title: primary_RHH1555

value: squamous cell carcinoma

value: primary tumor

value: single cell


title: total RNA-seq from G1E-ER4 (ENCLB992KNY)

status: Public on Jul 12 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR538CVD/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse G1E-ER4+E2 100ng rRNA-depeleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR538CVD
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB992KNY
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J G1E-ER4 immortalized cell line treated with 10 nM 17beta-estradiol for 24 hours

tag: line

value: immortalized cell line

tag: description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: biosample encode accession

tag: dev stage

value: postnatal

tag: treatments

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; duration:24; duration_units:hour; UCSC-ENCODE-cv:diffProtD_24hr;

tag: lab

value: Ross Hardison, PennState

tag: age

value: 0 day

tag: Sex

value: male

tag: link

value: ENCBS870UYF at ENCODE; https://www.encodeproject.org/ENCBS870UYF/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: primary_RHH1553

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

description:
Primary cancer
PolyA+ RNA
Processed data file: expression.txt

data_processing:
BAM files produced using Tophat-2.1.0.
FPKM obtained using Cuffdiff-2.2.1.
The RefSeq genes are tracked for analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: expression.txt: The tab-delimited text file contains the log2(1+pQ normalized FPKM) expression matrix for all individual cells. For details about pQ normalization, see Sengupta, Debarka, et al. "Fast, scalable and accurate differential expression analysis for single cells." bioRxiv (2016): 049734.

organism: Homo sapiens

source_name: squamous cell carcinoma, primary tumor

extract_protocol:
RNA isolated from cells using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech).
Library construction: In accordance to protocol from Fluidigm describing the use of the C1 system to generate cDNA library for single cell RNA-seq. Briefly, cDNA was synthesized using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System from Clontech; library was constructed using Nextera XT DNA Sample Preparation Kit and Nextera XT DNA Library Preparation Index Kits from Illumina.

tag: disease status

tag: tissue

tag: sample type


title: primary_RHH1552


title: primary_RHH1550


title: 3KO_myoblast_2

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Casava software was used for base calling
Reads were de-multiplexed using fastq-tools and quality was confirmed using FastQC. Reads were then mapped to either the human (hg19) or mouse (mm10) genome using HISAT2 and mapped, primary alignments were retrieved using SAMtools.
Alternative splicing analysis was performed using MISO, differential gene expression analysis was performed using Olego, Quantas, and EdgeR, and polyA-seq analysis was performed using Olego and Quantas.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text file including exon PSI values and confidence intervals for each sample.

source_name: myoblast

growth_protocol: For myoblast RNA-seq datasets, primary wild-type and 3KO myolasts were grown in myoblast growth media until the time of experiment.

extract_protocol:
All samples were collected into TRIzol or flash-frozen in liquid nitrogen and stored at -80°C until RNA was isolated.
RNA-seq libraries were prepared using rRNA-depleted RNA as per the manufacturer's protocol.

treatment_protocol: For myoblast RNA-seq datasets, wild-type and 3KO myoblasts were switch to differentiation media for 0 or 6 hours prior to collection.

tag: strain

value: mixed:C57BL/6 & Sv/129

value: myoblast

tag: genotype

value: Mbnl3 knockout


title: 3KO_myoblast_1


title: total RNA-seq from G1E-ER4 (ENCLB835WGS)

description:
https://www.encodeproject.org/experiments/ENCSR538CVD/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse G1E-ER4+E2 100ng rRNA-depeleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR538CVD
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB835WGS
size range: 200-1000
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: ENCBS031ZRK at ENCODE; https://www.encodeproject.org/ENCBS031ZRK/


title: primary_RHH1561


title: WT_myoblast_2

value: wild type


title: met_RHH1567

description:
Metastatic cancer
PolyA+ RNA
Processed data file: expression.txt

source_name: squamous cell carcinoma, metastatic tumor

value: squamous cell carcinoma

value: metastatic lymph node tumor


title: WT_myoblast_1


title: TKO_P0quad_3

source_name: quadriceps

value: quadriceps

value: post natal day 0

value: Mbnl1; Mbnl2; Mbnl3; Myog-Cre conditional triple knockout


title: primary_RHH1547

value: primary tumor

value: single cell


title: total RNA-seq from granulocyte monocyte progenitor cell (ENCLB326JJG)

description:
https://www.encodeproject.org/experiments/ENCSR277DPB/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse GMP 100ng rRNA-depleted RNA-seq via ScriptSeq
experiment encode accession: ENCSR277DPB
assay title: total RNA-seq
assembly: mm10
encode release date: 2017-01-04
lab: Ross Hardison, PennState
library encode accession: ENCLB326JJG
size range: 200-712
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J granulocyte monocyte progenitor primary cell male adult (5-6 weeks)

value: granulocyte monocyte progenitor cell

value: primary cell

value: granulocyte monocyte progenitor

value: adult

value: Ross Hardison, PennState

value: 5-6 week

tag: health state

value: unknown

value: ENCBS127MVP at ENCODE; https://www.encodeproject.org/ENCBS127MVP/


title: primary_RHH1549


title: primary_RHH1548


title: primary_RHH1544


title: TKO_P0quad_1

value: mixed:C57BL/6 & Sv/129


title: DKO_P0quad_3

value: Mbnl1; Mbnl2; Myog-Cre conditional double knockout


title: DKO_P0quad_2


title: primary_RHH1546

value: squamous cell carcinoma


title: primary_RHH1545


title: TKO_P0quad_2


title: DKO_P0quad_1


title: primary_RHH1541


title: WT_P0quad_3

value: wild type


title: WT_P0quad_2

value: quadriceps


title: primary_RHH1540


title: primary_RHH1537


title: primary_RHH1539


title: primary_RHH1538


title: primary_RHH1534


title: primary_RHH1533


title: primary_RHH1532


title: primary_RHH1530


title: CDM_2_polyaseq

molecule: polyA RNA

source_name: biceps brachii

value: biceps brachii

value: 3 months

value: congenital myotonic dystrophy


title: CDM_1_polyaseq

value: 15 months


title: SMA_3_polyaseq

value: 4 months

value: spinal muscular atrophy, type 1


title: primary_RHH1527

value: primary tumor

value: single cell


title: primary_RHH1526


title: CDM_3_polyaseq

value: 5 months


title: SMA_2_polyaseq


title: primary_RHH1525


title: primary_RHH1524


title: primary_RHH1523


title: WT_P0quad_1

value: post natal day 0


title: SMA_1_polyaseq


title: primary_RHH1520


title: primary_RHH1521


title: primary_RHH1522


title: primary_RHH1518


title: primary_RHH1519


title: primary_RHH1516


title: primary_RHH1529


title: met_RHH1579

value: metastatic lymph node tumor


title: primary_RHH1528


title: primary_RHH1535


title: primary_RHH1514


title: primary_RHH1511


title: primary_RHH1510


title: primary_RHH1513


title: primary_RHH1515


title: DFL_E12_Inv_Hoxd13VP

city: Lausanne

first: Pierre

middle: J

last: Fabre

address: Station 19

department: ISREC

country: Switzerland

institute: EPFL

description: Distal limb mouse E12.5_Hoxd13VP_Inv

library_source: genomic

data_processing:
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the mm10 (GRCm38) mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters “-n 2 --best -strata -m 5”. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
4C figures were made using smoothed/normalized data that were obtained by applying a running mean algorithm with a window size of eleven fragments and normalized to the same total intensity, such as to see only changes in contacts distribution and to minimize PCR complexity bias in each samples.
Genome_build: mm10
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph), one per viewpoint, per tissue

