title: GFP-DMSO-2_3pDGE

description:
GFP-DMSO-2
Well-A5

value: knockout

value: DMSO

value: AATCAA


title: mon128

status: Public on Mar 28 2019

type: SRA

city: Edinburgh

first: Jeffrey

middle: W

last: Pollard

state: Scotland

address: 47 Little France Cres

department: MRC Centre for Reproductive Health,

country: United Kingdom

institute: Queen's Medical Research Institute, The University of Edinburgh

description: Monocytes Protocol

library_source: transcriptomic

data_processing:
FastQ files of 2x100bp paired-end reads were quality checked using FastQC. Samples were filtered for low quality reads (Phred score >= 20) and adapters were removed when necessary using Cutadapt. Quality controlled reads were then aligned to the Human reference genome (GRCh37/hg19) using STAR aligner (Dobin et al., 2013) (version 2.3). Quantification of genes was performed using the count function of HTSeq (Anders et al., 2015). Reads were counted at the gene level and the unstranded option was used (-s no).
Genome_build: GENCODE Human reference genome Release 19 (GRCh37.p13)
Supplementary_files_format_and_content: tab-delimited files per sample  include raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Monocytes Protocol:  Monocytes were isolated from healthy and cancer individuals using Fluorescent- activated cell sorting (FACS) with the following markers (CD45+/CD3-CD19-CD56- /HLA-DR+MHC II+/CD14+CD16+). Immediately after FACS sorting, all samples were centrifuged at 450 RCF for 10 min at 4°C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions. Macrophages/TAMs Protocol: Isolation and Fluorescence-activated cell sorting (FACS) of human tissue macrophages was performed as described (Cassetta et al. 2016). Briefly, markers for FACS isolation of macrophages included CD45+/CD3-CD19-CD56- /CD11b+/CD14+CD163+. Immediately after sorting, all samples were centrifuged at 450 RCF for 10 min at 4C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions.
RNA quantity was determined by QUBIT (Invitrogen); total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated; samples that had a RIN > 7 were selected for RNA amplification and sequencing. RNA was amplified with Ovation RNAseq Amplification kit v2 (Nugen)

tag: cell type

value: monocytes

tag: condition

value: Normal

tag: sequencing batch

tag: pathology


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-9

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

country: USA

institute: national Institute of Health

library_source: genomic

data_processing:
Raw Sequence reads were aligned to the reference human genome (UCSC, hg18) by Bowtie2 (bowtie2 -D 20 -R 3 -N 1 -L 16 -i S,1,0.5 -X 1000  -p 20 -q -5 0 -3 30). The reads with mapping quality (MAPQ ≤10) or redundant reads that mapped to the same location with the same orientation were removed from further analysis in each single cell library. For scH3K4me3,  To avoid the possibility of doublet (or triplet) outliers, four cells were removed. A cell is defined as a doublet outlier if it satisfies the following two requirements.    1. The log-library size of the cell is larger the averaged the log-library size over all cells.    2. Cells are sorted based on their log-library size. With any of the selected window sizes, the log-library size of the cell is larger than three local scaled median absolute deviation (MAD) from the local median within the sliding window. A number of window sizes are tested. Finally, the remaining 281 cells are used for genome browser visualization and identification of peaks for pooled cells.
Peaks/Enriched regions for the 281 pooled single cell H3K4me3 data were identified using SICER (gap size = 200 bp, window size =200bp and frag size= 150bp). 22293 peaks are identified for the pooled H3K4me3 scChIC-seq data. Peaks/Enriched regions for the 106  pooled single cell H3K4me3 data were identified using SICER (gap size = 600 bp, window size =200bp and frag size= 150bp). 21,465 peaks are identified for the pooled H3K27me3 scChIC-seq data.
For each single cell library (both scH3K4me3 and scH3K27me3), we filtered the reads that are not located in the identified peak regions (22,293 peaks and 21,465 peaks for scH3K4me3 and scH3K27me3 libraries, respectively). Therefore, the *filtered.txt files are obtained for the downstream analysis.
Genome_build: hg18
Supplementary_files_format_and_content: *filtered.txt: bed 6 file. Each line is a peak region. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bed: Bed 6 file. Each line is a read. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bedgraph: bed 4 file. Each line is a bin, with bin size = 200bp. The four columns are chrom, start position, end position,read density.
Library strategy: scChIC-seq

molecule: genomic DNA

source_name: white blood cells

extract_protocol:
The DNAs were end-repaired using the End-It™ DNA End-Repair Kit (Lucigen, Radnor, PA, USA). The reaction was done in 10 µL reaction volume according to the manufacturer’s instruction. The reaction was terminated by adding 115 µL 10 mM Tris-Cl buffer (pH7.5) containing 1 mM EDTA, and the DNAs were extracted by the phenol-chloroform extraction, followed by the ethanol precipitation as described above. The precipitate is re-suspended in 5 µL Qiagen Buffer EB (10 mM Tris-Cl buffer (pH 8.5)). The addition of 3’ A overhangs to the end-repaired DNA fragments was done using the Klenow fragment (3’→5’ exo-) (New England BioLabs, Ipswich, MA, USA) and 1 mM deoxyadenosine triphosphate in the reaction buffer. The DNA fragments were incubated at 37°C for 20 min and the enzymes were inactivated at 75°C for 20 min. The Illumina Adaptor Oligo Mix (Illumina, San Diego, CA, USA) was ligated to the 3’ A overhangs of the DNA fragments using the T4 DNA ligase (New England BioLabs) by incubating at room temperature for 3 hr.
The DNA fragment with the adaptors bound was PCR amplified using the Phusion High-Fidelity PCR Master Mix (New England BioLabs) and the 125 nM PE PCR Primer 1.0 (Illumina). The PCR was done under the following condition: 98°C for 10 min, followed by a cycle of 30 sec at 68°C and 30 sec at 72°C (repeat 18 cycles in the case of 3,000 cells or 25 cycles in the case of a single cell). The 2% [w/v] agarose gel electrophoresis was done to isolate the 140-350 bp fragments and purify using the QIAquick Gel Extraction kit (Qiagen). The concentration of the purified DNAs was measured using Qubit dsDNA HS kit (Thermo Fisher Scientific). The paired-end sequencings were run using the Illumina MiSeq and HiSeq2000.

value: white blood cells

tag: antibody-mnase

value: H3K27me3 Ab + PA-MNase


title: GFP-DMSO-1_3pDGE

city: Medford

first: Eric

middle: R

last: Reed

state: MA

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

description:
GFP-DMSO-1
Well-A4

data_processing:
All reads containing bases with quality lower than Q10 are filtered out.
Reads that pass filter are assigned to a well and aligned to the transcriptome (UCSC RefSeq hg19) which includes mitochondrial genes using BWA aln version 0.7.10. Reads that only align to multiple isoforms of the same gene are considered uniquely mapped.
Genome_build: UCSC RefSeq hg19
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts.  File names are denoted by the nomencalture {genotypic perturbation}-{chemical perturbation}-{replicateID}.txt. Technical replicates of the same sample have an additional digit.

growth_protocol: Cells were subcultured using Clonetics ReagentPack subculture reagents (Lonza, Portsmouth NH). In preparation for exposure, cells were plated into 24-well plates and allowed to reach confluency for 24 hours.

extract_protocol:
Cells were thawed on ice and each sample was lysed using 1uL of 1mg/mL Proteinase K (ThermoFisher Scientific) followed by incubation at 50oC for 15 min, then 95oC for 10 min uncovered to evaporate all liquid.
Single Cell RNA Barcoding and Sequencing (SCRB-seq) was performed as described in Soumillon M., Cacchiarelli D., Semrau S., van Oudenaarden A. and Mikkelsen T.S. (2014). Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv. 10.1101/003236. Sequencing generates two files: read1 and read2.  Read1 contains 17 base reads (6 base barcode + 10 base UMI + an N in the 17th position).  Read2 contains the 46 bp cDNA sequence.

treatment_protocol: Cell culture media was replaced, and compounds added at a concentration of 24 μg/ml CSC, 173μM BaP, 490μM NNK or DMSO. NNK and BaP compounds were obtained from Sigma-Aldrich (St. Louis MO) and CSC obtained from Murty Pharmaceuticals (Lexington, KY). Genotypic perturbations included CRISPR knockouts of FAT1, and CDKN2A, as well as overexpression of NRF2 (NFE2L2), FGFR1, NRG1 and PIK3CA. Cells transfected with a pSpCas9-EGFP (GFP) plasmid (PX458) in the absence of sgRNAs were used as controls for the CRISPR perturbations while overexpression of an empty vector containing the reporter HcRed served as control for the overexpression experiments.

tag: cell line

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

tag: genotypic perturbation

value: GFP

tag: genotypic perturbation type

tag: chemical perturbation

tag: well id

tag: barcode

value: AATAAC


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-14


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-8


title: HCRED-DMSO-3_3pDGE

description:
HCRED-DMSO-3
Well-A3

value: HCRED

value: overexpression

value: AACTAA


title: FGFR1-DMSO-3_3pDGE

description:
FGFR1-DMSO-3
Well-A9

value: AGATAT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-6


title: mon127

description: Monocytes Protocol


title: HCRED-DMSO-2_3pDGE

description:
HCRED-DMSO-2
Well-A2

value: AAATGT


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-5


title: mon132

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-7


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-16


title: FGFR1-DMSO-2_3pDGE

description:
FGFR1-DMSO-2
Well-A8

value: ACTATT


title: mon131

description: Monocytes Protocol


title: mon117

description: Monocytes Protocol

value: Breast cancer


title: mon130

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-3


title: PIK3CA-DMSO-3_3pDGE

description:
PIK3CA-DMSO-3
Well-A12

value: DMSO

value: ATAGTA


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-10


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-2


title: mon116

description: Monocytes Protocol

value: monocytes


title: PIK3CA-DMSO-1_3pDGE

description:
PIK3CA-DMSO-1
Well-A10

value: AGTTAA


title: mon115

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-1

value: white blood cells


title: PIK3CA-DMSO-2_3pDGE

description:
PIK3CA-DMSO-2
Well-A11

value: ATAATG


title: human white blood cells single cells H3K4me3 Ab-Mnase-285

value: H3K4me3 Ab-MNase


title: mon118

description: Monocytes Protocol

value: DCIS


title: human white blood cells single cells H3K4me3 Ab-Mnase-284


title: human white blood cells single cells H3K4me3 Ab-Mnase-283


title: mon114

description: Monocytes Protocol


title: HCRED-DMSO-1_3pDGE

description:
HCRED-DMSO-1
Well-A1

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

value: AAACTA


title: mon113

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-281


title: human white blood cells single cells H3K4me3 Ab-Mnase-282


title: human white blood cells single cells H3K4me3 Ab-Mnase-280


title: human white blood cells single cells H3K4me3 Ab-Mnase-276


title: human white blood cells single cells H3K4me3 Ab-Mnase-277


title: mon112

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-279


title: mon111

description: Monocytes Protocol


title: mon110

description: Monocytes Protocol


title: human white blood cells single cells H3K27me3 Ab+PA-Mnase-4

value: H3K27me3 Ab + PA-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-278


title: human white blood cells single cells H3K4me3 Ab-Mnase-275


title: human white blood cells single cells H3K4me3 Ab-Mnase-273


title: human white blood cells single cells H3K4me3 Ab-Mnase-274


title: human white blood cells single cells H3K4me3 Ab-Mnase-272


title: human white blood cells single cells H3K4me3 Ab-Mnase-271


title: mon109

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-270


title: mon107

description: Monocytes Protocol

value: Normal


title: human white blood cells single cells H3K4me3 Ab-Mnase-269


title: human white blood cells single cells H3K4me3 Ab-Mnase-268


title: human white blood cells single cells H3K4me3 Ab-Mnase-265


title: mon105

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-267


title: mon106

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-263


title: human white blood cells single cells H3K4me3 Ab-Mnase-264


title: human white blood cells single cells H3K4me3 Ab-Mnase-261


title: human white blood cells single cells H3K4me3 Ab-Mnase-262


title: human white blood cells single cells H3K4me3 Ab-Mnase-266


title: mon104

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-259


title: human white blood cells single cells H3K4me3 Ab-Mnase-258


title: human white blood cells single cells H3K4me3 Ab-Mnase-260


title: mon108

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-255


title: xE-SCC-Zeb1KO.2

city: Cambridge

first: Cornelia

last: Kroeger

address: 455 Main St

institute: Whitehead Institute

description: Sample 10 (Duplicate of Sample 4)

data_processing:
RNASeq single-end reads from Illumina 1.5 encoding were aligned using TopHat (v 2.0.13) to the human genome (GRCh37) with Ensembl annotation (GRCh37.75) in gtf format: default parameters were used, except for base encoding.  HTSeq-count was used to obtain counts with intersection-strict mode and strand=reverse.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw counts from HTSeq-count

molecule: polyA RNA

source_name: epithelial HMLER single cell clone with knocked-out Zeb1

growth_protocol: All cells were grown in mammary epithelial growth medium (MEGM; Lonza)

