title: Neuron Nup98 IgG ChIP-Seq

city: La Jolla

first: William

middle: Harvey

last: Light

state: California

address: 10010 N Torrey Pines Rd

department: MCBL-Z

institute: The Salk Institute for Biological Studies

description:
HUES6-derived neurons.
Nup98 ChIP-Seq

data_processing:
Grooming performed using Genomatix Software.
Mapping performed using genome build hg19 and Genomatix Software.
Peak calling was performed using Genomatix Software based on Audic-Claverie algorithim for NGSAnalyzer.
Transcription Factor motif analysis was performed using Genomatix Software.
Genome_build: GRCh37
Supplementary_files_format_and_content: Bed files.

source_name: Neurons, Nup98 ChIP

growth_protocol:
Human embryonic stem cell line HUES6 was grown under feeder-free conditions in mTeSR1 medium. HUES6-derived neural progenitor cells were grown in DMEM/F12 supplemented with N2/B27. Early passage IMR90 cells were grown in DMEM, 15% FBS and MEM nonessential amino acids.
Human embryonic stem cell line HUES6 was grown in mTeSR1 medium (STEMCELL Technologies). To obtain neuroprogenitor cells, embryoid bodies were formed by mechanically lifting HUES6 cells and transferring them to low-adherence dishes in HUES6 medium without FGF2 for approximately 7 days. After that, embryoid boides were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 supplemented with N2 and B27 (Invitrogen). Rosettes were visible to collect after 5-7 days. Rosettes were then dissociated with TripLE (Invitrogen) diluted 1:5 in PBS and plated again onto poly-ornithine/laminin-coated dishes with the same medium but now with the addition of 10ng/ml FGF2. Homogeneous populations of neuroprogenitor cells were achieved after 1-2 passages with TripLE in the same conditions. HUES6-derived neural progenitor cells were grown in DMEM/F12/Glutamax (Invitrogen) supplemented with N-2 (Invitrogen), B-27 (Invitrogen), 20ng/ml FGF2 (Stemgent), and 1μg/ml laminin (Invitrogen). For differentiation into neurons, neural progenitor cells (NPCs) were plated at low density and cultured in DMEM/F12/Glutamax supplemented with N-2, B-27, 20ng/ml BDNF (Brain-derived neurotrophic factor, Peprotech), 20ng/ml GDNF (Glial-derived neurotrophic factor, Peprotech) and 1μg/ml laminin for 1 month.

extract_protocol:
Cells were fixed in 1% formaldehyde (Polysciences) for 10min. Fixation was stopped by adding glycine to a final concentration of 125mM. Fixed cells were lysed and sonicated. DNA was immunoprecipitated, eluted, de-crosslinked, treated with RNase and protease, and purified.
Library was constructed using Illumina ChIP-Seq DNA sample prep kit and sequencing was done on Illumina GAII.

tag: cell line

value: neurons

value: Nup98 (Cell Signaling #2292 )


title: IMR90 Normal IgG ChIP-Seq

status: Public on Jul 17 2013

type: SRA

country: USA

description: IgG ChIP-Seq

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: IMR90, IgG ChIP

tag: cell type

value: lung fibroblasts

tag: chip antibody

value: Normal Rabbit IgG (Cell Signaling #2729)


title: IMR90 Nup98IgGAb2 ChIP-Seq

description: Nup98 ChIP-Seq

source_name: IMR90, Nup98 ChIP

value: Nup98 (Cell Signaling #2598)


title: NPC Nup98-IgG ChIP-Seq

description:
HUES6-derived NPCs.
Nup98 ChIP-Seq

source_name: Neural progenitor cells, Nup98 ChIP

value: neural progenitor cells


title: ES normal IgG ChIP-Seq

description: IgG ChIP-Seq

source_name: HUES6, IgG ChIP

value: embryonic stem (ES) cells


title: ES Nup98-IgG ChIP-Seq

description: Nup98 ChIP-Seq

source_name: HUES6, Nup98 ChIP


title: EGDe WT Rhamnose-1

city: Bedford Park

first: Joelle

middle: K

last: Salazar

state: IL

address: 6502 S Archer Rd

institute: Illinois Institute of Technololgy

description:
mRNA-seq
purified mRNA

library_source: transcriptomic

data_processing:
Deep RNA sequencing was conducted on an Illumina HiSeq 2000 instrument (12.5 filter-passed 50 + 50 nt paired-end reads) (Illumina Inc., San Diego, CA).
Reads were mapped to the L. monocytogenes 10403S sequence available at the Broad Institute using GSNAP3.
Gene and transcript expressions were computed using Cufflinks, FPKM.
Quality control of transcripts was performed using FastQC.
Genome_build: Listeria monocytogenes 10403S Supercontig 6.1, Broad Institute
Supplementary_files_format_and_content: GSE47721_Gene_FPMK.txt.gz: Tab-delimited text file includes gene symbols and FPKMs.