molecule: genomic DNA

source_name: Forelimb

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 limbs either from wild type or mutant embryos were dissected, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 8 distal or proximal limbs were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. Hoxd13_inverse_forward: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAAAATCCTAGACCTGGTCAT, Hoxd13-inverse_reverse: CAAGCAGAAGACGGCATACGAGGCCGATGGTGCTGTATAG, Isl_II forward primer: GCATTCATCAAGCTGTGATTAGCA, Isl_II reverse primer: TCCCATAATATGTAGACTGTAGTGTTGC.
For sample 9 we used a series of four different barcoded primers for Hoxd13 forward such as barcode 1: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTATCGAAAAATCCTAGACCTGGTCATG; iHoxd13 forward:  barcode 2: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGACAAAAAATCCTAGACCTGGTCATG; iHoxd13 forward: barcode3: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTTGACAAAAATCCTAGACCTGGTCATG; and iHoxd13 forward: barcode4: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGGTAAAAAATCCTAGACCTGGTCATG


title: primary_RHH1508


title: primary_RHH1509


title: primary_RHH1506


title: primary_RHH1543


title: primary_RHH1504


title: primary_RHH1517


title: primary_RHH1503


title: primary_RHH1500


title: DFL_E12_del4_Hoxd13VP

description: Distal limb mouse E12.5_Hoxd13VP_del4


title: DFL_E12_del3_Hoxd13VP

description: Distal limb mouse E12.5_Hoxd13VP_del3


title: primary_RHH1499


title: DFL_E12_del1_Hoxd13VP

description: Distal limb mouse E12.5_Hoxd13VP_del1


title: DFL_E12_WT2_Hoxd13VP

description: Distal limb mouse E12.5 WT_Hoxd13VP2


title: DFL_E12_WT3_Hoxd13VP

description: Distal limb mouse E12.5 WT_Hoxd13VP3


title: primary_RHH1498


title: DFL_E12_WT_Island-IIVP

description: Distal limb mouse E12.5 WT_Isl-II_VP


title: primary_RHH1495


title: primary_RHH1493


title: DFL_E12_Inv_Island-IIVP

description: Distal limb mouse E12.5_Isl-II_VP_Inv


title: DFL_E12_WT_Hoxd13VP_250bp

description: Distal limb mouse E12.5 WT_Hoxd13VP_250bp


title: met_RHH1632


title: DFL_E12_del2_Hoxd13VP

description: Distal limb mouse E12.5_Hoxd13VP_del2


title: DFL_E12_WT_Hoxd13VP

description: Distal limb mouse E12.5 WT_Hoxd13 viewpoint


title: primary_RHH1505


title: primary_RHH1491


title: primary_RHH1492


title: invDFL

data_processing:
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) with bowtie2 with parameters --end-to-end --sensitive -k 20
Reads Per Kilobase per Million reads (RPKM) for each transcript were calculated from the raw counts with program rnacounter 1.5.2 (https://pypi.python.org/pypi/rnacounter)
Genome_build: mm9
Supplementary_files_format_and_content: One density file per strand (bigWig) and one tab-delimited text file with raw counts and RPKM per transcript.

source_name: distal limb

extract_protocol:
Total RNA from E12.5 embryonnic forelimb tissues was extracted shortly after dissection in cold PBS and isolated using Trizol.
Library preparation using the Illumina TruSeq protocol is applied with a Poly A selection

value: distal limb

tag: developmental stage

value: invDFL


title: primary_RHH1489


title: primary_RHH1488


title: primary_RHH1502


title: primary_RHH1487


title: RNA-seq invitro late 2-cell rep2

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

country: China

institute: Tsinghua University

description:
processed data file:
alpha_amanitin_experiments_RNAseq_FPKM.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: RNA-seq invitro late 2-cell

extract_protocol: RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males.

value: C57BL/6N x PWK/PhJ

value: Preimplantation embryo


title: PFL_E12_WT_Hoxd13VP

description: Proximal limb mouse E12.5 WT_Hoxd13 viewpoint

value: wild type


title: primary_RHH1485

value: squamous cell carcinoma


title: primary_RHH1484


title: primary_RHH1486


title: wtFL

value: wtFL


title: primary_RHH1482


title: primary_RHH1480


title: primary_RHH1496


title: Neuron_RNAseq

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings. Aligned reads were used to generate pileup for each base with Samtools v0.1.18.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: mm9
Supplementary_files_format_and_content: Counts for each refseq genes

source_name: Cortex

extract_protocol:
Heterozygous Nestin-GFP mice were bred with homozygous DCX-mRFP mice to yield GFP/RFP double positive embryos. The cortices derived from the double positive embryos were dissociated by trituration in HBSS with 2mM of EDTA and 25 ug/ml of DNase I. Cells were washed once with HBSS and re-suspended in DMEM/F12. Fluorescence-activated cell sorting (FACS) was used to acquire neural progenitor cells (NPCs, green color) and neurons (double color). Total RNA was extracted using TRIzol.
Following Illumina's True-seq RNA-seq library prep kit

value: cortex

tag: cell type

value: Neuron

value: Embryonic day 15.5


title: 12390_Neuron_H3K27me3_ChIPSeq

data_processing:
Bases were called using Illumina's CASAVA v1.8.2
Sequences were aligned to mm9 genome using Novoalign, only unique aligned reads were kept
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using in house R scripts

extract_protocol:
Heterozygous Nestin-GFP mice were bred with homozygous DCX-mRFP mice to yield GFP/RFP double positive embryos. The cortices derived from the double positive embryos were dissociated by trituration in HBSS with 2mM of EDTA and 25 ug/ml of DNase I. Cells were washed once with HBSS and re-suspended in DMEM/F12. Fluorescence-activated cell sorting (FACS) was used to acquire neural progenitor cells (NPCs, green color) and neurons (double color). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA samples after ChIP were subjected to amplification with MicroPlex Library Preparation kit (AB-004-0012, Diagenode) according to the instruction.

value: Neurons


title: RNA-seq invitro 8-cell rep2

source_name: RNA-seq invitro 8-cell


title: primary_RHH1478


title: primary_RHH1479


title: primary_RHH1481


title: primary_RHH1476


title: DFL_E12_WT_CTCF

description: Distal forelimb mouse E12.5 WT CTCF ChIPseq

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed ChIP-seq reads were mapped against the mouse GRC38/mm10 genome assembly using the BBCF HTSstation (http://htsstation.epfl.ch and (David et al., 2014)) platform.
Genome_build: GCR38/mm10
Supplementary_files_format_and_content: Bigwig files of the ChiP seq mapped reads

extract_protocol:
Micro-dissected distal segments of E12.5 limbs from wild type CD1 mice, were used for ChIP-seq. Samples were fixed in 1% formaldehyde/PBS for 10 minutes at room temperature, washed three times with cold PBS containing protease inhibitor and stored at -80°C.  One hundred milligrams of tissue  were used. Nuclei were extracted by incubating them in a cell lysis buffer provided in the ChIP IT high sensitivity kit (Active motif) during at least 10 minutes and with the aid of A Dounce homogenizer type B (Active motif). The isolated nuclei were pelleted and lysed in sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH=8.0 and protease inhibitor) for 10 min on ice, and fragmented to a range of 200-500 bp using a Vibracell tip sonicator. DNA concentration was estimated using the Qubit ds DNA HS assay kit following manufacturer instruction and 25 ugr of chromatin were diluted ten times in ChIP dilution buffer (20mM HEPES, 150mM NaCl, 0.1% NP40) and incubated overnight at 4C with 4mgr of anti-CTCF antibody (Active motif) on a rotating platform. The next day chromatin-antibody complexes were incubated with protein A/G agarose beads during 3h at 4C and successively  washed following manufacturer instructions. Finally they were eluted and purified by phenol:chlorophorm extraction and precipitation. A total of 10ngr of immunoprecipitated DNA were sequenced with a 50bp single-end Illumina HiSeq flow cell.
For ChIP-seq, 10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