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus kit
Libraries were prepared using the TruSeq stranded mRNA protocol as described in the kit (Illumina; Catalog # RS-122-2101) manual. Libraries were pooled together and sequenced on the HiSeq 2500 sequencer using the Standard sequencing protocols. Images analysis and base calling was done using the Standard Illumina pipeline, and then demultiplexed into fastq files

value: HMLER

tag: cell state

value: epithelial

tag: genotype

value: knocked-out Zeb1


title: E-SCC-Zeb1KOSnZmt.2

description: Sample 12 (Duplicate of Sample 6)

source_name: epithelial HMLER single cell clone with knocked-out Zeb1 and Snail overexpression and mtZeb1 rescue


title: E-SCC-Zeb1KOSn.2

description: Sample 11 (Duplicate of Sample 5)

source_name: epithelial HMLER single cell clone with knocked-out Zeb1 and Snail overexpression


title: xM.2

description: Sample 9 (Duplicate of Sample 3)

source_name: extreme mesenchymal derivatives of HMLER derived by FACS sorting for CDD4+ C104+ cells

value: extreme mesenchymal

value: wildtype


title: human white blood cells single cells H3K4me3 Ab-Mnase-256


title: human white blood cells single cells H3K4me3 Ab-Mnase-251


title: E/M.2

description: Sample 8 (Duplicate of Sample 2)

source_name: Epithelial/Mesenchymal hybrid derivatives of HMLER derived by FACS sorting for CDD4+ C104+ cells

value: Epithelial/Mesenchymal hybrid


title: human white blood cells single cells H3K4me3 Ab-Mnase-252


title: human white blood cells single cells H3K4me3 Ab-Mnase-254


title: human white blood cells single cells H3K4me3 Ab-Mnase-257


title: human white blood cells single cells H3K4me3 Ab-Mnase-250


title: E-SCC-Zeb1KOSnZmt

description: Sample 6

value: knocked-out Zeb1 and Snail overexpression and mtZeb1 rescue


title: human white blood cells single cells H3K4me3 Ab-Mnase-253


title: human white blood cells single cells H3K4me3 Ab-Mnase-248


title: E.2

description: Sample 7 (Duplicate of Sample 1)

source_name: Immortalized human mammary epithelial cells


title: E-SCC-Zeb1KOSn

description: Sample 5

value: knocked-out Zeb1 and Snail overexpression


title: human white blood cells single cells H3K4me3 Ab-Mnase-245

value: white blood cells


title: human white blood cells single cells H3K4me3 Ab-Mnase-249


title: human white blood cells single cells H3K4me3 Ab-Mnase-246


title: xE-SCC-Zeb1KO

description: Sample 4


title: human white blood cells single cells H3K4me3 Ab-Mnase-243


title: human white blood cells single cells H3K4me3 Ab-Mnase-244


title: xM

description: Sample 3


title: human white blood cells single cells H3K4me3 Ab-Mnase-241


title: human white blood cells single cells H3K4me3 Ab-Mnase-240


title: human white blood cells single cells H3K4me3 Ab-Mnase-242


title: E/M

description: Sample 2


title: human white blood cells single cells H3K4me3 Ab-Mnase-239


title: E

description: Sample 1


title: human white blood cells single cells H3K4me3 Ab-Mnase-235


title: MAC35: Endometrial cancer

description: Macrophages/TAMs Protocol

source_name: Tissue

extract_protocol:
Monocytes Protocol:  Monocytes were isolated from healthy and cancer individuals using Fluorescent- activated cell sorting (FACS) with the following markers (CD45+/CD3-CD19-CD56- /HLA-DR+MHC II+/CD14+CD16+). Immediately after FACS sorting, all samples were centrifuged at 450 RCF for 10 min at 4°C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions. Macrophages/TAMs Protocol: Isolation and Fluorescence-activated cell sorting (FACS) of human tissue macrophages was performed as described (Cassetta et al. 2016). Briefly, markers for FACS isolation of macrophages included CD45+/CD3-CD19-CD56- /CD11b+/CD14+CD163+. Immediately after sorting, all samples were centrifuged at 450 RCF for 10 min at 4C. Cell pellets were re-suspended in 350 ul of RLT lysis buffer and RNA extracted with RNAeasy Microkit (Qiagen) according to manufacturer’s instructions.
RNA quantity was determined by QUBIT (Invitrogen); total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated; samples that had a RIN > 7 were selected for RNA amplification and sequencing. RNA was amplified with Ovation RNAseq Amplification kit v2 (Nugen)
paired-end RNA-seq  illumina Hi-Seq

value: tumour associated macrophages

value: Endometrial cancer

value: Batch 5

value: UPSC

tag: age


title: tiny124 rep2

city: Ames

first: Yanhai

last: Yin

state: IA

address: 1035D Roy J. Carver Co-Lab

department: Genetic Development and Cell Biology

institute: Iowa State University

data_processing:
BlueBee A. thaliana (TAIR10) Lexogen QuantSeq 2.2.2 FWD pipeline
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: .csv file containing raw counts for each gene and DESeq2 differential expression analysis

organism: Arabidopsis thaliana

source_name: tiny124_whole rosette

growth_protocol: 4-week-old plants grown in long day (16 hour light/8 hour dark) conditions

extract_protocol:
Zymo DirecZol kit RNA extraction
QuantSeq 3’ mRNA-Seq Library Prep FWD Kit

tag: genotype/variation

tag: tissue

value: whole rosette


title: tiny124 rep3


title: TINYOE rep3

source_name: TINYOE_whole rosette


title: human white blood cells single cells H3K4me3 Ab-Mnase-238

value: H3K4me3 Ab-MNase


title: MAC33: Endometrial cancer

description: Macrophages/TAMs Protocol

value: Carcinosarcoma


title: MAC32: Endometrial cancer

description: Macrophages/TAMs Protocol

value: Endometrioid


title: human white blood cells single cells H3K4me3 Ab-Mnase-230


title: human white blood cells single cells H3K4me3 Ab-Mnase-233


title: TINYOE rep2


title: human white blood cells single cells H3K4me3 Ab-Mnase-232


title: human white blood cells single cells H3K4me3 Ab-Mnase-231


title: TINYOE rep1


title: human white blood cells single cells H3K4me3 Ab-Mnase-229


title: human white blood cells single cells H3K4me3 Ab-Mnase-228


title: WT rep3

source_name: WT_whole rosette

value: WT


title: human white blood cells single cells H3K4me3 Ab-Mnase-227


title: MAC30: Normal Endometrial

description: Macrophages/TAMs Protocol

value: Normal Endometrial

value: Benign


title: tiny124 rep1


title: human white blood cells single cells H3K4me3 Ab-Mnase-226


title: WT rep2


title: MAC31: Normal Endometrial

description: Macrophages/TAMs Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-225


title: human white blood cells single cells H3K4me3 Ab-Mnase-236


title: human white blood cells single cells H3K4me3 Ab-Mnase-237


title: human white blood cells single cells H3K4me3 Ab-Mnase-234


title: human white blood cells single cells H3K4me3 Ab-Mnase-224


title: MAC29: Breast cancer

description: Macrophages/TAMs Protocol

value: Breast cancer

value: Invasive Breast cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-223


title: WT rep1


title: MAC28: Normal Breast

description: Macrophages/TAMs Protocol

value: Normal Breast

value: Normal tissue


title: mTCP4#10_cotyledon

city: New Haven

first: jie

last: dong

state: Connecticut

address: 165 prospect st, OML 257

department: MCDB

institute: yale university

data_processing:
Base-calling was performed using built-in software of Illumina Hiseq 2500
Adaptor sequences were removed and low quality reads were trimmed by Seqtk v.1.2
Pair-end reads were mapped to Arabidopsis genome TAIR10 using HISAT2 v.2.1.0 using default parameters
Aligned reads were calculated using HTSeq (v.0.9.1) and normalized by library size using DESeq2 (v.1.10.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: csv file containing count number of each gene in each genotype

source_name: cotyledons

growth_protocol: Seeds were stratified at 4 ℃ for 3 days and induced for germination by white light for 3-4 hours. Then the seeds were transferred to darkness for 4 days and cotyledons were isolated for total RNA extraction.

extract_protocol:
Total RNA was extracted following the instructions of Rneasy Plant Mini kit of Qiagen
Library was constructed following standard Illumina procotol

value: 4-day-old dark grown

value: TCP4 overexpression line#10

value: cotyledons


title: MAC27: Breast cancer

description: Macrophages/TAMs Protocol

value: tumour associated macrophages

value: Batch 4


title: mTCP4#4_cotyledon

value: TCP4 overexpression line#4


title: human white blood cells single cells H3K4me3 Ab-Mnase-220

value: white blood cells


title: human white blood cells single cells H3K4me3 Ab-Mnase-219

value: H3K4me3 Ab-MNase


title: MAC25: Endometrial cancer

description: Macrophages/TAMs Protocol

value: Endometrial cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-221


title: human white blood cells single cells H3K4me3 Ab-Mnase-217


title: human white blood cells single cells H3K4me3 Ab-Mnase-247


title: Col_cotyledon

value: wild type


title: human white blood cells single cells H3K4me3 Ab-Mnase-218


title: mTCP4_Input

data_processing:
Reads were mapped to the Arabidopsis genome TAIR10 using Bowtie v0.12.9
Peak calling was performed between mTCP4_ChIP and Col_ChIP with MACS2 v2.1.1 using parameters as follows:-- nomodel –g 1.1e8 –p 0.00001 --shift 100 --extsize 200 --slocal 1000 --llocal 2000 --bw 300
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak results(bed file)

source_name: seedling

growth_protocol: Seeds were stratified at 4 ℃ for 3 days and induced for germination by white light for 3-4 hours. Then the seeds were transferred to darkness for 4 days and seedlings were harvested for ChIP assay.

