title: Caltech_RnaSeq_C2C12_2x75_EqS_2.0pct_60hr (superseded by GSE90175)

status: Public on May 10 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
****************************
GSM929775 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90175
****************************

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeCaltechRnaSeq

tag: lab

value: Caltech-m

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

tag: readtype

tag: readtype description

value: Paired 75 nt reads

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

value: immortalized

tag: age description

value: Immortal cells

tag: labexpid

tag: mapalgorithm

tag: mapalgorithm description

value: TopHat v1.3.1

tag: replicate

tag: strain description

value: Strain C3H, Very related to C57BL/6


title: Caltech_RnaSeq_C2C12_2x75 (superseded by GSE90173)

type: SRA

state: CA

country: USA

description:
****************************
GSM929774 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90173
****************************

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: lab

tag: lab description

value: No special treatment or protocol applies

tag: age

tag: strain


title: Caltech_RnaSeq_10T1/2_2x75 (superseded by GSE90174)

description:
****************************
GSM929773 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90174
****************************

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages.


title: CMU

status: Public on May 16 2012

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: Tissue from three females were pooled.

data_processing:
The reads that passed through a series of additional filters are called "mappable reads", which are sequences that satisfy the following criteria from the statistics of mammalian miRNAs in miRBbase 16.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing more than nine repeats of any dimer, more than five repeats of any trimer, or more than four repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database). All identical reads were counted and combined into one kind.

The UCSC pig reference genome (~2.26 Gbp) (Sscrofa9.2; ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/) was used for mapping using NCBI Local BLAST, which included several major steps:
(a) map the mappable reads to known porcine and other mammalian pre-miRNAs from miRBase 16.0 in order;
(b) map the mapped reads in step (a) to the pig genome to obtain their genomic locations and annotations;
(c) cluster the unmapped sequences in step (b) (which are mapped to miRBase sequences, but not to the pig genome) as potential novel miRNAs from the gaps of the genome; and
(d) hairpin RNA structures encompassing reads not-mapped to miRBase in step (a) were predicated from the adjacent 60 nt sequences in either direction using UNAFold complying with criteria from the statistics of mammalian pre-miRNAs in miRBbase 16.0. To avoid the reads being assigned to the ambiguous multiple positions in the pig genome, herein, only the reads longer than 18 nt in length been included.

molecule: total RNA

organism: Sus scrofa

source_name: cardiac muscle

extract_protocol: Eight different adipose tissues, two phenotypically distinct skeletal muscles, and cardiac muscle of three female Landrace pigs (a leaner, Western breed) were used for small RNA sequencing. Total RNA was extracted using the mirVana miRNA isolation kit (Ambion) following the manufacturer's procedure. For each tissue, equal quantities (5ug) of small RNA isolated from three female Landrace pigs were pooled. Approximately 15 ug of small RNA representing each tissue was used for library preparation and sequencing. The small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and each small RNA library was sequenced individually using the Illumina Genome Analyzer II according to manufacturer instructions.

tag: breed

value: Landrace

tag: gender

value: female

tag: developmental stage

value: adult

value: 210 days

tag: tissue

value: cardiac muscle


title: Caltech_RnaSeq_10T1/2_2x75_EqS_2.0pct_60hr (superseded by GSE90172)

description:
****************************
GSM929772 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90172
****************************

value: Caltech-m

value: Wold - Califonia Institute of Technology

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: cell description

tag: cell sex

tag: readtype

tag: readtype description

tag: treatment

tag: treatment description

tag: age description

tag: labexpid


title: ChIP_Seq_p300_IMR90

city: LA JOLLA

first: Nisha

last: Rajagopal

address: 9106 REGENTS RD APT F

institute: UCSD

library_source: genomic

data_processing:
base-calling using Illumina software with output as Fastq files
Sample 1 and 2:alignment and mapping with Bowtie with seed length 32bp,maximum matches 1 and maximum mismatches 2.Output was bowtie_output or BAM file.; Sample 3: alignment and mapping with Illumnia's ELAND software using seed length of 25bp and maximum number of mismatches 2
Bed files were created using custom perl scripts. Read length of 36bp was used and only reads that mapped uniquely were used. Polyclonal reads were reduced to one instance.
Genome_build: hg18
Supplementary_files_format_and_content: bed files

