title: 561NT

description:
561NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 552NT

status: Public on Mar 31 2012

type: SRA

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park Ave

department: Pulmonary Medicine

country: USA

institute: Albert Einstein College of Medicine

description:
552NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

library_source: transcriptomic

data_processing: The microRNA analytical pipeline identifies microRNA sequences through adaptor removal, genomic alignment, and comparison with the miRBase database. The algorithm works as follows. First, the 3' Illumina adaptor is stripped off. Then, sequences ranging from 17 - 27 bases (the size of mature microRNAs) are aligned to genomic and RefSeq libraries (hg19) using Bowtie. Sequences that align to annotated regions of the genome are compared with known microRNAs in miRBase 16. A hit is defined as an aligned sequence that overlaps at least 50% with coordinates of a miRBase-defined microRNA.

molecule: total RNA

organism: Homo sapiens

source_name: Lung tissue

extract_protocol:
Total RNA isolation from tissue samples; 50mg of snap frozen lung tissue was added to a tube containing 1 ml of ice cold trizol and homogenized until tissue was totally homogenized. After incubation for 5 min at room temperature, 0.2 ml of chloroform was added; tube was shaked vigorously by hand for 15 sec and then incubated for 3 min at room temperature. Then samples were centrifuged for 20 min at 12000g at 4C. Aqueous phase was transfered to a clean 1.5-ml tube and 0.5 ml of isopropyl alcohol was added into the aqueous phase. Incubate the samples at room temperature for 10 min and centrifuge for 20 min at 12000g at 4C. Remove the supernatant and wash the RNA pellet with 75% ethanol. Air-dry the pellet and dissolve it in 20 ul of RNase-free water. Use nanodrop to measure RNA concentration and use agilent 2100 bioanalyzer to check RNA quality.
Libraries were prepared according to Illumina's instructions accompanying Small RNA Sample Prep Kit (CAT#:FC-102-1009).Briefly, ligate 3' RNA adapter to 3'-end of small RNA and ligate 3' RNA adapter to 3'-end of small RNA. Then perform RT-PCR amplification and gel-purify the small RNA library.

tag: tissue (t=tumor, nt=non-tumor)

value: NT

tag: phenotype (sq=squamous lung cancer, ad=adenocarcinoma lung cancer)

value: benign


title: 581T

description:
581T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

value: T

value: Sq


title: 561T

description:
561T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 541NT

description:
541NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 558T

description:
558T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

value: Ad


title: 543NT

description:
543NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 541T

description:
541T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 304NT

description:
304NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 534NT

description:
534NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 325T

description:
325T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 159NT

description:
159NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: Foxtail millet spica

city: Shenzhen

first: Zhijun

last: Zheng

address: #11 Building 2/F│Beishan Industrial Zone│Yantian District

country: China

institute: BGI

description: Sequenced reads were generated from millet tassel

data_processing:
Align reads against millet genome using Tophat v1.2.0 with parameters set to be "--max-intron-length 20000 -m 1 -r 20 --mate-std-dev 20  --coverage-search --microexon-search". This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AGTC00000000.
Genome_build: AGTC01000000

organism: Setaria italica

source_name: spica (tassel)

growth_protocol: seeding on nutrient medium, grew in greenhouse for 40days

extract_protocol: total RNA extraction protocol and standard 200bp library protocol provided by Illumina

tag: landrace

value: Zhang-gu

tag: developmental stage

value: adult

tag: tissue

value: tassel


title: 159T

description:
159T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: Foxtail millet leaf

description: Sequenced reads were generated from millet leaf

source_name: leaf

value: leaf


title: 304T

description:
304T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: 581NT

description:
581NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: small RNA from lung tissue in Mouse Strain Cast infected with SARS