tag: tissues

value: Distal forelimb

tag: antibody

value: CTCF (Active motif REF# 61311)


title: 12385_Neuron_H3K4me3_ChIPSeq


title: 12386_Neuron_H3K4me3_ChIPSeq


title: 12384_NPC_H3K4me3_ChIPSeq

value: Neural progenitor cells


title: 12383_NPC_H3K4me3_ChIPSeq


title: 6050_Neuron_IgG control_ChIPSeq

description: Neuron_IgG control_ChIPSeq


title: NPC_RNAseq

value: Neural progenitor cell


title: primary_RHH1475

value: primary tumor

value: single cell


title: primary_RHH1474


title: 6049_NPC_IgG control_ChIPSeq

description: NPC_IgG control_ChIPSeq


title: met_RHH1598

value: metastatic lymph node tumor


title: 12388_NPC_H3K27me3_ChIPSeq


title: 12376_NPC_Pol II-Ser2P_ChIPSeq

description: NPC_Pol II-Ser2P_ChIPSeq


title: 12378_Neuron_Pol II-Ser2P_ChIPSeq

description: Neuron_Pol II-Ser2P_ChIPSeq


title: primary_RHH1472


title: 12377_Neuron_Pol II-Ser2P_ChIPSeq

description: Neuron_Pol II-Ser2P_ChIPSeq


title: primary_RHH1470


title: 12375_NPC_Pol II-Ser2P_ChIPSeq

description: NPC_Pol II-Ser2P_ChIPSeq


title: 12374_Neuron_Pol II-nonP_ChIPSeq

description: Neuron_Pol II-nonP_ChIPSeq


title: 12387_NPC_H3K27me3_ChIPSeq


title: 12389_Neuron_H3K27me3_ChIPSeq


title: 7006_Neuron_Pol II-total_ChIPSeq

description: Neuron_Pol II-total_ChIPSeq


title: 7008_Neuron_Pol II-Ser5P_ChIPSeq

description: Neuron_Pol II-Ser5P_ChIPSeq


title: 12372_NPC_Pol II-nonP_ChIPSeq

description: NPC_Pol II-nonP_ChIPSeq


title: 12371_NPC_Pol II-nonP_ChIPSeq

description: NPC_Pol II-nonP_ChIPSeq


title: 12373_Neuron_Pol II-nonP_ChIPSeq

description: Neuron_Pol II-nonP_ChIPSeq


title: primary_RHH1477


title: 5790_NPC_Pol II-Ser5P_ChIPSeq

description: NPC_Pol II-Ser5P_ChIPSeq


title: 5791_Neuron_Pol II-Ser5P_ChIPSeq

description: Neuron_Pol II-Ser5P_ChIPSeq


title: 5789_Neuron_Pol II-total_ChIPSeq

description: Neuron_Pol II-total_ChIPSeq


title: 7005_NPC_Pol II-total_ChIPSeq

description: NPC_Pol II-total_ChIPSeq


title: 5788_NPC_Pol II-total_ChIPSeq

description: NPC_Pol II-total_ChIPSeq


title: RNA-seq alpha-amanitin 45h rep1

description: alpha_amanitin_experiments_RNAseq_FPKM.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Preimplantation embryo

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. PN3 zygotes were treated with 100ug/ml alpha-amanitin for 45h.

value: preimplantation embryo


title: RNA-seq invitro 8-cell rep1

value: C57BL/6N x PWK/PhJ


title: RNA-seq alpha-amanitin 20h rep1

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. PN3 zygotes were treated with 100ug/ml alpha-amanitin for 20h.


title: RNA-seq invitro late 2-cell rep1


title: primary_RHH1473


title: Hi-C cortex rep2

data_processing:
Library strategy: HiC-seq
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

extract_protocol: HiC libraries were prepared using sisHi-C similar with in situ Hi-C method developed by Rao et al.

treatment_protocol: Cortex was isolated from 4 week-old PWK/PhJ X C57BL/6N F1 mice.

value: Cortex


title: RNA-seq alpha-amanitin 45h rep2


title: 7007_NPC_Pol II-Ser5P_ChIPSeq

description: NPC_Pol II-Ser5P_ChIPSeq


title: Spi1_Hoxb8FL

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: fastq (unmapped reads)

data_processing:
Reads aligned to mm10 using Bowtie2.
bedGraphs created using bedtools.
bigWigs created using UCSC utilities.
Peaks called using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig: density profile of mapped reads.
Supplementary_files_format_and_content: bed: peaks

source_name: Multipotent haematopoietic progenitor, Spi1 ChIP

growth_protocol: Grown in RPMI 1640 with 10% fetal bovine serum, mercaptoethanol, estradiol, FLT3 and penicillin, streptomycin and glutamine.

extract_protocol:
HoxB8 cells were fixed with either 1% or 0.4% formaldehyde for 10 mins. Chromatin was isolated, sonicated for 7 mins (30 sec on, 30 sec off), and specific antibodies were used to pull down the transcription factors of interest after a pre-clearing step. Chromatin was washed, de-crosslinked, amplified, size selected by gel purification and sequenced.
As described in Wilson et al., Cell Stem Cell. 2010 Oct 8;7(4):532-44 (PMID 20887958).
Library construction: According to Illumina TruSeq DNA Sample Prep Kit.

tag: cell line

value: LMPP-like

tag: chip antibody

value: Spi1 (Santa Cruz, cat no. sc-352x, lot B0314)


title: Runx1_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Runx1 ChIP

value: Runx1 (Abcam, cat no. ab23980, lot GR37372-1)


title: Tal_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Tal1 ChIP

value: Tal1 (Santa Cruz, cat no. sc-12984x, lot B2511)


title: Meis1_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Meis1 ChIP

value: Meis1 (Santa Cruz, cat no. sc-10599x, lot D2310)


title: Lmo2_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Lmo2 ChIP

value: Lmo2 (R&D Systems, cat no. AF2726, lot VHX0110111)


title: IgG_R_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, IgG ChIP

value: IgG Rabbit


title: Gfi1b_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Gfi1b ChIP

value: Gfi1b (Santa Cruz, cat no. sc8559x, lot E1409)


title: Lyl1_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Lyl1 ChIP


title: Cebpa_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Cebpa ChIP

value: Cebpa (Santa Cruz, cat no. sc-61x, lot F2811)


title: Fli1_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Fli1 ChIP


title: Cebpb_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Cebpb ChIP

value: Cebpb (Santa Cruz, cat no. sc-150x, lot F0711)


title: Gfi1_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Gfi1 ChIP

value: Gfi1 (Abcam, cat no. ab21061, lot 151880)


title: Erg_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Erg ChIP

value: Erg (Santa Cruz, cat no. sc-354x, lot A2510)


title: RNA-seq alpha-amanitin 20h rep2


title: ChIP-seq from DOHH2 (ENCLB969TTG)

description:
https://www.encodeproject.org/experiments/ENCSR562NOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR562NOP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2017-01-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB969TTG
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens DOHH2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

tag: line

value: immortalized cell line

tag: description

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

tag: biosample encode accession

value: 60 year

tag: dev stage

value: adult

value: male

value: Bradley Bernstein, Broad

value: ENCBS652PBR at ENCODE; https://www.encodeproject.org/ENCBS652PBR/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from H1-hESC (ENCLB601IKH)

description:
https://www.encodeproject.org/experiments/ENCSR774YGM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR774YGM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB601IKH
size range: 300-800