extract_protocol:
Chromains were isolated and sonicated. Then genomic DNA were immunoprecipited by anti-Myc antibody and purified by phenol/chloroform extraction.
Library was constructed following standard Illumina procotol

value: seedling

value: TCP4 overexpression

tag: growth condition

tag: chip antibody


title: MAC24: Endometrial cancer

description: Macrophages/TAMs Protocol

tag: cell type

tag: condition

value: Endometrioid


title: human white blood cells single cells H3K4me3 Ab-Mnase-215


title: human white blood cells single cells H3K4me3 Ab-Mnase-216


title: mon103

description: Monocytes Protocol

value: monocytes

value: Normal

tag: sequencing batch

tag: pathology


title: Col_Input


title: MAC23: Endometrial cancer

description: Macrophages/TAMs Protocol


title: mTCP4_ChIP

value: anti-Myc (sigma, C3956)


title: human white blood cells single cells H3K4me3 Ab-Mnase-212

tag: antibody-mnase


title: human white blood cells single cells H3K4me3 Ab-Mnase-214


title: human white blood cells single cells H3K4me3 Ab-Mnase-222


title: human white blood cells single cells H3K4me3 Ab-Mnase-211


title: Col_ChIP


title: human white blood cells single cells H3K4me3 Ab-Mnase-209


title: MAC19: Endometrial cancer

description: Macrophages/TAMs Protocol


title: MAC21: Endometrial cancer

description: Macrophages/TAMs Protocol

value: UPSC


title: human white blood cells single cells H3K4me3 Ab-Mnase-210


title: human white blood cells single cells H3K4me3 Ab-Mnase-208


title: human white blood cells single cells H3K4me3 Ab-Mnase-207


title: MAC17: Normal Endometrial

description: Macrophages/TAMs Protocol

value: Normal Endometrial

value: Benign


title: MAC16: Normal Endometrial

description: Macrophages/TAMs Protocol


title: esggal4NREG80_RNAi_w2_C

city: Paris cedex 05

first: Marius

last: van den Beek

state: Ile-de-France

address: 11-13 rue Pierre et Marie Curie, Equipe Bardin/UMR3215/Batiment BDD

department: GENETICS AND DEVELOPMENTAL BIOLOGY

country: France

institute: Institut Curie

data_processing:
Using the damidseq_pipeline reads in fastq files were aligned to the Drosophila melanogaster reference genome version 6 using bowtie2 and alignments were extended to 300 nucleotides or the first GATC site, whichever occurred first.
GATC sites in mappable regions read coverage was counted using bedtools coverage and GATC sites with fewer than 5 counts on average were discarded.
The remaining GATC sites were split into control counts and DamID fusion counts and tested for statistically significant differences using DESeq2, which also estimates a variance stabilized log2 fold enrichment values for each GATC site
Peaks were called by merging 2 or more consecutive significant GATC sites (adjusted p-value < 0.01, log2 fold change > 0). Genes were classified as bound by a protein if 2 consecutive GATC sites within the gene body were occupied with an adjusted p-value < 0.01.
RNA Pol II occupancy was determined by considering mean ratios (Dam-RNA Pol II/Dam-only) across annotated transcripts using “polii.gene.call” script and false discovery rates (FDR) were assigned. Genes with an FDR < 0.01 were used as genes active in ISC.
Reads were quasi-mapped against the Drosophila reference transcriptome fasta using Salmon.
Differential gene expression testing was performed using tximportData, RUVseq.
Genes with an adjusted p-value < 0.01 were considered differentially expressed.
Genome_build: Flybase, release 6.13

organism: Drosophila melanogaster

source_name: intestine

growth_protocol: Crosses and adults were kept at 18°C, the GAL80 permissive temperature. 3 day old flies were shifted to 29°C for 2 days to induce RNAi expression

extract_protocol:
RNA was extracted from FACS sorted ISC of 100 females dissected midguts via Arcturus PicoPure RNA isolation Kit and amplified using Arcturus RiboAmp HS plus Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestinal stem cells (ISC)

value: esg-gal4ts NREGal80>UAS_RNAi_WHITE

value: adult intestine


title: esggal4NREG80_RNAi_w1_A


title: human white blood cells single cells H3K4me3 Ab-Mnase-204


title: esggal4NREG80_RNAi_Trr3_J

value: esg-gal4ts NREGal80>UAS_RNAi_TRR


title: human white blood cells single cells H3K4me3 Ab-Mnase-205

value: white blood cells


title: human white blood cells single cells H3K4me3 Ab-Mnase-203

value: H3K4me3 Ab-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-213


title: human white blood cells single cells H3K4me3 Ab-Mnase-206


title: MAC12: Breast cancer

description: Macrophages/TAMs Protocol

value: tumour associated macrophages

value: Breast cancer

value: Batch 4

value: Invasive Breast cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-201


title: MAC22: Endometrial cancer

description: Macrophages/TAMs Protocol

value: Endometrial cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-202


title: MAC14: Normal Endometrial

description: Macrophages/TAMs Protocol


title: MAC9: Breast cancer

description: Macrophages/TAMs Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-199


title: esggal4NREG80_RNAi_Trr2_I


title: esggal4NREG80_RNAi_Trr1_G


title: human white blood cells single cells H3K4me3 Ab-Mnase-198


title: human white blood cells single cells H3K4me3 Ab-Mnase-200


title: human white blood cells single cells H3K4me3 Ab-Mnase-197


title: human white blood cells single cells H3K4me3 Ab-Mnase-196


title: MAC5: Normal Breast

description: Macrophages/TAMs Protocol

value: Normal Breast

value: Normal tissue


title: esggal4NREG80_RNAi_w3_E


title: esggal4NREG80_RNAi_Kis4_H

value: esg-gal4ts NREGal80>UAS_RNAi_KIS


title: MAC4: Normal Breast

description: Macrophages/TAMs Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-195


title: human white blood cells single cells H3K4me3 Ab-Mnase-194


title: esggal4NREG80_RNAi_Kis3_F


title: human white blood cells single cells H3K4me3 Ab-Mnase-193


title: MAC3: Normal Breast

description: Macrophages/TAMs Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-192


title: MON112: Endometrial cancer

description: Monocytes Protocol

value: monocytes

value: Batch 5

value: Endometrioid


title: human white blood cells single cells H3K4me3 Ab-Mnase-191


title: human white blood cells single cells H3K4me3 Ab-Mnase-190


title: human white blood cells single cells H3K4me3 Ab-Mnase-189


title: MON121: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-186


title: esggal4NREG80_RNAi_kis1_B

value: intestinal stem cells (ISC)


title: PIK3CA-NNK-3_SFL

data_processing:
Adapter sequences were trimmed from raw sequence files using Cutadapt v1.12
Quality assessment of trimmed SFL sequence files as well as raw full coverage RNA-seq sequencing files was performed with FastQC v0.11.5
Reads were aligned to human genome (UCSC RefSeq hg19) with STAR v2.5.2b
Expression quantification in RefSeq genes was carried out with featureCounts (subread) v1.5.0
Genome_build: UCSC RefSeq hg19
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts. File names are denoted by the nomencalture {genotypic perturbation}-{chemical perturbation}-{replicateID}.txt

extract_protocol:
RNA was isolated using a standard Qiazol and Qiacube protocol from Qiagen (Valencia, CA).
The dual-barcoded SFL libraries were pooled from 96 individual samples and then sequenced on the Illumina® NextSeq 550 to generate more than 400 million Single-Read 75-bp reads.

tag: cell line

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

tag: genotypic perturbation

value: overexpression

value: NNK


title: human white blood cells single cells H3K4me3 Ab-Mnase-187

value: white blood cells

value: H3K4me3 Ab-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-185


title: MON118: Breast cancer

description: Monocytes Protocol

value: Breast cancer


title: PIK3CA-NNK-2_SFL

tag: genotypic perturbation type

tag: chemical perturbation


title: human white blood cells single cells H3K4me3 Ab-Mnase-188


title: MON119: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-182


title: PIK3CA-NNK-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-181


title: PIK3CA-DMSO-3_SFL

value: DMSO


title: human white blood cells single cells H3K4me3 Ab-Mnase-179


title: PIK3CA-DMSO-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-183


title: esggal4NREG80_RNAi_kis2_D

value: adult intestine


title: MON97: Breast cancer

description: Monocytes Protocol

value: Invasive Breast cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-184


title: PIK3CA-DMSO-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-180


title: human white blood cells single cells H3K4me3 Ab-Mnase-177


title: MON95: Breast cancer

description: Monocytes Protocol


title: MON120: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-176


title: human white blood cells single cells H3K4me3 Ab-Mnase-175


title: PIK3CA-CSC-3_SFL

value: CSC


title: human white blood cells single cells H3K4me3 Ab-Mnase-174


title: PIK3CA-CSC-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-173


title: MON93: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-172


title: PIK3CA-CSC-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-171


title: human white blood cells single cells H3K4me3 Ab-Mnase-170


title: MON107: Normal

description: Monocytes Protocol

value: Normal


title: PIK3CA-BaP-2_SFL

value: BaP


title: PIK3CA-BaP-3_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-169


title: MON106: Normal

description: Monocytes Protocol

value: monocytes


title: human white blood cells single cells H3K4me3 Ab-Mnase-168


title: human white blood cells single cells H3K4me3 Ab-Mnase-178


title: MON96: Breast cancer

description: Monocytes Protocol

value: Batch 5


title: human white blood cells single cells H3K4me3 Ab-Mnase-167


title: MON105: Normal

description: Monocytes Protocol


title: PIK3CA-BaP-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-166


title: MON94: Breast cancer

description: Monocytes Protocol


title: MON104: Normal

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-164


title: NRG1-NNK-3_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-165


title: human white blood cells single cells H3K4me3 Ab-Mnase-163


title: human white blood cells single cells H3K4me3 Ab-Mnase-162


title: MON103: Normal

description: Monocytes Protocol


title: NRG1-NNK-2_SFL


title: MON87: Breast cancer

description: Monocytes Protocol

value: Batch 4


title: MON85: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-161


title: human white blood cells single cells H3K4me3 Ab-Mnase-159


title: NRG1-DMSO-3_SFL


title: MON84: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-157


title: human white blood cells single cells H3K4me3 Ab-Mnase-158


title: MON83: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-156


title: human white blood cells single cells H3K4me3 Ab-Mnase-155


title: human white blood cells single cells H3K4me3 Ab-Mnase-154


title: NRG1-DMSO-2_SFL


title: NRG1-DMSO-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-153


title: MON82: Breast cancer

description: Monocytes Protocol


title: NRG1-CSC-3_SFL


title: MON80: Endometrial cancer

description: Monocytes Protocol

value: Endometrial cancer

value: iEndometrioid


title: human white blood cells single cells H3K4me3 Ab-Mnase-151


title: NRG1-CSC-2_SFL

value: AALE

value: immortalized human bronchial epithelial cells (AALE)


title: MON81: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-152


title: human white blood cells single cells H3K4me3 Ab-Mnase-160


title: human white blood cells single cells H3K4me3 Ab-Mnase-150


title: NRG1-NNK-1_SFL

value: overexpression

value: NNK


title: human white blood cells single cells H3K4me3 Ab-Mnase-147

value: white blood cells

value: H3K4me3 Ab-MNase


title: NRG1-CSC-1_SFL


title: MON79: Endometrial cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-148