molecule: total RNA

organism: Listeria monocytogenes

source_name: Bacterial culture, WT

growth_protocol: L. monocytogenes cultures were grown overnight in BHI at 37°C, washed three times with PBS, and sub-cultured 1:100 into 100-ml phenol-red broth containing rhamnose as the sole carbon source. Bacteria were grown at 37C for 4 h to mid-log phase.

extract_protocol:
Total RNA was extracted using Ambion RiboPure Bacterial Kit (Life Technologies Corporation, Carlsbad, CA). Total RNA from two biological replicates was prepared from independent cultures on different days to ensure the reproducibility of RNA-seq data.
mRNA was purified using the NuGEN Prokaryotic RNA-Seq system (NuGEN, San Carlos, CA).

tag: strain/background

value: EGDe

tag: lineage

value: LII

tag: genotype/variation

value: wild-type

tag: carbon source

value: L-rhamnose

tag: media

value: phenol-red broth


title: IMR90 Nup98IgGAb1 ChIP-Seq

description: Nup98 ChIP-Seq


title: Brf1 - IP

city: Bethesda

first: Nagarajavel

last: Vivekananthan

state: Maryland

address: 9500 Rockville Pike, Buld 6A/Rm 2A14

department: NICHD

institute: National Institutes of Health

description:
Immuno-purified MNase digested DNA
415-IP-1

data_processing:
Nucleosomes: For wild type - experiment, ELAND was used to align the reads to the NCBI Saccharomyces cerevisiae genome sequence Build 2.1
Nucleosomes: For wild type repeat sample,  BWA was used to align the reads to Saccharomyces cerevisiae genome sequence
Samples were aligned with either BWA (413-Input, 413-IP, 416-1-Input, 416-1-IP, 415-1-Input, 415-1-IP)  or Bowtie 2 (416-1-Input, 416-3-IP, 415-2-Input, 415-2-IP)  to the Saccharomyces cerevisiae genome sequence (SacCer2).

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.

extract_protocol:
Nuclei were digested with micrococcal nuclease. Nucleosomes: mono-nucleosomal DNA was gel-purified. IP experiments: DNA was extracted from a fraction of the MNase digest (Input) for paired-end sequencing. The rest of the digest was immunoprecipitated using anti-FLAG antibody and eluted with 3-FLAG peptide (IP) and the DNA was extracted and sequenced.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: strain

tag: genotype

value: MATalpha ADE2 can1 his3 leu2 lys2delta trp1 ura3 BRF1:3XFLAG:KanMX

tag: antibody

value: anti-FLAG


title: NPC normal IgG ChIP-Seq

description:
HUES6-derived NPCs.
IgG ChIP-Seq

source_name: Neural progenitor cells, IgG ChIP


title: Wild type - nucleosomes

description:
gel-purified nucleosomal DNA (MNase)
78-1

value: MATalpha can1-100 his3-11,15 leu2-3, 112 lys2-delta trp1-1 ura3-1


title: IgH Col LP mouse 2

status: Public on Jul 16 2013

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

description:
5'RACE with C mu primer
IgH_Col_LP.txt

data_processing:
Approximate clonotypes were inferred using the Antigen Receptor Probalistic Parser (ARPP; Kepler, 2013).
Unmutated precursor CDR3 were refined and reads assigned to clones using reiterated hypothesis tests of equality of V gene mutation frequency and CDR3 mutation frequency described in Kepler (F1000Research, 2013)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files with V gene segment usage frequencies

organism: Mus musculus

source_name: lamina propria from mice colonized for 7 days

growth_protocol: RAG2-GFP mice were housed in regular SFP facility. GF mice were germ-free and Col mice were littermates of the GF mice that were cohoused with SPF mice for 7 days.

extract_protocol:
Bone marrow was extracted by crushing femurs and passing through 70 micron filter. Splenocytes were prepared by pushing through 70 micron filter. Lamina propria lymphocytes were prepared by washing cleaned, minced small intestinal samples in EDTA solution followed by collagenase extraction of lymphocytes.
RNA prepared from Trizol was extracted and subjected to 5' RACE using either IgH C mu or IgK C kappa primers.

tag: ig chain

value: IgH

value: Swiss Webster

tag: tissue

value: Lamina Propria


title: IgH Col LP mouse 1

description:
5'RACE with C mu primer
IgH_Col_LP.txt


title: control - Input

description:
MNase digested DNA
413-Input-1

value: MATalpha ADE2 his3-11 leu2-3,112  lys2delta  trp1-1  ura3-1


title: Wild type -nucleosomes - Repeat

description:
gel-purified nucleosomal DNA (MNase)
78-2


title: s02_MCF7_ER_rep2

city: Cambridge

first: Mauro

middle: Antonio

last: Alves Castro

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description: In-house id: mf002_MCF7_ERa_E2_45min_CRI01

