title: LIN28ES CLIPseq

first: Gene

last: Yeo

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

institute: UCSD

description: Cross-linking IP against LIN28

data_processing:
Read mapping from CLIP-seq experiments and data processing was performed as published (Polymenidou et al., 2011). Briefly, reads were processed and mapped to the human genome (hg18 http://genome.ucsc.edu; Bowtie version 0.12.2, with parameters -q -p 4 -e 70 -y -l 25 -n 2 -m 5 --best --strata) and assigned to 21,605 genes (as annotated previously (Yeo et al., 2009)).
Genome Build:
LIN28ES_CLIPseq_clusters.BED: hg18

source_name: H9 human ES cells

growth_protocol: HEK293 cells containing an integrated Flp-In site (Flp-In-293; Life Technologies) were cultured in DMEM media supplemented with 10% FBS and 2mM L-glutamine and passaged using TrypLE (LifeTechnologies). Human ES cell-lines H9 and HUES6 were grown in feeder-free conditions with mTeSR media (Stemcell Technologies) and on Matrigel (BD Biosciences) for support. Cells were passaged manually or with Dispase (BD Biosciences) every 5-7 days.

extract_protocol: Confluent human H9 or LIN28-V5 293 cells were subjected to UV cross-linking on ice. CLIP-seq libraries were constructed for LIN28 as previously described (Yeo et al., 2009) using an antibody against endogenous LIN28 (Abcam ab46020) in H9 cells, or an antibody to the V5 epitope (Sigma V8137) in LIN28-V5 293 cells. The Illumina adapter sequence TCGTATGCCGTCTTCTGCTTG was used in library preparation.

treatment_protocol: To generate the LIN28-V5 293 stable cell line, pEF5/FRT/LIN28-V5 plasmid was co-transfected along with the FLP Recombinase expressing plasmid pOG44 into Flp-In-293 cells using Lipofectamine-2000 (Life Technologies) according to the manufacturer’s instructions. Recombination and insertion of LIN28-V5 at the Flp-In site confers stable integration and expression of the LIN28-V5 fusion protein and hygromycin resistance. Stably transected clones were selected and propagated in media supplemented with 75-100 μg/ml hygromycin B (Life Technologies).

tag: cell line

value: LIN28 (Abcam ab46020)

tag: antibody manufactuer

tag: antibody catalog number


title: LICR_ChipSeq_SmIntestine_Input_adult-8wks

status: Public on Sep 10 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: SmIntestine

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: SmIntestine

tag: cell organism

value: mouse

tag: cell description

value: Small Intestine

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion

value: Bowtie

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Limb_Input_E14.5

source_name: Limb

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Limb

value: U

value: Embryonic day 14.5


title: LICR_ChipSeq_BAT_H3K4me1_adult-24wks

source_name: BAT

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: BAT

tag: cell organism

tag: cell description

value: Brown adipocytes tissue

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

tag: antibody targetdescription

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: Adult 24 weeks

value: Pooled & filtered

value: MACS


title: LICR_ChipSeq_SmIntestine_H3K27ac_adult-8wks

value: ChipSeq

value: Chromatin IP Sequencing

value: SmIntestine

value: mouse

value: Small Intestine

value: M

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K27ac

value: Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

tag: controlid

tag: labversion


title: H9 small RNA

city: La Jolla

description: strand-specific smallRNAseq

library_source: transcriptomic

data_processing:
Small RNA reads were mapped to the human (hg19) genome using Bowtie short read aligner (Langmead et al., 2009) and associated with coordinates of known miRNAs from mirBase18 (Griffiths-Jones, 2004; Kozomara and Griffiths-Jones, 2011). We required exact 5' end alignment to the canonical miRNAs for read alignments. An expression value for each miRNA was calculated using the metric RPM; reads mapped to the mature miRNA normalized to the number of million mapped reads. Changes in miRNA expression were calculated by Z-score analyses of the log2 fold change (RPM LIN28-V5 over RPM Flp-In-293 cells) for all miRNAs with an RPM >= 1.  Mature miRNAs with an absolute Z-score >= 2 and an RPM > 1 in both cell types were considered significantly changed.
Genome Build:
H9_smallRNA_RPM.txt: hg19

molecule: total RNA

organism: Homo sapiens

extract_protocol: Small RNA libraries were generated from total RNA isolated from H9, untreated Flp-In-293, and LIN28-V5 293 cell line. H9 RNA was treated as described in Illumina's Small RNA Digital Gene Expression v1.5 protocol, using the supplied adapters. RNA extracted from Flp-In-293 and LIN28-V5 293 cells was treated as described in Illumina's Small RNA Digital Gene Expression v1.5 protocol, with the exception of custom oligonucleotide adapters and primers used which matched those of Illumina's TruSeq Small RNA Sample Preparation protocol. For all samples, 2µg total RNA was ligated with a 3' pre-adenylated adaptor using T4 RNA ligase 2, truncated (NEB), followed by ligation of a 5' adaptor using T4 RNA ligase 1 (NEB). First-strand cDNA synthesis was performed using Superscript II (Life Technologies). DNA was amplified using 13 cycles of PCR with Phusion polymerase (Finnzymes). DNA products (H9: 85-115bp; Flp-In-293 and LIN28-V5 293: 135-160bp) were purified using a 6% non-denaturing TBE acrylamide gel (Life Technologies). Flp-In-293 and LIN28-V5 293 libraries contained the Illumina Truseq barcode indices 6 and 5, respectively. DNA products were eluted by diffusion, filtered using Spin-X columns (Costar), and precipitated. DNA was quantified using Quant-It PicoGreen (Life Technologies). If barcoded, libraries were mixed, and 17.5fmol of cDNA per flow cell lane was sequenced on the Illumina GAII for 36 cycles.

tag: cell line

tag: treatment

value: Untreated H9 human ES cells


title: LIN28V5-293 small RNA

description: strand-specific smallRNAseq

data_processing:
Small RNA reads were mapped to the human (hg19) genome using Bowtie short read aligner (Langmead et al., 2009) and associated with coordinates of known miRNAs from mirBase18 (Griffiths-Jones, 2004; Kozomara and Griffiths-Jones, 2011). We required exact 5' end alignment to the canonical miRNAs for read alignments. An expression value for each miRNA was calculated using the metric RPM; reads mapped to the mature miRNA normalized to the number of million mapped reads. Changes in miRNA expression were calculated by Z-score analyses of the log2 fold change (RPM LIN28-V5 over RPM Flp-In-293 cells) for all miRNAs with an RPM >= 1.  Mature miRNAs with an absolute Z-score >= 2 and an RPM > 1 in both cell types were considered significantly changed.
Genome Build:
LIN28V5_smallRNA_RPM.txt: hg19

source_name: human LIN28-V5 293 stable cells

value: LIN28 Flp-In-293


title: LIN28KD H9 RNAseq

description: strand-specific RNAseq

data_processing:
Strand-specific RNA-seq reads were mapped to our annotated gene structure hg18 database (Bowtie version 0.12.2, with parameters –q -e 70 –y –l 25 –n 2 –m 5 –k 5 --best --strata). We measured gene expression as the number of reads uniquely mapped to exons of a gene, per kilobase of exon sequence for that gene, normalized by the total number of million mapped reads to genes (RPKM). Differentially expressed genes were identified using a Z-score analysis as previously described with a cutoff of Z < -2 (downregulated) or Z > 2 (upregulated) (Polymenidou et al., 2011).
Genome Build:
LIN28KD_H9_rnaseq_RPKM.txt: hg18

growth_protocol: Human ES cell-lines H9 and HUES6 were grown in feeder-free conditions with mTeSR media (Stemcell Technologies) and on Matrigel (BD Biosciences) for support. Cells were passaged manually or with Dispase (BD Biosciences) every 5-7 days.