title: human white blood cells single cells H3K4me3 Ab-Mnase-146


title: NRG1-BaP-3_SFL


title: MON78: Breast cancer

description: Monocytes Protocol

value: Breast cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-145


title: human white blood cells single cells H3K4me3 Ab-Mnase-144


title: NRG1-BaP-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-143


title: human white blood cells single cells H3K4me3 Ab-Mnase-141


title: MON76: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-140


title: NRF2-NNK-3_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-142


title: MON75: Normal

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-139


title: MON74: Normal

description: Monocytes Protocol


title: NRF2-NNK-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-136


title: human white blood cells single cells H3K4me3 Ab-Mnase-138


title: human white blood cells single cells H3K4me3 Ab-Mnase-149


title: MON73: Normal

description: Monocytes Protocol


title: NRF2-NNK-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-137


title: human white blood cells single cells H3K4me3 Ab-Mnase-135


title: NRF2-DMSO-3_SFL

value: DMSO


title: MON72: Normal

description: Monocytes Protocol


title: MON71: Normal

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-133


title: MON70: Normal

description: Monocytes Protocol


title: NRG1-BaP-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-131


title: human white blood cells single cells H3K4me3 Ab-Mnase-129


title: NRF2-DMSO-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-134


title: MON69: Normal

description: Monocytes Protocol


title: NRF2-CSC-3_SFL


title: MON68: Normal

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-125


title: human white blood cells single cells H3K4me3 Ab-Mnase-126


title: human white blood cells single cells H3K4me3 Ab-Mnase-124


title: NRF2-CSC-1_SFL


title: MON66: Normal

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-123


title: human white blood cells single cells H3K4me3 Ab-Mnase-122


title: human white blood cells single cells H3K4me3 Ab-Mnase-132


title: MON65: Endometrial cancer

description: Monocytes Protocol

value: Batch 3


title: human white blood cells single cells H3K4me3 Ab-Mnase-121


title: human white blood cells single cells H3K4me3 Ab-Mnase-120


title: human white blood cells single cells H3K4me3 Ab-Mnase-130


title: human white blood cells single cells H3K4me3 Ab-Mnase-119


title: NRF2-DMSO-2_SFL


title: NRF2-BaP-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-128


title: human white blood cells single cells H3K4me3 Ab-Mnase-117


title: HCRED-NNK-3_SFL

value: HCRED


title: human white blood cells single cells H3K4me3 Ab-Mnase-118


title: MON61: Breast cancer

description: Monocytes Protocol

value: Invasive Breast cancer


title: MON59: Breast cancer

description: Monocytes Protocol


title: human white blood cells single cells H3K4me3 Ab-Mnase-116


title: NRF2-CSC-2_SFL

value: CSC


title: human white blood cells single cells H3K4me3 Ab-Mnase-115


title: human white blood cells single cells H3K4me3 Ab-Mnase-114


title: human white blood cells single cells H3K4me3 Ab-Mnase-127


title: MON67: Normal

description: Monocytes Protocol

value: monocytes

value: Normal


title: HCRED-NNK-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-113


title: HCRED-NNK-1_SFL


title: MON57: Normal

description: Monocytes Protocol


title: NRF2-BaP-3_SFL

value: BaP


title: NRF2-BaP-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-111


title: human white blood cells single cells H3K4me3 Ab-Mnase-109


title: human white blood cells single cells H3K4me3 Ab-Mnase-112


title: human white blood cells single cells H3K4me3 Ab-Mnase-110


title: HCRED-DMSO-3_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-108


title: HEK293T-empty-rep2

city: Baltimore

first: Kathleen

middle: Helen

last: Burns

address: 733 N. Broadway, MRB 447

department: Pathology

institute: Johns Hopkins University School of Medicine

data_processing:
RNA-seq data were aligned to UCSC hg38 build chromosomes and L1RP plasmid sequence  using SQuIRE (version 0.97) Map
Alignments to UCSC hg38 RepeatMasker TEs and L1RP sequence were quantified with SQuIRE (version 0.97) Count
Genome_build: UCSC hg38
Supplementary_files_format_and_content: TE count files (.txt) were generated at the locus and subfamily level; the columns are: tx_start = start position of left most read aligning to TE,tx_stop = stop position of right most read aligning to TE,TE_ID = unique ID concatenating RepeatMasker coordinates, strand and milliDiv (see below) - can have two entries per TE_ID, one for each ,strand if RNA-seq data is stranded,fpkm = fragments per kilobase transcribed length per million aligned fragments,tx strand = strand of TE transcription,alignedsize = number of fragments  with valid unique or multi alignments,TE_start = annotated RepeatMasker start,TE_stop = annotated RepeatMasker stop,TE_strand = annotated RepeatMasker strand (orientation of TE insertion),milliDiv = Base mismatches in parts per thousand (from RepeatMasker) ,uniq_count = # uniquely aligning reads,tot_count = # uniquely aligning reads + sum of multimapping fractions aligned to TE,tot_reads = # multi-mapping reads aligned to TE,score = tot_count/tot_reads * 100, which approximates how likely the TE is expressed with at least the tot_count,subFcount.txt files (subfamily - level counts) ,copies = # copies of particular subfamily in reference RepeatMasker annotation

source_name: HEK293T cells

growth_protocol: 37 degrees celsius, 5% CO2 incubator. DMEM media with 10% FBS.

extract_protocol:
Cells were washed with PBS, then RNA was extracted using the Zymo QuickRNA microprep kit.
The RiboZero Stranded Library Preparation kit was used. Samples were sequenced paired-end, 101bp reads and sequenced on 8 lanes of an Illumina HiSeq 2500 lane.

treatment_protocol: 500,000 cells were plated, then 24 hours later they were transfected with plasmids using the Promega Fugene HD reagent. 24 hours later, media was replaced with fresh media supplemented with 1ug/ml puromycin. Cells were selected with puromycin for 72 hours prior to sample extraction.

tag: clonal cells

value: Tet-On

tag: transfection

value: empty vector (DA019 plasmid)


title: MON63: Endometrial cancer

description: Monocytes Protocol

value: Endometrial cancer

value: iEndometrioid


title: HCRED-DMSO-2_SFL

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

value: overexpression


title: HEK293T-L1RP-rep3

value: L1RP (MT302 plasmid)


title: human white blood cells single cells H3K4me3 Ab-Mnase-107

value: white blood cells

value: H3K4me3 Ab-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-106


title: HCRED-DMSO-1_SFL

value: DMSO


title: HEK293T-L1RP-rep2


title: human white blood cells single cells H3K4me3 Ab-Mnase-105


title: human white blood cells single cells H3K4me3 Ab-Mnase-104


title: HEK293T-L1RP-rep1


title: human white blood cells single cells H3K4me3 Ab-Mnase-102


title: HCRED-CSC-3_SFL

value: HCRED


title: HCRED-CSC-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-100


title: human white blood cells single cells H3K4me3 Ab-Mnase-99


title: human white blood cells single cells H3K4me3 Ab-Mnase-101


title: HEK293T-empty-rep3


title: HCRED-CSC-1_SFL


title: HCRED-BaP-3_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-96


title: human white blood cells single cells H3K4me3 Ab-Mnase-97


title: human white blood cells single cells H3K4me3 Ab-Mnase-95


title: human white blood cells single cells H3K4me3 Ab-Mnase-98


title: human white blood cells single cells H3K4me3 Ab-Mnase-93


title: human white blood cells single cells H3K4me3 Ab-Mnase-94


title: HCRED-BaP-1_SFL


title: GFP-NNK-2_SFL

value: GFP

value: knockout

value: NNK


title: GFP-NNK-3_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-89


title: Loxp/loxp, Myh6,Cre+ rep5

city: Philadelphia

last: Field

state: PA

address: 1313 BRB II/III U

department: Pharmacology

institute: University of Pennsylvania

data_processing:
Experiment A was aligned to mm10 by the Ion Torrent Suite and Experiment B was aligned to the reference genome mm10 by STAR v2.6.0c
Experiment A was quantified by ENSEMBL annotations and normalized using Deseq algorithm by the StrandNGS program
Experiment B was qunatified using ENSEMBLv93 annotations and normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization (-v0.8.5b-beta)
Genome_build: mm10
Supplementary_files_format_and_content: For both experiments A and B,  tab-delimited text file of gene-level count data, normalized

organism: Mus musculus

source_name: heart

extract_protocol:
heart were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Fibrous RNAeasy kit.
Experiment A was constructed with Ion Total RNA-Seq Kit v2 and Experiment B was prepared with Illumina TruSeq RNA Stranded mRNA HT Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain

tag: organ

value: heart

tag: genotype

value: Loxp/Loxp, Cre+

tag: gender

value: male

tag: experiment

value: B


title: human white blood cells single cells H3K4me3 Ab-Mnase-103


title: human white blood cells single cells H3K4me3 Ab-Mnase-91


title: human white blood cells single cells H3K4me3 Ab-Mnase-88


title: ISC_Dam_1d_replicate_11

description: control for ISC_DamTrr_1d_replicate_3

data_processing:
Library strategy: DamID
Using the damidseq_pipeline reads in fastq files were aligned to the Drosophila melanogaster reference genome version 6 using bowtie2 and alignments were extended to 300 nucleotides or the first GATC site, whichever occurred first.
GATC sites in mappable regions read coverage was counted using bedtools coverage and GATC sites with fewer than 5 counts on average were discarded.
The remaining GATC sites were split into control counts and DamID fusion counts and tested for statistically significant differences using DESeq2, which also estimates a variance stabilized log2 fold enrichment values for each GATC site
Peaks were called by merging 2 or more consecutive significant GATC sites (adjusted p-value < 0.01, log2 fold change > 0). Genes were classified as bound by a protein if 2 consecutive GATC sites within the gene body were occupied with an adjusted p-value < 0.01.
RNA Pol II occupancy was determined by considering mean ratios (Dam-RNA Pol II/Dam-only) across annotated transcripts using “polii.gene.call” script and false discovery rates (FDR) were assigned. Genes with an FDR < 0.01 were used as genes active in ISC.
Reads were quasi-mapped against the Drosophila reference transcriptome fasta using Salmon.
Differential gene expression testing was performed using tximportData, RUVseq.
Genes with an adjusted p-value < 0.01 were considered differentially expressed.
Genome_build: Flybase, release 6.13

growth_protocol: Crosses and adults were kept at 18°C, the GAL80 permissive temperature. 3 day old flies were shifted to 29°C for 1 day to induce Dam expression

extract_protocol:
DNA was extracted from 60 dissected intestine via Qiagen QIAmp DNA Micro Kit following manufacturers' instructions, digested with DpnI, ligated with DamID adaptors, digested with DpnII before amplification by PCR.
DNA was then sonicated to 300bp and adaptors were removed with AlwI before beeing end-repaired and A-tailed. Finally sequencing adaptors were ligated to the fragments before PCR amplification.

value: intestinal stem cells (ISC)

value: esg-gal4ts NREGal80>UAS-Dam

tag: tissue

value: adult intestine


title: GFP-NNK-1_SFL

value: AALE

tag: cell type

value: immortalized human bronchial epithelial cells (AALE)


title: human white blood cells single cells H3K4me3 Ab-Mnase-90


title: human white blood cells single cells H3K4me3 Ab-Mnase-87


title: human white blood cells single cells H3K4me3 Ab-Mnase-86


title: human white blood cells single cells H3K4me3 Ab-Mnase-84


title: human white blood cells single cells H3K4me3 Ab-Mnase-85


title: GFP-DMSO-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-82


title: GFP-DMSO-1_SFL


title: GFP-DMSO-3_SFL


title: ISC_Dam_1d_replicate_10

description: control for ISC_DamTrr_1d_replicate_2


title: HCRED-BaP-2_SFL

value: overexpression

value: BaP


title: human white blood cells single cells H3K4me3 Ab-Mnase-83

value: white blood cells

value: H3K4me3 Ab-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-80


title: human white blood cells single cells H3K4me3 Ab-Mnase-81


title: ISC_Dam_1d_replicate_8

description: ISC_DamHP1_1d_replicate_3 and ISC_DamH1_1d_replicate_3 and ISC_DamBrm_1d_replicate_3


title: ISC_Dam_1d_replicate_9

description: control for ISC_DamTrr_1d_replicate_1


title: GFP-CSC-3_SFL

value: CSC


title: human white blood cells single cells H3K4me3 Ab-Mnase-92


title: human white blood cells single cells H3K4me3 Ab-Mnase-78


title: human white blood cells single cells H3K4me3 Ab-Mnase-79


title: ISC_Dam_1d_replicate_7

description: control for ISC_DamPolycomb_1d_replicate_3


title: ISC_Dam_1d_replicate_6

description: control for ISC_DamHP1_1d_replicate_2 and ISC_DamH1_1d_replicate_2 and ISC_DamBrm_1d_replicate_2


title: GFP-CSC-2_SFL

value: GFP


title: human white blood cells single cells H3K4me3 Ab-Mnase-77


title: human white blood cells single cells H3K4me3 Ab-Mnase-76


title: human white blood cells single cells H3K4me3 Ab-Mnase-75


title: human white blood cells single cells H3K4me3 Ab-Mnase-73


title: human white blood cells single cells H3K4me3 Ab-Mnase-72


title: human white blood cells single cells H3K4me3 Ab-Mnase-74


title: GFP-BaP-3_SFL

value: knockout


title: GFP-CSC-1_SFL


title: ISC_Dam_1d_replicate_4

description: control for ISC_DamPolycomb_1d_replicate_1 and ISC_DamHP1_1d_replicate_1 and ISC_DamH1_1d_replicate_1 and ISC_DamBrm_1d_replicate_1


title: GFP-BaP-2_SFL


title: ISC_DamTrr_1d_replicate_3

description:
processed data file: Galaxy33-[DamID_deseq2_to_peaks_on_Trr].bed
processed data file: Galaxy14-[Interpolate_GATC_signal_on_Trr].bedgraph

value: esg-gal4ts NREGal80>UAS-DamTrr


title: human white blood cells single cells H3K4me3 Ab-Mnase-70


title: GFP-BaP-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-68


title: ISC_DamTrr_1d_replicate_2


title: FGFR1-NNK-3_SFL

value: NNK


title: human white blood cells single cells H3K4me3 Ab-Mnase-67


title: ISC_DamTrr_1d_replicate_1


title: FGFR1-NNK-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-66


title: human white blood cells single cells H3K4me3 Ab-Mnase-64


title: ISC_DamBrm_1d_replicate_3

description:
processed data file: Galaxy25-[DamID_deseq2_to_peaks_on_Brahma].bed
processed data file: Galaxy9-[Interpolate_GATC_signal_on_Brahma].bedgraph

value: esg-gal4ts NREGal80>UAS-DamBrm


title: human white blood cells single cells H3K4me3 Ab-Mnase-65


title: ISC_Dam_1d_replicate_5

description: control for ISC_DamPolycomb_1d_replicate_2


title: FGFR1-NNK-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-63


title: 3T3 fixed frozen 3000 cells  H3K27me3 Ab + PA-MNase, 400 mM salt wash buffer

source_name: NIH/3T3 tet-on 3G cells

value: NIH/3T3 tet-on 3G cells

value: H3K27me3 Ab + PA-MNase


title: ISC_DamBrm_1d_replicate_2

value: intestinal stem cells (ISC)


title: FGFR1-DMSO-3_SFL

value: DMSO


title: human white blood cells single cells H3K4me3 Ab-Mnase-71

source_name: white blood cells


title: ISC_DamBrm_1d_replicate_1

value: adult intestine


title: FGFR1-DMSO-2_SFL

value: AALE


title: human white blood cells single cells H3K4me3 Ab-Mnase-62


title: ISC_DamH1_1d_replicate_3

description:
processed data file: Galaxy32-[DamID_deseq2_to_peaks_on_H1].bed
processed data file: Galaxy12-[Interpolate_GATC_signal_on_H1].bedgraph

value: esg-gal4ts NREGal80>UAS-DamH3


title: FGFR1-DMSO-1_SFL

value: immortalized human bronchial epithelial cells (AALE)

value: overexpression


title: 3T3 fixed frozen 3000 cells  IgG Ab + PA-MNase, RIPA buffer +150 mM salt wash

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
scChIC-seq reads were mapped to the mouse genome (mm9) using Bowtie2 (bowtie2 -p 18 -q -5 0 -3 0). The reads with MAPQ <=10 or redundant reads were removed for further analysis in each library.
The enriched regions were identified using SICER. For H3K4me3, Gap size = 200, win size = 200 fragment = 150.  For H3K27me3, Gap size = 600, win size = 200 fragment = 150,
Genome_build: mm9
Supplementary_files_format_and_content: scoreisland: plan text file. Each line is a peak region. The four columns are chrom, start position, end position, score.
Supplementary_files_format_and_content: bed: Bed 6 file. Each line is a read. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bedgraph: bed 4 file. Each line is a bin, with bin size = 200bp. The four columns are chrom, start position, end position,read density.
Library strategy: scChIC-seq

value: IgG Ab + PA-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-69

value: white blood cells

value: H3K4me3 Ab-MNase


title: ISC_DamH1_1d_replicate_2

value: esg-gal4ts NREGal80>UAS-DamH2


title: 3T3 fixed frozen 3000 cells  H3K4me3 Ab + PA-MNase, 400 mM salt wash buffer rep2

value: H3K4me3 Ab + PA-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-60


title: ISC_DamH1_1d_replicate_1

value: esg-gal4ts NREGal80>UAS-DamH1


title: 3T3 fixed frozen 3000 cells  H3K4me3 Ab + PA-MNase, RIPA buffer+150 mM salt wash


title: human white blood cells single cells H3K4me3 Ab-Mnase-59


title: FGFR1-CSC-2_SFL

value: CSC


title: 3T3 fixed frozen 3000 cells IgG Ab + PA-MNase, 400 mM salt wash buffer


title: FGFR1-BaP-3_SFL

value: BaP


title: ISC_DamHP1_1d_replicate_2

description:
processed data file: Galaxy31-[DamID_deseq2_to_peaks_on_HP1].bed
processed data file: Galaxy11-[Interpolate_GATC_signal_on_HP1].bedgraph

value: esg-gal4ts NREGal80>UAS-DamHP2


title: 3T3 fixed frozen 3000 cells  H3K4me3 Ab + PA-MNase, 400 mM salt wash buffer rep1

value: NIH/3T3 tet-on 3G cells


title: human white blood cells single cells H3K4me3 Ab-Mnase-58


title: human white blood cells single cells H3K4me3 Ab-Mnase-57


title: FGFR1-BaP-2_SFL


title: 3T3 fixed frozen 3000 cells  IgG Ab + PA-MNase, 300 mM salt wash buffer


title: 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase, RIPA buffer+150 mM salt wash buffer rep4


title: human white blood cells single cells H3K4me3 Ab-Mnase-56


title: ISC_DamHP1_1d_replicate_1

value: intestinal stem cells (ISC)

value: esg-gal4ts NREGal80>UAS-DamHP1


title: human white blood cells single cells H3K4me3 Ab-Mnase-61


title: ISC_DamPolycomb_1d_replicate_3

description:
processed data file: Galaxy30-[DamID_deseq2_to_peaks_on_Polycomb].bed
processed data file: Galaxy10-[Interpolate_GATC_signal_on_Polycomb].bedgraph

value: esg-gal4ts NREGal80>UAS-DamPolycomb

value: adult intestine


title: FGFR1-BaP-1_SFL

value: AALE


title: 3T3 fixed frozen 3000 cells  H3K4me3 Ab + PA-MNase, 300 mM salt wash buffer


title: ISC_DamPolycomb_1d_replicate_2


title: FGFR1-CSC-3_SFL

value: immortalized human bronchial epithelial cells (AALE)


title: human white blood cells single cells H3K4me3 Ab-Mnase-54


title: ISC_DamPolycomb_1d_replicate_1


title: human white blood cells single cells H3K4me3 Ab-Mnase-55


title: FAT1-NNK-2_SFL

value: knockout

value: NNK


title: FAT1-NNK-1_SFL


title: 3T3 fixed frozen 3000 cells IgG Ab-MNase, RIPA buffer +150 mM salt wash

value: IgG Ab-MNase


title: ISC_DamPolII_1d_replicate_3

description:
processed data file: Galaxy15-[DamID_deseq2_to_peaks_on_Pol_II].bed
processed data file: Galaxy8-[Interpolate_GATC_signal_on_Pol_II].bedgraph

value: esg-gal4ts NREGal80>UAS-DamPolII


title: human white blood cells single cells H3K4me3 Ab-Mnase-52

value: white blood cells

value: H3K4me3 Ab-MNase


title: FAT1-DMSO-3_SFL

value: DMSO


title: ISC_DamPolII_1d_replicate_2


title: ISC_DamPolII_1d_replicate_1


title: human white blood cells single cells H3K4me3 Ab-Mnase-51


title: FAT1-DMSO-2_SFL


title: 3T3 fixed frozen 3000 cells IgG Ab-MNase, 400 mM salt wash buffer


title: 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase, RIPA buffer +150 mM salt wash


title: human white blood cells single cells H3K4me3 Ab-Mnase-53


title: human white blood cells single cells H3K4me3 Ab-Mnase-50


title: 3T3 fixed frozen 3000 cells IgG Ab + PA-MNase, 200 mM salt wash buffer

value: IgG Ab + PA-MNase


title: ISC_DamKis_1d_replicate_3

description:
processed data file: Galaxy21-[DamID_deseq2_to_peaks_on_Kismet].bed
processed data file: Galaxy13-[Interpolate_GATC_signal_on_Kismet].bedgraph

value: esg-gal4ts NREGal80>UAS-DamKis


title: human white blood cells single cells H3K4me3 Ab-Mnase-49


title: FAT1-NNK-3_SFL


title: ISC_DamKis_1d_replicate_2


title: FAT1-CSC-3_SFL

value: CSC


title: 3T3 fixed frozen 3000 cells H3K4me3 Ab + PA-MNase, 200 mM salt wash buffer

value: NIH/3T3 tet-on 3G cells

value: H3K4me3 Ab + PA-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-48


title: 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase, 300 mM salt wash buffer


title: human white blood cells single cells H3K4me3 Ab-Mnase-47


title: FAT1-CSC-2_SFL


title: 3T3 fixed frozen 3000cells IgG Ab-MNase, 200 mM salt wash buffer rep3


title: FAT1-DMSO-1_SFL


title: 3T3 fixed frozen 3000 cells IgG Ab-MNase, 300 mM salt wash buffer


title: ISC_DamHP1_1d_replicate_3

value: intestinal stem cells (ISC)

value: esg-gal4ts NREGal80>UAS-DamHP3


title: FAT1-CSC-1_SFL


title: ISC_Dam_1d_replicate_3

description: control for ISC_DamKis_1d_replicate_3 and ISC_DamPolII_1d_replicate_3

value: esg-gal4ts NREGal80>UAS-Dam

value: adult intestine


title: ISC_DamKis_1d_replicate_1


title: human white blood cells single cells H3K4me3 Ab-Mnase-46


title: ISC_Dam_1d_replicate_2

description: control for ISC_DamKis_1d_replicate_2 and ISC_DamPolII_1d_replicate_2


title: human white blood cells single cells H3K4me3 Ab-Mnase-45


title: mouse Naïve CD4 fixed frozen 3000 cells IgG Ab-MNase

source_name: Naïve CD4

value: Naive CD4 primary cells


title: 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase, 200 mM salt wash buffer rep3


title: FAT1-BaP-1_SFL

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

value: knockout

value: BaP


title: human white blood cells single cells H3K4me3 Ab-Mnase-44

value: white blood cells


title: ISC_Dam_1d_replicate_1

description: control for ISC_DamKis_1d_replicate_1 and ISC_DamPolII_1d_replicate_1


title: mouse Naïve CD4 fixed frozen 3000 cells H3K4me3 Ab-MNase

value: H3K4me3 Ab-MNase


title: FAT1-BaP-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-43


title: Rhino ChIPseq from nxf3 knock-out ovaries

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

data_processing:
HiSeq data was basecalled with the instruments RTA (Run time analysis version 1.18.66.3): SCS (PN:RTA DS:Controlling software on instrument VN:2.2.68)
NextSeq data was basecalled with the instruments RTA (Run time analysis version 2.4.11): SCS (PN:RTA DS:Controlling software on instrument VN:2.2.0.4)
for small RNA sequencing and PROseq fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings and the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini)
reads were mapped with bowtie v0.12.7 or STAR (RNAseq and RIPseq data only) to D. mel. genome (dm6, r6.18)
BigWig files were generated with Homertools v4.6
Genome_build: Drosophila melanogaster dm6, release 6.18
Supplementary_files_format_and_content: The processed data files are normalized bigwig tracks with uniquely mapping reads only

source_name: Adult ovaries

growth_protocol: Flies were kept at strandard conditions at 25º C.

extract_protocol:
Lysis and sonication of formaldehyde-crosslinked ovaries
NEBNext Ultra II DNA Library Prep Kit for Illumina
Ovaries were hand-dissected into ice-cold PBS

tag: fly genotype

tag: antibodies used

value: anti-Rhino rabbit polyclonal antibody (PMID:24906153)


title: CDKN2A-NNK-3_SFL

value: NNK


title: Input sample of Rhino ChIPseq from nxf3 knock-out ovaries


title: CDKN2A-NNK-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-42


title: 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase, 400 mM salt wash buffer


title: mouse ES fixed frozen 3000 cells H3K4me3 Ab-MNase

source_name: mES

value: mESC


title: Rhino ChIPseq from rhino knock-out ovaries


title: FAT1-BaP-3_SFL


title: Input sample of Rhino ChIPseq from rhino knock-out ovaries


title: CDKN2A-NNK-1_SFL


title: Rhino ChIPseq from w1118 (wildtype) ovaries


title: CDKN2A-DMSO-3_SFL

value: DMSO


title: human white blood cells single cells H3K4me3 Ab-Mnase-41


title: mouse ES fixed frozen 3000 cells IgG Ab-MNase

value: IgG Ab-MNase


title: mouse 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase rep2

value: NIH/3T3 tet-on 3G cells


title: mouse 3T3 fixed frozen 100 cells IgG Ab-MNase


title: CDKN2A-DMSO-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-39


title: Input sample of Rhino ChIPseq from w1118 (wildtype) ovaries


title: human white blood cells single cells H3K4me3 Ab-Mnase-38


title: CDKN2A-DMSO-1_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-37


title: human white blood cells single cells H3K4me3 Ab-Mnase-36


title: CDKN2A-CSC-2_SFL

value: CSC


title: CDKN2A-CSC-3_SFL


title: mouse 3T3 fixed frozen 300 cells H3K4me3 Ab-Mnase rep1


title: mouse 3T3 fixed frozen 300 cells IgG Ab-MNase


title: RNAseq (rRNA-depleted by RNase H treatment) from w1118 (wildtype) ovaries

extract_protocol:
Total RNA extraction with TRIzol
rRNA-depleted by RNase H treatment
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
Ovaries were hand-dissected into ice-cold PBS


title: RNAseq (rRNA-depleted by RNase H treatment) from nxf3 knock-out ovaries


title: mouse 3T3 fixed frozen 3000 cells IgG Ab-MNase rep2


title: human white blood cells single cells H3K4me3 Ab-Mnase-40


title: mouse 3T3 fixed frozen 1000 cells IgG Ab-MNase


title: small RNA sequencing from nxf3_D434R_-GFP knock-in ovaries

description: small RNAs

extract_protocol:
Total RNA extraction with TRIzol
small RNA sequencing as described in PMID: 21890899
Ovaries were hand-dissected into ice-cold PBS


title: CDKN2A-BaP-3_SFL


title: CDKN2A-CSC-1_SFL


title: mouse 3T3 fixed frozen 1000 cells H3K4me3 Ab-MNase


title: human white blood cells single cells H3K4me3 Ab-Mnase-34


title: CDKN2A-BaP-2_SFL


title: human white blood cells single cells H3K4me3 Ab-Mnase-33


title: small RNA sequencing from CG13741 knock-out ovaries, replicate 2

description: small RNAs


title: human white blood cells single cells H3K4me3 Ab-Mnase-32


title: mouse 3T3 fixed frozen 3000 cells IgG Ab-MNase rep 1


title: CDKN2A-BaP-1_SFL


title: mouse 3T3 fixed frozen 300 cells H3K4me3 Ab-Mnase rep2


title: mouse 3T3 fixed frozen 3000 cells H3K4me3 Ab-MNase rep 1


title: RNAseq (rRNA-depleted by RNase H treatment) from rhino knock-out ovaries


title: human white blood cells single cells H3K4me3 Ab-Mnase-31


title: small RNA sequencing from nxf3 knock-out ovaries, replicate 2

description: small RNAs


title: human white blood cells single cells H3K4me3 Ab-Mnase-35


title: GC-JC-7819-H05_S40

city: London

first: Vlatka

last: Antolovic

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

institute: University College London

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_47

data_processing:
Paired-end reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat version 2.0.9 (parameters: -r 300 -p 4 -g 1).
Reads for each gene were counted with htseq-count (parameters: -m union -s no -a 0).
Insert size was calculated with picard 1.119 (CollectInsertSizeMetrics)
Genome_build: dicty_2.7
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each replicate.

organism: Dictyostelium discoideum

source_name: mound stage cell

growth_protocol: Cells were cultured in petri dishes in HL5 media (Formedium). For development, cells were washed in KK2 (20mM KPO4 pH 6.2) then plated on KK2/1.5% agar in 35mm petri dishes with 1-5 x 106 cells. The dishes were incubated at 22°C for 14h. Aggregates were disaggregated to single cells by taking them up in 1ml KK2/10mM EDTA and repeatedly passing the structures through a 20G needle.

extract_protocol:
Cells were loaded onto Integrated Fluidic Circuit chips (IFC; Fluidigm).  We identified capture of multiple cells and empty wells using brightfield illumination, with validation of single cell capture also carried out using a genetically-encoded red fluorescent nuclear marker. Cell lysis, reverse transcription and cDNA pre-amplification were performed in the C1 Single-Cell Auto Prep IFC using the SMARTer PCR cDNA Synthesis Kit (Clontech) and the Advantage 2 PCR Kit, as specified by the manufacturer (protocol 100-7168 A2). ERCC RNA spike-in control mix (92 transcripts; ThermoFisher) was added to the chambers at a 1:1000 ratio.
cDNA was harvested and the libraries were prepared using the Nextera XT DNA Sample Preparation Kit and the Nextera Index Kit (Illumina), according to the manufacturer's recommendations (protocol 100-7168 A2). Libraries from one chip were pooled, and paired-end 75bp sequencing was performed on 4 lanes of an Illumina NextSeq500.

value: AX3 with H2B-mCherry inserted in the rps30 locus

tag: replicate number

tag: developmental stage

value: mound


title: GC-JC-7819-H06_S48

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_48


title: small RNA sequencing from nxf3 knock-out ovaries, replicate 1

description: small RNAs


title: small RNA sequencing from nxf3-GFP knock-in ovaries

description: small RNAs

value: w[1118]; ; nxf3-GFP-V5-3xFLAG[knock-in]


title: human white blood cells single cells H3K4me3 Ab-Mnase-29

tag: antibody-mnase


title: GC-JC-7819-H04_S32

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_46


title: human white blood cells single cells H3K4me3 Ab-Mnase-30


title: small RNA sequencing from rhino knock-out ovaries, replicate 2

description: small RNAs


title: GC-JC-7819-H03_S24

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_45


title: human white blood cells single cells H3K4me3 Ab-Mnase-27


title: small RNA sequencing from w1118 (wildtype) ovaries, replicate 2

description: small RNAs


title: GC-JC-7819-H02_S16

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_44


title: small RNA sequencing from rhino knock-out ovaries, replicate 1

description: small RNAs


title: human white blood cells single cells H3K4me3 Ab-Mnase-25


title: small RNA sequencing from w1118 (wildtype) ovaries, replicate 1

description: small RNAs


title: small RNA sequencing from CG13741 knock-out ovaries, replicate 1

description: small RNAs


title: human white blood cells single cells H3K4me3 Ab-Mnase-26


title: GC-JC-7819-G06_S47

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_42


title: Poly_3_96h

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

data_processing:
Trimming and filtering of reads was performed with Trimmomatic version 0.33. TruSeq adapters were removed from read ends; additionally bases with a quality score smaller than 20 (less than 99 % base call accuracy) were removed from both read ends and further quality trimming was done using a 5 bp wide sliding window requiring an average quality score of 20. Finally, only reads of a length of at least 50 bp after trimming were retained.
Reads were mapped to the D. melanogaster transcriptome with TopHat2 2.1.0 (default parameters) using genome assembly BDGP6 and genome annotation BDGP6.84
Reads were counted using HTSeq 0.6.1 with options as follows: mode = "union", stranded = "reverse", alignment quality minimum = 10, and nonunique = "none".
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample

source_name: Poly, 96h, accessory gland

growth_protocol: Virgin males from all six experimental evolution lines were collected and aged for 48 and 96 h, respectively. For dissections, males were chilled on ice and reproductive tracts (RTs: AG, testes and ejaculatory duct) were dissected in phosphate buffered saline. Thirty RTs were pooled for each line and time point, snap frozen in liquid nitrogen and transferred to -80 °C until RNA extraction.

extract_protocol:
RNA was extracted from the pooled male RTs using the RNeasy Mini Kit (Qiagen).
Stranded libraries were generated using TruSeq Stranded Total RNA Library Prep kit (Illumina).

treatment_protocol: Six populations were established from the IV population of D. melanogaster: three (M1, M2, and M3) were held under enforced monogamy by randomly pairing one male and one virgin female, whereas the other three (P1, P2, and P3) experienced mating in polygamous groups of five females and five males. After two days of sexual interactions, males were discarded and females were allowed to lay eggs for three days in groups of 50, which assured similar degree of non-sexual competition. The populations had undergone 168 generations of experimental evolution when AG size and whole-transcriptome gene expression were measured; for further details, see paper.

tag: selection regime

value: polygamy

tag: population

tag: timepoint

value: 96 hours

value: Male reproductive tract (accessory glands, testes, ejaculatory duct)


title: human white blood cells single cells H3K4me3 Ab-Mnase-23

extract_protocol:
The DNAs were end-repaired using the End-It™ DNA End-Repair Kit (Lucigen, Radnor, PA, USA). The reaction was done in 10 µL reaction volume according to the manufacturer’s instruction. The reaction was terminated by adding 115 µL 10 mM Tris-Cl buffer (pH7.5) containing 1 mM EDTA, and the DNAs were extracted by the phenol-chloroform extraction, followed by the ethanol precipitation as described above. The precipitate is re-suspended in 5 µL Qiagen Buffer EB (10 mM Tris-Cl buffer (pH 8.5)). The addition of 3’ A overhangs to the end-repaired DNA fragments was done using the Klenow fragment (3’→5’ exo-) (New England BioLabs, Ipswich, MA, USA) and 1 mM deoxyadenosine triphosphate in the reaction buffer. The DNA fragments were incubated at 37°C for 20 min and the enzymes were inactivated at 75°C for 20 min. The Illumina Adaptor Oligo Mix (Illumina, San Diego, CA, USA) was ligated to the 3’ A overhangs of the DNA fragments using the T4 DNA ligase (New England BioLabs) by incubating at room temperature for 3 hr.
The DNA fragment with the adaptors bound was PCR amplified using the Phusion High-Fidelity PCR Master Mix (New England BioLabs) and the 125 nM PE PCR Primer 1.0 (Illumina). The PCR was done under the following condition: 98°C for 10 min, followed by a cycle of 30 sec at 68°C and 30 sec at 72°C (repeat 18 cycles in the case of 3,000 cells or 25 cycles in the case of a single cell). The 2% [w/v] agarose gel electrophoresis was done to isolate the 140-350 bp fragments and purify using the QIAquick Gel Extraction kit (Qiagen). The concentration of the purified DNAs was measured using Qubit dsDNA HS kit (Thermo Fisher Scientific). The paired-end sequencings were run using the Illumina MiSeq and HiSeq2000.


title: Poly_3_48h

source_name: Poly, 48h, accessory gland

value: 48 hours


title: GC-JC-7819-G04_S31

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_40


title: GC-JC-7819-G05_S39

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_41


title: human white blood cells single cells H3K4me3 Ab-Mnase-24


title: human white blood cells single cells H3K4me3 Ab-Mnase-22


title: human white blood cells single cells H3K4me3 Ab-Mnase-28


title: Spleen_injected CdCl2_10μmol/kg_rep2

type: RNA

city: Zhenjiang

first: Haifeng

last: Shi

state: Jiangsu

address: 301 Xuefu Rd

department: Institute of life sciences

country: China

institute: Jiangsu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Spleen_injected CdCl2_10μmol/kg

label_protocol: Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina  System

growth_protocol: The ICR mice, 28 days of age, 18-22g of weight, administered a single subcutaneous injection of cadmium chloride at a dose of 0 μmol/kg, 5 μmol/kg, 10 μmol/kg body weight (in 200 μL saline) for 24 h (n =7-8). The blank control mice received an equal volume of saline only.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: administered a single subcutaneous injection of cadmium chloride at a dose of 0umol/kg, 5umol/kg, 10umol/kg  body weight (in 200 uL saline) for 24h (n = 7–8). The blank control mice received an equal volume of saline only.

tag: strain background

value: ICR

tag: age

tag: treatment

value: 10μmol/kg CdCl2

value: spleen


title: GC-JC-7819-G03_S23

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_39

tag: strain


title: Spleen_injected CdCl2_10μmol/kg_rep1


title: Spleen_injected Saline_rep1

source_name: Spleen_injected Saline

value: saline control


title: Poly_2_48h


title: Poly_2_96h


title: Spleen_injected Saline_rep2


title: GC-JC-7819-H01_S8

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_43


title: Spleen_injected CdCl2_5μmol/kg_rep1

source_name: Spleen_injected CdCl2_5μmol/kg

value: 5μmol/kg CdCl2


title: human white blood cells single cells H3K4me3 Ab-Mnase-20

value: white blood cells

value: H3K4me3 Ab-MNase


title: Poly_1_96h


title: human white blood cells single cells H3K4me3 Ab-Mnase-21


title: human white blood cells single cells H3K4me3 Ab-Mnase-19


title: GC-JC-7819-G01_S7

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_37


title: Poly_1_48h


title: Spleen_injected CdCl2_5μmol/kg_rep2


title: GC-JC-7819-F06_S46

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_36


title: Mono_3_96h

source_name: Mono, 96h, accessory gland

value: monogamy


title: GC-JC-7819-F05_S38

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_35


title: Mono_3_48h

source_name: Mono, 48h, accessory gland


title: DR500, sample 3

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

hyb_protocol: Mouse Gene 1.0 ST Array

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (ThermoFisher).

data_processing: Microarray analyses were carried out with R, a free software environment available at http://www.r-project.org/. After quantification of gene expression with robust multi-array normalization using the  BioConductor package Affy, (http://www.bioconductor.org/) significance of differential gene expression was determined by computing moderated t-statistics and false discovery rates (FDR) with the limma package (63). Annotation was based on the genome version NCBI Build 36 (Feb. 2006). The obtained p-values were corrected for multiple testing by calculating estimated false discovery rates (FDR) using the method of Benjamini-Hochberg. The transcriptional factors enrichment analysis was then performed by using MetaCore from Thomson Reuters (version 6.11) by filter with thresholds 1.5 and p-value 0.01. Heatmaps were produced by color-coding gene-wise standardized log gene expression levels (mean zero standard deviation one).

label: biotin

source_name: 4T1 cells, selected with up to 500ng/ml methotrexate

label_protocol: Expression profiling by array

growth_protocol: 10e6 4T1 tumor cells were plated in 10 cm cell cuture dish one day prior treatment.

extract_protocol: Triplicates wells of 4T1 WTR- and DR500 cells grown in culture were used for RNA extraction using RNeasy kit (QIAGEN, Basel, Switzerland).

treatment_protocol: For Doxorubicin selection, cells were treated with the lower dosage (IC50) in culture medium. The medium with Doxorubicin were replaced in 2nd and 3rd day and then every 2-3 days. The Doxorubicin concentration for treatment was gradually increased upto 500ng/ml from day 7 to day 14. The treatment was continued for up to 2 weeks until single colonies os surviving cells were visible.

tag: cell line

value: up to 500ng/ml methotrexate


title: Mono_2_96h


title: human white blood cells single cells H3K4me3 Ab-Mnase-17

data_processing:
Raw Sequence reads were aligned to the reference human genome (UCSC, hg18) by Bowtie2 (bowtie2 -D 20 -R 3 -N 1 -L 16 -i S,1,0.5 -X 1000  -p 20 -q -5 0 -3 30). The reads with mapping quality (MAPQ ≤10) or redundant reads that mapped to the same location with the same orientation were removed from further analysis in each single cell library. For scH3K4me3,  To avoid the possibility of doublet (or triplet) outliers, four cells were removed. A cell is defined as a doublet outlier if it satisfies the following two requirements.    1. The log-library size of the cell is larger the averaged the log-library size over all cells.    2. Cells are sorted based on their log-library size. With any of the selected window sizes, the log-library size of the cell is larger than three local scaled median absolute deviation (MAD) from the local median within the sliding window. A number of window sizes are tested. Finally, the remaining 281 cells are used for genome browser visualization and identification of peaks for pooled cells.
Peaks/Enriched regions for the 281 pooled single cell H3K4me3 data were identified using SICER (gap size = 200 bp, window size =200bp and frag size= 150bp). 22293 peaks are identified for the pooled H3K4me3 scChIC-seq data. Peaks/Enriched regions for the 106  pooled single cell H3K4me3 data were identified using SICER (gap size = 600 bp, window size =200bp and frag size= 150bp). 21,465 peaks are identified for the pooled H3K27me3 scChIC-seq data.
For each single cell library (both scH3K4me3 and scH3K27me3), we filtered the reads that are not located in the identified peak regions (22,293 peaks and 21,465 peaks for scH3K4me3 and scH3K27me3 libraries, respectively). Therefore, the *filtered.txt files are obtained for the downstream analysis.
Genome_build: hg18
Supplementary_files_format_and_content: *filtered.txt: bed 6 file. Each line is a peak region. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bed: Bed 6 file. Each line is a read. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bedgraph: bed 4 file. Each line is a bin, with bin size = 200bp. The four columns are chrom, start position, end position,read density.
Library strategy: scChIC-seq


title: human white blood cells single cells H3K4me3 Ab-Mnase-16


title: GC-JC-7819-F04_S30

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_34


title: MR20_3, biological replicate 3

source_name: 4T1 cells, selected with 20ug/ml methotrexate

extract_protocol: Triplicates of 4T1 WT and MR20 tumor cells were subjected to RNA extraction using RNeasy kit according to Manufacturer's instructions (QIAGEN, Basel, Switzerland). Extracted RNA content and quality were determined by NanoDrop spectrophotometer.

treatment_protocol: For MTX selection, cells were treated with 20 ug/ml methotrexate directly added into the culture medium. The medium with MTX was replaced at 2nd and 3rd days and then every 2-3 days. The treatment was continued for up to 2 weeks until single colonies were visible. All the survival cells (MR20) were then cultured in normal, MTX-free medium for additional 2 weeks for their recovery before RNA extraction. The same batch of 4T1 tumor cells was cultured in parallel in normal culture medium, without MTX, as control (WT).

value: 20ug/ml methotrexate


title: HopX_P3_3 [RNA-Seq]

first: Yijing

last: Su

address: Levy 326

department: Department of Oral Medicine

data_processing:
Basecalls performed using BCl2fastq
RNA-seq reads were aligned to the mm9 genome assembly using Bowtie with the default setting
Data was process by cufflink
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: HopX+ cells

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Standard Illumina scanning protocol

value: neural progenitor cells


title: human white blood cells single cells H3K4me3 Ab-Mnase-15


title: DR500, sample 2


title: GC-JC-7819-G02_S15

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_38

value: AX3 with H2B-mCherry inserted in the rps30 locus

value: mound


title: Mono_2_48h


title: DR500, sample 1


title: HopX_P3_1 [RNA-Seq]


title: WT_2, biological replicate 2

source_name: 4T1 cells, untreated

value: untreated


title: MR20_2, biological replicate 2


title: Mono_1_96h

value: 96 hours


title: MR20_1, biological replicate 1


title: GC-JC-7819-F01_S6

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_31


title: WT_3, biological replicate 3


title: WT_1, biological replicate 1


title: Mono_1_48h

value: Male reproductive tract (accessory glands, testes, ejaculatory duct)


title: HopX_E15_1 [RNA-Seq]


title: P180181_S09: U2OS_TET_WT_+Dox_RNA-seq_rep_3

city: Oxford

first: Skirmantas

last: Kriaucionis

address: Old Road Campus Research Building

institute: Ludwig Institute for Cancer Research

description: RNA-seq using ribo-RNA depleted total RNA

data_processing:
RNA-Seq: Base calls performed using X. The reads from each lane were merged for each sample and aligned to the hg19 genome using STAR (v2.4.2), allowing for uniquely mapped reads only ( --outFilterMultimapNmax 1). The number of reads overlapping each gene (on each strand) were counted using multiBamSummary from deeptools (v3.0.2). Only those genes with at least one read were kept. The count tables were converted into GRanges objects (GenomicRanges v1.34.0) in R (v3.5.1) and split according to strand into sense and antisense. We used DESeq2 (v1.22.1) with default parameters to calculate differential expression between conditions with "design = ~ Sample + Condition", where Sample is the batch. We used "apeglm" shrinkage when generating the results tables.
genome_build: hg19
processed_data_files_format_and_content: A DESeq2 result table for each comparison is output in tab-delimited format into separate sheets in an Excel document. AS indicates analyses on the antisense strand. For RNA-Seq there are 4 grouped Excel files in total: Supplementary Table 1 (TET1-CD effect in HEK293 cells), Supplementary Table 2 (5-aza-2'-deoxycytidine and TET1-CD effect in U2OS cells), Supplementary Table 3 (5-aza-2'-deoxycytidine, UVA, and 4-Thio-2'-deoxythymidine effect in HEK293 cells), Supplementary Table 6 (MeBP analyses in HEK293 cells).

growth_protocol: all cells were cultured in DMEM (high glucose) containing antibiotics, L-glutamine, 10% FBS at 37°C, 5%CO2

extract_protocol:
RNeasy Mini kit with DNase I treatment, Ribo-Zero rRNA Removal Kit
TruSeq Stranded Total RNA kit (Illumina)

value: 1 μg/mL Doxycycline for 48 hours

tag: genotype/variation

value: TET-CD-GFP


title: GC-JC-7819-E06_S45

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_30


title: human white blood cells single cells H3K4me3 Ab-Mnase-12


title: P180181_S08: U2OS_TET_WT_+Dox_RNA-seq_rep_2


title: GC-JC-7819-E05_S37

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_29


title: GC-JC-7819-F03_S22

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_33


title: HopX_Adult_3 [RNA-Seq]

value: Adult


title: human white blood cells single cells H3K4me3 Ab-Mnase-11


title: GC-JC-7819-F02_S14

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_32


title: HopX_E15_2 [RNA-Seq]


title: P180181_S07: U2OS_TET_WT_+Dox_RNA-seq_rep_1


title: GC-JC-7819-E03_S21

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_27


title: human white blood cells single cells H3K4me3 Ab-Mnase-14


title: human white blood cells single cells H3K4me3 Ab-Mnase-9


title: P180181_S06: U2OS_TET_WT_+Aza_RNA-seq_rep_3

value: 55 nM 5-aza-2'-deoxycytidine for 48 hours


title: HopX_P3_3

data_processing:
Basecalls performed using BCl2fastq
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtiw with the default setting
peaks were called using MACS, with p < 0.05 as cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: bed

extract_protocol: ADD

tag: chip antibody


title: human white blood cells single cells H3K4me3 Ab-Mnase-13


title: P180181_S05: U2OS_TET_WT_+Aza_RNA-seq_rep_2


title: GC-JC-7819-E02_S13

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_26


title: HopX_Adult_1 [RNA-Seq]