data_processing:
ChIP-Seq reads were aligned to genome build hg18 and filtered by removing reads either with quality less than 5 or overlapping "signal artefact" regions (regions obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/). Peaks were called using model-based analysis for ChIP-Seq (MACS) (Zhang et al., Genome Biology, 9(9):R137, 2008), run using default parameters. Quality control of the raw sequenced data was conducted using the FastQC software (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and good quality scores across all bases were observed.
To evaluate the consistency of signal between replicates we measured the read coverage over all genomic regions covering peak regions that were called in at least two of the three replicates. There is a good correlation between pairs of replicates, with Spearman’s correlation coefficients ranging from 0.51 to 0.74
Genome_build: hg18
Supplementary_files_format_and_content: Files produced by MACS that report peak positons, summit and statistics. The files named NAME_peaks.bed are in BED format which contains the peak locations and in the 5th column is the -10*log10pvalue of peak region. The files names NAME_summits.bed is in BED format, which contains the peak summits locations for every peaks, and in the 5th column in this file is the summit height of fragment pileup.

source_name: MCF-7 breast cancer cell line

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% heat-inactivated foetal calf serum and 1% penicillin-streptomycin.

extract_protocol:
ChIP of DNA was performed as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001
Illumina sequencing libraries were prepared as described in Schmidt et al., Methods (2009) doi: 10.1016/j.ymeth.2009.03.001

treatment_protocol: Cells growing asynchronously in full media were fixed for ChIP.

value: MCF-7 breast cancer cell line

value: ERα (sc543; Santa Cruz Biotechnology)

tag: chip treatment conditions

value: 10nM E2, 45 minutes


title: IgH GF LP mouse 2

description:
5'RACE with C mu primer
IgH_GF_LP.txt

source_name: lamina propria from germ free mice


title: IgH GF LP mouse 3

description:
5'RACE with C mu primer
IgH_GF_LP.txt


title: IgH GF LP mouse 1

description:
5'RACE with C mu primer
IgH_GF_LP.txt


title: EGDe 0753 Rhamnose-1

description:
mRNA-seq
purified mRNA

source_name: Bacterial culture, lmo0753 deletion


title: Igk Col LP mouse 2

description:
5'RACE with C kappa primer
Igk_Col_ LP.txt

value: IgK


title: Igk GF LP mouse 3

description:
5'RACE with C kappa primer
Igk_GF_LP.txt


title: IgH Col LP mouse 3

description:
5'RACE with C mu primer
IgH_Col_LP.txt


title: Igk GF LP mouse 2


title: HL3168 E3 RNA-Seq

city: Shanghai

first: Weibing

last: Liu

address: Meilong Road 130

country: China

institute: East China University Of Science And Technology

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to Saccharopolyspora erythraea NRRL 2338 ribosome RNA sequence using bowtie version 2.0.0.beta5 with parameters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
Unmapped rRNA reads were aligned to Saccharopolyspora erythraea NRRL 2338 genome using bowtie version 2.0.0.beta5 with parameters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
Gene abundance measurements were generationed and normalized  using  The normalized standard were Mapped gene Reads Per Kilobase of exon per Megabase of library size (RPKM)
Differential expression were analysed  using perl program et.al
Genome_build: Saccharopolyspora erythraea NRRL 2338/ASM6288v1
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each sRNA predicted in silico.

organism: Saccharopolyspora erythraea

source_name: cell

extract_protocol:
Total RNA was isolated after 72h incubation using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. The RNA sample harvested was used for deep-sequencing analysis.
NUGEN PROKARYOTIC RNA-SEQ SYSTEM KIT  protocol was using to construction library