extract_protocol: We used one round of polyA selection with Oligo (dT)25 Dynabeads (Life Technologies) according to manufacturer’s recommendations to isolate mRNA from 3-9 µg total RNA. This mRNA was then fragmented with the Ambion RNA Fragmentation kit (AM8740) according to the manufacturer’s instructions. The fragmented RNA was phosphorylated with T4 polynucleokinase (PNK), and subjected to the small RNA-seq protocol v1.5 (Illumina) as per manufacturer’s instruction and bands corresponding to 110-160bp fragments extracted for sequencing.

treatment_protocol: To achieve knockdown of LIN28 in hES cells, we utilized an shRNA construct targeting human LIN28A in the pLKO.1 vector (TRCN0000102579; Open Biosystems). As a control, a pLKO.1 vector containing an shRNA toward GFP was used (Open Biosystems). Lentivirus expressing these constructs was prepared in 293T cells, as previously described (Yeo et al., 2009). Human ES cells were treated with Accutase to generate single cell suspensions and infected with LIN28 or matched control GFP virus. The media was changed daily and cells were harvested 72 hours after infection.

value: LIN28 shRNA (TRCN0000102579; Open Biosystems)


title: Flp-In-293 small RNA

description: strand-specific smallRNAseq

data_processing:
Small RNA reads were mapped to the human (hg19) genome using Bowtie short read aligner (Langmead et al., 2009) and associated with coordinates of known miRNAs from mirBase18 (Griffiths-Jones, 2004; Kozomara and Griffiths-Jones, 2011). We required exact 5' end alignment to the canonical miRNAs for read alignments. An expression value for each miRNA was calculated using the metric RPM; reads mapped to the mature miRNA normalized to the number of million mapped reads. Changes in miRNA expression were calculated by Z-score analyses of the log2 fold change (RPM LIN28-V5 over RPM Flp-In-293 cells) for all miRNAs with an RPM >= 1.  Mature miRNAs with an absolute Z-score >= 2 and an RPM > 1 in both cell types were considered significantly changed.
Genome Build:
Flp-In-293_smallRNA_RPM.txt: hg19

source_name: human Flp-In-293 cells

value: Untreated Flp-In-293


title: LIN28V5 CLIPseq

description: Cross-linking IP against LIN28-V5

data_processing:
Read mapping from CLIP-seq experiments and data processing was performed as published (Polymenidou et al., 2011). Briefly, reads were processed and mapped to the human genome (hg18 http://genome.ucsc.edu; Bowtie version 0.12.2, with parameters -q -p 4 -e 70 -y -l 25 -n 2 -m 5 --best --strata) and assigned to 21,605 genes (as annotated previously (Yeo et al., 2009)).
Genome Build:
LIN28V5_CLIPseq_clusters.BED: hg18

value: V5 (Sigma V8137)

tag: antibody manufactuer

value: Sigma

tag: antibody catalog number


title: 75°C_biological_replicate2

status: Public on Sep 09 2012

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description:
H10
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 75°C-replicate2.

data_processing:
The yeast genome was downloaded from the Saccharomyces Genome Database (SGD, http://www.yeastgenome.org). The yeast transcriptome was assembled using SGD annotations (downloaded June 2008). The length of the untranslated regions (UTRs) for each transcript was taken from Nagalakshmi et al., 2008 (PMID 18451266).
Raw reads were mapped to the yeast transcriptome using SHRiMP2.
V1 reads were normalized to the library size of each sequencing lane. This size could be simply estimated by the total mapped reads of that lane. But this estimate can be severely biased (Bullard et al., 2010; Li, J., Witten, D. M., Johnstone, I.,Tibshirani, R., 2011; Robinson and Oshlack, 2010) as reads at melted bases are dispersed to other bases. To reduce this bias, we instead applied PoissonSeq (Li, J., Witten, D. M., Johnstone, I., Tibshirani, R., 2012 (PMID 22003245)), which makes an estimate of those bases that are likely to be stable under different temperatures based on the Poisson goodness-of-fit statistic and then estimates the sizes using reads of these bases. Since the inclusion of positions with few reads lowers the accuracy of PoissonSeq, the data that we input into PoissonSeq was not reads on all bases, but only at bases that are peaks in both duplicated libraries of at least one of the five temperatures. In each library, a peak was defined as a base whose number of reads is larger than (1) the base on its left and the base on its right, (2) the average of bases on the same gene, and (3) the average of all bases. In total, 231,068 bases were selected. Using these estimated library sizes, we divided counts from each sample by the corresponding size. The log2 of these normalized reads were then treated as the V1 scores.
Genome_build: June 2008 (SGD/sacCer2)
Supplementary_files_format_and_content: Tab-delimited text file (GSE39680_processed.txt) with genes and their base readings for each sample. This file is linked to the Series record as a supplementary file.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: polyA RNA, RNase V1 at 75°C

growth_protocol: Yeast strain S288C was grown at 30°C to log phase (~4x10^7 cells/ml) in YPD medium.

extract_protocol: RNA was isolated from yeast cells using the Poly(A)Purist MAG Kit (Life Technologies). The cleavage sites were captured and cloned using SOLiD™ Small RNA Expression Kit (Ambion).

treatment_protocol: PolyA-isolated RNA was folded and structure probed at 23°C, 30°C, 37°C, 55°C and 75°C.

tag: strain

tag: growth phase

value: log

tag: folding and cutting temperature


title: 75°C_biological_replicate1

description:
H9
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 75°C-replicate1.


title: uninfected H9 RNAseq

description: strand-specific RNAseq

data_processing:
Strand-specific RNA-seq reads were mapped to our annotated gene structure hg18 database (Bowtie version 0.12.2, with parameters –q -e 70 –y –l 25 –n 2 –m 5 –k 5 --best --strata). We measured gene expression as the number of reads uniquely mapped to exons of a gene, per kilobase of exon sequence for that gene, normalized by the total number of million mapped reads to genes (RPKM). Differentially expressed genes were identified using a Z-score analysis as previously described with a cutoff of Z < -2 (downregulated) or Z > 2 (upregulated) (Polymenidou et al., 2011).
Genome Build:
uninfected_H9_rnaseq_RPKM.txt: hg18

extract_protocol: We used one round of polyA selection with Oligo (dT)25 Dynabeads (Life Technologies) according to manufacturer’s recommendations to isolate mRNA from 3-9 µg total RNA. This mRNA was then fragmented with the Ambion RNA Fragmentation kit (AM8740) according to the manufacturer’s instructions. The fragmented RNA was phosphorylated with T4 polynucleokinase (PNK), and subjected to the small RNA-seq protocol v1.5 (Illumina) as per manufacturer’s instruction and bands corresponding to 110-160bp fragments extracted for sequencing. The Illumina adapter sequence ATCTCGTATGCCGTCTTCTGCTTG was used in library preparation.