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
For the global classification, the trimmed reads were aligned sequentially to mouse ribosomal sequences (rRNA) from GenBank, tRNA sequences (tRNA) from the genome browser of the University of California, Santa Cruz (UCSC), (http://genome.ucsc.edu), small cytoplasmic RNA (scRNA), small nuclear RNA (snRNA), and small nucleolar RNAs (snoRNA) sequences from NCBI RefSeq annotation, piwiassociated small RNA (piRNA) sequences from the functional RNA database (44), microRNA (miRNA) precursor sequences from miRBase (http://www.mirbase.org, release 16), the mouse reference genome (mm9, July 2007, NCBI build 37, reference strain C57BL/6J), and SARSCoV (GenBank accession no. DQ497008) or influenza virus (GenBank accession no. AF389115 to AF389122) genomic sequences.
mature.rpm.txt: data matrix with rows are mature microRNAs and columns are samples. Only miRNAs with at least one non-zero value are kept in the matrix. The identifiers were based on miRBase release 16. The first column are identifiers formatted as .ID=m-mmu-let-7d*-h-mmu-let-7d +., where each identifier has three parts:
1) mature miRNA (.mmu-let-7d*.), the part after .-m-..
2) precursor miRNA or hairpin (.mmu-let-7d.), the part after .-h-.;
3) the strand of mature miRNA sequences (not genomic sequence) where reads mapped to at the end (.+.), which is separated from other pieces by one space.
The expression values were represented as RPM: the number of reads per million (rpm) mapped for each sample.

organism: Mus musculus

source_name: small RNA_Strain Cast infected with SARS

extract_protocol:
The individual lung lobes were homogenized using Trizol and a Magnalyser system (Roche) according to the manufacturer’s instructions. RNA was further purified using an miRNeasy Mini kit (Qiagen) according to the nufacturer’s instructions. RNA samples were spectroscopically verified for purity, and the quality of the intact RNA was assessed using an Agilent 2100 Bioanalyzer. The assay also confirmed that the RNA samples were free of genomic DNA contamination.
For SARS MA15-infected samples, small RNA libraries were prepared with a Small RNA v1.5 sample preparation kit following the manufacturer’s instructions (Illumina, San Diego, CA). Total RNA was ligated with a 3 = RNA adaptor (5=-/5rApp/ATCTCGTATGCCGTCTTCTGCTTG/3ddC/) specifically modified to target miRNAs and other small RNAs that have a 3 = hydroxyl group resulting from cleavage by Dicer and other RNA-processing enzymes and then with a 5 = RNA adaptor (5=-GUUCAGAGUUCUACAGUCCGACGAUC) at the 5 = end of RNA with a phosphate group. The 5 = adaptor also included the sequencing primer. RT-PCR amplification was then done using the adaptors as primers, selectively enriching the fragments that had adaptors on both ends. The resulting double-stranded DNA libraries were polyacrylamide gel electrophoresis (PAGE) (6% Novex Tris-borate-EDTA [TBE] PAGE; Invitrogen) purified and size selected to eliminate dimerized adaptors. For influenza virus-infected samples, small RNA libraries were prepared using a TruSeq Small RNA sample preparation kit (Illumina, San Diego, CA) following the manufacturer’s instructions.

tag: strain

value: CAST/EiJ (CAST)

tag: age

value: 10 weeks

value: lung

tag: infected with

value: severe acute respiratory syndrome coronavirus (SARS-CoV; rMA15)

tag: dpi

value: 2 days post infection


title: small RNA from lung tissue in Mouse Strain PWK infected with Mock

source_name: small RNA_Strain PWK infected with Mock

value: PWK/PhJ (PWK)

value: phosphate-buffered saline (PBS) alone (Mock)


title: small RNA from lung tissue in Mouse Strain WSB infected with Mock

source_name: small RNA_Strain WSB infected with Mock

value: WSB/EiJ (WSB)


title: small RNA from lung tissue in Mouse Strain Cast infected with Mock

source_name: small RNA_Strain Cast infected with Mock


title: 552T

description:
552T
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.