tag: age


title: NRRL23338 RNA-Seq


title: Igk GF LP mouse 1


title: IgH total spleen pool 4

description:
5'RACE with C mu primer
IgH_total_spl.txt

source_name: spleen

value: Spleen


title: IgH total spleen pool 3


title: IgH total spleen pool 1


title: IgH RAG2+ BM pool 2

description:
5'RACE with C mu primer
IgH_RAG2_BM.txt

source_name: RAG+ B lineage cells from bone marrow

value: RAG+ B lineage cells from bone marrow

value: Bone Marrow


title: IgH RAG2+ BM pool 1

description:
5'RACE with C mu primer
IgH_RAG2_BM.txt


title: IgH RAG2+ BM pool 4

description:
5'RACE with C mu primer
IgH_RAG2_BM.txt


title: IgH RAG2+ LP pool 4

description:
5'RACE with C mu primer
IgH_RAG2_LP.txt

source_name: RAG+ B lineage cells from small intestinal lamina propria


title: IgH RAG2+ LP pool 3

description:
5'RACE with C mu primer
IgH_RAG2_LP.txt

value: RAG+ B lineage cells from small intestinal lamina propria


title: IgH RAG2+ LP pool 2

description:
5'RACE with C mu primer
IgH_RAG2_LP.txt


title: IgH RAG2+ LP pool 1

description:
5'RACE with C mu primer
IgH_RAG2_LP.txt


title: Igk RAG2+ BM pool 8

description:
5'RACE with C kappa primer
Igk_RAG2_BM.txt


title: Igk RAG2+ BM pool 7


title: Igk RAG2+ BM pool 6


title: Igk RAG2+ BM pool 5


title: Igk RAG2+ BM pool 4


title: Igk Col LP mouse 3


title: Igk Col LP mouse 1

description:
5'RACE with C kappa primer
Igk_Col_LP.txt


title: Igk RAG2+ BM pool 2


title: Igk RAG2+ LP pool 8

description:
5'RACE with C kappa primer
Igk_RAG2_LP.txt


title: Igk RAG2+ BM pool 3


title: Igk RAG2+ BM pool 1


title: Igk RAG2+ LP pool 7


title: Igk RAG2+ LP pool 4


title: Igk RAG2+ LP pool 6


title: IgH total spleen pool 2


title: IgH RAG2+ BM pool 3

description:
5'RACE with C mu primer
IgH_RAG2_BM.txt


title: Igk RAG2+ LP pool 3


title: Igk RAG2+ LP pool 1


title: Igk RAG2+ LP pool 5


title: Mouse Adult Small Intestine

status: Public on Jul 15 2013

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description: Small RNA

data_processing:
454 instrument data processing to fastA files.
Filtering and adaptor trimming were performed on Sequery - www.medicine.nevada.edu/yan/sequery.html.
Mapping to known small RNA sequences was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html.
Alignment to mm9 Mus musculus genome was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html.
Removal of novel endo-siRNA detection was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html.
Removal of novel miRNA detection was performed using MIREAP - http://sourceforge.net/projects/MIREAP.
Novel piRNA-like detection was determined by remaining unannotated sequence lengths (24-32 nts).
Genome_build: MGSCv37
Supplementary_files_format_and_content: .GFF file contains novel pilRNAs and their genomic locations.

source_name: Small Intestine

extract_protocol:
ICC were FACS sorted by c-kit antibodies, frozen and lysed. Sm Int was collected, flash frozen, and whole tissue homogenized and lysed. sncRNA were collected with the mirVana isolation kit.
Barcoded and prepared per 454 library preparation protocol.

tag: developmental stage

value: adult

value: small intestine

tag: tissue/cell preparation

value: homogenized tissue

tag: sample type

value: pooled


title: Mouse Adult Interstitial Cells of Cajal

description: Small RNA

source_name: Interstitial cells of Cajal

value: interstitial cells of Cajal

value: purified cells


title: DW replicate

city: Beijing

first: zhang

last: jingyu

address: Nanxincun #20

institute: Institute od botany

data_processing:
Illumina GA Pipeline v1.5 used for basecalling.
After removing sequences corresponding to known rRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and repeats/transposons (http://www.sanger.ac.uk/Software/Rfam, http://www.girinst.org/server/RepBase/),  the remaining sequences were mapped to the Brachypodium genome (http://www.brachypodium.org) using bowtie, allowing one mismatch. After three 5' end randome nucleotides being removed, 26 nucleotides at the 5' end of the remaining sequence were used for further analysis. Low quality reads and low frequency reads (≤5) were omitted from further analysis. For PARE reads mapped to multiple positions, reads were divided among different positions. Brachypodium draft genome sequences and V1.2 annotation was obtained from http://www.brachypodium.org.
Custom Perl scripts were used to identify the total reads for specific transcripts.
Genome_build: Brachypodium distachyon
Supplementary_files_format_and_content: text file showing reads for all the genes

organism: Brachypodium distachyon

source_name: Seedling

growth_protocol: Seeds of the Brachypodium distachyon (L.) Beauv. diploid line ABR5 were placed in petri dishes containing two layers of damp sterile filter paper. The seeds were first stratified at 4 °C for one week to promote synchronous germination, then grown in a growth chamber at 24 °C under a 16 hour/8 hour (light/dark) photoperiod with light intensity of approximately 5,000 lux.

extract_protocol:
Total RNA was extracted from 12-day-old ABR5 seedlings using the mirVana miRNA Isolation Kit (Ambion, Austin, USA) following the manufacturer's protocol.
PARE libraries were prepared as described previously (Nature Protocols 2009, 4:356-362.). Modification was made according to (Plant Cell 2010, 22:1090-1103). Sequencing was performed on Illumina GAIIx.

treatment_protocol: The aerial part of seedlings treated or untreated with cold stress (4 °C for 24 h) were pooled and used for  library construction.

tag: ecotype

tag: growth stage

value: 12 day old

tag: treatment

value: no treatment


title: DW


title: DC

value: with cold teatment (4℃, 24h)


title: DC replicate


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC H1 Cells; renlab.H3K27me3.hESC.H1.02.01

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in hESC H1 cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY830
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17187
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.17186
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line.; renlab.H3K27me3.hESC.H1.02.01