title: LICR_ChipSeq_Spleen_H3K36me3_adult-8wks

source_name: Spleen

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

value: Spleen

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K36me3

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts.

value: Abcam

value: Standard input signal for most experiments.

value: Pooled & filtered

tag: softwareversion

value: MACS

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_BMDM_H3K4me1_adult-8wks

source_name: BMDM

value: Chromatin IP Sequencing

value: BMDM

value: mouse

value: Bone marrow derived macrophage

value: F

tag: antibody

value: rabbit polyclonal. Antibody Target:H3K4me1

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: antibody vendorname

tag: antibody vendorid

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

tag: controlid

tag: labversion


title: LICR_ChipSeq_SmIntestine_H3K27me3_adult-8wks

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: tissue

value: Small Intestine

tag: Sex

value: M

value: rabbit polyclonal. Antibody Target:H3K27me3

value: Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci.

value: Millipore

tag: strain


title: 55°C_biological_replicate1

description:
H7
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 55°C-replicate1.

source_name: polyA RNA, RNase V1 at 55°C

tag: growth phase

value: log

tag: folding and cutting temperature


title: 37°C_biological_replicate1

description:
H5
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 37°C-replicate1.

source_name: polyA RNA, RNase V1 at 37°C


title: 37°C_biological_replicate2

description:
H6
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 37°C-replicate2.


title: 30°C_biological_replicate1

description:
H3
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 30°C-replicate1.

source_name: polyA RNA, RNase V1 at 30°C


title: 30°C_biological_replicate2

description:
H4
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 30°C-replicate2.


title: 23°C_biological_replicate1

description:
H1
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 23°C-replicate1.

source_name: polyA RNA, RNase V1 at 23°C


title: nTreg_Input_Biotin_ChIPseq

status: Public on Sep 07 2012

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

data_processing:
Basecalls performed using CASAVA v1.4
Bowtie v0.12.7 was used to identify sequences mapping uniquely to the genome
Peak calls were determined using MACS v1.4
Overlapping peaks between antibody and biotin ChIP methods were merged
Genome_build: mm9
Supplementary_files_format_and_content: BED files for uniquely mapping reads and called MACS peaks for Antibody, Biotin, and overlapping peaks are provided

source_name: nTreg cells, Foxo1tagBirA mice

extract_protocol: Foxo1 Ab- and Streptavidin-precipitated chromatin DNA samples were extracted with Phenol-Chloroform-Isoamyl Alcohol, and then precipitated with 1/10V 3M Sodium Acetate (pH5.2) and 2V ethanol. Lysates were clarified from sonicated nuclei and Foxo1-DNA complexes were isolated with antibody or Streptavidin. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a kit from Epicentre. The blunt, phosphorylated ends were treated with Taq DNA polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-19 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: nTreg, Foxo1tagBirA strepdavidin Input

tag: chip antibody


title: CTCF #2

status: Public on Sep 08 2012

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

data_processing: Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/) on 1/15/10.!Sample_data_processing = Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.!Sample_data_processing = SNP-containing reads were extracted using custom scripts.!Sample_data_processing = Genome_build: mm9!Sample_data_processing = Supplementary_files_format_and_content: WIG and BED files were generated from mm9 alignments, and reported read ends reflect average fragment size of corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.

source_name: F1 C/B trophoblast stem cells

growth_protocol: TSCs were grown under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To eliminate feeder cell contamination of TSC RNA and chromatin preparations, TSC cultures grown on sub-lethally irradiated feeders were trypsinized and pre-plated for 40 minutes before transferring to new plates. TSC cultures were then split an additional 2x or 4x before harvesting cells for chromatin and RNA, respectively.

extract_protocol: Strand-specific RNA-Seq libraries were prepared according to (Ingolia NT, et al. Science. 2009). ChIP-Seq libraries were prepared according to Illumina instructions. FAIRE-Seq libraries were prepared according to  (Giresi PG, Lieb JD. Methods. 2009). DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2009).

tag: antibody

value: CTCF (Pugacheva et. al. 2005 Hum Mol Genet 14, 953-965)

value: F1 C/B trophoblast stem cells

tag: data type

value: ChIP-Seq

tag: parent of origin

value: CAST/EiJ mother X C57BL/6J father

tag: tsc passage number

tag: total obtained reads


title: Mouse P6 Sertoli Cells

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description: Two nucleotide barcode tag for Sertoli sequences is NA

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
Novel endo-siRNA detection was performed using Sequery - www.medicine.nevada.edu/yan/sequery.html
Novel miRNA detection was performed using MIREAP - http://sourceforge.net/projects/MIREAP
Novel snoRNA detection was performed using snoREPORT - http://www.bioinf.uni-leipzig.de/Software/snoReport
Novel piRNA-like detection was determined by remaining unannotated sequence lengths (24-32 nts).
Genome_build: mm9
Supplementary_files_format_and_content: gff file contains novel small RNAs and their genomic locations

source_name: Sertoli Cells

extract_protocol:
Ro S, Yan W. Small RNA Cloning. In: Sioud M (ed.) RNA Therapeutics: Function, Design, and Delivery: Humana Press Inc; 2010: 271-283
Barcoded and Prepared per 454 library preparation protocol.

tag: age

value: post-natal day 6

value: pooled Sertoli cells

tag: cell purity

tag: molecule subtype

value: small RNA


title: M_Cux2_ChIPSeq_G62M1_M3

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Chromatin IP using Cux2 antibody

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

source_name: liver tissue

growth_protocol: Male and female CD-1 mice (Charles River Laboratories), 8 weeks old, were euthanized and their livers extracted.

extract_protocol: Multiplexed samples were prepared for Illumina sequencing using standard Illumina methods. For the CUX2 antibody, a GST protein fused to CUX2 amino acids 356 to 415 was gifted to us from Dr. Alain Nepveu.  The GST-CUX2 356 protein was used to inoculate New Zealand white rabbits by Pro Sci, Inc (Poway, CA) and we affinity purified the serum through GST and GST-CUX2 356 columns.

value: CD-1 (Charles River)

value: male

value: 8 weeks old


title: nTreg_Input_Ab_ChIPseq

source_name: nTreg cells

value: nTreg, Foxo1 Ab Input


title: nTreg_Foxo1_Ab_ChIPseq

value: nTreg, Foxo1 Ab, ChIP

value: Foxo1 antibody (Abcam, Ab39670, lot#GR16346-7)


title: nTreg_Foxo1_Biotin_ChIPseq

value: nTreg, Foxo1tagBirA strepdavidin ChIP

value: Strepdavidin


title: 55°C_biological_replicate2

description:
H8
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 55°C-replicate2.