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: embryonic

tag: Sex

tag: age

value: unknown

value: healthy

tag: lab

tag: link

value: ENCBS284CPV at ENCODE; https://www.encodeproject.org/ENCBS284CPV/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from H1-hESC (ENCLB126YGP)

description:
https://www.encodeproject.org/experiments/ENCSR418RRF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR418RRF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB126YGP
size range: 300-600

value: ENCBS364BFI at ENCODE; https://www.encodeproject.org/ENCBS364BFI/


title: ChIP-seq from H1-hESC (ENCLB693VHC)

description:
https://www.encodeproject.org/experiments/ENCSR418RRF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR418RRF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB693VHC
size range: 300-600


title: ChIP-seq from H1-hESC (ENCLB933RWS)

description:
https://www.encodeproject.org/experiments/ENCSR663WAR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR663WAR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB933RWS
size range: 300-1000

value: REST


title: CDM_3

source_name: biceps brachii

tag: strain

tag: tissue

value: biceps brachii

value: 5 months

value: congenital myotonic dystrophy


title: ChIP-seq from MCF-7 (ENCLB629WGA)

description:
https://www.encodeproject.org/experiments/ENCSR460YHB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR460YHB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR768LHG
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB629WGA
size range: 200-600
nucleic acid starting quantity: 633.6
nucleic acid starting quantity units: ng

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: adult

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: passage number

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: ChIP-seq from MCF-7 (ENCLB446QOT)

description:
https://www.encodeproject.org/experiments/ENCSR460YHB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR460YHB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR768LHG
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB446QOT
size range: 200-600
nucleic acid starting quantity: 3.614
nucleic acid starting quantity units: ng

value: Bradley Bernstein, Broad

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/


title: Gata2_Hoxb8FL

description: fastq (unmapped reads)

source_name: Multipotent haematopoietic progenitor, Gata2 ChIP

tag: cell type

value: LMPP-like

value: Gata2 (Santa Cruz, cat no. sc-9008x, lot I0109)


title: Hi-C cortex rep1

source_name: Cortex

value: C57BL/6N x PWK/PhJ

tag: developmental stage

value: Cortex


title: ChIP-seq from SK-N-MC (ENCLB841KOB)

description:
https://www.encodeproject.org/experiments/ENCSR526PZM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against H3K36me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR526PZM
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB841KOB
size range: 200-600

source_name: Homo sapiens SK-N-MC immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b4b48e6e-d14b-4359-96de-5e8c782c7bcf/@@download/attachment/TF_ChIP_Protocol_from_Shawn.pdf

tag: antibody

value: SK-N-MC

value: Please note:This cell line was previously described as a neuroepithelioma (ATCC HTB-10).  However recent evidence reveals it is Ewing's Sarcoma (http://www.ncbi.nlm.nih.gov/pubmed/15548687, http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903).

value: child

value: 14 year

value: Ewing's sarcoma

value: ENCBS556HGY at ENCODE; https://www.encodeproject.org/ENCBS556HGY/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/

value: ENCODE dbxrefs Cellosaurus CVCL_0530; http://web.expasy.org/cellosaurus/CVCL_0530


title: SMA_2

value: biceps brachii

value: 4 months

tag: genotype

value: spinal muscular atrophy, type 1


title: SMA_1


title: SMA_3


title: CDM_1

value: 15 months

value: congenital myotonic dystrophy


title: iPSC single cell 63

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Reads were trimmed of adapter sequences TCGTATGCCGTCTTCTGCTTG, ATCTCGTATGCCGTCTTCTGCTTG, CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC using cutadapt v1.8.1
Trimmed reads were aligned to RepBase v18.05 using STAR v2.4.01
Reads that didn't align to RepBase were aligned to hg19 using STAR v2.4.01 and a splice junction database derived from GENCODE v19
Transcripts per million (TPM) per transcript was calculated from reads that didn't align to RepBase were quasi-aligned to GENCODE v19 protein coding and lincRNA transcripts using Sailfish v0.6.3
TPM per gene was calculated by summing the TPM for all transcripts of a gene
Percent spliced-in (Psi) was calculated from junction read output from STAR aligner (SJ.out.tab) were used to create a de novo splicing index in conjunction with GENCODE v19 gene annotations, using outrigger
Outlier cells were calculated using K-means clustering with k=3 on the expression matrix and omitting cells which clustered into a group consisting of a majority of other cell types
Modality was calculated using anchor on the psi scores for all events detected in at least 10 cells, for each cell type
Waypoints were calculated using bonvoyage on the psi scores for all events detected in at least 10 cells, for each cell type
Splicing events were annotated using poshsplice to annotate corresponding genes, splice site strength using MaxEntScan, intron and exon lengths, conservation of alternative splicing from Merkin et al Science 2012,
Genes were annotated with attributes available in Gencode v19, Phylostrata for the matching ENSEMBL identifiers in Domazet-Loso et al MBE 2008, and TF or RBP category from Gerstberger et al Nat Rev Gen 2014
Genome_build: hg19
Supplementary_files_format_and_content: "metadata.csv.gz" contains sample metadata, "splicing.csv.gz" contains Psi scores, "splicing_feature.csv.gz" contains metadata for splicing events, "expression.csv.gz" contains TPM values for genes, "expression_feature.csv.gz" contains metadata for genes, "mapping_stats.csv.gz" contains the number and percentages of reads mapped for each samples

source_name: Induced pluripotent cells

growth_protocol: iPSCs were cultured on matrigel coated plated using mTeSR(Stem Cell Technologies) media with mTeSR supplement at 37C incubator with 5% CO2.

extract_protocol:
Motor neurons were directly differentiated from iPSCs as previous described (Chambers S, Nature Biotechnology, 2009). Briefly, iPSCs were cultured on matrigel coated plates until fully confluent in mTeSR then switch to knock-out serum replacement media (KSR) containing Dorsomorphin(1uM) and SB431542(10uM). Upon day 4 of differentiation, increasing amounts of N2 media (25%, 50%) was added to the KSR. From day 7 of differentiation, 1.5uM retinoic acid and 200nM Smoothened Agonist (SAG, EMD Millipore) were added to induce patterning. Cells were dissociated on day 17 of differentiation and replated in poly-D-lysine and laminin coated plates. Maturation was performed using BDGF(2ng/ml), GDNF(2ng/ml), CNTF(2ng/ml), ascorbid acid, sonic hedgehog and retinoic acid in N2 and B27 media up until 35 days of differentiation.
Single cells were captured on C1 auto prep platform (Fluidigm, CA) according to manufacturer's instructions. C1 auto prep chips were visually inspected with a light microscopy at 20X to ensure singularity of captured cells. All non-single cells were discarded from analysis. SMARTer Ultra Low RNA cDNA Synthesis Kit (Clontech) was used to reverse transcribe polyA-tailed RNA. cDNA was amplified using Advantage 2 Polumerase Mix by PCR at 95¡C for 1 minutes, followed by 21 cylcles of 15 secondes at 95¡C, 30 seconds at 65¡C and 6 minutes at 68¡C, followed by another 10 minutes at 72¡C as a final extension. cDNAs were inspected using Agilent Bioanalyzer High Sensitivity DNA chips and quantitated by PicoGreen dsDNA Assay kit (ThermoFisher). cDNAs were diluted to 1ng to generate libraries using the Nextera XT DNA kit(Illumina, CA).  Libraries were multiplexed and sequenced on Illumina HiSeq200 to generate 100bp PE reads.

treatment_protocol: Neuron progenitor cells were differentiated from iPSCs. Briefly, iPSCs were cultured in Matrigel coated plates and dislodged by dispase. To form embryonic bodies, the dislodged colonies were cultured in DMEM/F12(invitrogen) with GlutaMax and N2 supplement in non-adhere petri dish. Media were replaced every other day for 7 days. EBs were then placed onto matrigel coated plate to allow rosette formation. Clean rosette were picked manually and maintained in EB media for 7 days and subsequently dissociated with accutase and cultured in NPC media (DMEM/F12, GlutaMax, N2 and B27 with 2ug/ml FGF) to allow neuron progenitor cell differentiation. NPCs were maintained in NPC media.

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

tag: gender

value: male

tag: sample type

value: Single Cell


title: iPSC single cell 62


title: ChIP-seq from PC-3 (ENCLB969DEQ)

description:
https://www.encodeproject.org/experiments/ENCSR695SCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR695SCQ
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR328AHC
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB969DEQ
size range: 300-600
nucleic acid starting quantity: 11.39
nucleic acid starting quantity units: ng
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol: extraction method: see document

tag: line

value: immortalized cell line

tag: description

value: prostate cancer cell line

value: adult

value: 62 year

value: grade IV, adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: iPSC single cell 60


title: iPSC single cell 58

tag: split library pair


title: iPSC single cell 57


title: iPSC single cell 56


title: iPSC single cell 59


title: iPSC single cell 55


title: iPSC single cell 53


title: iPSC single cell 54


title: BPH89BE

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description:
Basal Epithelia from Tissue without Basal Cell Hyperplasia
089B

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling followed by bcl2fastq2 version 2.17.1.14 to generate fastq files.
Reads were trimmed using Trimmomatic version 0.32.
Reads were mapped to GRCh37 using TopHat version 2.1.12, with Bowtie2 version 2.2.3).
Mapped reads were filtered using SAMtools version 0.1.19 to remove those with a quality score MAPQ less than 10.
Quality-filtered mapped reads were quantified using Cufflinks' (version 2.2.1) CuffQuant and CuffNorm to generate FPKM.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: Human prostate basal epithelia

extract_protocol:
Total RNA from 500K FACS-purified basal cells was extracted using RNEasy micro columns (Qiagen). RNA quality and quantity were measured by a Bioanalyzer and NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fresh surgical tissue samples were transported in ice-cold saline and immediately processed for an overnight enzymatic digestion into single cells at 37ºC. Single cells were flow sorted to isolate basal epithelia (CD326+/CD49fHI/CD26-).

tag: phenotype

value: non-BCH

tag: facs ab profile


title: BPH85BE

description:
Basal Epithelia from Tissue without Basal Cell Hyperplasia
085B


title: iPSC single cell 52


title: CDM_2

value: biceps brachii

tag: age

value: 3 months


title: ChIP-seq from H1-hESC (ENCLB717OWZ)

description:
https://www.encodeproject.org/experiments/ENCSR267YDT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267YDT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB717OWZ
size range: 300-800

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/97a73f1c-6372-4dd2-b275-0b8e855cbd5a/@@download/attachment/Cell_Paper_ChIP_protocol.pdf

value: stem cell

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: unknown

value: healthy

tag: lab

tag: link

value: ENCBS284CPV at ENCODE; https://www.encodeproject.org/ENCBS284CPV/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: BPH114BE

description:
Basal Epithelia from Tissue without Basal Cell Hyperplasia
114B


title: iPSC single cell 51

tag: cell type

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male

value: Single Cell


title: BPH110BE

description:
Basal Epithelia from Tissue with Basal Cell Hyperplasia
110B

value: BCH


title: BPH117BE

description:
Basal Epithelia from Tissue with Basal Cell Hyperplasia
117B


title: iPSC single cell 50


title: ChIP-seq from HCT116 (ENCLB197PCN)

description:
https://www.encodeproject.org/experiments/ENCSR494CCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494CCN
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197PCN
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

value: immortalized cell line

value: cells obtained from ATCC

tag: health state

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: iPSC single cell 49


title: iPSC single cell 61


title: iPSC single cell 48


title: iPSC single cell 46


title: BCOT_input_br2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Arabidopsis genome (TAIR10) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.19).
Peaks were identified using the PeakSeq algorithm of CisGenome (v2.0), using default parameters except min peak length=50.
Genome_build: TAIR10
Supplementary_files_format_and_content: peak coordinates (chr, start, end) are in the standard bed format, quantitative data (log2FC).

organism: Arabidopsis thaliana

source_name: bent cotyledon-stage seeds

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the seeds were ground in cold EB1 buffer using a glass tissue grinder (Kontes), the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of the anti-GFP (Neuromab 75-131) antibodies.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Bent cotyledon-stage seeds were harvested from Arabidopsis plants carrying the LEC1:LEC1-GFP:LEC1 transgene.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: lec1-1 LEC1:LEC1-GFP:LEC1

tag: tissue

value: bent cotyledon stage seeds

tag: antibody


title: BCOT_input_br1

tag: genotype


title: iPSC single cell 45

tag: gender

tag: sample type


title: iPSC single cell 44


title: BCOT_chip_br1

value: anti-GFP (Neuromab, catalog# 75-131, lot# 455-1JD-56)


title: iPSC single cell 41


title: BPH118BE

description:
Basal Epithelia from Tissue without Basal Cell Hyperplasia
118B

value: non-BCH


title: iPSC single cell 42


title: BCOT_chip_br2


title: iPSC single cell 40


title: ChIP-seq from A673 (ENCLB694WYI)

description:
https://www.encodeproject.org/experiments/ENCSR435FGK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR435FGK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR196CXJ
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB694WYI
size range: 200-600
nucleic acid starting quantity: 0.437
nucleic acid starting quantity units: ng

source_name: Homo sapiens A673 immortalized cell line

tag: line

tag: description

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: female

value: 15 year

value: ENCBS385OLC at ENCODE; https://www.encodeproject.org/ENCBS385OLC/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: iPSC single cell 39

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male

value: Single Cell


title: ChIP-seq from A549 (ENCLB576KOQ)

description:
https://www.encodeproject.org/experiments/ENCSR798EGJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR798EGJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576KOQ
size range: 200-600
nucleic acid starting quantity: 1.52
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

value: immortalized cell line

value: adult

tag: passage number

value: Bradley Bernstein, Broad

value: 58 year

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from A549 (ENCLB795RFC)

description:
https://www.encodeproject.org/experiments/ENCSR798EGJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR798EGJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB795RFC
size range: 200-600
nucleic acid starting quantity: 26.8
nucleic acid starting quantity units: ng

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/


title: BPH132INBE

description:
Basal Epithelia from Tissue with Basal Cell Hyperplasia
132INB

tag: phenotype

value: BCH

tag: facs ab profile


title: iPSC single cell 37


title: iPSC single cell 47


title: iPSC single cell 38


title: ChIP-seq from A549 (ENCLB165ISA)

description:
https://www.encodeproject.org/experiments/ENCSR787VQB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR787VQB
assay title: ChIP-seq
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB165ISA
size range: 200-600

value: Control

tag: biosample encode accession

tag: age


title: iPSC single cell 35


title: ChIP-seq from transverse colon (ENCLB814FIR)

description:
https://www.encodeproject.org/experiments/ENCSR791LZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR791LZY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2017-01-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB814FIR
size range: 200-600

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

tag: dev stage

value: 53 year

tag: Sex

value: female

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from A549 (ENCLB973LVG)

description:
https://www.encodeproject.org/experiments/ENCSR787VQB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR787VQB
assay title: ChIP-seq
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB973LVG
size range: 200-600

value: immortalized cell line

tag: lab

value: male

tag: link


title: ChIP-seq from A549 (ENCLB039UAN)

description:
https://www.encodeproject.org/experiments/ENCSR787VQB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR787VQB
assay title: ChIP-seq
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039UAN
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: iPSC single cell 33

tag: cell type

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: Single Cell


title: iPSC single cell 32


title: iPSC single cell 34


title: ChIP-seq from neutrophil (ENCLB659FNH)

description:
https://www.encodeproject.org/experiments/ENCSR785YRL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR785YRL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR557RDB
encode release date: 2016-12-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB659FNH
size range: 200-600

source_name: Homo sapiens neutrophil primary cell

value: CTCF

value: neutrophil

value: primary cell

value: Neutrophils were isolated by centrifuging heparinized venous blood over Histopaque 1119 (Sigma-Aldrich) and subsequently over a discontinuous Percoll (Amersham Biosciences) gradient.  Cells provided by Max Planck Institute for Infection Biology, Berlin

value: unknown

value: not collected

value: ENCBS462VZJ at ENCODE; https://www.encodeproject.org/ENCBS462VZJ/

value: Derived from ENCODE donor ENCDO055UKA; https://www.encodeproject.org/ENCDO055UKA/


title: iPSC single cell 43


title: iPSC single cell 29


title: iPSC single cell 30


title: iPSC single cell 31


title: ChIP-seq from neutrophil (ENCLB994JYV)

description:
https://www.encodeproject.org/experiments/ENCSR785YRL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR785YRL
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR557RDB
encode release date: 2016-12-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB994JYV
size range: 200-600

value: ENCBS360EQL at ENCODE; https://www.encodeproject.org/ENCBS360EQL/


title: ChIP-seq from H1-hESC (ENCLB206FBF)

description:
https://www.encodeproject.org/experiments/ENCSR774YGM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR774YGM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB206FBF
size range: 200-600
nucleic acid starting quantity: 19.94
nucleic acid starting quantity units: ng

value: stem cell

value: embryonic

tag: health state

value: healthy

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: iPSC single cell 28

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male


title: ChIP-seq from gastrocnemius medialis (ENCLB797RDW)

description:
https://www.encodeproject.org/experiments/ENCSR785DJD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR785DJD
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001UFN
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB797RDW
size range: 200-600

source_name: Homo sapiens gastrocnemius medialis tissue female adult (53 years)

tag: antibody

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: adult

value: female

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS866HOM at ENCODE; https://www.encodeproject.org/ENCBS866HOM/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from body of pancreas (ENCLB672ZYK)

description:
https://www.encodeproject.org/experiments/ENCSR774CFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR774CFO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR099LGH
encode release date: 2016-07-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB672ZYK
size range: 200-600

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: body of pancreas

value: 54 year

value: ENCBS209WBW at ENCODE; https://www.encodeproject.org/ENCBS209WBW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: iPSC single cell 27

value: Single Cell


title: ChIP-seq from gastrocnemius medialis (ENCLB566MIR)

description:
https://www.encodeproject.org/experiments/ENCSR776EAH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR776EAH
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR001UFN
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB566MIR
size range: 200-600


title: ChIP-seq from right atrium auricular region (ENCLB341CVJ)

description:
https://www.encodeproject.org/experiments/ENCSR793PLF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793PLF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR195BZZ
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB341CVJ
size range: 200-600

source_name: Homo sapiens right atrium auricular region tissue female adult (53 years)

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/


title: iPSC single cell 24

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male


title: iPSC single cell 26


title: iPSC single cell 25


title: ChIP-seq from GM12878 (ENCLB735HPS)

description:
https://www.encodeproject.org/experiments/ENCSR751CJG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR751CJG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB735HPS
size range: 200-600
nucleic acid starting quantity: 30.6
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: unknown

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: ChIP-seq from GM12878 (ENCLB249IUE)

description:
https://www.encodeproject.org/experiments/ENCSR751CJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR751CJG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249IUE
size range: 200-600
nucleic acid starting quantity: 18.4
nucleic acid starting quantity units: ng

value: adult

value: female

value: Bradley Bernstein, Broad

value: ENCBS330WEW at ENCODE; https://www.encodeproject.org/ENCBS330WEW/


title: ChIP-seq from thyroid gland (ENCLB229WTB)

description:
https://www.encodeproject.org/experiments/ENCSR761WVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR761WVQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR475NOQ
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB229WTB
size range: 200-600

source_name: Homo sapiens thyroid gland tissue female adult (53 years)

value: thyroid gland

value: tissue

value: 53 year

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: iPSC single cell 20

value: Single Cell


title: iPSC single cell 36

tag: split library pair


title: ChIP-seq from right atrium auricular region (ENCLB089NUE)

description:
https://www.encodeproject.org/experiments/ENCSR791KFQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR791KFQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR195BZZ
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089NUE
size range: 200-600

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/


title: iPSC single cell 23

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

tag: gender

value: male


title: iPSC single cell 22

tag: sample type


title: iPSC single cell 18


title: ChIP-seq from breast epithelium (ENCLB045LGY)

description:
https://www.encodeproject.org/experiments/ENCSR770WSE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR770WSE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR247XFQ
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB045LGY
size range: 200-600

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue

value: ENCBS433LAO at ENCODE; https://www.encodeproject.org/ENCBS433LAO/


title: iPSC single cell 21


title: iPSC single cell 15


title: ChIP-seq from body of pancreas (ENCLB264NMN)

description:
https://www.encodeproject.org/experiments/ENCSR748TFF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR748TFF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR833HBT
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB264NMN
size range: 200-600

source_name: Homo sapiens body of pancreas tissue female adult (53 years)

value: body of pancreas

value: adult

value: female

value: ENCBS359OQR at ENCODE; https://www.encodeproject.org/ENCBS359OQR/


title: iPSC single cell 19


title: iPSC single cell 16


title: iPSC single cell 14


title: ChIP-seq from A549 (ENCLB634MKD)

description:
https://www.encodeproject.org/experiments/ENCSR740DXC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR740DXC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB634MKD
size range: 200-600
nucleic acid starting quantity: 80
nucleic acid starting quantity units: ng

tag: line

value: immortalized cell line

value: Bradley Bernstein, Broad

value: 58 year

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from ACC112 (ENCLB465BUD)

description:
https://www.encodeproject.org/experiments/ENCSR741GJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR741GJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR836XKP
encode release date: 2016-10-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB465BUD
size range: 200-600

source_name: Homo sapiens ACC112 immortalized cell line

tag: description

value: adenoid cystic carcinoma cell line supplied by Lurdes Queimado, M.D., Ph.D.Phone:405-271-4232 (office); 405-271-4279 (lab); cells immortalized by infection with a retrovirus expressing HPV16 E6 and E7

value: 70 year

value: submaxillar tumor

value: ENCBS827JIC at ENCODE; https://www.encodeproject.org/ENCBS827JIC/

value: Derived from ENCODE donor ENCDO085ZKK; https://www.encodeproject.org/ENCDO085ZKK/

value: ENCODE dbxrefs Cellosaurus CVCL_Y492; http://web.expasy.org/cellosaurus/CVCL_Y492


title: ChIP-seq from A549 (ENCLB845IDR)

description:
https://www.encodeproject.org/experiments/ENCSR740DXC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR740DXC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB845IDR
size range: 200-600
nucleic acid starting quantity: 82.6
nucleic acid starting quantity units: ng

tag: passage number

value: male

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/


title: iPSC single cell 17

source_name: Induced pluripotent cells

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: Single Cell


title: ChIP-seq from K562 (ENCLB653ZRV)

description:
https://www.encodeproject.org/experiments/ENCSR735JCD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR735JCD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AKY
encode release date: 2017-01-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB653ZRV
size range: 200-600
nucleic acid starting quantity: 0.22
nucleic acid starting quantity units: ng

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: female

value: ENCBS984VNR at ENCODE; https://www.encodeproject.org/ENCBS984VNR/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from esophagus muscularis mucosa (ENCLB919IPT)

description:
https://www.encodeproject.org/experiments/ENCSR743KZR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR743KZR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR474WLZ
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919IPT
size range: 200-600

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

value: esophagus muscularis mucosa

value: tissue

value: EnTEX:Esophagus - Muscularis

value: Bradley Bernstein, Broad

value: ENCBS071FUE at ENCODE; https://www.encodeproject.org/ENCBS071FUE/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from ascending aorta (ENCLB900MRP)

description:
https://www.encodeproject.org/experiments/ENCSR736PKV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR736PKV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR494YJW
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB900MRP
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (51 year)

value: ascending aorta

value: EnTEX:Artery- Aorta

value: 51 year

value: ENCBS273PSC at ENCODE; https://www.encodeproject.org/ENCBS273PSC/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: iPSC single cell 13

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male

value: Single Cell


title: ChIP-seq from K562 (ENCLB541ZLR)

description:
https://www.encodeproject.org/experiments/ENCSR735JCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR735JCD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AKY
encode release date: 2017-01-31
lab: Bradley Bernstein, Broad
library encode accession: ENCLB541ZLR
size range: 200-600
nucleic acid starting quantity: 7.482
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS979ZKW at ENCODE; https://www.encodeproject.org/ENCBS979ZKW/


title: ChIP-seq from tibial nerve (ENCLB983BAB)

description:
https://www.encodeproject.org/experiments/ENCSR771YJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR771YJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR154SJE
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB983BAB
size range: 200-600

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

value: tibial nerve

value: tissue

value: EnTEX:Nerve - Tibial

value: Bradley Bernstein, Broad

value: ENCBS248LIK at ENCODE; https://www.encodeproject.org/ENCBS248LIK/


title: ChIP-seq from ACC112 (ENCLB663RSK)

description:
https://www.encodeproject.org/experiments/ENCSR726ZZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR726ZZX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR836XKP
encode release date: 2016-10-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB663RSK
size range: 200-600

value: adenoid cystic carcinoma cell line supplied by Lurdes Queimado, M.D., Ph.D.Phone:405-271-4232 (office); 405-271-4279 (lab); cells immortalized by infection with a retrovirus expressing HPV16 E6 and E7

value: 70 year

value: submaxillar tumor

value: ENCBS827JIC at ENCODE; https://www.encodeproject.org/ENCBS827JIC/

value: Derived from ENCODE donor ENCDO085ZKK; https://www.encodeproject.org/ENCDO085ZKK/

value: ENCODE dbxrefs Cellosaurus CVCL_Y492; http://web.expasy.org/cellosaurus/CVCL_Y492


title: ChIP-seq from upper lobe of left lung (ENCLB929TAJ)

description:
https://www.encodeproject.org/experiments/ENCSR738SXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR738SXD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2016-11-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB929TAJ
size range: 200-600

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

value: upper lobe of left lung

value: ENCBS684YJH at ENCODE; https://www.encodeproject.org/ENCBS684YJH/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from spleen (ENCLB603CIJ)

description:
https://www.encodeproject.org/experiments/ENCSR726HTS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR726HTS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB603CIJ
size range: 200-600

source_name: Homo sapiens spleen tissue female adult (53 years)

value: spleen

value: adult

value: 53 year

value: female

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/


title: iPSC single cell 9

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male

value: Single Cell


title: iPSC single cell 11


title: iPSC single cell 8


title: iPSC single cell 6


title: iPSC single cell 7


title: iPSC single cell 10


title: ChIP-seq from thyroid gland (ENCLB527LRM)

description:
https://www.encodeproject.org/experiments/ENCSR699FHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR699FHH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB527LRM
size range: 200-600
nucleic acid starting quantity: 224
nucleic acid starting quantity units: ng

source_name: Homo sapiens thyroid gland tissue male adult (54 years)

value: thyroid gland

value: tissue

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS050AKF at ENCODE; https://www.encodeproject.org/ENCBS050AKF/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: ChIP-seq from ascending aorta (ENCLB035VIQ)

description:
https://www.encodeproject.org/experiments/ENCSR707AEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR707AEW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007WYC
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB035VIQ
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (53 years)

value: ascending aorta

value: EnTEX:Artery- Aorta

value: ENCBS801NKM at ENCODE; https://www.encodeproject.org/ENCBS801NKM/


title: iPSC single cell 5


title: iPSC single cell 4


title: ChIP-seq from thyroid gland (ENCLB838IRP)

description:
https://www.encodeproject.org/experiments/ENCSR716FUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR716FUH
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR475NOQ
encode release date: 2016-11-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB838IRP
size range: 200-600

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: iPSC single cell 3


title: iPSC single cell 2


title: ChIP-seq from sigmoid colon (ENCLB288ISF)

description:
https://www.encodeproject.org/experiments/ENCSR682GOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR682GOI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR844YME
encode release date: 2017-01-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB288ISF
size range: 200-600

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: adult

value: 53 year

value: ENCBS555KUV at ENCODE; https://www.encodeproject.org/ENCBS555KUV/


title: iPSC single cell 12

value: Skin fibroblast-derived induced pluripotent cells (iPSCs)

value: male

value: Single Cell


title: iPSC single cell 1


title: ChIP-seq from gastroesophageal sphincter (ENCLB927ZZP)

description:
https://www.encodeproject.org/experiments/ENCSR677LBH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR677LBH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178MWD
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927ZZP
size range: 200-600

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (53 years)

value: gastroesophageal sphincter

value: tissue

value: EnTEX:Esophagus - Gastroesophageal Junction

value: female

value: ENCBS783BYN at ENCODE; https://www.encodeproject.org/ENCBS783BYN/


title: NPC single cell 73

source_name: Neural progenitor cells

value: iPSC-derived neural progenitor cells


title: ChIP-seq from body of pancreas (ENCLB684KTL)

description:
https://www.encodeproject.org/experiments/ENCSR719COF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR719COF
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR833HBT
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB684KTL
size range: 200-600

value: body of pancreas

value: Bradley Bernstein, Broad

value: ENCBS359OQR at ENCODE; https://www.encodeproject.org/ENCBS359OQR/


title: ChIP-seq from H1-hESC (ENCLB706HVA)

description:
https://www.encodeproject.org/experiments/ENCSR663WAR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR663WAR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR000AMI
encode release date: 2017-01-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB706HVA
size range: 200-600

source_name: Homo sapiens H1-hESC stem cell male embryo

value: REST

value: stem cell

value: embryonic

value: unknown

value: healthy

value: ENCBS952IPA at ENCODE; https://www.encodeproject.org/ENCBS952IPA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from PC-3 (ENCLB701YDY)

description:
https://www.encodeproject.org/experiments/ENCSR695SCQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR695SCQ
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR328AHC
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB701YDY
size range: 300-600
nucleic acid starting quantity: 30.226
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

value: immortalized cell line

value: prostate cancer cell line

value: adult

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: NPC single cell 72

value: iPSC-derived neural progenitor cells

value: Single Cell


title: ChIP-seq from neuroepithelial stem cell (ENCLB200JGZ)

description:
https://www.encodeproject.org/experiments/ENCSR662PLB/
***************
biological replicate number: 3
technical replicate number: 3
description:
experiment encode accession: ENCSR662PLB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR803UDX
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200JGZ
size range: 200-600

source_name: Homo sapiens neuroepithelial stem in vitro differentiated cells female embryo (5 days) derived from H9 stably expressing C-terminal eGFP-HES5 fusion protein

value: neuroepithelial stem cell

value: in vitro differentiated cells

value: Neuroepithelial cells were collected at day 12 of differentiation (see protocol)

value: embryonic

value: female

value: 5 day

value: Bradley Bernstein, Broad

value: ENCBS435FHS at ENCODE; https://www.encodeproject.org/ENCBS435FHS/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: NPC single cell 71

value: male


title: ChIP-seq from neuroepithelial stem cell (ENCLB445WPO)

description:
https://www.encodeproject.org/experiments/ENCSR662PLB/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR662PLB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR803UDX
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB445WPO
size range: 200-600

value: healthy

value: ENCBS562NPI at ENCODE; https://www.encodeproject.org/ENCBS562NPI/


title: NPC single cell 70


title: NPC single cell 69


title: ChIP-seq from fibroblast of arm (ENCLB288UHO)

description:
https://www.encodeproject.org/experiments/ENCSR673OPX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR673OPX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR922FLS
encode release date: 2017-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB288UHO
size range: 200-600
nucleic acid starting quantity: 837.5
nucleic acid starting quantity units: ng

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: ChIP-seq from ascending aorta (ENCLB171AZH)

description:
https://www.encodeproject.org/experiments/ENCSR723IKM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR723IKM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR007WYC
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB171AZH
size range: 200-600

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: female

value: ENCBS801NKM at ENCODE; https://www.encodeproject.org/ENCBS801NKM/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: NPC single cell 68

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: ChIP-seq from A549 (ENCLB157FBK)

description:
https://www.encodeproject.org/experiments/ENCSR659LJJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR659LJJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB157FBK
size range: 200-600
nucleic acid starting quantity: 10.82
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 immortalized cell line

value: immortalized cell line

value: Bradley Bernstein, Broad

value: 58 year

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: NPC pooled 3

value: Pooled


title: ChIP-seq from A549 (ENCLB556KTF)

description:
https://www.encodeproject.org/experiments/ENCSR659LJJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR659LJJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB556KTF
size range: 200-600
nucleic acid starting quantity: 26
nucleic acid starting quantity units: ng

value: adult

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/


title: ChIP-seq from spleen (ENCLB747JAN)

description:
https://www.encodeproject.org/experiments/ENCSR659RJP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR659RJP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB747JAN
size range: 200-600

value: spleen

value: tissue

value: 53 year

value: ENCBS913XPU at ENCODE; https://www.encodeproject.org/ENCBS913XPU/


title: NPC single cell 67


title: ChIP-seq from neural progenitor cell (ENCLB940SYA)

description:
https://www.encodeproject.org/experiments/ENCSR656MXA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR656MXA
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR603SVD
encode release date: 2017-02-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB940SYA
size range: 200-600

source_name: Homo sapiens neural progenitor in vitro differentiated cells female embryo (5 days) derived from H9

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: NPC single cell 66

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: NPC single cell 65


title: NPC single cell 64


title: NPC single cell 63


title: ChIP-seq from neural progenitor cell (ENCLB061HLX)

description:
https://www.encodeproject.org/experiments/ENCSR656MXA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR656MXA
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR603SVD
encode release date: 2017-02-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB061HLX
size range: 200-600
nucleic acid starting quantity: 10.824
nucleic acid starting quantity units: ng

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/


title: ChIP-seq from GM12878 (ENCLB148PNW)

description:
https://www.encodeproject.org/experiments/ENCSR649WUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR649WUM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB148PNW
size range: 200-600
nucleic acid starting quantity: 45.4
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: adult

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS900QPF at ENCODE; https://www.encodeproject.org/ENCBS900QPF/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: ChIP-seq from GM12878 (ENCLB537JDJ)

description:
https://www.encodeproject.org/experiments/ENCSR649WUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR649WUM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB537JDJ
size range: 200-600
nucleic acid starting quantity: 25.4
nucleic acid starting quantity units: ng

value: ENCBS330WEW at ENCODE; https://www.encodeproject.org/ENCBS330WEW/


title: NPC single cell 62


title: NPC single cell 61


title: ChIP-seq from A549 (ENCLB719JOV)

description:
https://www.encodeproject.org/experiments/ENCSR639GWS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR639GWS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB719JOV
size range: 200-600
nucleic acid starting quantity: 13.2
nucleic acid starting quantity units: ng

value: 58 year

value: ENCBS998UBJ at ENCODE; https://www.encodeproject.org/ENCBS998UBJ/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from Peyer's patch (ENCLB737BHF)

description:
https://www.encodeproject.org/experiments/ENCSR621BZD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR621BZD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR124GAS
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB737BHF
size range: 200-600

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

value: Peyer's patch

value: tissue

value: EnTEX:Small Intestine - Terminal Ileum

value: female

value: 53 year

value: ENCBS766ILR at ENCODE; https://www.encodeproject.org/ENCBS766ILR/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: ChIP-seq from Peyer's patch (ENCLB235MQE)

description:
https://www.encodeproject.org/experiments/ENCSR621BZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR621BZD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR124GAS
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB235MQE
size range: 200-600

value: adult


title: ChIP-seq from ascending aorta (ENCLB751UIO)

description:
https://www.encodeproject.org/experiments/ENCSR645FBM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR645FBM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR494YJW
encode release date: 2017-06-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB751UIO
size range: 200-600

source_name: Homo sapiens ascending aorta tissue female adult (51 year)

value: ascending aorta

value: EnTEX:Artery- Aorta

value: 51 year

value: ENCBS273PSC at ENCODE; https://www.encodeproject.org/ENCBS273PSC/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: NPC single cell 60

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: NPC single cell 59


title: ChIP-seq from A549 (ENCLB017ZHO)

description:
https://www.encodeproject.org/experiments/ENCSR639GWS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639GWS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB017ZHO
size range: 200-600
nucleic acid starting quantity: 2.08
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Bradley Bernstein, Broad

value: 58 year

value: ENCBS117POP at ENCODE; https://www.encodeproject.org/ENCBS117POP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023


title: ChIP-seq from thyroid gland (ENCLB638RCU)

description:
https://www.encodeproject.org/experiments/ENCSR658VPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR658VPF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR475NOQ
encode release date: 2016-11-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB638RCU
size range: 200-600

source_name: Homo sapiens thyroid gland tissue female adult (53 years)

value: thyroid gland

value: tissue

value: 53 year

value: female

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/


title: NPC single cell 58


title: ChIP-seq from A549 (ENCLB826RGQ)

description:
https://www.encodeproject.org/experiments/ENCSR616MOB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR616MOB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR787VQB
encode release date: 2016-11-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB826RGQ
size range: 200-600
nucleic acid starting quantity: 5.98
nucleic acid starting quantity units: ng

value: adult


title: microRNA-seq from midbrain (ENCLB231NMV)

description:
https://www.encodeproject.org/experiments/ENCSR625ESQ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR625ESQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB231NMV
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (16.5 days)

value: midbrain

value: Midbrain from 37 embryonic 16.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS463JSE at ENCODE; https://www.encodeproject.org/ENCBS463JSE/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: NPC single cell 57

value: iPSC-derived neural progenitor cells

value: male

value: Single Cell


title: NPC single cell 56


title: ChIP-seq from adrenal gland (ENCLB521JWR)

description:
https://www.encodeproject.org/experiments/ENCSR620TXL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR620TXL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR754WVA
encode release date: 2016-08-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB521JWR
size range: 200-600
nucleic acid starting quantity: 392.5
nucleic acid starting quantity units: ng

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

value: adrenal gland

value: EnTEX:Adrenal Gland

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS232HQQ at ENCODE; https://www.encodeproject.org/ENCBS232HQQ/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: microRNA-seq from hindbrain (ENCLB736TOV)

description:
https://www.encodeproject.org/experiments/ENCSR571RHM/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR571RHM
assay title: microRNA-seq
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB736TOV
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (16.5 days)

value: hindbrain

value: tissue

value: Hindbrain from 37 embryonic 16.5 day mice

value: ENCBS281ZLI at ENCODE; https://www.encodeproject.org/ENCBS281ZLI/