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

tag: sample alias

tag: sample common name

value: H1 Cell Line

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

tag: medium

value: mTeSER

tag: Sex

value: Male

tag: batch

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: RW

data_processing:
Illumina GA Pipeline v1.3  used for basecalling.
After  low quality reads being removed, the remaining Illumina sequencing reads were  mapped to the Brachypodium genome (v1.2 ,http://www.brachypodium.org) using SOAP.
The gene expression level is calculated by using RPKM  (Reads Per kb per Million reads) method (Mortazavi et al, 2008, Nature Methods. 5: 621-8.)
Genome_build: Brachypodium distachyon
Supplementary_files_format_and_content: text file showing  RPKM value for all the samples

extract_protocol:
Total RNA was extracted from 12-day-old ABR5 seedlings using the mirVana miRNA Isolation Kit (Ambion, Austin, USA) following the manufacturer's protocol.
The mRNAs were enriched by using oligo(dT) magnetic beads and broken into short fragments (about 200 bp). The first strand cDNA was synthesized using random hexamer primer with mRNA fragments as templates. DNA polymerase I (Epicentre® Biotechnologies, Madison, USA) was used to synthesize the second strand. The double-strand cDNA was purified with the QiaQuick PCR extraction kit (Qiagen). Then, sequencing adaptors were added and the obtained fragments were purified using agarose gels and enriched by PCR amplification. The resultant products were used for sequencing analysis via Illumina HiSeq™ 2000.

treatment_protocol: The aerial part of seedlings treated or untreated with cold stress (4 °C for 24 h) were pooled and used for  library construction


title: RC


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: RNA-Seq analysis of placenta (amniotic membrane) tissue from CTL03 (A19265) using Illumina HiSeq 2000
library name: A19265
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.2
RNA_PREPARATION_INITIAL_RNA_QNTY: 2.46 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 250-470 bp
****************
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: GSM1127108_UCSF-UBC.Placenta_Amnion.mRNA-Seq.CTL03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19265-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Amnion, Donor CTL03 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.16987
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 393,679,856
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.05
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

ANALYSIS FILE NAME: GSM1127108_UCSF-UBC.Placenta_Amnion.mRNA-Seq.CTL03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19265-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Amnion, Donor CTL03 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.17003
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PA mRNA 03 65
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion mRNA-Seq Donor CTL03 Library A19265 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 393,679,856
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.05
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: body site

value: Placenta

tag: histological type

value: Amnion tissue

tag: is tumor

value: No

value: primary tissue

value: placenta (amniotic membrane) tissue


description:
design description: RNA-Seq analysis of placenta (trophoblast) tissue from CTL02 (A19261) using Illumina HiSeq 2000
library name: A19261
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 312-531 bp
****************
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: GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19261-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Trophoblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Trophoblast Primary Cells, Donor CTL02 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.16990
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 312,136,881
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19261-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Trophoblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Trophoblast Primary Cells, Donor CTL02 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.17006
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PT mRNA 02 61
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Trophoblast Primary Cells mRNA-Seq Donor CTL02 Library A19261 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 312,136,881
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Trophoblast

value: placenta (trophoblast) tissue


description:
design description: RNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL01 (A19255) using Illumina HiSeq 2000
library name: A19255
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.1
RNA_PREPARATION_INITIAL_RNA_QNTY: 4.13 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 287-478 bp
****************
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: GSM1127107_UCSF-UBC.Placenta_Chorion_Smooth.mRNA-Seq.CTL01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19255-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Chorion Smooth, Donor CTL01 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.16988
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 396,008,992
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127107_UCSF-UBC.Placenta_Chorion_Smooth.mRNA-Seq.CTL01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19255-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Chorion Smooth, Donor CTL01 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.17004
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PCS mRNA 01 55
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth mRNA-Seq Donor CTL01 Library A19255 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 396,008,992
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: female

value: Chorion smooth tissue


title: Igk RAG2+ LP pool 2

tag: ig chain

value: IgK

tag: cell type

value: RAG+ B lineage cells from small intestinal lamina propria

tag: strain

tag: tissue

value: Lamina Propria


description:
design description: RNA-Seq analysis of placenta (villi) tissue from CTL01 (A19254) using Illumina HiSeq 2000
library name: A19254
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 6.9
RNA_PREPARATION_INITIAL_RNA_QNTY: 4.28 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 289-481 bp
****************
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: GSM1127102_UCSF-UBC.Placenta_Villi.mRNA-Seq.CTL01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19254-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Villi mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Villi, Donor CTL01 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.16993
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 401,459,650
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.52
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127102_UCSF-UBC.Placenta_Villi.mRNA-Seq.CTL01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19254-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Villi mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Villi, Donor CTL01 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.17009
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PV mRNA 01 54
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Villi mRNA-Seq Donor CTL01 Library A19254 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 401,459,650
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.52
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Villi tissue

value: placenta (villi) tissue


description:
design description: RNA-Seq analysis of breast luminal epithelial cell from RM084 (A17918) using Illumina HiSeq 2000
library name: A17918
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.9
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 208-442 bp
****************
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: GSM1127103_UCSF-UBC.Breast_Luminal_Epithelial_Cells.mRNA-Seq.RM084.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17918-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Luminal Epithelial Cells, Donor RM084 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.16992
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 356,720,402
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.06
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.53