value: log


title: input DNA

status: Public on Sep 06 2012

city: Research Triangle Park

first: Franco

last: DeMayo

address: Building 101, Room F191 111 T.W. Alexander Drive

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

data_processing:
3_uterus_Input_s_5_aligned.xls; genome build: mm9
DNA libraries were sent to Illumina Sequencing Services for sequencing on a Genome Analyzer II. Sequences (35 bases) were aligned to the mouse genome (NCBI Build 37, July 2007) using Eland software. Aligns were extended in silico at their 39-ends to a length of 110-200 bp and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Peak locations were determined by applying a threshold of 18 (5 consecutive bins containing .18 aligns) and storing the resulting intervals in BED files (Affymetrix TAS software). These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Mouse uterus

growth_protocol: 8 week old ovariectomized mice

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit. Briefly, DNA ends were polished and 59-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. Addition of 3’ adenine to blunt ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size-fractionated to 175–225 bp on a 2% agarose gel. After amplification for 18 cycles with Phusion polymerase, the resulting DNA libraries were tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions

treatment_protocol: treated subcutaneously with oil/P4 for 1 hr

tag: tissue

value: uterus

value: 8 week


title: PR_P4_ChIPSeq

data_processing:
2_PR_P4_s_1_aligned.xls; genome build: mm9
DNA libraries were sent to Illumina Sequencing Services for sequencing on a Genome Analyzer II. Sequences (35 bases) were aligned to the mouse genome (NCBI Build 37, July 2007) using Eland software. Aligns were extended in silico at their 39-ends to a length of 110-200 bp and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Peak locations were determined by applying a threshold of 18 (5 consecutive bins containing .18 aligns) and storing the resulting intervals in BED files (Affymetrix TAS software). These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

value: PR

tag: treatment


title: Ell2-KD rep2

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
Basecalling was done in colorspace calls using the standard SOLiD tool and ribosomal sequences were filtered out.
RNA-Seq reads were aligned to the mm9 genome assembly and the exon-exon junctions derived from RefSeq using Bioscope with the default parameters
From the set of aligned reads properly paired reads were extracted using samtools (v. 0.1.11).
The number of reads falling in the RefSeq genes were counted using HTSeq-count (v. 0.5.3).
The differential expressed genes were detected using DESeq (v. 1.4.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample. The read counts were counted using HTSeq-count (v. 0.5.3).

growth_protocol: MPC11 cells were transduced overnight with pLKO.1-shGFP or pLKO.1-shELL2-1C7 lentivirus and polybrene according to standard protocols in a six-well plate format. After 18 hours, media was removed and fresh media with puromycin added, with selection allowed to occur for 72 hours. Cells were split and expanded for an addition 72 hours, whereupon cells were harvested and mRNA purified.

extract_protocol: RNA was purified using Qiagen RNeasy columns, with ELL2 transcript levels as well as mIg/sIg ratios analyzed prior to RNA-Seq to ensure the appropriate phenotype. Two biological replicates of total RNA for each treatment group were prepared for SOLiD RNA-Seq according to the manufacturers recommendations.

treatment_protocol: MPC11 cell line was purchased from ATCC and cultured in RPMI + 10% FBS.

value: plasmacytoma cell line

tag: cell line

tag: genotype/variation


title: PR_Oil_ChIPSeq

data_processing:
1_PR_oil_s_4_aligned.xls; genome build: mm9
DNA libraries were sent to Illumina Sequencing Services for sequencing on a Genome Analyzer II. Sequences (35 bases) were aligned to the mouse genome (NCBI Build 37, July 2007) using Eland software. Aligns were extended in silico at their 39-ends to a length of 110-200 bp and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Peak locations were determined by applying a threshold of 18 (5 consecutive bins containing .18 aligns) and storing the resulting intervals in BED files (Affymetrix TAS software). These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

tag: strain

value: oil


title: Ell2-KD rep1


title: LICR_ChipSeq_CH12_H3K27ac_immortalized

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: line

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27ac

tag: antibody targetdescription

value: Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

value: immortalized

value: immortalized cell line

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

value: Pooled & filtered

tag: softwareversion

value: MACS

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: shGFP rep2

tag: cell type

value: plasmacytoma cell line

tag: cell line

tag: genotype/variation

value: shGFP


title: LC_S49_nor

city: Houston

first: Won-Chul

last: Lee

address: 1881 East Road

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA sequencing reads were aligned to the NCBI human reference genome assembly (build 37.1) using GSNAP (Wu and Nacu, Bioinformatics, 2010) with allowance for 5% mismatches.
RNA sequencing reads were also aligned to a cDNA set consisting of 161,250 mRNA sequences obtained from public databases (36,742 RefSeq, 73,671 UCSC, and 161,214 Ensembl) to decrease the false positives and false negatives in variant detection from RNA sequencing data (Ju et al., Nature Genetics, 2011; Ju et al., Genome Researcg, 2012).
For each gene, the number of reads aligned to it (raw read count) was normalized by RPKM (reads per kilobase per million mapped reads) (Mortazavi et al., Nature Methods, 2008).
Genome_build: human NCBI genome build 37.1
Supplementary_files_format_and_content: The 'LC-87_RPKM_expression.txt' file includes RPKM values for each sample. "accession" represents NCBI RefSeq accession number, "chrom" represents chromosome number, "start" represents the gene's genomic start position, "end" represents the gene's genomic end position and "strand" represents the gene's trascribed strand.

source_name: Adjacent lung normal cells

extract_protocol: RNAs were extracted from tissue using RNAiso Plus (Takara Bio Inc.), followed by purification using RNeasy MinElute (Qiagen Inc.). RNAs were assessed for quality and was quantified using an RNA 6000 Nano LabChip on a 2100 Bioanalyzer (Agilent Inc.).

tag: gender

value: female

value: never smoker

tag: Stage


title: LC_S47_nor


title: LC_S48_nor


title: 23°C_biological_replicate2

description:
H2
cDNA
RNA structure probing and deep sequencing of double-stranded regions in the yeast transcriptome at 23°C-replicate2.

tag: strain

tag: growth phase

value: log

tag: folding and cutting temperature


title: LC_S50_nor


title: LC_S44_nor


title: LC_S46_nor

value: male


title: LC_S45_nor


title: Epith_P4_ChIPSeq

data_processing:
4_epith_P4_s_1_aligned.xls; genome build: mm9
DNA libraries were sent to Illumina Sequencing Services for sequencing on a Genome Analyzer II. Sequences (35 bases) were aligned to the mouse genome (NCBI Build 37, July 2007) using Eland software. Aligns were extended in silico at their 39-ends to a length of 110-200 bp and assigned to 32-nt bins along the genome. The resulting histograms were stored in BAR (Binary Analysis Results) files. Peak locations were determined by applying a threshold of 18 (5 consecutive bins containing .18 aligns) and storing the resulting intervals in BED files (Affymetrix TAS software). These files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals).
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Mouse uterus epithelium