title: small RNA from lung tissue in Mouse Strain PWK infected with SARS

source_name: small RNA_Strain PWK infected with SARS


title: Foxtail millet root

description: Sequenced reads were generated from millet root

source_name: root

value: root


title: small RNA from lung tissue in Mouse Strain WSB infected with SARS

source_name: small RNA_Strain WSB infected with SARS


title: small RNA from lung tissue in Mouse Strain 129 infected with Mock

source_name: small RNA_Strain 129 infected with Mock


title: small RNA from lung tissue in Mouse Strain 129 infected with SARS

source_name: small RNA_Strain 129 infected with SARS


title: small RNA from lung tissue in Mouse Strain WSB infected with Flu, rep1

source_name: small RNA_Strain WSB infected with Flu

value: influenza A virus strain A/Pr/8/34 (H1N1; PR8)

value: 2 days postinfection


title: small RNA from lung tissue in Mouse Strain WSB infected with Flu, rep2


title: small RNA from lung tissue in Mouse Strain PWK Mock, rep1

source_name: small RNA_Strain PWK Mock


title: small RNA from lung tissue in Mouse Strain PWK infected with Flu, rep2

source_name: small RNA_Strain PWK infected with Flu


title: 325NT

description:
325NT
small RNA sequencing
Patient recruitment and sample collection: This study was comprised of 32 consenting individuals undergoing lung resectional surgery for clinically suspected carcinoma. As previously describe, recruits were part of the pulmonary medicine or thoracic surgery practices at Albert Einstein College of Medicine of Montefiore Medical Center in the Bronx and were otherwise destined for bronchoscopy or lung resectional surgery for clinical indications, under a protocol approved by Albert Einstein College of Medicine and New York State Department of Health institutional review boards. Lung tissue samples were snap frozen in liquid nitrogen within 15 min of surgical resection, and stored in a −180°C tissue bank until analyzed. The assigned clinical surgical pathologist confirmed the diagnosis of lung cancer, per clinical routine, and classified the samples as adenocarcinoma, squamous cell carcinoma, mixed non–small cell carcinoma, or benign process of lung, according to the 1999 WHO histologic classification of lung and pleural tumors.

value: NT

value: benign


title: small RNA from lung tissue in Mouse Strain Cast Mock, rep1

source_name: small RNA_Strain Cast Mock


title: small RNA from lung tissue in Mouse Strain PWK infected with Flu, rep1


title: small RNA from lung tissue in Mouse Strain Cast infected with Flu, rep1

source_name: small RNA_Strain Cast infected with Flu


title: small RNA from lung tissue in Mouse Strain Cast infected with Flu, rep2


title: small RNA from lung tissue in Mouse Strain 129 infected with Flu, rep1

source_name: small RNA_Strain 129 infected with Flu


title: small RNA from lung tissue in Mouse Strain 129 infected with Flu, rep2


title: small RNA from lung tissue in Mouse Strain 129 Mock, rep1

source_name: small RNA_Strain 129 Mock


title: Oryza sativa L. ssp. japonica Nipponbare seedlings sRNA

status: Public on Mar 30 2012

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput sequencing of small RNA

data_processing: The raw data was acquired by Illumina base calling, all the reads containing ambiguous 'N' were eliminated from raw data, remained data was submitted to our following bioinformatics study, including sRNA annotation, phasiRNA prediction and motif analysis etc.

organism: Oryza sativa

source_name: young seedlings

growth_protocol: The rice 93-11 and Nipponbare seedlings were grown on Murashige and Skoog medium with a daylength of 16h and a night of 8h at 25 centigrade. And the panicles were collected from plants which were grown on field.