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

ANALYSIS FILE NAME: GSM1127103_UCSF-UBC.Breast_Luminal_Epithelial_Cells.mRNA-Seq.RM084.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17918-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM084 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.17008
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BLEC mRNA 84 18
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells mRNA-Seq Donor RM084 Library A17918 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 356,720,402
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.06
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.53

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

value: Breast

value: Luminal epithelial cell

value: primary cell

value: breast luminal epithelial cell


description:
design description: RNA-Seq analysis of placenta (basal plate and villi) tissue from CTL01 (A19253) using Illumina HiSeq 2000
library name: A19253
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.1
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 285-477 bp
****************
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: GSM1127098_UCSF-UBC.Placenta_Basal_Plate.mRNA-Seq.CTL01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19253-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Basal Plate mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Basal Plate, Donor CTL01 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.16994
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 369,315,787
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.1
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1127098_UCSF-UBC.Placenta_Basal_Plate.mRNA-Seq.CTL01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19253-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Basal Plate mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Basal Plate, Donor CTL01 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.17010
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PBP mRNA 01 53
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Basal Plate mRNA-Seq Donor CTL01 Library A19253 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 369,315,787
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.1
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

value: Placenta

value: Basal plate tissue

value: No

value: placenta (basal plate and villi) tissue


description:
design description: RNA-Seq analysis of breast fibroblast from RM070 (A18760) using Illumina HiSeq 2000
library name: A18760
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.2
RNA_PREPARATION_INITIAL_RNA_QNTY: 2.58 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 268-478 bp
****************
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: GSM1127101_UCSF-UBC.Breast_Fibroblast_Primary_Cells.mRNA-Seq.RM070.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18760-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Fibroblast Primary Cells, Donor RM070 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.16997
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 324,348,540
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.11
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1127101_UCSF-UBC.Breast_Fibroblast_Primary_Cells.mRNA-Seq.RM070.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18760-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM070 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.17013
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BF mRNA 70 60
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells mRNA-Seq Donor RM070 Library A18760 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 324,348,540
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.11
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

value: Fibroblast cultured cell

value: primary cell culture

value: breast fibroblast


description:
design description: RNA-Seq analysis of breast progenitor enriched cell from RM084 (A17920) using Illumina HiSeq 2000
library name: A17920
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.7
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.44 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 210-480 bp
****************
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: GSM1127099_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM084.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17920-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Stem Cells, Donor RM084 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.17000
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 465,720,995
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.28
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.44

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

ANALYSIS FILE NAME: GSM1127099_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM084.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A17920-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Stem Cells, Donor RM084 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.17016
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BSC mRNA 84 20
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Stem Cells mRNA-Seq Donor RM084 Library A17920 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 465,720,995
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.28
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.44

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

value: female

value: Progenitor enriched cell

value: breast progenitor enriched cell


description:
design description: RNA-Seq analysis of brain (cerebellum) tissue from HuFGM01 (A15610) using Illumina HiSeq 2000
library name: A15610
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.1
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.05 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 217-475 bp
****************
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: GSM1127104_UCSF-UBC.Brain_Cerebellum.mRNA-Seq.HuFGM01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15610-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Cerebellum mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Brain Cerebellum, Donor HuFGM01 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.16989
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 357,821,017
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.54
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127104_UCSF-UBC.Brain_Cerebellum.mRNA-Seq.HuFGM01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15610-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cerebellum mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Brain Cerebellum, Donor HuFGM01 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.17005
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BC mRNA 01 10
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Cerebellum mRNA-Seq Donor HuFGM01 Library A15610 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 357,821,017
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.54
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Brain

value: Cerebellum tissue

value: primary tissue

value: brain (cerebellum) tissue


description:
design description: RNA-Seq analysis of pancreas islet from ZD4 273 (A18759) using Illumina HiSeq 2000
library name: A18759
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.7
RNA_PREPARATION_INITIAL_RNA_QNTY: 4.86 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 275-470 bp
****************
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: GSM1127105_UCSF-UBC.Pancreatic_Islets.mRNA-Seq.ZD4_273.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18759-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Pancreatic Islets, Donor ZD4 273 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.16991
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 393,795,743
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.41
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127105_UCSF-UBC.Pancreatic_Islets.mRNA-Seq.ZD4_273.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18759-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Pancreatic Islets, Donor ZD4 273 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.17007
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI mRNA 73 59
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets mRNA-Seq Donor ZD4 273 Library A18759 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 393,795,743
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.41
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Pancreas

value: Islet

value: primary cell

value: pancreas islet


description:
design description: RNA-Seq analysis of breast variant human mammary epithelial cell from RM071 (A18761) using Illumina HiSeq 2000
library name: A18761
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.24 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 280-509 bp
****************
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: GSM1127094_UCSF-UBC.Breast_vHMEC.mRNA-Seq.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18761-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast vHMEC mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast vHMEC, Donor RM071 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.16985
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 365,385,279
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.87
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