tag: tissue

value: uterus

tag: age

value: 8 week

tag: chip antibody

value: PR

tag: treatment


title: LC_S52_nor

value: smoker


title: LC_S41_nor


title: LC_S42_nor


title: LC_S39_nor


title: LC_S38_nor

value: current smoker


title: LC_S40_nor


title: shGFP rep1


title: LC_S36_nor


title: LC_S37_nor


title: LC_S35_nor


title: LC_S33_nor


title: LC_S34_nor


title: LC_S29_nor


title: LC_S28_nor


title: LC_S32_nor


title: LC_S31_nor


title: LC_S27_nor


title: LC_S23_nor


title: LC_S24_nor


title: LC_S25_nor


title: LC_S30_nor


title: LC_S22_nor


title: LC_S43_nor


title: LC_S26_nor


title: LC_S19_nor


title: LC_S20_nor


title: LC_S18_nor


title: LC_S17_nor


title: LC_S16_nor


title: LC_S14_nor


title: ControlKD H9 RNAseq

description: strand-specific RNAseq

data_processing:
Strand-specific RNA-seq reads were mapped to our annotated gene structure hg18 database (Bowtie version 0.12.2, with parameters –q -e 70 –y –l 25 –n 2 –m 5 –k 5 --best --strata). We measured gene expression as the number of reads uniquely mapped to exons of a gene, per kilobase of exon sequence for that gene, normalized by the total number of million mapped reads to genes (RPKM). Differentially expressed genes were identified using a Z-score analysis as previously described with a cutoff of Z < -2 (downregulated) or Z > 2 (upregulated) (Polymenidou et al., 2011).
Genome Build:
controlKD_H9_rnaseq_RPKM.txt: hg18

source_name: H9 human ES cells

value: GFP shRNA


title: LC_S15_nor


title: LC_S8_nor


title: LC_S13_nor


title: LC_S11_nor


title: LC_S10_nor


title: LC_S9_nor


title: LC_S6_nor


title: LC_S4_nor


title: LC_S3_nor


title: LC_S2_nor


title: LC_S1_nor


title: LC_S21_nor


title: LC_C36_nor


title: LC_C34_nor


title: LC_C29_nor


title: LC_C35_nor


title: LC_C28_nor


title: LC_C22_nor


title: LC_C21_nor


title: LC_C20_nor


title: LC_C19_nor


title: LC_C18_nor


title: LC_C17_nor


title: LC_S5_nor


title: LC_C14_nor


title: LC_C16_nor


title: LC_C12_nor


title: LC_C10_nor


title: LC_C11_nor


title: LC_C9_nor


title: LC_C33_nor


title: LC_C3_nor


title: LC_C5_nor


title: LC_C7_nor


title: LC_C2_nor


title: LC_C30_nor


title: LC_C25_nor


title: LC_C24_nor


title: LC_C31_nor


title: LC_C1_nor


title: LC_S51

source_name: Lung cancer cells


title: LC_S52


title: LC_S49


title: LC_S47


title: LC_S45


title: LC_S48


title: F_Cux2_ChIPSeq_G62M2_M4_G33

description: Chromatin IP using Cux2 antibody

value: CD-1 (Charles River)

tag: Sex

value: 8 weeks old

tag: antibody


title: LC_S50


title: LC_S46


title: LC_S44


title: LC_S43


title: LC_S42


title: LC_S41


title: LC_S40


title: LC_S37


title: LC_S35


title: LC_S39


title: LC_S36


title: LC_S38


title: LC_S34


title: LC_S32


title: LC_S28


title: LC_S27


title: LC_S30


title: LC_S33


title: LC_S25


title: LC_S29


title: LC_S22


title: LC_S23


title: LC_S24


title: LC_S26


title: LC_S19


title: LC_S21


title: LC_S18


title: LC_S20


title: LC_S31


title: LC_S15


title: LC_S14


title: LC_S13


title: LC_S12


title: LC_S17


title: LC_S9


title: LC_S5


title: LC_S4


title: LC_S10


title: LC_S8


title: LC_S2


title: LC_S3


title: LC_C36


title: LC_C35


title: LC_S1


title: LC_C33


title: LC_C34


title: LC_C31


title: LC_C32


title: LC_C26


title: LC_C27


title: LC_S16


title: LC_C28


title: LC_C30


title: LC_C29


title: LC_C23


title: LC_C22


title: LC_S11


title: LC_C20


title: LC_C24


title: LC_C19


title: LC_S6


title: LC_C17


title: LC_C21


title: LC_C16


title: LC_C15


title: LC_C18


title: LC_C14


title: LC_C13


title: LC_C9


title: LC_C10


title: LC_C25


title: LC_C11


title: LC_C7


title: LC_C8


title: LC_C6


title: LC_C5


title: LC_C3


title: LC_C1


title: LC_C4


title: LC_C2


title: w1118

status: Public on Sep 05 2012

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

data_processing:
Illumina Casava 1.7 was used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded.
Reads were then aligned against the D. melanogaster genome (dm3 genome assembly, BDGP Release 5.38) using Bowtie mapper (version 0.12.7)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools.
To compute gene expression, D. melanogaster GFF3 genome annotation from FlyBase (version 5.38) was used. All overlapping regions between alignments and referenced exons were counted.
Technical replicates coming from paired-end reads were first summed. Then, all samples were normalized together. Data were normalized according to the scaling normalization proposed by Robinson and Oshlack and implemented in the edgeR package version 1.6.10
A Fisher's Exact Test was then performed using the sage.test function of the statmod package version 1.4.6. Finally, a Benjamini and Hochberg (BH) P-value adjustment was made.
Genome_build: dm3 genome assembly, BDGP Release 5.38
Supplementary_files_format_and_content: tab-delimited text files include abundance estimation for each Sample. ID: transcript ID from modEncode Drosophila database, Type: feature annotation type according to the GFF format definition, Chromosome: chromsome reference, Start: genomic start position of the feature, End: genomic end position of the feature, Strand: genomic strand position + or - of the feature, length: full length of the feature, FullCovered: boolean that indicates is the feature is fully covered by reads, BasesNotCovered: the number of bases not covered by any reads after mapping, Ratio: the feature abundance among all the feature list, Count: the raw read count covering the feature

organism: Drosophila melanogaster

source_name: pools of wing imaginal discs

extract_protocol: Wing imaginal discs of third instar larvae (one disc per larva) were dissected by batches of 50 in PBS and frozen in liquid nitrogen. 300 discs (6 batches) were pooled and homogenized in lysis buffer using a FastPrep-24 during 20 s at 4m.s-1 (MP Biomedicals, Lysing Matrix D). Total RNA were extracted using RNeasy® kit (Quiagen). Library preparation and Illumina sequencing (multiplexed 50 bp paired-end sequencing on HiSeq 2000) were performed at the BC Cancer Agency Genome Sciences Center (Canada) following the manufacturer's protocol.

value: Wing imaginal discs

tag: developmental stage

value: Third instar larvae

tag: genotype


title: sd::Gal4/+


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: RNA-Seq analysis of cortex neural stem and progenitor cells from HuFNSC04 (A15298) using Illumina HiSeq 2000
library name: A15298
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 10
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 234-473 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: GSM958176_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15298-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC04 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.13746
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 375,100,761
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 82.85
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.74

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

ANALYSIS FILE NAME: GSM958176_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.mRNA-Seq.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15298-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC04 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.13754
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 8
BROWSER_TRACK_NAME: NCD mRNA 04 98
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC04 Library A15298 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 375,100,761
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 82.85
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.74

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

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: Brain

tag: histological type

value: Cortex neurosphere culture

tag: is tumor

value: No

value: primary cell culture

value: cortex neural stem and progenitor cells


description:
design description: RNA-Seq analysis of UCSF-4 embryonic stem cell line (A11831) using Illumina HiSeq 2000
library name: A11831
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
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 215-431 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: GSM958179_UCSF-UBC.UCSF-4star.mRNA-Seq.A11831.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11831-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the UCSF-4* Cell Line, Library A11831 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.13743
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 377,507,263
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.83
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM958179_UCSF-UBC.UCSF-4star.mRNA-Seq.A11831.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11831-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4star Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the UCSF-4star Cell Line, Library A11831 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.13751
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 8
BROWSER_TRACK_NAME: UCSF4* mRNA 31
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line mRNA-Seq Library A11831 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 377,507,263
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.83
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

value: cell line

tag: line

value: female

value: Embryo ICM

value: Embryonic stem cell


description:
design description: RNA-Seq analysis of UCSF-4 embryonic stem cell line (A11832) using Illumina HiSeq 2000
library name: A11832
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 10
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 221-431 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: GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11832-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the UCSF-4* Cell Line, Library A11832 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.13744
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 387,057,821
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM958175_UCSF-UBC.UCSF-4star.mRNA-Seq.A11832.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A11832-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4star Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the UCSF-4star Cell Line, Library A11832 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.13752
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 8
BROWSER_TRACK_NAME: UCSF4* mRNA 32
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line mRNA-Seq Library A11832 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 387,057,821
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.63
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.65

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


description:
design description: RNA-Seq analysis of foreskin keratinocyte from skin03 (A15293) using Illumina HiSeq 2000
library name: A15293
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 10
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 236-451 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: GSM958177_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.mRNA-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15293-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13750
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 355,501,933
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.65
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM958177_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.mRNA-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15293-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.13758
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 8
BROWSER_TRACK_NAME: PFK mRNA 03 93
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin03 Library A15293 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 355,501,933
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.65
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

value: male

value: Penis

value: Keratinocyte

tag: cell type

value: foreskin keratinocyte


description:
design description: RNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC03 (A15295) using Illumina HiSeq 2000
library name: A15295
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 9.8
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 232-451 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: GSM958173_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.mRNA-Seq.HuFNSC03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15295-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC03 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.13747
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 367,509,492
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.26
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.73

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

ANALYSIS FILE NAME: GSM958173_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.mRNA-Seq.HuFNSC03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15295-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC03 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.13755
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 8
BROWSER_TRACK_NAME: NGED mRNA 03 95
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC03 Library A15295 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 367,509,492
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.26
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.73

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

value: Ganglionic eminence neurosphere culture


title: LC_C12

tag: gender

tag: Stage


description:
design description: RNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A15299) using Illumina HiSeq 2000
library name: A15299
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 10
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 232-458 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: GSM958172_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.mRNA-Seq.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15299-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.13748
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 313,871,523
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.23
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.73

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

ANALYSIS FILE NAME: GSM958172_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.mRNA-Seq.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15299-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.13756
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 8
BROWSER_TRACK_NAME: NGED mRNA 04 99
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC04 Library A15299 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 313,871,523
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.23
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.73

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


title: LC_S51_nor

value: current smoker


title: FH-cortoCD

value: Wing imaginal discs


title: RpL12-Myc

value: Third instar larvae


description:
design description: RNA-Seq analysis of foreskin melanocyte from skin03 (A15294) using Illumina HiSeq 2000
library name: A15294
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 9.9
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 238-432 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: GSM958174_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.mRNA-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15294-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13745
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 384,752,915
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.87
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.47

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

ANALYSIS FILE NAME: GSM958174_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.mRNA-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15294-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.13753
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 8
BROWSER_TRACK_NAME: PFM mRNA 03 94
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin03 Library A15294 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 384,752,915
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.87
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.47

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

value: Melanocyte

value: foreskin melanocyte


title: LS180_NCoR_Veh

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

description: ChIP-DNA

data_processing:
ChIP-seq runs were all 36bp.  All samples were mapped from fastq files using Bowtie [-m 1 -- best] to hg18 [UCSC human genome build 18]. Replicate lanes were validated separately for reproducibility and then combined for greater read depth.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding with the following exception: clonal filter = 5.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: hg18
Supplementary_files_format_and_content: Bowtie files are the bowtie aligned files, bedGraph files are for display in the UCSC genome browser and the peaks.bed files are the resulting peaks found with QuEST and HOMER

growth_protocol: Cells were grown in normal MEM-alpha with 10% standard FBS serum, 1% Non-essential Amino Acids, 1% Sodium Pyruvate and 1% Penicillin-Streptomycin

extract_protocol: Chromatin immunoprecipitation was performed by treating LS180 cells for 3 hrs with vehicle or 10-7M 1,25(OH)2D3 as was optimized as previously reported. ChIP samples were created from 100 million cells per sample.  The treated cells were washed several times with PBS and then subjected to a 15 minute cross-linking reaction with 1.5% formaldehyde.  After the cross-linking reaction, isolated cell extracts were sonicated to prepare chromatin fragments (average DNA size of 500-600 bp DNA as assessed by agarose gel electrophoresis) using a Fisher Model 100 Sonic Dismembranator at a power setting of 2.  Pre-cleared samples were subjected to immunoprecipitation using either a control IgG antibody or the indicated experimental antibody.  The precipitated DNA was then washed, the cross-links reversed and the DNA fragments purified using Qiagen QIAquick PCR Purification Kits (Valencia, CA).  The isolated DNA (or DNA acquired prior to precipitation (input)) was then subjected to quantitative real time PCR (qPCR) and further preparation for ChIP-chip or ChIP-seq analysis.  ChIP-DNA was prepared and amplified using the Illumina ChIP-seq DNA preparation kit (1003473, #11257047 RevA), clusters formed and sequenced on the Illumina GAIIx sequencers by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center.  DNA clusters were generated using either a Standard Cluster Generation kit (ver. 4) on an Illumina cluster station (Illumina, San Diego, CA), [for all samples sequenced before April, 2010] or using a cBot Single Read Cluster Generation kit on an Illumina cBot (Illumina) [after April, 2010] according to the manufacturer's instructions, to obtain an average of 2.0×107 clusters for each lane on a flowcell.  All sequencing runs for 36mers were performed on an Illumina Genome Analyzer IIx using the Illumina Sequencing kit (ver. 4).

treatment_protocol: Cells were treated with 10-7M 1,25(OH)2D3 [125] or with ethanol vehicle [Veh] for 3 hours prior to ChIP assay

tag: cell line

value: LS180 cells

tag: passage number

value: cultured CRC cells

value: NCoR (Santa Cruz, C-20, sc-1609)


title: LS180_SMRT_125

description: ChIP-DNA

value: SMRT (Affinity Bioreagents, PA1-843)


title: LS180_NCoR_125

description: ChIP-DNA


title: LS180_MED1_125

description: ChIP-DNA

value: MED1 (Santa Cruz, M-255, sc-8998)


title: LS180_CBP_125

description: ChIP-DNA

value: CBP (Santa Cruz, A-22, sc-3996)


title: WT SAM #2

status: Public on Sep 04 2012

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

institute: Michigan State University

description:
Each plant was dissected down to P3 or P4 and the apices were cut at the base of P4 (pool of 15)
SAM_e1_WT.diff