title: human white blood cells single cells H3K4me3 Ab-Mnase-8


title: human white blood cells single cells H3K4me3 Ab-Mnase-10


title: P180181_S04: U2OS_TET_WT_+Aza_RNA-seq_rep_1


title: human white blood cells single cells H3K4me3 Ab-Mnase-7


title: GC-JC-7819-E01_S5

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_25


title: GC-JC-7819-D06_S44

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_24


title: P180181_S03: U2OS_TET_WT_Untreated_RNA-seq_rep_3


title: GC-JC-7819-E04_S29

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_28


title: HopX_Adult_2 [RNA-Seq]


title: human white blood cells single cells H3K4me3 Ab-Mnase-6


title: HopX_E15_2


title: P180181_S02: U2OS_TET_WT_Untreated_RNA-seq_rep_2


title: GC-JC-7819-D05_S36

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_23


title: human white blood cells single cells H3K4me3 Ab-Mnase-5


title: HopX_E15_1


title: HopX_P3_2


title: GC-JC-7819-D04_S28

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_22


title: human white blood cells single cells H3K4me3 Ab-Mnase-4


title: P180181_S01: U2OS_TET_WT_Untreated_RNA-seq_rep_1


title: P170694_S26: HEK293_MeBP_TKO_G37_+Dox_RNA-seq_rep_3


title: HopX_Adult_3


title: HopX_Adult_2


title: P170694_S23: HEK293_MeBP_TKO_G37_+Dox_RNA-seq_rep_2


title: human white blood cells single cells H3K4me3 Ab-Mnase-3


title: P170694_S20: HEK293_MeBP_TKO_G37_+Dox_RNA-seq_rep_1


title: GC-JC-7819-D01_S4

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_19


title: GC-JC-7819-D03_S20

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_21


title: GC-JC-7819-C06_S43

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_18


title: human white blood cells single cells H3K4me3 Ab-Mnase-2


title: ERG_Crispr_818PTEN_ERG_H3K27AcIP

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

description:
IP H3K27Ac
Sample_ERG_Crispr_818PTEN_ERG_H3K27AcIP_IGO_06778_12

data_processing:
Alignment of raw reads to hg19 using bowtie aligner
Quality control using RSeQC and Picard
Picard MarkDuplicates
Peak calling by MACS2
Peak annotation by homer annotatePeaks.pl
reads density by deeptools
Genome_build: hg19
Supplementary_files_format_and_content: bam file

source_name: Prostate cancer

growth_protocol: Cells  were grown in prostate epithelial organoid media as 2D layer in vitro and split at 70% confluency.

extract_protocol:
cells are fixed by 0.8%PFA and lysised in  low-salt wash buufer with 0.1% SDS and 1% Triton X-100
CHIP-Seq was performed by New York genome center. DNA was adenylated, ligated to Illumina sequencing adapters, and amplified by PCR (using 10 cycles).  Final libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems), Next generation sequencing was carried out on an Illumina HiSeq2000 plateform with 50 bp or 100 bp single reads.

treatment_protocol: No treatment

tag: genotype

value: Pten-/- Rosa26-Tmprss2-ERG

tag: manipulation

value: CRISPR-ERG

tag: tissue

value: Prostate cancer


title: human white blood cells single cells H3K4me3 Ab-Mnase-1

source_name: white blood cells

tag: cell type

value: white blood cells

value: H3K4me3 Ab-MNase


title: P170694_S27: HEK293_MeBP_TKO_G37_+Aza_RNA-seq_rep_3

value: 880 nM 5-aza-2'-deoxycytidine for 48 hours


title: ERG_Crispr_818PTEN_ERG_ERGIP

description:
IP ERG
Sample_ERG_Crispr_818PTEN_ERG_ERGIP_IGO_06778_6


title: ERG_Crispr_818PTEN_ERG_ARIP

description:
IP AR
Sample_ERG_Crispr_818PTEN_ERG_ARIP_IGO_06778_9


title: P170694_S24: HEK293_MeBP_TKO_G37_+Aza_RNA-seq_rep_2

description: RNA-seq using ribo-RNA depleted total RNA


title: GC-JC-7819-C05_S35

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_17

tag: replicate number


title: Control_818PTEN_ERG_H3K27AcIP

description:
IP H3K27Ac
Sample_Control_818PTEN_ERG_H3K27AcIP_IGO_06778_10

value: Control


title: P170694_S21: HEK293_MeBP_TKO_G37_+Aza_RNA-seq_rep_1


title: Caki-1 cell line si-HOIL-1#1

city: Beijing

first: Sifan

last: Yu

address: Fucheng Road 52#

institute: Peking University Cancer Hospital & Institute

description:
Institute of Basic Medical Sciences, CAMS/PUMC
Si1

data_processing:
Basecalls performed using Tophat2 viersion 2.1.0
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the hg19. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced)
Genome_build: hg19
Supplementary_files_format_and_content: text file include gene name, position,log2(Fold_change),p-value,q-value for each Sample

source_name: clear cell renal cell carcinoma

extract_protocol:
RNA was harvested using Trizol reagent(Life Technologies). Illumina NEB Ultra directional RNA library Prep Kit was used with 1 ug of total RNA for the construction sequencing libraries.
Total RNA was extracted and ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre, Madison, WI, USA).Fragmented RNA were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA). The libraries were paired-end sequenced at Guangzhou RiboBio Co., Ltd. using IlluminaHiSeq 3000 platform.

value: clear cell renal cell carcinoma


title: GC-JC-7819-C04_S27

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_16

value: AX3 with H2B-mCherry inserted in the rps30 locus

tag: developmental stage


title: GC-JC-7819-D02_S12

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_20

value: mound


title: Caki-1 cell line si-Control

description:
Institute of Basic Medical Sciences, CAMS/PUMC
NC


title: GC-JC-7819-C03_S19

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_15


title: P170694_S25: HEK293_MeBP_TKO_G37_Untreated_RNA-seq_rep_3


title: Control_818PTEN_ERG_ARIP

description:
IP AR
Sample_Control_818PTEN_ERG_ARIP_IGO_06778_7


title: Control_818PTEN_ERG_ERGIP

description:
IP ERG
Sample_Control_818PTEN_ERG_ERGIP_IGO_06778_4


title: Armi-R949A mut FAST-iCLIP rep2

city: Tokyo

first: Hirotsugu

last: Ishizu

address: 35 Shinanomachi

country: Japan

institute: Keio University

description:
IndexCHKPEI85216100038_RA_rep2_1
processed data file:
Armi_mutant_RPM.txt

data_processing:
Reads were filtered for quality, and PCR duplicates removed using the random barcode. 3' adaptor sequences were trimmed using Cutadapt, and reads were mapped to the Drosophila genome (dm6) using STAR. 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
RIP-seq: Piwi associated small RNA sequencing data was analyzed as described previously (PMID: 27425411). 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
Armi-CLIPPARE* samples: Reads were filtered for quality, and PCR duplicates removed using the random barcode. 3' adaptor sequences were trimmed using Cutadapt, and reads were mapped to the Drosophila genome (dm6) using STAR. 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Armi-R949A mut FAST-iCLIP

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase T1 (Roche) and immunoprecipitation of RNA-protein complexes with an anti-Armi antibody (PMID: 20966047). After dephosphorylation with T4 PNK (NEB), a preadenylated DNA adapter was ligated to the 3’ end with T4 RNA Ligase2, truncated KQ (NEB). Ligations were performed on-bead. Samples were then run on NuPAGE gels (Life Technologies) and transferred to nitrocellulose membranes. After cutting out the region of nitrocellulose containing RNA–protein complexes, RNAs were removed from the membrane by Proteinase K (Roche) digestion.
Samples were processed for reverse transcription, cDNA purification, and cDNA circularization as previously described in (PMID: 25411354). Libraries were then amplified with Q5 DNA polymerase (NEB) and size-selected via polyacrylamide gel electrophoresis. Each sequencing read conatins 5 random bases (N) at the 5’ end "NNNGGTTNN".

treatment_protocol: OSCs were crosslinked with UV (254 nm, 200 mJ/cm2). Cells were then isolated with cell scrapers and precipitated by centrifugation for 2 min at 10000 rpm.

value: Ovarian Somatic Cells (OSC)

value: Myc-Armi-R949A transfection

tag: ip antibody

value: anti-c-Myc antibody 9E10 (Sigma)


title: GC-JC-7819-C02_S11

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_14


title: P170694_S22: HEK293_MeBP_TKO_G37_Untreated_RNA-seq_rep_2


title: GC-JC-7819-C01_S3

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_13


title: Armi-D862A mut FAST-iCLIP rep2

description:
IndexCHKPEI85216100038_DA_rep2_1
processed data file:
Armi_mutant_RPM.txt

source_name: Armi-D862A mut FAST-iCLIP

value: Myc-Armi-D862A transfection


title: P170694_S17: HEK293_MeBP_TKO_G16_+Dox_RNA-seq_rep_3

value: 1 μg/mL Doxycycline for 48 hours

value: TET-CD-GFP


title: AR_Crispr_818PTEN_ERG_ERGIP

description:
IP ERG
Sample_AR_Crispr_818PTEN_ERG_ERGIP_IGO_06778_5

value: CRISPR-AR


title: AR_Crispr_818PTEN_ERG_H3K27AcIP

description:
IP H3K27Ac
Sample_AR_Crispr_818PTEN_ERG_H3K27AcIP_IGO_06778_11

value: Pten-/- Rosa26-Tmprss2-ERG


title: P170694_S19: HEK293_MeBP_TKO_G37_Untreated_RNA-seq_rep_1


title: GC-JC-7819-B06_S42

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_12

source_name: mound stage cell


title: GC-JC-7819-B05_S34

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_11


title: Armi-D862A mut FAST-iCLIP rep1

description:
IndexCHKPEI85216100038_DA_rep1_1
processed data file:
Armi_mutant_RPM.txt


title: AR_Crispr_818PTEN_ERG_ARIP

description:
IP AR
Sample_AR_Crispr_818PTEN_ERG_ARIP_IGO_06778_8


title: Caki-1 cell line si-HOIL-1#2

description:
Institute of Basic Medical Sciences, CAMS/PUMC
Si2


title: Armi-WT FAST-iCLIP rep2

description:
IndexCHKPEI85216100038_WT_rep2_1
processed data file:
Armi_mutant_RPM.txt

source_name: Armi-WT FAST-iCLIP

value: Myc-Armi-WT transfection


title: GC-JC-7819-B04_S26

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_10


title: Armi-WT FAST-iCLIP rep1

description:
IndexCHKPEI85216100038_WT_rep1_1
processed data file:
Armi_mutant_RPM.txt


title: P170694_S11: HEK293_MeBP_TKO_G16_+Dox_RNA-seq_rep_1

description: RNA-seq using ribo-RNA depleted total RNA


title: GC-JC-7819-B03_S18

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_9


title: Armi FAST-iCLIP from Yb-KD rep2

description:
IndexCHKPEI85216100038_Yb_rep2_1
processed data file:
Armi_iCLIP_RNAi_RPM.txt

source_name: Armi FAST-iCLIP from Yb-KD

value: Yb RNAi

value: anti-Armi antibody (PMID:20966047)


title: P170694_S14: HEK293_MeBP_TKO_G16_+Dox_RNA-seq_rep_2


title: P170694_S18: HEK293_MeBP_TKO_G16_+Aza_RNA-seq_rep_3


title: Armi-R949A mut FAST-iCLIP rep1

description:
IndexCHKPEI85216100038_RA_rep1_1
processed data file:
Armi_mutant_RPM.txt


title: Armi FAST-iCLIP from Yb-KD rep1

description:
IndexCHKPEI85216100038_Yb_rep1_1
processed data file:
Armi_iCLIP_RNAi_RPM.txt


title: GC-JC-7819-B01_S2

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_7


title: P170694_S15: HEK293_MeBP_TKO_G16_+Aza_RNA-seq_rep_2