ANALYSIS FILE NAME: GSM1127094_UCSF-UBC.Breast_vHMEC.mRNA-Seq.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18761-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast vHMEC, Donor RM071 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.17001
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Bv mRNA 71 61
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast vHMEC mRNA-Seq Donor RM071 Library A18761 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 365,385,279
PERCENT_READS_MAPPING_TO_UCSC_GENES: 95.87
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

value: Breast

value: Variant human mammary epithelial cell culture

value: No


description:
design description: RNA-Seq analysis of placenta (amniotic membrane) tissue from CTL01 (A19256) using Illumina HiSeq 2000
library name: A19256
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN N/A
RNA_PREPARATION_INITIAL_RNA_QNTY: 4.10 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 222-318 bp
****************
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: GSM1127095_UCSF-UBC.Placenta_Amnion.mRNA-Seq.CTL01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19256-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Amnion, Donor CTL01 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.16986
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 417,718,630
PERCENT_READS_MAPPING_TO_UCSC_GENES: 85.08
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

ANALYSIS FILE NAME: GSM1127095_UCSF-UBC.Placenta_Amnion.mRNA-Seq.CTL01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19256-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Amnion, Donor CTL01 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.17002
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PA mRNA 01 56
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion mRNA-Seq Donor CTL01 Library A19256 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 417,718,630
PERCENT_READS_MAPPING_TO_UCSC_GENES: 85.08
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

value: Placenta

value: Amnion tissue

value: placenta (amniotic membrane) tissue


title: K562

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

description: chronic myelogenous leukemia (CML)

data_processing:
Human genome (release 55) from Ensembl database was used as reference to do read mapping. We also constructed an Exon–exon Junction Database for reads mapping with randomly combination of 49 bp sequences near each exonic junction points. We first mapped the full length 50 bp reads to the ribosomal RNA database to wipe off the disturbance of remnants of rRNA. The left data were then aligned with Human genome and exon junction database for annotation, with the allowance of five mismatches, and then the last 5 bp were cut off from unmapped tags for the next matching with chromosome and exon junction database (allowing five mismatches) to increase annotation rate of raw data. We repeated this step until remained length of the reads was 25bp and reduced the number of mismatches gradually from five to two. Finally, after these six steps, tags with matching information were collected for subsequent gene expression analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Mortazavi A, et al., Nature methods, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for K562

source_name: bone marrow

growth_protocol: K562 cells were culture  in the culture flask containing RPMI 1640 medium (Gibco) supplied with 10% fetal bovine serum (Hylone) and penicillin (100 U/ml)-streptomycin (0.1 mg/ml) (Invitrogen, Carlsbad, CA).

extract_protocol: SOLiD RNA-seq with Invitrogen ribominus kit

value: blood

tag: cell line


description:
design description: RNA-Seq analysis of placenta (basal plate and villi) tissue from CTL03 (A19262) using Illumina HiSeq 2000
library name: A19262
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.3
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 250-470 bp
****************
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: GSM1127096_UCSF-UBC.Placenta_Basal_Plate.mRNA-Seq.CTL03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19262-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Basal Plate mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Basal Plate, Donor CTL03 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.16996
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 351,811,061
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.6
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1127096_UCSF-UBC.Placenta_Basal_Plate.mRNA-Seq.CTL03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19262-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Basal Plate mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Basal Plate, Donor CTL03 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.17012
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PBP mRNA 03 62
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Basal Plate mRNA-Seq Donor CTL03 Library A19262 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 351,811,061
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.6
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

value: Basal plate tissue

value: placenta (basal plate and villi) tissue


description:
design description: RNA-Seq analysis of breast fibroblast from RM071 (A18472) using Illumina HiSeq 2000
library name: A18472
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.7
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 266-470 bp
****************
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: GSM1127100_UCSF-UBC.Breast_Fibroblast_Primary_Cells.mRNA-Seq.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18472-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Fibroblast Primary Cells, Donor RM071 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.16998
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 387,151,529
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1127100_UCSF-UBC.Breast_Fibroblast_Primary_Cells.mRNA-Seq.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18472-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 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.17014
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BF mRNA 71 72
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells mRNA-Seq Donor RM071 Library A18472 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 387,151,529
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

value: female

value: Fibroblast cultured cell

value: primary cell culture

value: breast fibroblast


title: polyA RNA sequencing of STL001 Spleen Cells; polyA-RNA-seq_STL001SX_r1a

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL001 Spleen Cells
Library name: polyA-RNA-seq_STL001SX_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15456
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15438
****************
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: GSM1120316_UCSD.Spleen.mRNA-Seq.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001SX_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Spleen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Spleen, Donor STL001 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.16726
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,867,274
PERCENT_READS_MAPPING_TO_UCSC_GENES: 77.8
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 0.45