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to the maize genome assembly version 2 using TopHat version 1.2.0 -G option using the gff file for Filtered Gene Set provided by maizegenome.org
Total number of reads to be considered in the next steps were counted from the alignment files. The gene region as appears for the protein-coding genes in the FGS gff provided by maizegenome.org. Reads were counted using the script htseq-count.py unique hits using union method and unique hits only.
Differential expression was tested between mutants and controls using DESeq version 1.4.1 with a P-value adjusted (this value is the P-value after FDR adjusted for multiple testing with the Benjamini-Hochberg procedure) < 0.01
Genome_build: Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: DESeq results for genes differentially expressed are reported as tabulated text files and reads count results as a excel spreadsheet

organism: Zea mays

source_name: shoot apical meristem from wild-type

growth_protocol: maize plants were grown in the greenhouse or the field as specified in column H

extract_protocol: Dissected tissue was flash frozen in liquid nitrogen and total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. Ligated cDNA were amplified for 13 cycles instead of the 15 cycles specified in the TruSeq protocol.

tag: inbred

tag: tissue

value: shoot apical meristem

tag: growth conditions

value: Greenhouse, large pots, 19 days after germination (6-7 visible leaves)


title: e1 SAM #2

source_name: shoot apical meristem from kn1-e1


title: LS180_MED1_Veh

description: ChIP-DNA


title: LS180_SRC1_Veh

description: ChIP-DNA

value: SRC-1 (Santa Cruz, M-341, sc-8495)


title: WT SAM #1


title: LS180_SRC1_125

description: ChIP-DNA


title: LS180_SMRT_Veh

description: ChIP-DNA


title: e1 ears #1

description:
dissected ears were between 4 and 5 mm (pool of 6-8)
Ears_e1_WT.diff

source_name: ear primordia from kn1-e1

value: ear primordia

value: Field (Gill Track, Albany, CA)


title: WT ears #2

description:
dissected ears were between 7 and 8 mm (pool of 6-8)
Ears_e1_WT.diff

source_name: ear primordia from wild-type


title: e1 ears #2


title: WT tassels #3

description:
dissected tassels were between 4 and 5.5 mm (pool of 10)
Tassels_e1_WT.diff

source_name: tassel primordia from wild-type

value: tassel primordia


title: WT ears #1


title: WT tassels #1


title: WT tassels #2


description:
design description: RNA-Seq analysis of foreskin fibroblast from skin03 (A15292) using Illumina HiSeq 2000
library name: A15292
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 10
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 232-438 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: GSM958178_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.mRNA-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15292-1.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13749
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 350,595,949
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.48
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.61

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

ANALYSIS FILE NAME: GSM958178_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.mRNA-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15292-1.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.13757
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 8
BROWSER_TRACK_NAME: PFF mRNA 03 92
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin03 Library A15292 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 350,595,949
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.48
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.61

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

tag: Sex

value: male

value: Penis

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


title: e1 tassels #2

description:
dissected tassels were between 2 and 3 mm (pool of 10)
Tassels_e1_WT.diff

source_name: tassel primordia from kn1-e1


title: e1 tassels #1


title: WT leaf #2

description:
dissected leaves were a tube of 1-2 mm by 7-8 mm (starting 2-3 mm above the SAM)
Leaf_Homo_WT.diff
Leaf_Het_WT.diff

source_name: young leaves from wild-type siblings

value: young immature leaves

value: Greenhouse, flat tray, 10 days after germination (2 visible leaves with the third one emerging from the whorl)


title: e1 tassels #3


title: WT leaf #1


title: Kn1-N leaf het #2

description:
dissected leaves were a tube of 1-2 mm by 7-8 mm (starting 2-3 mm above the SAM)
Leaf_Het_WT.diff
Leaf_Homo_Het.diff

source_name: young leaves from Kn1-N heterozygote


title: Kn1-N leaf het #1


title: LS180_CBP_Veh

description: ChIP-DNA

value: LS180 cells

value: cultured CRC cells

tag: antibody


title: Kn1-N leaf homo #2

description:
dissected leaves were a tube of 1-2 mm by 7-8 mm (starting 2-3 mm above the SAM)
Leaf_Homo_WT.diff
Leaf_Homo_Het.diff

source_name: young leaves from Kn1-N homozygote


title: e1 SAM #1


title: Kn1-N leaf homo #1


title: ear1-Total input

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-Seq reads were aligned to the maize genome assembly version 2 using Bowtie.
MACS ver. 1.4.0beta was used for calling peaks by using uniquely aligned reads.
Genome_build: Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: *.bed files generated by MACS contains information of peak positions (genome coordinates) and hights.

source_name: ear primordia

growth_protocol: Plant were grown in the field (Gill Track, Albany, CA)

extract_protocol: Inflorescences primordia were dissected, fixed for 10 minutes in 1% formaldehyde and nuclei isolated. Fragmented (sonicated) chromatin was incubated with anti-KN1 antibodies to pull down KN1-bound regions. ChIP-seq libraries were prepared according to the standard Illumina protocol using Illumina adapters and oligos (ear libraries), or custom made adapters containing a barcode for pooling multiple samples per sequencing lane (tassel libraries), while other reagents were obtained from major manufacturers (Promega, NEB). Prior to ChIP, chromatin from ear and tassel primordia was sonicated to obtain an average size of about 100 and 400 bp, respectively. One notable modification to the standard Illumina protocol was that the gel selection of fragments 150-350 bp was performed after the PCR amplification step (18 cycles) for the ear libraries, and was omitted for the tassel libraries.

value: ear

tag: chip antibody


title: ear1-ChIP


title: tassel1-Total input

source_name: tassel primordia

value: tassel


title: Ma_Y04-03__Yn04-28_hi_15

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing: Reads were aligned to the genome and RefSeq using bfast.  Up to one mismatch was allowed.  Only reads that aligned to one genomic location were used.

organism: Macaca mulatta

source_name: macaque, hippocampus

extract_protocol: RNA extracted using Qiagen Rneasy kit; library made using Illumina DpnII protocol

tag: brain region

value: hippocampus

tag: isolate


title: tassel1-ChIP


title: Y0430

city: Atlanta

first: Jia

last: Zeng

state: GA

address: Georgia Institute of Technology

department: School of Biology

institute: Georgia Institute of Technology

data_processing:
Basecalls performed using CASAVA version 1.8.2
All Cs were converted to Ts both in the reads and in the reference genomes, then aligned the converted reads to the converted reference genomes using the Bowtie algorithm. If multiple reads have identical external coordinates, we only retained the reads with the highest mapping quality. Besides, we  allowed up to two mismatches per read.
The output of the mapping reulsts were convert to BAM format. We used the samtools and custom perl scripts to get the base-pair resolution methylation maps.
Genome_build: GRCh37/HG19 for human, and CGSC2.1/panTro2 for chimpanzee.
Supplementary_files_format_and_content: methylation_CG.gff files are tab-delimited text files that include fractional methylation values for each Sample.
Supplementary_files_format_and_content: methylation_nonCG.gff files are tab-delimited text files that contain the base-pair resolution methylation  map for the cytosines in non-CpG context.

organism: Pan troglodytes

source_name: Brain

extract_protocol: BS-seq libraries for Illumina sequencing were custom-constructed from ~1 μg of genomic DNA which was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit. Five to ten ng of bisulfite-converted libraries was PCR amplified with the following condition: 2.5 U of ExTaq DNA polymerase (Takara), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). The thermocyling was as follows: 95°C  3 min, then 14-16 cycles of 95°C 30 sec, 65°C 30 sec and 72°C 60 sec. The enriched libraries were purified twice with SPRI method using AMPure beads.

value: prefrontal cortex

tag: organism

value: Chimpanzees

tag: age

value: Male


title: tassel2 and 3-ChIP


title: Y0404


title: Ma_Y04-05__Ryd-1_hi_11


title: Y06147


title: Ma_Y04-03__Yn04-28_ca_10

source_name: macaque, caudate nucleus

value: caudate nucleus


title: Ma_Y04-05__Ryd-1_ca_6


title: Ma_Y04-20__Rke-6_ca_7


title: Ma_Y04-03__Yn04-28_FP_5

source_name: macaque, frontal pole

value: frontal pole


title: Ma_Y04-20__Rke-6_FP_3


title: Ch_Y04-04__Pt_hi_35

source_name: chimp, hippocampus


title: Ch_Yn07-25_Pt_hi_34


title: Ch_Y05-12__Pt_hi_31


title: Ch_Y06-147__Pt_hi_30


title: Ch_Y04-04__Pt_ca_28

source_name: chimp, caudate nucleus


title: Ch_Yn07-25__Pt_ca_27


title: Ch_Y05-12__Pt_ca_25


title: tassel2 and 3-Total input


title: Ch_Y05-12Pt_FP_23

source_name: chimp, frontal pole


title: Ma_Y04-20__Rke-6_hi_12


title: Ma_Y04-21__Run-3_hi_13


title: Ch_Yn06-108__Pt_FP_22


title: Ch_Y06-147__Pt_FP_20


title: Ch_Y03-09__Pt_FP_21


title: Ma_Y04-21__Run3_FP_4


title: Ch_Yn07-147__Pt_hi_37


title: sat_thy_226

city: Rehovot

first: Gilad

last: Landan

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
4C PCR product
library strategy: 4C-Seq

data_processing:
Processing of sequenced 4C-seq reads is performed using a special purpose computational analysis pipeline, 4Cseqpipe, which can be downloaded along with a detailed manual at: http://compgenomics.weizmann.ac.il/tanay/?page_id=367 .
Briefly, sequenced reads are mapped to a pre-built database of restriction fragment locations and fragment end sequences, representing a reduced genome defined by the primary and secondary restriction enzymes.
Mapping takes into account fragment end uniqueness and mappability, and utilizes base-calling qualities to partially apportion reads according to mismatch probabilities.
Dense genomic profiles are created for four distinct classes of fragment ends by linear interpolation of mapped reads.
One interpolated profile is selected and the three other profiles are quantile-normalized to match its distribution. Resulting profiles are combined by direct summation, resulting in a coverage profile.
Finally, medians of normalized coverage, as well as 20th and 80th percentiles, are calculated for sliding windows ranging from 2kb to 50kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins.  Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns:
column 1 – the starting coordinate of the 1kb bin
column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin
column 3 – the 80th percentile of values in the window
column 4 – the 20th percentile of values in the window
column 5-148 – as columns 2-4, but with linearly increasing window size, going up to 50kb

source_name: Adult thymus

growth_protocol: 1 adult thymus was resuspended in DMEM supplemented with 10% FCS. Approximately 4 × 10^7 cells were diluted to 50 ml with DMEM (10% FCS).

extract_protocol: The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics), remain unchanged. Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with a primary restriction enzyme and subsequently ligated under dilute conditions. After reversal of the cross inks the DNA is purified and treated with the second restriction enzyme. After a second re-ligation step the sample is purified and a 4C inverse PCR is perfomed using primers annealing to the viewpoint fragment-end of interest. Primers contain non-annealing dangles with Illumina adapter sequences, allowing immediate sequencing of purified PCR products.

treatment_protocol: cells were cross-linked using 2% formaldehyde for 10 minutes at room temperature in PBS (10% FCS)

tag: strain

tag: developmental stage

value: adult

value: thymus

tag: 1st restriction enzyme

value: NlaIII

tag: 2nd restriction enzyme

tag: viewpoint

value: Satb1 promoter (+1.5kb)


title: sat_FB_535

description:
4C PCR product
library strategy: 4C-Seq

source_name: Fetal brain

growth_protocol: 10-12 14.5 dpc embryo brains were resuspended in DMEM supplemented with 10% FCS. The equivalent of four fetal brains (approximately 4 × 10^7 cells) was diluted to 50 ml with DMEM (10% FCS).

value: fetal

value: brain

value: DpnII

value: Satb1 promoter


title: sat_l6_es_1562

description:
4C PCR product
library strategy: 4C-Seq

source_name: Embryonic stem cells

growth_protocol: Mouse ES (mES) cells were grown in buffalo rat liver cell-conditioned medium combined with DMEM GlutaMAX (Gibco) containing 15% fetal bovine serum (Invitrogen), leukemia inhibitory factor (LIF), 2-β-mercaptoethanol, and non-essential amino acids.

value: IB10/E14 cell line

value: embryonic stem cells

value: Satb1 promoter -470kb


title: Paraquat STR RNA-Seq

first: Seema

last: Gollamudi

state: New York

address: 525 East 68th Street A501

department: Neurology and Neuroscience

institute: Weill Cornell Medical College

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
PQ_STR.txt: mm9

extract_protocol: mRNA libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq sample preparation kit (part number:1004814).  Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 3 month old C57Bl6 mice were administered pesticides using subcutaneous alzet pumps for one week. After one week the mice were harvested and ventral mid brain and striatum collected for RNA isolation. RNA was purified followed by qualitative and quantitative analysis.

value: 3 month old mice

value: Striatum (STR)

tag: treatment

value: Paraquat


title: Control STR RNA-Seq

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
Control_STR.txt: mm9

value: Control


title: Ch_Y04-04__Pt_FP_19


title: Ma_Y04-21__Run-3_ca_8

value: caudate nucleus


title: Maneb + Paraquat STR RNA-Seq

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
MnPQ_STR.txt: mm9

value: Maneb + Paraquat


title: Pyridaben STR RNA-Seq

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
PY_STR.txt: mm9

value: Pyridaben


title: Maneb + Paraquat VMB RNA-Seq

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
MnPQ_VMB.txt: mm9

value: Ventral mid brain (VMB)


title: sat_l6_thy_643

description:
4C PCR product
library strategy: 4C-Seq

value: adult

value: thymus


title: Pyridaben VMB RNA-Seq

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
PY_VMB.txt: mm9


title: sat_thy_515

description:
4C PCR product
library strategy: 4C-Seq

value: NlaIII


title: oct_es_629

description:
4C PCR product
library strategy: 4C-Seq

value: Oct4 promoter


title: oct_es_234

description:
4C PCR product
library strategy: 4C-Seq


title: HS62_FL_343

description:
4C PCR product
library strategy: 4C-Seq

source_name: Fetal liver

growth_protocol: 10-12 14.5 dpc embryo livers were resuspended in DMEM supplemented with 10% FCS. The equivalent of two fetal livers (approximately 4 × 10^7 cells) was diluted to 50 ml with DMEM (10% FCS).

value: fetal

value: liver

value: DpnII

value: beta-globin HS-62


title: 3hs1_FB_685

description:
4C PCR product
library strategy: 4C-Seq

value: brain

value: beta-globin 3' HS-1