extract_protocol: Total RNA was extracted from seedling and panicles using Trizol reagent (Invitrogen). The low molecular weight (LMW) RNA was enriched by adding equal volume of 8M LiCl, incubating on ice for 1 hour and centrifuging at 12,000 rpm for 5 min at 4°C. Approximately 150µg of low molecular weight RNA was resolved in formamide and loaded into 15% PAGE gel with 7M urea and 1×TBE buffer. The gel fragments ranging between 15-30 nt were excised from gel for further purification. The purified small RNA was then ligated with a 5’ adaptor GUUCAGAGUUCUACAGUCCGACGAUC using T4 RNA ligase (NEB) at 20℃ for 6 hours and the ligation product ranging between 40-60 nt was purified again. The purified product was further ligated to the 3’ adaptor pUCGUAUGCCGUCUUCUGCUUGidT, which has a phosphate group in the 5’ terminal and an inverted deoxythymidine in the 3’ terminal, using T4 RNA ligase. The 2nd ligation product between 60-90 nt was separated within 10% Urea-PAGE gel and the purified product was reverse transcription (RT) using primer CAAGCAGAAGACGGCATACGA. The RT product was then amplified by PCR using p5 (AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA) and p7 (CAAGCAGAAGACGGCATACGA) primers for 15 cycles. The amplified products (90-95 nt) was excised from a 6% PAGE gel without urea and purified eventually. The purified product was resolved in 1×TE buffer and submitted to SBS sequencing after quality control (QC) assay in Beijing Genomics Institution.

treatment_protocol: Collected materials were ground into a fine powder in liquid nitrogen and processed following with Trizol reagent (Invitrogen) kit to extract total RNA.

tag: genotype/variation

value: Wild-type

value: seedlings


title: small RNA from lung tissue in Mouse Strain WSB Mock, rep1

source_name: small RNA_Strain WSB Mock


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in BMP4 Trophoblast Cells; renlab.H3K4me3.BMP4T.03.01

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY65
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11916
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906405_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me3.AY65.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.BMP4T.03.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY65, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13496
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,095,791
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.6262
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.6521
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9998
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6311
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906405_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me3.AY65.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.BMP4T.03.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY65, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13616
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K4me3 65
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me3 Library AY65 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,095,791
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.6262
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.6521
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9998
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6311
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

molecule: genomic DNA

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K4me3.BMP4T.03.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: U87 glioblastoma cell line

city: Los Angeles

first: Gang

last: Li

address: 611 Charles E. Young Drive Rm. 660

institute: UCLA

description: cDNA from control U87

data_processing: only raw data provided

source_name: Glioblastoma

growth_protocol: U87MG cells were maintained in DMEM high glucose medium supplemented with pyruvate, L-glutamine, and 10% fetal bovine serum (FBS).

extract_protocol: We used the standard Illumina protocol to prepare libraries for RNA-Seq (http://www.illumina.com/support/documentation.ilmn). Briefly, 10Î¼g total RNA was first processed via poly-A selection and fragmentation. We generated first-strand cDNA using random hexamer-primed reverse transcription and subsequently used it to generate second-strand cDNA using RNase H and DNA polymerase. Sequencing adapters were ligated using the Illumina Paired-End sample prep kit. Fragments of ~200 bp were isolated by gel electrophoresis, amplified by 15 cycles of PCR and sequenced.

tag: cell line

tag: cell type

value: glioblastoma


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in BMP4 Trophoblast Cells; renlab.H2BK5ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY73
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11924
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906391_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK5ac.AY73.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK5ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY73, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13524
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,105,108
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.417
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9532
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4827
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM906391_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK5ac.AY73.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY73, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13644
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H2BK5ac 73
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY73 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,105,108
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.417
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9532
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4827
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H2BK5ac.BMP4T.01.01

value: Histone H2BK5ac


title: WT macrophage_SMRT_ChIPSeq

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: Chromatin IP against SMRT

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) mm9 genome using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.

source_name: wild-type primary bone marrow-derived macrophages

growth_protocol: Bone marrow was purified and differentiated in DMEM containing 20% fetal bovine serum, 30% L929 conditioned media, and antibiotics for 5 days, then re-plated in macrophage serum free media (Invitrogen) overnight.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the ChIP seq sample prep kit (IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.

tag: strain

value: 10 month old

tag: gender

value: male

tag: antibody

value: anti-SMRT


title: Bcl6 KO macrophage_SMRT_ChIPSeq

description: Chromatin IP against SMRT

source_name: Bcl6 knockout primary bone marrow-derived macrophages

tag: age


title: WT macrophage_NCoR_ChIPSeq

description: Chromatin IP against NCoR

value: anti-NCoR


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in BMP4 Trophoblast Cells; renlab.H2BK120ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK120ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY71
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11928
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906389_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK120ac.AY71.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY71, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13542
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,379,897
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2361
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4276
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9139
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5346
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

**********************************************************************

ANALYSIS FILE NAME: GSM906389_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK120ac.AY71.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY71, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13662
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H2BK120ac 71
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY71 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,379,897
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.2361
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4276
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9139
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5346
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H2BK120ac.BMP4T.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Histone H2BK120ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in BMP4 Trophoblast Cells; renlab.H3K4me1.BMP4T.03.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY64
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11897
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906403_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me1.AY64.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.BMP4T.03.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY64, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13493
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,025,516
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.4533
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5067
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9911
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5813
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906403_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me1.AY64.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.BMP4T.03.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY64, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13613
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K4me1 64
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY64 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,025,516
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.4533
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5067
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9911
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5813
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K4me1.BMP4T.03.01

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Male

value: Histone H3K4me1

value: Abcam


title: Chromatin accessibility assay of H1 Derived Mesenchymal Stem Cells; DS21042

first: Northwest

last: REMC

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS21042
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11905
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906381_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS21042.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells ChromatinAccessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Derived Mesenchymal Stem Cells, Library DS21042 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13375
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,319,010
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.5177
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5563
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9941
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5809
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906381_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS21042.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells ChromatinAccessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 Derived Mesenchymal Stem Cells, Library DS21042 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13378
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HDMSC DNase 42
BROWSER_TRACK_DESCRIPTION: UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,319,010
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.5177
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5563
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9941
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5809
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; DS21042

extract_protocol: Library construction protocol: Single read - Illumina

value: H1 Derived Mesenchymal Stem Cells

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

value: Chromatin Accessibility

value: Qiagen minElut


title: Bcl6 KO macrophage_NCoR_ChIPSeq

description: Chromatin IP against NCoR

value: 10 month old

value: male


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in BMP4 Trophoblast Cells; renlab.H3K36me3.BMP4T.03.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY67
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11918
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906401_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K36me3.AY67.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.BMP4T.03.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY67, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13517
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,462,303
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.5638
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.5556
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.631
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM906401_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K36me3.AY67.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.BMP4T.03.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY67, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13637
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K36me3 67
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY67 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,462,303
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.5638
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.5556
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.631
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K36me3.BMP4T.03.01

value: genomic DNA

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: input DNA for TCF7

city: PALO ALTO

first: Jiaqian

last: Wu

address: 1501 California Avenue

institute: Stanford University

description: input DNA

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: EML cells

growth_protocol: EML cell culture was maintained in  expansion medium (IMDB, 20% heat inactivated horse serum, 100 ng/ml SCF [PeproTech])

extract_protocol: Cell lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with antibody.  DNA sequencing followed the instructions of the mRNA-Sequencing Sample Prep Kit (Illumina).

tag: sequence type

value: Illumina; single-end;35bp reads

value: Lin-SCA+CD34+ cells


title: Chromatin accessibility assay of H1 Derived Mesenchymal Stem Cells; DS20671

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20671
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11911
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906380_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS20671.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20671.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells ChromatinAccessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Derived Mesenchymal Stem Cells, Library DS20671 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13376
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,839,693
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4814
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5087
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9967
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5279
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906380_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS20671.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20671.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells ChromatinAccessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 Derived Mesenchymal Stem Cells, Library DS20671 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13379
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HDMSC DNase 71
BROWSER_TRACK_DESCRIPTION: UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS20671 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,839,693
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4814
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5087
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9967
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5279
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; DS20671

tag: sample alias

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Male


title: input DNA for RUNX1

description: input DNA


title: Reference Epigenome: ChIP-Seq Analysis of H2A.Z in BMP4 Trophoblast Cells; renlab.H2A.Z.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2A.Z in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY68
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11920
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2A.Z ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY68, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13515
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,332,005
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2243
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3979
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9339
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4865
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

ANALYSIS FILE NAME: GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2A.Z ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY68, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13635
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H2A.Z 68
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,332,005
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2243
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3979
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9339
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4865
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H2A.Z.BMP4T.01.01

tag: sample common name

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Histone H2A.Z

value: Abcam


title: Chromatin accessibility assay of H1 Derived Neuronal Progenitor Cultured Cells; DS20153

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS20153
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11899
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7871
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906379_UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS20153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20153.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells ChromatinAccessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Derived Neuronal Progenitor Cultured Cells, Library DS20153 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13374
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,984,280
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2487
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2482
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.996
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3223
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906379_UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS20153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS20153.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells ChromatinAccessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 Derived Neuronal Progenitor Cultured Cells, Library DS20153 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13377
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HDNP DNase 53
BROWSER_TRACK_DESCRIPTION: UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS20153 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,984,280
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2487
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2482
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.996
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3223
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; DS20153

tag: molecule

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Between 20 and 30

value: Chromatin Accessibility

value: Qiagen minElut


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in BMP4 Trophoblast Cells; renlab.H2AK5ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY69
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11926
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906388_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2AK5ac.AY69.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2AK5ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY69, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13463
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,301,069
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.212
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3257
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.939
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5067
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906388_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2AK5ac.AY69.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2AK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY69, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13583
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H2AK5ac 69
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY69 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,301,069
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.212
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3257
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.939
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5067
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H2AK5ac.BMP4T.01.01

value: genomic DNA

tag: disease

value: Histone H2AK5ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: RUNX1_ChIPSeq_Rep2

description: Chromatin IP against RUNX1

value: Illumina; single-end;35bp reads

value: anti-AML(RUNX1) rabbit polyclonal antibody

tag: vendor

value: CalBiochem

tag: catalog

value: Lin-SCA+CD34+ cells


title: RUNX1_ChIPSeq_Rep1

description: Chromatin IP against RUNX1


title: Digital Genomic Footprinting assay of H1 BMP4 Derived Trophoblast Cultured Cells; DGF.DS19317

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS19317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11937
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7847
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906382_UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19317.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS19317.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on the H1 BMP4 Derived Trophoblast Cultured Cells, Library DGF.DS19317 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13111
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 183,594,616
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2205
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2658
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3091
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM906382_UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.Digital_Genomic_Footprinting.DGF.DS19317.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS19317.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  the H1 BMP4 Derived Trophoblast Cultured Cells, Library DGF.DS19317 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13116
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT DGF 17
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 183,594,616
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2205
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2658
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3091
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; DGF.DS19317

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

tag: passage

value: Male

value: Digital Genomic Footprinting

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: TCF7_ChIPSeq

description: Chromatin IP against TCF7

value: TCF7 goat polyclonal antibody TCF1(H18)

value: Santa Cruz Biotechnology


title: DCIS

status: Public on Mar 29 2012

city: Detroit

first: RAYMOND

middle: R

last: MATTINGLY

state: MI

address: 540 East Canfield

department: Pharmacology

institute: Wayne State University

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes using novoalign with default parameters. Only the reads that map to the unique genome positions were considered.
Genome Build:
DCIS_2_novo.bed: hg18
DCIS_3_novo.bed: hg18

source_name: ductal carcinoma in situ cells

growth_protocol: All the experiments in the present study were conducted using in vitro three dimensional (3D) organotypic culture models with reconstituted basement membrane (rBM).  In the 3D rBM overlay protocol, single cells were seeded onto culture dishes previously coated with polymerized rBM (Cultrex®) and were overlaid with media containing 2% rBM when the cells had attached.

extract_protocol: We used Trizol to extract the RNA from our samples. Libraries of template molecules for high throughput DNA sequencing were prepared using Illumina mRNA Sequencing Sample Preparation kit.  First, using Sera-Mag oligo (dT) beads, mRNA molecules were purified from the total RNA. Then the purified mRNA samples were fragmented under elevated temperature conditions.  Subsequently, first strand cDNA synthesis was done from the cleaved RNA fragments using reverse transcriptase and random primers.  This was followed by second strand synthesis using DNA polymerase I and RNaseH (using SuperScript II from Invitrogen).  These cDNA fragments were then subjected to repair end process with T4 DNA polymerase and Klenow.   The 3’ ends were then adenylated to prepare for adapter ligation.  After paired end ligation of adapters, the samples were purified on 1.2% agarose recovery FlashGelTM.  The library of products of desired size (150-200bp) was then selected for further enrichment with 15 cycles of polymerase chain reaction (PCR) amplification.

value: DCIS

tag: disease status

value: ductal carcinoma in situ

tag: Stage

value: premalignant stage


title: Sum102

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes using novoalign with default parameters. Only the reads that map to the unique genome positions were considered.
Genome Build:
Sum102_1_novo.bed: hg18
Sum102_2_novo.bed: hg18

tag: cell line


title: Sum225

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes using novoalign with default parameters. Only the reads that map to the unique genome positions were considered.
Genome Build:
Sum225_1_novo.bed: hg18
Sum225_2_novo.bed: hg18


title: control

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

country: Germany

institute: University of Giessen

data_processing: Alignments against the human genome (assembly hg19) and exon-junctions (based on human mRNA and EST data) were done using BWA (Burrows-Wheeler Aligner). The alternative splicing targets were predicted using both read-density and junction-read-counts information (Rösel et al., EMBO J. 2011).

source_name: control

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyrivate, Pen-Strep, and 50 uM beta-mercaptoethanol.

extract_protocol: Libraries were constructed from total RNA and the mRNA-Seq libraries were prepared for Solexa high-throughput sequencing by Illumina standard protocols. Sequencing was done in a single-read, 76-base mode.

treatment_protocol: DG75 cells were transfected with 2 ug LL-V5-His plasmid, or as a control, 1 ug eGFP.


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in BMP4 Trophoblast Cells; renlab.H3K9me3.BMP4T.03.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY66
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11922
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906408_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9me3.AY66.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.BMP4T.03.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY66, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13550
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,847,876
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.4376
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4887
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9658
IROC_PERCENTILE: 94
POISSON_SCORE: 0.539
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM906408_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9me3.AY66.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.BMP4T.03.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY66, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13670
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H3K9me3 66
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library AY66 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,847,876
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 16
FINDPEAKS_SCORE: 0.4376
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4887
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9658
IROC_PERCENTILE: 94
POISSON_SCORE: 0.539
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K9me3.BMP4T.03.01

value: genomic DNA

tag: medium

tag: Sex

tag: batch

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in BMP4 Trophoblast Cells; renlab.H2BK12ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK12ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY72
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11930
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM906390_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK12ac.AY72.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK12ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY72, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13506
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,600,690
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2838
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3915
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.963
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5196
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM906390_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK12ac.AY72.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK12ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY72, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13626
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: HBDT H2BK12ac 72
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY72 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,600,690
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2838
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3915
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.963
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5196
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H2BK12ac.BMP4T.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: Histone H2BK12ac