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

ANALYSIS FILE NAME: GSM1120316_UCSD.Spleen.mRNA-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001SX_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Spleen, Donor STL001 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.16761
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Spleen mRNA 01
BROWSER_TRACK_DESCRIPTION: UCSD Spleen mRNA-Seq Donor STL001 Library polyA-RNA-seq_STL001SX_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,867,274
PERCENT_READS_MAPPING_TO_UCSC_GENES: 77.8
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 0.45

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

extract_protocol: Library construction protocol: Four µg of total RNA was extracted from frozen cell pellets using the RNeasy Mini Kit (Qiagen, Valencia, CA). PolyA RNA was isolated from total RNA using Dynabeads oligo(dt)25 (Invitrogen). PolyA selected RNA was eluted in 2x Superscript III buffer supplemented with 10mM DTT and was fragmented by incubation at 94°C for 4 minutes. First-strand cDNA was synthesized with the following reaction composition: 0.5 µL random hexamer, 0.5 µL RNase Out, 1 µL DTT (100 mM), 0.5 µL dNTP (25 mM), 0.5 µL SuperScript III (20 µL final). The reaction was incubated at 25°C for 10 min then 50°C for 50 min.  Single-stranded cDNA was isolated by purification with RNAClean XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing second-strand was synthesized with the following reaction: 1.5 µL NEBuffer 2 (NEB), 1 µL dNTP mix (10 mM dATP, dCTP, dGTP, and dUTP), 0.2 µL RNase H, 1 µL DNA Polymerase I (E. coli) (New England Biolabs) (15 µL final). The reaction was incubated at 16°C for 2.5 hours. The dUTP-containing cDNA was isolated by purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing cDNA was then end repaired and a 3'A base was added. TruSeq adapters (Illumina, San Diego, CA) were ligated to the dUTP-containing cDNA at 16°C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated cDNA was isolated by two rounds of purification with AMPure XP beads. The dUTP-containing strands were digested at 37°C for 30 min with uracil DNA glycosylase (Enzymatics). Adapter-ligated, single-stranded DNA molecules were enriched by 10 cycles of PCR with the following reaction composition: 5 µL TruSeq PCR Primer Cocktail (Illumina), 25 µL TruSeq PCR Master Mix (Illumina) (50 µL final). The thermocycling parameters were: 98°C 30 sec, then 10-15 cycles of 98°C 10 sec, 60°C 30 sec and 72°C 30 sec, ending with one 72°C 5 min step. The reaction products were purified using AMPure XP beads.

tag: sample alias

tag: sample common name

value: Spleen

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: polyA RNA sequencing of STL002 Spleen Cells; polyA-RNA-seq_STL002SX_r1a

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL002 Spleen Cells
Library name: polyA-RNA-seq_STL002SX_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15457
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14062
****************
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: GSM1120317_UCSD.Spleen.mRNA-Seq.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002SX_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Spleen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Spleen, Donor STL002 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.16727
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,541,066
PERCENT_READS_MAPPING_TO_UCSC_GENES: 79.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.49

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

ANALYSIS FILE NAME: GSM1120317_UCSD.Spleen.mRNA-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002SX_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Spleen, Donor STL002 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.16762
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Spleen mRNA 02
BROWSER_TRACK_DESCRIPTION: UCSD Spleen mRNA-Seq Donor STL002 Library polyA-RNA-seq_STL002SX_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,541,066
PERCENT_READS_MAPPING_TO_UCSC_GENES: 79.96
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.49

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

value: Spleen

tag: sra sample accession

tag: disease

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)


title: polyA RNA sequencing of STL002 Small Bowel Cells; polyA-RNA-seq_STL002SB_r1a

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL002 Small Bowel Cells
Library name: polyA-RNA-seq_STL002SB_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15453
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14055
****************
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: GSM1120313_UCSD.Small_Intestine.mRNA-Seq.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002SB_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Small Intestine, Donor STL002 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.16725
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,944,319
PERCENT_READS_MAPPING_TO_UCSC_GENES: 80.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.36

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

ANALYSIS FILE NAME: GSM1120313_UCSD.Small_Intestine.mRNA-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002SB_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Small Intestine, Donor STL002 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.16760
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SI mRNA 02
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine mRNA-Seq Donor STL002 Library polyA-RNA-seq_STL002SB_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,944,319
PERCENT_READS_MAPPING_TO_UCSC_GENES: 80.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.36

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

source_name: Small Intestine tissue; polyA-RNA-seq_STL002SB_r1a

value: Small Intestine

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL