5_HC2WJBBXX_L5_1.fastq.gz


title: H3K4me3_CNS_U251_rep2

description:
Chromatin IP against H3K4me3
GAWSU324-U251-H3K4me3-ChIP-rep2-101927_GATCAG_S39_L007


title: H3K4me3_BR_MDA-MB-231_rep2

description:
Chromatin IP against H3K4me3
GAWSU462-MDA-MB-231-H3K4me3-ChIP-rep2_AGTCAA_CKDL200155697-1a-13_HC2WJBBXX_L5_1.fastq.gz


title: H3K4me3_BR_MCF7_rep2

description:
Chromatin IP against H3K4me3
GAWSU190-MCF7-H3K4me3-ChIP-rep2-99296_ATCACG_S1_L006


title: H3K4me3_BR_MDA-MB-468_rep2

description:
Chromatin IP against H3K4me3
GAWSU594-MDA-MB-468-H3K4me3-ChIP-rep2_ATCACG_GAWSU594_CKDL200157353-1a-1_HC3LFBBXX_L6_1.fastq.gz


title: H3K4me3_BR_BT-549_rep2

description:
Chromatin IP against H3K4me3
GAWSU332-BT549-H3K4me3-ChIP-rep2-101935_GTAGAG_S47_L007


title: H3K4me3_BR_HS_578T_rep2

description:
Chromatin IP against H3K4me3
GAWSU458-HS-578T-H3K4me3-ChIP-rep2_GATCAG_CKDL200155697-1a-9_HC2WJBBXX_L5_1.fastq.gz


title: H3K4me3_LC_EKVX_rep2

description:
Chromatin IP against H3K4me3
GAWSU198-EKVX-H3K4me3-ChIP-rep2-99304_GATCAG_S9_L006


title: H3K4me3_CO_HT29_rep2

description:
Chromatin IP against H3K4me3
GAWSU498-HT29-H3K4me3-ChIP-rep2_ATCACG_GAWSU498_CKDL200157350-1a-1_HC3LFBBXX_L3_1.fastq.gz


title: CART19_only (RNA-seq)

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with trimmomatic, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression
Genome_build: CRCh38
Supplementary_files_format_and_content: tab-delimited text files contain the gene expression counts for each sample; csv is DeSeq2 dataset

source_name: CART cells

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CART19 cells were thawed and stimulated with irradiated Jeko-1 cells (120 Gy) for 24 hours with 3 biological replicates of CLL-derived EVs. CART19 were isolated to a purity of 100% using CD19 microbeads (Miltenyi).  JeKo-1 were co-cultured for 24 hours with the same 3 biological replicates of CLL-derived EVs. Total RNA was isolated from all CART19 and JeKo-1 samples.

value: Untreated

tag: stimulation

value: Unstimulated

tag: ev sample

tag: ev dose


title: CART19_No_EV (RNA-seq)

value: Antigen-Stimulated


title: CART19_1_1_EV__5 (RNA-seq)

value: EV-treated


title: CART19_1_1_EV__4 (RNA-seq)


title: CART19_1_1_EV__13 (RNA-seq)


title: CART19_10_1_EV__5 (RNA-seq)


title: ChIP_Input_TK-10

description: Direct sequencing following sonication of x-linked chromatin

value: cancer cell

tag: antibody


title: ChIP_Input_UO-31


title: CART19_10_1_EV__13 (RNA-seq)


title: ChIP_Input_SN12C


title: CART19_10_1_EV__4 (RNA-seq)


title: ChIP_Input_RXF 393


title: ChIP_Input_CAKI-1


title: ChIP_Input_A498


title: ChIP_Input_ACHN

value: ACHN


title: ChIP_Input_PC-3


title: ChIP_Input_IGROV1


title: ChIP_Input_OVCAR-3


title: ChIP_Input_UACC-257


title: ChIP_Input_NCI_ADR-RES


title: ChIP_Input_SK-MEL-5


title: ChIP_Input_DU-145


title: ChIP_Input_SK-OV-3


title: ChIP_Input_OVCAR-8


title: ChIP_Input_OVCAR-5


title: ChIP_Input_MDA-MB-435


title: ChIP_Input_OVCAR-4


title: ChIP_Input_MALME-3M


title: ChIP_Input_SK-MEL-28


title: ChIP_Input_UACC-62


title: ChIP_Input_SK-MEL-2


title: ChIP_Input_M14


title: ChIP_Input_LOX IMVI


title: ChIP_Input_MOLT-4


title: ChIP_Input_HL-60


title: ChIP_Input_SR


title: ChIP_Input_NCI-H522


title: ChIP_Input_786-0


title: ChIP_Input_CCRF-CEM

value: CCRF-CEM


title: ChIP_Input_RPMI-8226


title: ChIP_Input_K-562


title: ChIP_Input_NCI-H226


title: ChIP_Input_HT29


title: ChIP_Input_EKVX


title: ChIP_Input_KM12


title: ChIP_Input_HOP-62


title: ChIP_Input_A549


title: ChIP_Input_HCC-2998


title: ChIP_Input_HCT-116


title: ChIP_Input_HCT-15


title: ChIP_Input_U251


title: ChIP_Input_SNB-75


title: ChIP_Input_NCI-H460


title: ChIP_Input_SNB-19


title: ChIP_Input_SF-295


title: ChIP_Input_COLO 205


title: ChIP_Input_SF-268


title: ChIP_Input_NCI-H23


title: ChIP_Input_NCI-H322M


title: ChIP_Input_T-47D


title: ChIP_Input_MDA-MB-231


title: ChIP_Input_MCF7


title: H4K20me3_OV_OVCAR-8

description: Chromatin IP against H4K20me3

value: Anti-H4K20me3 antibody (Abcam; ab9053)


title: ChIP_Input_SF-539


title: ChIP_Input_BT-549


title: H4K20me3_RE_TK-10

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_A549

description: Chromatin IP against H4K20me3


title: ChIP_Input_HS 578T


title: ChIP_Input_MDA-MB-468


title: ChIP_Input_SW-620


title: ChIP_Input_HOP-92


title: H4K20me3_RE_RXF_393

description: Chromatin IP against H4K20me3


title: H4K20me3_RE_SN12C

description: Chromatin IP against H4K20me3


title: H4K20me3_RE_A498

description: Chromatin IP against H4K20me3


title: H4K20me3_RE_ACHN

description: Chromatin IP against H4K20me3


title: H4K20me3_DU-145

description: Chromatin IP against H4K20me3


title: H4K20me3_OV_OVCAR-4

description: Chromatin IP against H4K20me3


title: H4K20me3_RE_CAKI-1

description: Chromatin IP against H4K20me3


title: H4K20me3_RE_786-0

description: Chromatin IP against H4K20me3


title: H4K20me3_PC-3

description: Chromatin IP against H4K20me3


title: H4K20me3_OV_SK-OV-3

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_UACC-62

description: Chromatin IP against H4K20me3


title: H4K20me3_OV_OVCAR-5

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_SK-MEL-5

description: Chromatin IP against H4K20me3


title: H4K20me3_OV_OVCAR-3

description: Chromatin IP against H4K20me3


title: H4K20me3_OV_IGROV1

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_UACC-257

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_SK-MEL-2

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_MDA-MB-435

description: Chromatin IP against H4K20me3


title: H4K20me3_LE_RPMI-8226

description: Chromatin IP against H4K20me3


title: H4K20me3_OV_NCI_ADR-RES

description: Chromatin IP against H4K20me3


title: H4K20me3_LE_SR

description: Chromatin IP against H4K20me3

value: SR


title: H4K20me3_RE_UO-31

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_MALME-3M

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_HOP-62

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_SK-MEL-28

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_M14

description: Chromatin IP against H4K20me3


title: H4K20me3_LE_MOLT-4

description: Chromatin IP against H4K20me3


title: H4K20me3_ME_LOX_IMVI

description: Chromatin IP against H4K20me3


title: H4K20me3_LE_K-562

description: Chromatin IP against H4K20me3


title: H4K20me3_LE_HL-60

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_NCI-H522

description: Chromatin IP against H4K20me3


title: H4K20me3_LE_CCRF-CEM

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_NCI-H460

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_NCI-H322M

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_NCI-H226

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_HOP-92

description: Chromatin IP against H4K20me3


title: H4K20me3_CO_SW-620

description: Chromatin IP against H4K20me3


title: H4K20me3_CO_KM12

description: Chromatin IP against H4K20me3


title: H4K20me3_CO_HCT-116

description: Chromatin IP against H4K20me3


title: H4K20me3_CO_HT29

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_EKVX

description: Chromatin IP against H4K20me3

value: EKVX


title: H4K20me3_CO_HCT-15

description: Chromatin IP against H4K20me3


title: H4K20me3_LC_NCI-H23

description: Chromatin IP against H4K20me3


title: H4K20me3_CNS_SF-295

description: Chromatin IP against H4K20me3


title: H4K20me3_CO_HCC-2998

description: Chromatin IP against H4K20me3


title: H4K20me3_CO_COLO_205

description: Chromatin IP against H4K20me3


title: H4K20me3_CNS_U251

description: Chromatin IP against H4K20me3


title: H4K20me3_BR_MDA-MB-468

description: Chromatin IP against H4K20me3


title: H4K20me3_CNS_SNB-19

description: Chromatin IP against H4K20me3


title: H4K20me3_CNS_SNB-75

description: Chromatin IP against H4K20me3


title: H4K20me3_BR_MDA-MB-231

description: Chromatin IP against H4K20me3


title: H4K20me3_CNS_SF-539

description: Chromatin IP against H4K20me3


title: HCT116_Dom_rep1

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from HCT116 cells treated with Domperidone, biological replicate 1

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Affymetrix background correction, quantile normalization, and summarization were done with the package oligo (version 1.50.0)

label: biotin

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

extract_protocol: RNA extraction was performed using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion

treatment_protocol: As described in the paper. Briefly, HCT116 cells were treated with Niclosamide ethanolamine (1.2 µM) and Domperidone (30 µM)


title: HCT116_Ctrl_rep3

description: Gene expression data from HCT116 cells control, biological replicate 3


title: HCT116_Ctrl_rep1

description: Gene expression data from HCT116 cells control, biological replicate 1


title: HCT116_NEN_Dom_rep3

description: Gene expression data from HCT116 cells treated with Niclosamide ethanolamine and Domperidone, biological replicate 3


title: HCT116_NEN_Dom_rep2

description: Gene expression data from HCT116 cells treated with Niclosamide ethanolamine and Domperidone, biological replicate 2


title: HCT116_NEN_rep2

description: Gene expression data from HCT116 cells treated with Niclosamide ethanolamine, biological replicate 2


title: HCT116_Ctrl_rep2

description: Gene expression data from HCT116 cells control, biological replicate 2


title: HCT116_Dom_rep3

description: Gene expression data from HCT116 cells treated with Domperidone, biological replicate 3


title: HCT116_NEN_Dom_rep1

description: Gene expression data from HCT116 cells treated with Niclosamide ethanolamine and Domperidone, biological replicate 1


title: H4K20me3_BR_T-47D

description: Chromatin IP against H4K20me3


title: H4K20me3_BR_BT-549

description: Chromatin IP against H4K20me3


title: HCT116_Dom_rep2

description: Gene expression data from HCT116 cells treated with Domperidone, biological replicate 2


title: H3K4me1_primed_rep3

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Library strategy: CUT&RUN
Standard Illumina base-calling pipeline.
CUT&RUN reads were trimmed using Trim Galore (v0.5.0) and aligned using Bowtie2 (v2.3.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: A tab-separated file of log2RPM read counts per 500bp. Fields are "chomosome", "start", "end", "log2 RPM"

source_name: Primed ESCs (NK2 H9 line)

extract_protocol:
WA09/H9 NK2 naive and primed PSCs were kindly provided by Austin Smith (Takashima et al., 2014) with permission from WiCell. All PSCs were cultured in 5% O2, 5% CO2 at 37°C. Naive PSCs were maintained as previously described (Takashima et al., 2014) in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2 supplement, 0.5x B27 supplement, 1x nonessential amino acids, 2mM L-Glutamine, 1x Penicillin/Streptomycin (all from ThermoFisher Scientific), 0.1mM β-mercaptoethanol (Sigma-Aldrich), 1 μM PD0325901, 1 μM CHIR99021, 20ng/ml human LIF (all from WT-MRC Cambridge Stem Cell Institute) and 2 μM Go6983 (PKCi; Tocris) on Matrigel–coated plates (Corning). Primed PSCs were maintained on Vitronectin-coated plates (0.5 μg/cm2; ThermoFisher Scientific) in TeSR-E8 medium (StemCell Technologies).
CUT&RUN samples were generated essentially as described (Skene et al., 2018). Libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina. Libraries were paired-end sequenced on an Illumina NextSeq machine at the Babraham Institute Sequencing Facility.

value: Human embryonic stem cells (ESCs)

value: Primed ESCs (NK2 H9 line)

value: H3K4me1 (Abcam ab8895)


title: H3K9me3_RE_UO-31

description: Chromatin IP against H3K9me3

value: Anti-H3K9me3 antibody (Abcam; ab8898)


title: H3K4me1_naive_rep2

source_name: Naive ESCs (NK2 H9 line)

value: Naive ESCs (NK2 H9 line)


title: H4K20me3_BR_MCF7

description: Chromatin IP against H4K20me3


title: H3K4me1_primed_rep2


title: HCT116_NEN_rep3

description: Gene expression data from HCT116 cells treated with Niclosamide ethanolamine, biological replicate 3


title: H3K9me3_RE_SN12C

description: Chromatin IP against H3K9me3


title: H3K9me3_RE_CAKI-1

description: Chromatin IP against H3K9me3


title: Non-exposed_rep1.fastq.gz

city: Kyoto

first: Hiroyuki

last: Matsui

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Hematology and Oncology

country: Japan

institute: Kyoto University

description: 5' capped RNA

data_processing:
Library strategy: CAGE-seq
Raw reads were trimmed and aligned to the combined sequence using HISAT2 with the following parameters: hisat2 -p 12 --trim3 2 -S.
Generated SAM files were converted into BAM files, and uniquely mapped reads with high mapping quality values (MAPQ ≥ 20) were retained using samtools version 1.9. Using bedtools v2.25.0 with the parameters of genomecov -5 -bg -strand + or genomecov -5 -bg -strand -, coverage of 5’ ends of reads were computed on FANTOM5-defined promoters that were downloaded from http://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/.
The resultant bedGraph files were converted to bigWig files with bedGraphtobigWig. Reads mapped to promoters were counted using bigWigAverageOverBed.
Genome_build: hg19

source_name: Jurkat T cells

extract_protocol:
Total RNA from each sample was extracted with miRNeasy Mini Kit (QIAGEN).
CAGE libraries were constructed using total RNAs based on the no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) protocol. Briefly, first strand cDNAs were synthesized through reverse transcription using random primers. Subsequently, 5’ caps of RNAs were oxidized and biotinylated. Samples were then treated with RNase I to remove single-stranded RNAs. Biotinylated RNA/cDNA molecules were purified using streptavidin magnetic beads. Single-stranded cDNAs were obtained by treating with RNase H and RNase I. After ligation of adapters and second strand synthesis of cDNAs, CAGE libraries were finalized.

treatment_protocol: Jurkat T cells were infected with HIVGKO. Infected cells were washed twice with PBS at 24h after infection and sorted out at 4 or 5 days after infection by FACS Aria II. Non-exposed samples are samples that were not exposed to HIVGKO.

value: Jurkat T cells

tag: infection type

value: Non-exposed


title: Non-exposed_rep2.fastq.gz

description: 5' capped RNA


title: HCT116_NEN_rep1

description: Gene expression data from HCT116 cells treated with Niclosamide ethanolamine, biological replicate 1


title: Latently infected Rep1

description: 5' capped RNA

data_processing:
Raw reads were trimmed and aligned to the combined sequence using HISAT2 with the following parameters: hisat2 -p 12 --trim3 2 -S.
Generated SAM files were converted into BAM files, and uniquely mapped reads with high mapping quality values (MAPQ ≥ 20) were retained using samtools version 1.9. Using bedtools v2.25.0 with the parameters of genomecov -5 -bg -strand + or genomecov -5 -bg -strand -, coverage of 5’ ends of reads were computed on FANTOM5-defined promoters that were downloaded from http://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/.
The resultant bedGraph files were converted to bigWig files with bedGraphtobigWig. Reads mapped to promoters were counted using bigWigAverageOverBed.
Genome_build: hg19
Supplementary_files_format_and_content: counts

treatment_protocol: Jurkat T cells were infected with HIVGKO. Infected cells were washed twice with PBS at 24h after infection and sorted out at 4 or 5 days after infection by FACS Aria II.

value: latently infected


title: H3K9me3_RE_A498

description: Chromatin IP against H3K9me3


title: Non-infected Rep2

description: 5' capped RNA

value: non-infected


title: H3K9me3_DU-145

description: Chromatin IP against H3K9me3


title: H3K9me3_OV_SK-OV-3

description: Chromatin IP against H3K9me3


title: H4K20me3_CNS_SF-268

description: Chromatin IP against H4K20me3


title: H4K20me3_BR_HS_578T

description: Chromatin IP against H4K20me3


title: H3K4me1_primed_rep1


title: EV_9_11_13 Final

city: Pittsburgh

first: Nayra

last: Cardenes

state: PA

address: 200 Lothrop st., BST W1230

department: PACCM

institute: University of Pittsburgh

data_processing:
Read alignment and quantification was done with Salmon v0.14.1. Run with parameters –seqBias -l A –numBootstraps 30
Normalized abundance measurements were generated by Sleuth v0.27.3. Transcript counts were aggregated by ENSEMBL Gene ID, and then normalized counts were generated with sleuth_to_matrix with the “obs_norm” data and “tpm” units.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing normalized gene expression in TPMs labeled by ENSEMBL Gene ID

source_name: Lung tissue

extract_protocol: Tissues from chronic lung diseases and normal lungs were collected at time 0 and end of EVLP (6hr), and quality RNA libraries were generated using Illumina TruSeq RNA Access library preparation kit. The coding regions of the transcriptome were then captured from this library using sequence-specific probes to create the final library. The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorometer and quality examined using Agilent Tapestation 2200. Cluster generation and 75 bp Paired-read dual-indexed sequencing was performed on Illumina NextSeq 500’s.

value: Lung

tag: disease

value: PAH

tag: time point

value: Final


title: H3K9me3_RE_TK-10

description: Chromatin IP against H3K9me3

value: cancer cell


title: EV_2_27_2015 Final

value: Emphysema


title: H3K9me3_RE_RXF_393

description: Chromatin IP against H3K9me3

value: RXF 393


title: H3K4me1_naive_rep1


title: EV_2_23_2015 Final

value: IPF


title: Productively infected Rep1

description: 5' capped RNA

value: productively infected


title: Productively infected Rep2

description: 5' capped RNA


title: H3K9me3_OV_OVCAR-4

description: Chromatin IP against H3K9me3


title: H3K9me3_OV_NCI_ADR-RES

description: Chromatin IP against H3K9me3

value: NCI/ADR-RES


title: H3K9me3_RE_ACHN

description: Chromatin IP against H3K9me3

value: ACHN


title: Latently infected Rep2

description: 5' capped RNA


title: EV_12_11_13 Final

value: Normal


title: H3K9me3_RE_786-0

description: Chromatin IP against H3K9me3

value: Anti-H3K9me3 antibody (Abcam; ab8898)


title: Non-infected Rep1

description: 5' capped RNA


title: H3K9me3_ME_UACC-62

description: Chromatin IP against H3K9me3


title: Exp_2_7_20_2012 Final


title: H3K9me3_PC-3

description: Chromatin IP against H3K9me3


title: EV2015-007 Final


title: EV_9_4_13 Final


title: H3K9me3_ME_SK-MEL-5

description: Chromatin IP against H3K9me3


title: H3K9me3_OV_OVCAR-8

description: Chromatin IP against H3K9me3


title: EV_5_2_14 Final


title: H3K9me3_ME_SK-MEL-28

description: Chromatin IP against H3K9me3


title: H3K9me3_OV_OVCAR-5

description: Chromatin IP against H3K9me3


title: Exp_2_7_20_2012 Baseline

value: Baseline


title: H3K9me3_ME_SK-MEL-2

description: Chromatin IP against H3K9me3


title: EV_2015-005 Final


title: H3K9me3_OV_IGROV1

description: Chromatin IP against H3K9me3


title: H3K9me3_OV_OVCAR-3

description: Chromatin IP against H3K9me3


title: EV2016-009 Final


title: EV2015-008 Final


title: EV_9_11_13 Baseline


title: H3K9me3_ME_MALME-3M

description: Chromatin IP against H3K9me3


title: H3K9me3_ME_UACC-257

description: Chromatin IP against H3K9me3


title: EV_9_4_13 Baseline


title: H3K9me3_ME_M14

description: Chromatin IP against H3K9me3


title: EV2015-004 Final


title: EV_5_2_14 Baseline


title: EV_2_23_2015 Baseline


title: EV2015-006 Final


title: H3K9me3_ME_LOX_IMVI

description: Chromatin IP against H3K9me3

value: LOX IMVI


title: EV2016-009 Baseline


title: EV_2015-005 Baseline


title: H3K9me3_LE_RPMI-8226

description: Chromatin IP against H3K9me3


title: EV_12_11_13 Baseline


title: H3K9me3_LE_MOLT-4

description: Chromatin IP against H3K9me3


title: H3K9me3_LE_K-562

description: Chromatin IP against H3K9me3


title: H3K9me3_ME_MDA-MB-435

description: Chromatin IP against H3K9me3


title: EV2015-008 Baseline


title: EV_2_27_2015 Baseline


title: H3K9me3_LE_HL-60

description: Chromatin IP against H3K9me3


title: H3K9me3_LE_SR

description: Chromatin IP against H3K9me3

value: SR


title: EV2015-007 Baseline


title: H3K9me3_LC_NCI-H522

description: Chromatin IP against H3K9me3


title: EV2015-006 Baseline


title: H3K9me3_LE_CCRF-CEM

description: Chromatin IP against H3K9me3

value: CCRF-CEM


title: H3K9me3_LC_NCI-H460

description: Chromatin IP against H3K9me3


title: EV2015-004 Baseline


title: H3K9me3_LC_NCI-H322M

description: Chromatin IP against H3K9me3


title: H3K9me3_LC_NCI-H23

description: Chromatin IP against H3K9me3


title: H3K9me3_LC_NCI-H226

description: Chromatin IP against H3K9me3


title: VCaP_Dox31 RNA-seq2

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
Raw read sequences from fastq files for each sample were quality trimmed using Trim Galore with a Phred score of 20.
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 using default parameters.
Total aligned reads for each sample at each features were then quantified using featureCounts and a transcript annotation reference for the hg19 genome build (V24).
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads were normalised to counts per million bases for each feature quantified using featureCounts are provided as text files.

source_name: VCaP_Dox RNA-seq

growth_protocol: LNCaP AR-V7 and VCaP AR-V7 cells grown in their corresponding medium were supplemented with 10% FBS and maintained under constant G418 antibiotic selection. Cells were ligand starved in 10% CSS medium for 24 hours before treatment.

extract_protocol:
LNCaP AR-V7 and VCaP AR-V7 cells treated with ethanol, 10uM R1881 or 20ng/mL DOX for 24 hours were harvested into PureXtract RNAzol solution. Total RNA was extracted, and column purified using RNAeasy kit (Qiagen, USA).
RNA-seq libraries were constructed using Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions. cDNA libraries were sequenced on the Illumina HiSeq 2500 platform at Genomic and RNA Profiling Core facility, Baylor College of Medicine.

treatment_protocol: Cells were treated with 10nM R1881 for hormone response and 20ng/mL Doxycycline for AR-V7 response.

tag: cell line background

value: VCaP

value: Immortalised prostate cancer cell line

tag: genotype/variation

value: expressing AR-V7 in response to doxycycline (LNCaP AR-V7)

tag: passages

value: 20ng/mL Doxycycline for 24hrs


title: VCaP_R1881-31 RNA-seq2

source_name: VCaP_R1881 RNA-seq

value: 10uM R1881 for 24 hrs


title: H3K9me3_LC_EKVX

description: Chromatin IP against H3K9me3

value: EKVX

value: cancer cell


title: H3K9me3_LC_HOP-62

description: Chromatin IP against H3K9me3


title: VCaP_Veh31 RNA-seq2

source_name: VCaP_Veh RNA-seq

value: ethanol (vehicle) for 24 hrs


title: VCaP_Veh13 RNA-seq1


title: H3K9me3_LC_A549

description: Chromatin IP against H3K9me3


title: VCaP_Dox13 RNA-seq1


title: H3K9me3_LC_HOP-92

description: Chromatin IP against H3K9me3


title: H3K9me3_CO_SW-620

description: Chromatin IP against H3K9me3


title: Naive CD4+ T cells donor 2 RNA-Seq

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Illumina's Real-Time Analysis software v2.4.6.
Reads were aligned to the human genome by Rsubread version 1.24.1.
Reads counts were quantified by Entrez Gene ID using featureCounts and Rsubread's inbuilt NCBI annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file (tsv). Columns represent Entrez Gene ID, total gene length (total base count of all merged exons) and the number of reads mapping to that gene.

source_name: Peripheral blood

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (QIAGEN, cat. no. 217084) following manufacturer's protocol.
Libraries were made following manufactur's protocol for Illumina's TruSeq Total Stranded RNA kit with Ribo-zero Gold.

tag: donor

value: CD4+ T lymphocyte cells

tag: activation status

value: Naive


title: H3K9me3_CO_KM12

description: Chromatin IP against H3K9me3


title: H3K9me3_CO_HT29

description: Chromatin IP against H3K9me3


title: Activated CD8+ T cells donor 2 RNA-Seq

value: CD8+ T lymphocyte cells

value: Activated


title: B cells donor 2 RNA-Seq

value: B lymphocyte cells


title: Activated CD4+ T cells donor 2 RNA-Seq


title: H3K9me3_CO_HCT-116

description: Chromatin IP against H3K9me3

value: Anti-H3K9me3 antibody (Abcam; ab8898)


title: B cells donor 1 RNA-Seq


title: VCaP_R1881-13 RNA-seq1

tag: treatment


title: H3K9me3_CO_HCT-15

description: Chromatin IP against H3K9me3

tag: cell type


title: Naive CD8+ T cells donor 1 RNA-Seq


title: H3K9me3_CO_HCC-2998

description: Chromatin IP against H3K9me3


title: H3K9me3_CNS_SNB-19

description: Chromatin IP against H3K9me3


title: Naive CD4+ T cells donor 1 RNA-Seq


title: H3K9me3_CNS_U251

description: Chromatin IP against H3K9me3


title: Naive CD8+ T cells donor 2 RNA-Seq


title: H3K9me3_CNS_SNB-75

description: Chromatin IP against H3K9me3


title: Activated CD8+ T cells donor 1 RNA-Seq


title: Activated CD4+ T cells donor 1 RNA-Seq


title: Activated CD4+ T cells 1 HiC

data_processing:
Reads pairs from each sample were aligned to the human genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The files are in Matrix Market Exchange (mtx) format, which is a compact space-delimited text format for representing a sparse matrix. The files have integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the corresponding read count. Bin pairs with no reads are omitted. The indices correspond to rows of the supplementary BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

extract_protocol: In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547).

treatment_protocol: To induce activation, cells were cultured for three days in Iscove’s Modified Dulbecco’s Medium containing 5% pooled, heat-inactivated, human serum, 100 nM non-essential aminoacids, 2mM of glutamine and 50 uM 2-mercaptoethanol (IP5) medium in the presence of Dynabeads Human T-Activator CD3/CD28 beads (Life Technologies, cat. no. 111.31D).

value: Activated CD4+ T lymphocyte cells


title: B cells 2 ATAC-Seq

data_processing:
FASTQ files were output using standard Illumina protocols and software.
ATAC-seq reads were aligned to the human genome assembly (hg38) using Bowtie2 v2.2.5.
For samples with two technical replicates, the BAM were merged using the samtools merge function.
Mitochondrial reads, ummapped reads and low mappability (<30) reads were filtered out using the samtools view function.
Peaks were called using MACS2 –callpeak (with parameters -- nomodel, --extsize 200, and --shift 100) after merging all the filtered reads from all the samples and both donors into a single file.
The number of read counts overlapping each peak was then obtained for all ten samples using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text (tsv) files. Columns represent the genomic location and the number of reads for each peak. Supplementary file PeakRegions.bed.gz provides the peak regions in BED format. Supplementary file PeakCounts.txt.gz provides read counts for all samples in a single file.

extract_protocol: ATAC-seq was performed as described by Buenrostro et al (Nature Methods, 2013, PMID: 24097267).

value: B cell


title: H3K9me3_CO_COLO_205

description: Chromatin IP against H3K9me3

value: COLO 205


title: Activated CD8+ T cells 1 ATAC-Seq

value: naive CD8+ T cells


title: H3K9me3_BR_MDA-MB-231

description: Chromatin IP against H3K9me3


title: H3K27ac_RE_UO-31

description: Chromatin IP against H3K27ac

value: Anti-H3K27ac antibody (Abcam; ab4729)


title: Activated CD8+ T cells 2 HiC

value: Activated CD8+ T lymphocyte cells


title: H3K9me3_CNS_SF-539

description: Chromatin IP against H3K9me3


title: H3K9me3_CNS_SF-268

description: Chromatin IP against H3K9me3


title: H3K9me3_BR_T-47D

description: Chromatin IP against H3K9me3


title: Activated CD8+ T cells 1 HiC


title: B cells 1 ATAC-Seq


title: H3K9me3_CNS_SF-295

description: Chromatin IP against H3K9me3


title: H3K9me3_BR_MDA-MB-468

description: Chromatin IP against H3K9me3


title: Activated CD8+ T cells 2 ATAC-Seq


title: H3K9me3_BR_MCF7

description: Chromatin IP against H3K9me3


title: Naive CD8+ T cells 1 ATAC-Seq


title: Naive CD8+ T cells 2 ATAC-Seq


title: H3K27ac_RE_SN12C

description: Chromatin IP against H3K27ac


title: Activated CD4+ T cells 2 HiC


title: H3K27ac_RE_A498

description: Chromatin IP against H3K27ac


title: Activated CD4+ T cells 2 ATAC-Seq

value: naive CD4+ T cells


title: RAJI untreated 1

city: Moncton

first: Rodney

last: Ouellette

address: 35 Providence St.

country: Canada

institute: ATLANTIC CANCER RESEARCH INSTITUTE

data_processing:
RNA-seq reads were mapped using the Two-mapping step strategy with STAR (version 2.5.2) and Bowtie2 (version 2.2.6) using hg19 version of index files.
parameters used are as follows with STAR: --chimSegmentMin 18 --chimScoreMin 12
parameters used are as follows with Bowtie2: --local --very-sensitive-local --mm
Raw counts extracted with Featurecounts (version 1.5.1)
Genome_build: hg19
Supplementary_files_format_and_content: CSV files with reads counts format

molecule: polyA RNA

source_name: Burkitt's lymphoma cell line, No Treatment

growth_protocol: KIS-1 cells stably transduced with empty vector or carrying a doxycycline-inducible EBF1 gene were treated with doxycycline for 48h and total RNA was extracted 48 hours later

extract_protocol:
RNA was extracted with trizol and subsequently the RNAeasy minikit
RNA was quantified and integrity was analyzed on Agilent Tape Station. Samples with RNA integration number of greater than 8 were selected for library preparation. Poly-A enrichment of mRNA was performed from 15ug of total RNA (Dyna beads mRNA direct Micro Kit). All samples were spiked in with ERCC spike in mix (Life Technologies) before poly-A enrichment for performance assessment of libraries. 100ng of poly-A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module (RNA Seq V2 kit, Life Technologies). Size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape. 50ng of fragmented poly A enriched RNA was used to prepare whole transcriptome library using RNA seq V2 kit( Life Technologies ) following manufacturer recommended protocols . Yield and size distribution of the  library was assessed on Agilent Tape Station using D1000 screen tape. Barcoded libraries were equally pooled and amplified onto Ion Sphere™ Particles (ISPs) supplied by Ion Pi HiQ OT2 kit (Life Technologies). ISPs loaded with libraries were sequenced on Ion Torrent Proton sequencer using Ion PI chip V3. Two samples were pooled together and sequenced in one chip (Ion PI HiQ sequencing kit).

treatment_protocol: Cells were treated with 100ng/ml doxycycline.

value: Burkitt's lymphoma cell line RAJI

value: No Treatment

tag: replicate


title: RAJI untreated 2

tag: cell line


title: H3K9me3_BR_HS_578T

description: Chromatin IP against H3K9me3

value: HS 578T

value: cancer cell


title: H3K27ac_RE_RXF_393

description: Chromatin IP against H3K27ac

value: RXF 393


title: H3K27ac_RE_786-0

description: Chromatin IP against H3K27ac


title: H3K27ac_RE_ACHN

description: Chromatin IP against H3K27ac

source_name: ACHN

value: ACHN


title: H3K9me3_BR_BT-549

description: Chromatin IP against H3K9me3


title: Naive CD4+ T cells 1 ATAC-Seq

value: Naive


title: H3K27ac_RE_TK-10

description: Chromatin IP against H3K27ac


title: KIS1 untreated 1

source_name: Diffuse large B-cell lymphoma cell line, No Treatment

value: Diffuse large B-cell lymphoma cell line KIS-1


title: KIS1 untreated 2


title: H3K27ac_PR_DU-145

description: Chromatin IP against H3K27ac


title: KIS1 Empty -DOX 2

source_name: Diffuse large B-cell lymphoma cell line, NO EBF1 - DOX

tag: transduction

value: NO EBF1

value: - DOX


title: Naive CD4+ T cells 2 ATAC-Seq


title: KIS1 Empty +DOX 3

source_name: Diffuse large B-cell lymphoma cell line, NO EBF1 + DOX

value: + DOX


title: H3K27ac_OV_SK-OV-3

description: Chromatin IP against H3K27ac


title: H3K27ac_PR_PC-3

description: Chromatin IP against H3K27ac


title: KIS1 Empty -DOX 1


title: H3K27ac_OV_OVCAR-8

description: Chromatin IP against H3K27ac


title: H3K27ac_RE_CAKI-1

description: Chromatin IP against H3K27ac


title: KIS1 Empty +DOX 2


title: KIS1 Empty +DOX 1


title: H3K27ac_OV_OVCAR-4

description: Chromatin IP against H3K27ac


title: KIS1 EBF1 -DOX 3

source_name: Diffuse large B-cell lymphoma cell line, EBF1 - DOX


title: KIS1 EBF1 +DOX 3

source_name: Diffuse large B-cell lymphoma cell line, EBF1 + DOX


title: H3K27ac_OV_NCI_ADR-RES

description: Chromatin IP against H3K27ac

source_name: NCI/ADR-RES

value: NCI/ADR-RES


title: H3K27ac_OV_IGROV1

description: Chromatin IP against H3K27ac


title: KIS1 EBF1 -DOX 1


title: KIS1 EBF1 -DOX 2


title: KIS1 EBF1 +DOX 2


title: KIS1 Empty -DOX 3


title: H3K27ac_ME_UACC-62

description: Chromatin IP against H3K27ac


title: KIS1 EBF1 +DOX 1


title: CPZWT3_65

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 70
Supplementary_files_format_and_content: Matrix table with RSEM-estimated raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Heart

growth_protocol: Experiments were conducted with E12.5 mouse embryos with C57BL/6 background from a single litter.

extract_protocol:
Total RNA was extracted from ventricular embryonic tissue collected from embryonic hearts by removing atria and valve region using QIAzol Lysis Reagent (Qiagen; CA; USA) and miRNeasy Mini Kit (Qiagen; CA; USA)
RNA was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific; MA; USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies; CA; USA). 500 ng of total RNA were used with the TruSeq RNA Sample Preparation v2 Kit (Illumina; CA; USA) to construct index-tagged cDNA libraries.
RNASeq libraries were sequenced (single-end mode and length of 75 bp) on the Genome Analyzer IIx system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.

tag: genotype

tag: developmental stage

tag: litter

tag: tissue

value: Heart


title: H3K27ac_ME_SK-MEL-28

description: Chromatin IP against H3K27ac

tag: antibody


title: H3K27ac_ME_SK-MEL-5

description: Chromatin IP against H3K27ac


title: H3K27ac_ME_UACC-257

description: Chromatin IP against H3K27ac


title: H3K27ac_ME_SK-MEL-2

description: Chromatin IP against H3K27ac


title: CPZWT2_64


title: H3K27ac_ME_MDA-MB-435

description: Chromatin IP against H3K27ac


title: H3K27ac_ME_M14

description: Chromatin IP against H3K27ac


title: CPZKO2_62


title: H3K27ac_OV_OVCAR-5

description: Chromatin IP against H3K27ac


title: H3K27ac_LE_RPMI-8226

description: Chromatin IP against H3K27ac


title: H3K27ac_OV_OVCAR-3

description: Chromatin IP against H3K27ac


title: H3K27ac_LE_K-562

description: Chromatin IP against H3K27ac


title: H3K27ac_LE_SR

description: Chromatin IP against H3K27ac

source_name: SR

value: SR


title: H3K27ac_LE_MOLT-4

description: Chromatin IP against H3K27ac

value: Anti-H3K27ac antibody (Abcam; ab4729)


title: K562_KO_PMA_H2AX_2

first: Haoqiang

last: Ying

state: Texas

institute: M. D. Anderson Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bwa
peaks and regions were called using HOMER software
Genome_build: hg19
Supplementary_files_format_and_content: gamma H2AX binding regions were generated by subtracting input using HOMER software

source_name: human immortalised myelogenous leukemia cell line

growth_protocol: K562 wild type or FANCL knockout cells were cultured in RPMI 1640 with 10% FBS at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody against gamma H2AX
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: One replicate was PMA (5nM) or mock treated for 72 hours

value: PMA

value: FANCL-KO

tag: chip antibody

value: anti-gamma H2AX


title: H3K27ac_LE_HL-60

description: Chromatin IP against H3K27ac


title: K562_KO_mock_H2AX_2

value: mock


title: H3K27ac_LE_CCRF-CEM

description: Chromatin IP against H3K27ac

source_name: CCRF-CEM

value: CCRF-CEM


title: K562_KO_mock_H2AX_1


title: CPZKO3_63


title: K562_KO_PMA_H2AX_1


title: K562_WT_PMA_H2AX_1

value: wild-type


title: H3K27ac_LC_NCI-H522

description: Chromatin IP against H3K27ac

value: cancer cell


title: H3K27ac_ME_LOX_IMVI

description: Chromatin IP against H3K27ac

source_name: LOX IMVI

value: LOX IMVI


title: High glucose MCPs (HG)

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

country: South Korea

institute: Inha university hospital

description: Pooling : HG 1 + HG 2 + HG 3 = HG

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing:
All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: The mouse penis cavernous primary pericytes was maintained in Dulbecco’s modified Eagle Medium (DMEM) containing 20% FBS, 1% penicillin/streptomycin, and 10 nM human pigment epithelium-derived factor (PEDF)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: MCPs cells at the density of 2 × 106 cells/well were exposed to the normal-glucose (5 mmol, Sigma-Aldrich) or high-glucose (30 mmol) condition for 72 hours.

tag: strain

value: High glucose (HG)

value: mouse cavernous primary pericytes (MCPs)


title: H3K27ac_ME_MALME-3M

description: Chromatin IP against H3K27ac


title: normal glucose MCPs (NG)

description: Pooling : normal 1 + normal 2 + normal 3 = normal

value: Normal glucose (NG)


title: K562_WT_PMA_H2AX_2


title: K562_WT_mock_H2AX_2


title: H3K27ac_LC_NCI-H226

description: Chromatin IP against H3K27ac


title: H3K27ac_LC_HOP-92

description: Chromatin IP against H3K27ac


title: K562_WT_mock_H2AX_1


title: Small_RNA seq_MCF-7 untreated_replicate_6

city: pune

first: vineet

last: jha

state: Maharashtra

address: 9 A/12 Pingale Aryabhatta Persistent Tower,

department: LABS

country: India

institute: Persistent systems

data_processing:
RNA seq Read Mapping ,TopHat version 2.1.1
Diffrential Gene Expression RNASeq ,Cufflinks 2.2.1
Small RNA Seq Read Mapping , Bowtie 2 Version 2.3.2
Diffrential Gene Expression small RNASeq ,Cufflinks 2.2.1
Small RNA Seq adapter trimming , cutadapt version 2.3
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output

growth_protocol: Neurons were differentiated from progenitor cells (derived from telencephalon region of a 10-15 week old aborted foetus) at 37°C/5% CO2. MCF-7 cells were cultured in DMEM high glucose media supplemented with 10% FBS, and incubated at 37°C/5% CO2.

extract_protocol:
RNA was isolated from monolayer cells using TRIzol, following manufacturer's protocol.
TruSeq Stranded Total RNA Sample Preparation Guide was followed for Total RNA sequencing and TruSeq Small RNA Library Prep Reference Guide was followed for Small RNA sequencing

treatment_protocol: Heat shock was given at 45°C (±0.2)  for 30 mins in a water bath. Subsequent to the treatment, cells were transferred to 37°C/5% CO2 for recovery and harvested after 1hr, 3hrs and 24hrs. Full length HIV-Tat treatment was performed for 6hrs with 100ng/ml Tat and cells were either harvested just after the treatment or allowed to recover at 37°C/5% CO2 for another 6hrs prior to harvesting.

value: Breast cancer cell line


title: H3K27ac_LC_NCI-H460

description: Chromatin IP against H3K27ac


title: Small_RNA seq_MCF-7 untreated_replicate_1


title: Small_RNA seq_Tat_6 hr recovery_Replicate_3

source_name: Primary neurons

value: Primary neurons


title: Small_RNA seq_MCF-7 untreated_replicate_5


title: H3K27ac_LC_NCI-H322M

description: Chromatin IP against H3K27ac


title: H3K27ac_LC_EKVX

description: Chromatin IP against H3K27ac

source_name: EKVX

value: EKVX


title: H3K27ac_LC_NCI-H23

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Tat_6 hr recovery_Replicate_1


title: H3K27ac_CO_HT29

description: Chromatin IP against H3K27ac


title: K562_WT_mock_input

value: none (input)


title: Small_RNA seq_MCF-7 untreated_replicate_2


title: Small_RNA seq_MCF-7 untreated_replicate_3


title: H3K27ac_LC_HOP-62

description: Chromatin IP against H3K27ac


title: H3K27ac_LC_A549

description: Chromatin IP against H3K27ac


title: H3K27ac_CO_SW-620

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Tat_6 hr recovery_Replicate_2


title: H3K27ac_CO_HCT-15

description: Chromatin IP against H3K27ac


title: H3K27ac_CO_HCT-116

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Tat_no recovery_Replicate_2


title: H3K27ac_CO_HCC-2998

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Tat_no recovery_Replicate_3


title: Small_RNA seq_MCF-7 untreated_replicate_4


title: H3K27ac_CO_KM12

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Heat_shock_24 hr recovery_Replicate_3


title: Small_RNA seq_Tat_no recovery_Replicate_1


title: H3K27ac_CNS_U251

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Heat_shock_24 hr recovery_Replicate_2


title: Small_RNA seq_Heat_shock_3 hr recovery_Replicate_3


title: Small_RNA seq_Heat_shock_24 hr recovery_Replicate_1


title: H3K27ac_CNS_SF-539

description: Chromatin IP against H3K27ac


title: H3K27ac_CNS_SNB-19

description: Chromatin IP against H3K27ac


title: H3K27ac_CNS_SF-295

description: Chromatin IP against H3K27ac


title: H3K27ac_CNS_SNB-75

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Heat_shock_1 hr recovery_Replicate_3


title: H3K27ac_BR_T-47D

description: Chromatin IP against H3K27ac


title: H3K27ac_BR_MDA-MB-231

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Heat_shock_1 hr recovery_Replicate_2


title: H3K27ac_BR_MDA-MB-468

description: Chromatin IP against H3K27ac


title: Small_RNA seq_Heat_shock_1 hr recovery_Replicate_1


title: Small_RNA seq_Heat_shock_3 hr recovery_Replicate_1


title: Small_RNA seq_Untreated_Replicate_3


title: H3K27ac_BR_HS_578T

description: Chromatin IP against H3K27ac

source_name: HS 578T

value: HS 578T


title: H3K27ac_BR_MCF7

description: Chromatin IP against H3K27ac

value: Anti-H3K27ac antibody (Abcam; ab4729)


title: H3K27ac_CO_COLO_205

description: Chromatin IP against H3K27ac

source_name: COLO 205

value: COLO 205


title: Small_RNA seq_Heat_shock_3 hr recovery_Replicate_2


title: Small_RNA seq_Untreated_Replicate_1


title: H3K4me3_RE_UO-31

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: RNA seq_Tat_6 hr recovery_Replicate_2


title: RNA seq_Tat_6 hr recovery_Replicate_1


title: H3K27ac_CNS_SF-268

description: Chromatin IP against H3K27ac


title: H3K27ac_BR_BT-549

description: Chromatin IP against H3K27ac


title: RNA seq_Tat_no recovery_Replicate_3


title: Activated CD4+ T cells 1 ATAC-Seq

source_name: Peripheral blood

value: naive CD4+ T cells

value: Activated


title: H3K4me3_RE_SN12C

description: Chromatin IP against H3K4me3


title: H3K4me3_RE_TK-10

description: Chromatin IP against H3K4me3


title: H3K4me3_RE_CAKI-1

description: Chromatin IP against H3K4me3


title: H3K4me3_RE_ACHN

description: Chromatin IP against H3K4me3

source_name: ACHN

value: ACHN


title: RNA seq_Tat_no recovery_Replicate_1


title: RNA seq_Tat_6 hr recovery_Replicate_3


title: H3K4me3_RE_RXF_393

description: Chromatin IP against H3K4me3

source_name: RXF 393

value: RXF 393


title: RNA seq_Tat_no recovery_Replicate_2


title: Small_RNA seq_Untreated_Replicate_2


title: H3K4me3_RE_786-0

description: Chromatin IP against H3K4me3

value: cancer cell


title: RNA seq_Heat_shock_24 hr recovery_Replicate_3


title: RNA seq_Heat_shock_24 hr recovery_Replicate_1


title: H3K4me3_RE_A498

description: Chromatin IP against H3K4me3


title: H3K4me3_PR_DU-145

description: Chromatin IP against H3K4me3


title: RNA seq_Heat_shock_24 hr recovery_Replicate_2


title: RNA seq_Heat_shock_3 hr recovery_Replicate_1


title: RNA seq_Heat_shock_3 hr recovery_Replicate_2


title: RNA seq_Heat_shock_3 hr recovery_Replicate_3


title: RNA seq_Heat_shock_1 hr recovery_Replicate_3


title: H3K4me3_OV_OVCAR-5

description: Chromatin IP against H3K4me3


title: RNA seq_Heat_shock_1 hr recovery_Replicate_1


title: H3K4me3_OV_OVCAR-4

description: Chromatin IP against H3K4me3


title: H3K4me3_OV_OVCAR-8

description: Chromatin IP against H3K4me3


title: H3K4me3_OV_OVCAR-3

description: Chromatin IP against H3K4me3


title: RNA seq_Untreated_Replicate_2


title: RNA seq_Untreated_Replicate_1


title: H3K4me3_OV_NCI_ADR-RES

description: Chromatin IP against H3K4me3

value: NCI/ADR-RES


title: RNA seq_Untreated_Replicate_3


title: RNA seq_Heat_shock_1 hr recovery_Replicate_2


title: H3K4me3_ME_UACC-257

description: Chromatin IP against H3K4me3


title: D90

city: Happy Valley

first: Alex

middle: Daniel

last: Chitsazan

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using HISATv2.1.0 with parameters --max-intronlen 500000 -p 11
Gene counts were called using HTSeq-count using the mode intersection-strict
Genome_build: GRCh38
Supplementary_files_format_and_content: hts files contain counts tables for each sample

source_name: Retina

growth_protocol: Stem cell were differentiated with modifications to Meyer et al. 2009 protocol.  Fetal retinal explants were grown on filters using the retinal medium (Methods)

extract_protocol:
All samples were extracted in TRIzol. RNA from these was purified using Qiagen Rneasy Micro kit and was used for RNAseq analysis. Genomic DNA of the retinas was precipitated from the interphase and phenol phase of the TRIzol solution using 100% ethanol. The DNA pellet was washed 3 times with 0.1 M sodium citrate/10% ethanol solution and once with 75% ethanol. The pellet was then resuspended in 8 mM NaOH buffer or concentrated using gDNA Clean and Concentrator kit (Zymo Research, Irvine, CA). . Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Following the desulphonation and wash steps, converted DNA was eluted in 12 µl of the M-Elution buffer  and was used for epigentic clock analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age at dissection (day)

tag: days in vitro

tag: tissue origin

value: H9-derived retinal organoids

tag: karyotype

value: WT

value: retina


title: H3K4me3_ME_SK-MEL-28

description: Chromatin IP against H3K4me3

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph


title: H3K4me3_ME_SK-MEL-5

description: Chromatin IP against H3K4me3


title: H3K4me3_PR_PC-3

description: Chromatin IP against H3K4me3


title: H3K4me3_OV_SK-OV-3

description: Chromatin IP against H3K4me3


title: H3K4me3_OV_IGROV1

description: Chromatin IP against H3K4me3


title: H3K4me3_ME_SK-MEL-2

description: Chromatin IP against H3K4me3


title: 134d-plus-ODIV

value: fetal


title: 134d-plus-21DIV


title: D30


title: D40


title: H3K4me3_ME_MDA-MB-435

description: Chromatin IP against H3K4me3


title: D89T21

value: Trisomy 21


title: H3K4me3_ME_LOX_IMVI

description: Chromatin IP against H3K4me3

value: LOX IMVI


title: H3K4me3_LE_SR

description: Chromatin IP against H3K4me3

value: SR


title: D110T21


title: H3K4me3_ME_M14

description: Chromatin IP against H3K4me3


title: 105d-plus-21DIV


title: 105d-plus-ODIV


title: H3K4me3_LE_HL-60

description: Chromatin IP against H3K4me3


title: D20


title: H3K4me3_LE_RPMI-8226

description: Chromatin IP against H3K4me3


title: H3K4me3_ME_UACC-62

description: Chromatin IP against H3K4me3


title: D60


title: H3K4me3_ME_MALME-3M

description: Chromatin IP against H3K4me3


title: H3K4me3_LE_MOLT-4

description: Chromatin IP against H3K4me3


title: D136T21