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung fibroblast

tag: strain

tag: antibody

value: p300 [Manufacturer:Santa Cruz, Catalog:SC-585XS, Lot#: E2209]

tag: cell type

value: Lung fibroblast


title: ChIP_Seq_Input_IMR90


title: p9 - 12 month male

city: Liverpool

first: Shona

middle: Hiedi

last: Wood

address: Crown street

department: Functional and Comparative Genomics

country: United Kingdom

institute: University of Liverpool

description: Ribodepleted RNA

data_processing:
p9_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.

organism: Rattus norvegicus

source_name: cerebral cortex_middle age

growth_protocol: Male BN rats (SubstrainBN/SsNOlaHSD) were obtained from Harlan UK at 21–28 days of age and maintained under barrier conditions on a 12-h light: 12-h dark cycle (08:00–20:00). All rats were fed ad libitum and sacrificed at 6, 12 and 28 months

extract_protocol: RNA was extracted from the cerebral cortex using Qiagen's tissuelyser II and RNeasy lipid tissue kit. The quality of the extracted RNA was assessed using the Agilent 2100 bioanalyser, all RNA integrity numbers (RINs) were above 8 indicating that good quality RNA had been extracted. The samples were pooled 2 by 2 (leaving 3 samples per age group). Ribosomal RNA was removed from the pooled samples using a Eukaryote ribominus kit (Invitrogen) and confirmed with the Agilent 2100 bioanalyser. The library preparation protocol was carried out according to the manufacturer’s instructions: the RNA was fragmented and cleaned up using spin columns (Invitrogen) and SOLiD RNA adapters were then hybridized and ligated to the samples. Reverse transcription was performed to generate cDNA. The cDNA was purified, size selected, amplified and then purified again (as detailed in the SOLiD protocol). The size distribution of the cDNA library was assessed using the bioanalyser. The samples were then subject to emulsion PCR and sequenced using the SOLiD system V4. Multiplex paired-end sequencing of RNA libraries with barcodes.

value: BN rats (Substrain BN/SsNOlaHSD)

value: male

tag: age

value: 12 month (middle age)

value: cerebral cortex


title: p8 - 12 month male

description: Ribodepleted RNA

data_processing:
p8_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.


title: p7 - 12 month male

description: Ribodepleted RNA

data_processing:
p7_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.


title: early maturation-stage cotyledon abaxial parenchyma compartment

status: Public on May 11 2012

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Cotyledon abaxial parenchyma compartment was captured from ten micron paraffin sections using the Leica LMD6000 system.

data_processing:
Basecalls were performed using RTA version 1.12.4.2.
Original data files from the Illumina sequencing pipeline were in the QSEQ format. Each lane of sequencing was in an individual file.
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches. The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: Tab-delimited text file including methylation level of each sampled cytosine. Column definitions are included in the supplementary README.txt file that is linked to the Series record.

organism: Glycine max

source_name: Laser-captured cotyledon abaxial parenchyma compartment from early-maturation stage cotyledons

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were harvested.

extract_protocol: Harvested seeds were fixed in 3:1(v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from ten-micron sections using a Leica LMD6000.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).  Approximately 300 nanogram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications.  We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion.  Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

value: early maturation stage

value: cotyledon abaxial parenchyma


title: MAD

description: Tissue from three females were pooled.

source_name: mesenteric adipose

tag: breed

value: Landrace

value: female

value: adipose:mesenteric adipose


title: p4 - 28 month male

description: Ribodepleted RNA

data_processing:
p4_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.

source_name: cerebral cortex_old

tag: gender

value: 28 month (old)


title: p3 - 6 month male

description: Ribodepleted RNA

data_processing:
p3_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.

source_name: cerebral cortex_young

value: 6 month (young)


title: p5 - 28 month male

description: Ribodepleted RNA

data_processing:
p5_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.


title: p6 - 28 month male

description: Ribodepleted RNA

data_processing:
p6_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.


title: Stam_WI-38_2_4OHTAM_20nM_72hr

status: Public on May 15 2012

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WI38_Stam_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase

tag: cell

tag: cell organism

value: human

value: Embryonic Lung Fibroblast Cells, hTERT immortalized, includes Raf1 construct

tag: cell karyotype

value: Normal (RAF)

tag: cell lineage

value: Fibroblast

value: F

tag: replicate


title: p2 - 6 month male

description: Ribodepleted RNA

data_processing:
p2_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.

value: BN rats (Substrain BN/SsNOlaHSD)

tag: tissue


title: p1 - 6 month male

description: Ribodepleted RNA

data_processing:
p1_counts.txt; genome build: rn4
counts: Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/) using the forward reads mapped by Bowtie.

value: male


title: GOM

description: Tissue from three females were pooled.

source_name: greater omentum

tag: developmental stage

value: adult

value: 210 days

value: adipose:greater omentum


title: LICR_RnaSeq_Heart_E14.5 (superseded by GSE93464)

description:
****************************
GSM929724 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93464
****************************

source_name: Heart

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

value: Heart

value: mouse

tag: cell description

tag: cell sex

value: U

value: Embryonic day 14.5

tag: labversion

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: softwareversion

value: TopHat

tag: strain description

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


title: IAD

description: Tissue from three females were pooled.

source_name: intermuscular adipose

tag: breed

value: Landrace

tag: gender

value: female

tag: age

value: adipose:intermuscular adipose


title: ASA

description: Tissue from three females were pooled.

source_name: abdominal subcutaneous adipose

value: adult

value: adipose:abdominal subcutaneous adipose


title: RAD

description: Tissue from three females were pooled.

source_name: retroperitoneal adipose

value: 210 days

value: adipose:retroperitoneal adipose


title: LICR_RnaSeq_Placenta_adult-8wks (superseded by GSE93462)

description:
****************************
GSM929722 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93462
****************************

source_name: Placenta

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: Placenta

tag: cell organism

value: F

tag: age description

value: Adult 8 weeks

tag: replicate

tag: strain


title: LICR_RnaSeq_SmIntestine_adult-8wks (superseded by GSE93467)

description:
****************************
GSM929716 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93467
****************************

source_name: SmIntestine

tag: lab

tag: lab description

tag: datatype

value: RnaSeq

value: Sequencing analysis of RNA expression

value: SmIntestine

value: mouse

value: Small Intestine

value: M


title: LICR_RnaSeq_Testis_adult-8wks (superseded by GSE93466)

description:
****************************
GSM929715 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93466
****************************

source_name: Testis

tag: datatype description

value: Testis

tag: cell description

tag: cell sex

value: Single 36 nt reads

value: TopHat

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


title: LICR_RnaSeq_ES-Bruce4_E0 (superseded by GSE93453)

description:
****************************
GSM929718 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93453
****************************

value: mouse embryonic stem cells

value: Embryonic day 0 (stem cell)

tag: labversion

tag: readtype

tag: readtype description

value: Single 30 nt read


title: LICR_RnaSeq_Liver_E14.5 (superseded by GSE93463)

description:
****************************
GSM929721 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93463
****************************

source_name: Liver

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: Liver

value: U

value: Embryonic day 14.5

tag: softwareversion

tag: strain description


title: PAD

description: Tissue from three females were pooled.

source_name: pericardial adipose

tag: breed

value: Landrace

tag: gender

value: female

tag: developmental stage

value: adult

tag: age

value: 210 days

tag: tissue

value: adipose:pericardial adipose


title: LICR_RnaSeq_OlfactBulb_adult-8wks (superseded by GSE93470)

description:
****************************
GSM929712 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93470
****************************

source_name: OlfactBulb

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: cell

value: OlfactBulb

tag: cell organism

value: mouse

value: Olfactory Bulb

value: M

tag: age description

value: Adult 8 weeks

tag: replicate

tag: strain


title: LICR_RnaSeq_Thymus_adult-8wks (superseded by GSE93469)

description:
****************************
GSM929714 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93469
****************************

source_name: Thymus

tag: lab

value: LICR-m

tag: lab description

tag: datatype

tag: datatype description

value: Thymus

tag: cell description

value: Single 36 nt reads

value: TopHat

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


title: LICR_RnaSeq_Limb_E14.5 (superseded by GSE93468)

description:
****************************
GSM929713 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93468
****************************

source_name: Limb

value: Ren - Ludwig Institue for Cancer Research

value: Limb

tag: cell sex

value: U

value: Embryonic day 14.5

tag: labversion

tag: readtype

tag: readtype description

tag: softwareversion


title: LICR_RnaSeq_BoneMarrow_adult-8wks (superseded by GSE93452)

description:
****************************
GSM929717 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93452
****************************

source_name: BoneMarrow

value: BoneMarrow

value: Bone Marrow

tag: age

value: Single 30 nt read

tag: strain description


title: LICR_RnaSeq_WholeBrain_E14.5 (superseded by GSE93465)

description:
****************************
GSM929723 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93465
****************************

source_name: WholeBrain

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: cell

value: WholeBrain

value: Whole Brain


title: LICR_RnaSeq_Spleen_adult-8wks (superseded by GSE93455)

description:
****************************
GSM929720 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93455
****************************

source_name: Spleen

value: Spleen

tag: cell organism

value: mouse

value: M

value: Adult 8 weeks


title: LICR_RnaSeq_BAT_adult-24wks (superseded by GSE93472)

description:
****************************
GSM929703 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93472
****************************

source_name: BAT

value: LICR-m

value: BAT

value: Brown adipocytes tissue

tag: age description

value: Adult 24 weeks

value: Single 36 nt reads

value: TopHat


title: LICR_RnaSeq_MEL_immortalized (superseded by GSE93471)

description:
****************************
GSM929704 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93471
****************************

source_name: MEL

value: Ren - Ludwig Institue for Cancer Research

value: MEL

value: Leukemia (K562 analog)

value: immortalized

value: Immortal cells

tag: replicate

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


title: ILB

description: Tissue from three females were pooled.

source_name: inner layer of backfat

tag: breed

value: Landrace

tag: gender

value: female

tag: developmental stage

value: adult

value: 210 days

tag: tissue

value: adipose:inner layer of backfat


title: LICR_RnaSeq_BMDM_adult-8wks (superseded by GSE93473)

description:
****************************
GSM929705 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93473
****************************

source_name: BMDM

tag: lab

value: LICR-m

tag: lab description

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

value: BMDM

value: mouse

value: Bone marrow derived macrophage

value: F

value: Adult 8 weeks

value: Single 30 nt read

tag: strain


title: ULB

description: Tissue from three females were pooled.

source_name: upper layer of backfat

value: adipose:upper layer of backfat


title: LICR_RnaSeq_Lung_adult-8wks (superseded by GSE93461)

description:
****************************
GSM929710 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93461
****************************

source_name: Lung

value: Ren - Ludwig Institue for Cancer Research

value: Lung

tag: cell description

tag: cell sex

value: M

tag: labversion

tag: readtype

tag: readtype description

value: Single 36 nt reads

value: TopHat


title: LICR_RnaSeq_Cerebellum_adult-8wks (superseded by GSE93456)

description:
****************************
GSM929709 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93456
****************************

source_name: Cerebellum

tag: cell

value: Cerebellum

tag: cell organism

tag: age

tag: softwareversion

tag: strain description

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


title: LICR_RnaSeq_Cortex_adult-8wks (superseded by GSE93457)

description:
****************************
GSM929708 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93457
****************************

source_name: Cortex

value: LICR-m

value: Cortex

tag: age description

tag: replicate


title: LICR_RnaSeq_Heart_adult-8wks (superseded by GSE93458)

description:
****************************
GSM929707 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93458
****************************

source_name: Heart

tag: lab

value: RnaSeq

value: Sequencing analysis of RNA expression

value: Heart


title: LICR_RnaSeq_Liver_adult-8wks (superseded by GSE93460)

description:
****************************
GSM929711 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93460
****************************

source_name: Liver

tag: lab description

value: Liver

value: mouse


title: LICR_RnaSeq_MEF_adult-8wks (superseded by GSE93454)

description:
****************************
GSM929719 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93454
****************************

source_name: MEF

tag: datatype

value: MEF

value: Mouse Embryonic Fibroblast

value: Adult 8 weeks


title: Snyder_F45C12.2_Input_L1_rep2 extraction2_seq1 aliquote 1

status: Public on May 09 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: OP212(official name :OP212 genotype :unc-119(ed3); wgIs212(F45C12.2:TY1 EGFP FLAG; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by :Mihail Sarov )

tag: developmental stage

value: fed L1

tag: genotype

tag: Sex

value: Hermaphrodite


title: LICR_RnaSeq_Kidney_adult-8wks (superseded by GSE93459)

description:
****************************
GSM929706 record metadata submitted on May 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93459
****************************

source_name: Kidney

value: Ren - Ludwig Institue for Cancer Research

tag: datatype description

value: Kidney

tag: cell description

tag: cell sex

value: M

value: Single 36 nt reads

tag: strain


title: Snyder_F45C12.2_Input_L1_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_NHR-116_Input_L2_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: OP226(official name :OP226 genotype :unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross :3 transgene :nhr-116 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by :M Sarov )

tag: transgene


title: Snyder_NHR-77_Input_L4_rep1 extraction1_seq1 aliquote 1

description: input DNA

value: OP353(official name :OP353 genotype :unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross :3 transgene :nhr-77 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by :R Waterston )


title: Snyder_NHR-77_GFP_L3_rep2 extraction2_seq1 aliquote 1

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220


title: Snyder_NHR-116_GFP_L2_rep2 extraction2_seq1 aliquote 1


title: Snyder_F45C12.2_GFP_L1_rep1 extraction1_seq1 aliquote 1


title: Snyder_NHR-77_Input_L4_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_NHR-77_GFP_L4_rep2 extraction2_seq1 aliquote 1


title: Snyder_NHR-116_Input_L2_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_NHR-77_GFP_L4_rep1 extraction1_seq1 aliquote 1


title: Snyder_NHR-116_GFP_L2_rep1 extraction1_seq1 aliquote 1


title: Snyder_NHR-77_GFP_L3_rep1 extraction1_seq1 aliquote 1


title: Snyder_NHR-77_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS220


title: Snyder_NHR-77_Input_L3_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_NHR-77_GFP_L2_rep2 extraction2_seq1 aliquote 1


title: Snyder_NHR-77_GFP_L2_rep1 extraction1_seq1 aliquote 1


title: Snyder_NHR-77_Input_L2_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_ZK377.2_GFP_L2_rep2 extraction2_seq1 aliquote 1

value: OP355(official name :OP355 genotype :unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by :R Waterston )


title: Snyder_ZK377.2_GFP_L2_rep1 extraction1_seq1 aliquote 1


title: Snyder_F45C12.2_GFP_L1_rep2 extraction2_seq1 aliquote 1


title: Snyder_ZK377.2_Input_L2_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_ZK377.2_Input_L2_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_FOS-1_Input_L4_rep2 extraction2_seq1

description: input DNA

value: OP304(official name :OP304 genotype :unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by :R Waterston )


title: Snyder_FOS-1_GFP_L4_rep2 extraction2_seq1


title: Snyder_FOS-1_GFP_L4_rep1 extraction1_seq1


title: Snyder_FOS-1_Input_L3_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_FOS-1_GFP_L3_rep2 extraction2_seq1 aliquote 1


title: Snyder_FOS-1_Input_L4_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_FOS-1_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: H3K27ac_48hpf, danRer7

status: Public on May 08 2012

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: chromatin IP against H3K27ac

data_processing: Reads were mapped to the D. rerio genome (ENSEMBL version Zv9) with the ELAND software (from Illumina CASAVA 1.8.2) using default settings. Reads with 0 or 1 mismatch were kept.

organism: Danio rerio

source_name: H3K27ac_48hpf, danRer7

growth_protocol: Danio rerio embryos used for ChIP assays were obtained from a natural mating procedure and dechorionated by pronase treatment prior to immunoprecipitation.

extract_protocol: The DNA ends were repaired and the 3-dA overhangs added. The adapters were then ligated. The library was size-selected (200-300 bp) and amplified by PCR.

tag: tissue

value: whole embryo

tag: antibody

value: Abcam

tag: antibody catalog

tag: antibody batch


title: Snyder_MEF-2_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: Enhanced Green Fluorescent Protein;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

value: OP301(official name :OP301 genotype :unc119(ed3);wgIs301(mef-2::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MEF-2::EGFP fusion protein is expressed in the correct mef-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MEF-2 transcription factor. made_by :R Waterston )


title: Snyder_MEF-2_Input_L1_rep2 extraction2_seq1 aliquote 1

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180


title: Snyder_NHR-77_Input_L2_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: H3K4me1_48hpf, danRer7

description: chromatin IP against H3K4me1

source_name: H3K4me1_48hpf, danRer7

tag: antibody vendor

value: Diagenode


title: Snyder_MEF-2_GFP_L1_rep2 extraction2_seq1 aliquote 1


title: Snyder_MEF-2_Input_L1_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: H3K4me1_24hpf, danRer7

description: chromatin IP against H3K4me1

source_name: H3K4me1_24hpf, danRer7


title: H3K4me1_dome, danRer7

description: chromatin IP against H3K4me1

source_name: H3K4me1_dome, danRer7

value: dome


title: H3K4me1_80%epi, danRer7

description: chromatin IP against H3K4me1

source_name: H3K4me1_80%epi, danRer7

value: 80% epiboly


title: Snyder_FOS-1_GFP_L3_rep1 extraction1_seq1 aliquote 1


title: H3K4me3_48hpf, danRer7

description: chromatin IP against H3K4me3

source_name: H3K4me3_48hpf, danRer7


title: H3K4me3_24hpf, danRer7

description: chromatin IP against H3K4me3

source_name: H3K4me3_24hpf, danRer7


title: H3K4me3_80%epi, danRer7

description: chromatin IP against H3K4me3

source_name: H3K4me3_80%epi, danRer7


title: H3K27ac_dome, danRer7

description: chromatin IP against H3K27ac

source_name: H3K27ac_dome, danRer7


title: H3K4me3_dome, danRer7

description: chromatin IP against H3K4me3

source_name: H3K4me3_dome, danRer7


title: H3K27ac_80%epi, danRer7

description: chromatin IP against H3K27ac

source_name: H3K27ac_80%epi, danRer7


title: H3K27ac_24hpf, danRer7

description: chromatin IP against H3K27ac

source_name: H3K27ac_24hpf, danRer7


title: H3K27ac_48hpf, danRer6

description: chromatin IP against H3K27ac

data_processing:
Reads were mapped to the D. rerio genome (ENSEMBL version Zv8) with the ELAND software (Ilumina pipeline). Only the alignments within 2 mismatches were included in further analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).

source_name: H3K27ac_48hpf, danRer6


title: H3K27ac_80%epi, danRer6

description: chromatin IP against H3K27ac

source_name: H3K27ac_80%epi, danRer6


title: H3K27ac_24hpf, danRer6

description: chromatin IP against H3K27ac

source_name: H3K27ac_24hpf, danRer6


title: H3K4me3_24hpf, danRer6

description: chromatin IP against H3K4me3

source_name: H3K4me3_24hpf, danRer6


title: H3K4me1_dome, danRer6

description: chromatin IP against H3K4me1

source_name: H3K4me1_dome, danRer6


title: H3K4me1_48hpf, danRer6

description: chromatin IP against H3K4me1

source_name: H3K4me1_48hpf, danRer6


title: H3K4me1_80%epi, danRer6

description: chromatin IP against H3K4me1

source_name: H3K4me1_80%epi, danRer6


title: H3K4me3_48hpf, danRer6

description: chromatin IP against H3K4me3

source_name: H3K4me3_48hpf, danRer6


title: H3K4me3_80%epi, danRer6

description: chromatin IP against H3K4me3

source_name: H3K4me3_80%epi, danRer6


title: H3K4me1_24hpf, danRer6

description: chromatin IP against H3K4me1

source_name: H3K4me1_24hpf, danRer6


title: H3K27ac_dome, danRer6

description: chromatin IP against H3K27ac

source_name: H3K27ac_dome, danRer6


title: H3K4me3_dome, danRer6

description: chromatin IP against H3K4me3

source_name: H3K4me3_dome, danRer6


title: IgG dividing rep2

city: Singapore

first: Pierre-Étienne

last: Jacques

address: 60 Biopolis Street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Casava v1.7 used for base calling and read mapping.
MACS v1.4.0 used to convert mapped reads into density files (resolution 10bp) using the parameters: --gsize 94093750 --wig -single-profile
In order to be directly comparable, each WIG file was next normalized using the total number of mapped read (per million).
Genome_build: TAIR9
Supplementary_files_format_and_content: WIG files contain the normalized histone density

organism: Arabidopsis thaliana

source_name: Meristem and younger leaves

growth_protocol: Plants were grown in short day conditions (8h light -16h dark, 20 to 22 °C) for 4 weeks after stratification at 4°C and in dark for 5 days. For harvesting the tissues, we dissected the plants with scalpels under a binocular scope.

extract_protocol: Libraries were constructed according to the guide lines described in the Illumina website. Briefly, 30 µl of chromatin-immuno-precipitated DNA was subjected to the following process: end repair by the addition of a single ‘A’ base, and then ligation of adapters specific for sequencing flow cell. These products were then purified and size-selected on gel to have fragments from 200 to 300bp and enriched by 20 cycles PCR to create the final cDNA library (22 cycles for experiment 1). This library was validated by loading 1 μl of the re-suspended constructs onto an Agilent Technologies 2100 Bioanalyzer DNA-1000 microfluidic chip. The final products showed a distinct band at 200-300bp

value: Columbia HTR5-GFP

tag: chip antibody

value: IgG

tag: genetic background

value: Columbia

value: Meristem and younger leaves

tag: chip antibody manufacturer

tag: chip antibody catalog #


title: Snyder_EOR-1_GFP_L3_rep2 extraction2_seq1 aliquote 1

status: Public on May 07 2012

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. The sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

value: OP81(official name :OP81 genotype :unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross :0 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by :R. Waterston and S. Kim )

tag: developmental stage

value: Hermaphrodite


title: H3 non-dividing rep1

source_name: Oldest 4 to 6 leaves

value: Columbia HTR13-GFP

value: Oldest 4 to 6 leaves


title: Stem

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

data_processing: All RNAseq reads from different libraries are merged into a single file: the read ids are prefixed with a unique id for the respective library to ensure uniqueness. Low quality regions are detected and trimmed using lucy v1.20(Chou and Holmes, 2001) (http://sourceforge.net/projects/lucy/) and the provided awk script zapping.awk. We run seqclean (http://sourceforge.net/projects/seqclean/) to screen for adapters, vectors and contaminant databases: smart clontech adapters, NCBI’s Univec (ftp://ftp.ncbi.nih.gov/pub/UniVec/), Escherichia coli genome (NC_000913.2), Tomato mosaic virus (NC_002692.1), and Solanum lycopersicum chloroplast genome (NC_007898.1). Duplicated reads are removed using bioperl version of nrdb (bp_nrdb.pl) to reduce the runtime for the following alignment. In each of the above steps, short reads (<50nt) are discarded. Tissue specific expression: For each read the best alignments are kept (95% alignment score threshold and 90% coverage threshold). Alignments are ordered by alignment score and in case of tie by coverage. Alignments per each library are expanded so that duplicated reads are removed only within each library and not across libraries.   For each library and based on the respective alignments and on CDS from iTAG annotation v2.3, we calculate tissue specific expression using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and specifically the python script htseq-count. We run htseq-count with default union mode and thus, reads that map across genes will not be counted. The stranded option is set to no as the RNAseq data are not from a strand-specific assay. The resulting raw expression values are converted to RPKM (Reads Per Kilobase of exon sequence, per Million reads) using the following formula:  RPKM = 10^9 × CDSReadCount / TotalReadCount × CDSLength  where CDSReadCount the raw number of reads mapped to CDS of a gene, TotalReadCount the sum of all mapped reads to CDS and CDSLength the transcript length.

organism: Solanum lycopersicum

source_name: Stem

growth_protocol: Plants of S. lycopersicum (cv MoneyMaker) or S. pimpinellifolium (LA0722) were grown in soil-filled pots in greenhouse under controlled conditions in Long day (16 hours light, 8 hours dark).

extract_protocol:
RNA was extracted from different tissues according to published methods(López-Gómez and Gomez-Lim, 1992). cDNA was produced according to the SMART cDNA PCR synthesis kit (Clontech) but using the SuperScriptII Reverse Transcriptase (Invitrogen), their quantity and quality were evaluated respectively by Nanodrop spectrophotometer and Agilent Bioanalyzer (DNA12000 assay). Tissues used for cDNA synthesis in S. lycopersicum were: root, stem, leaf, flower and fruit at 3 different maturation stages: mature green, breaker and ripe. S. pimpinellofolium tissues used for synthesis were leaf and berry ripe.
cDNA libraries were produced following the 454 Titanium Rapid Library Preparation protocol instructions, then fixed to micro beads and clonally amplified by emulsion PCR (emPCR Method Manual-Lib-L). The beads have been enriched to keep only those carrying identical PCR products, and then each sample has been loaded on a half picotiter plate to obtain at least 350000 reads with a medium length of 400bp. Each sample was sequenced on a half picotiterplate.

tag: cultivar/accession

value: MoneyMaker

value: Stem

value: upper stem, below apical meristem


title: Flower

source_name: Flower

value: Flower

value: flower, complete (excluding sepals). Full anthesis


title: Fruit Mature Green

source_name: Fruit Mature Green

value: Fruit Mature Green

value: fruit at mature green stage (fully expanded, green)


title: Leaf pimpinellifolium

organism: Solanum pimpinellifolium

source_name: Leaf

value: Leaf

value: fully expanded leaf, 2-4 weeks old


title: Fruit Ripe pimpinellifolium

source_name: Fruit Ripe

value: Fruit Ripe

value: fruit at ripe stage (fully expanded, red)


title: Fruit Ripe


title: Leaf

value: fully expanded leaf, 2-3 weeks old


title: Fruit Breaker

source_name: Fruit Breaker

value: Fruit Breaker

value: fruit at breaker stage (fully expanded, turning color)


title: Snyder_EOR-1_GFP_L3_rep1 extraction1_seq1 aliquote 1

value: OP81(official name :OP81 genotype :unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross :0 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by :R. Waterston and S. Kim )

tag: genotype

tag: Sex

value: Hermaphrodite


title: Root

source_name: Root

value: Root

value: grown root (hypogeous)


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of foreskin melanocyte from skin01 (m01583) using Illumina Genome Analyzer IIx
library name: m01583
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.1
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 3.512 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM817251_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01583-1.hg19.level.1.release6
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01 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.12568
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,424,189
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 44.69
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817251_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin01.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01583-1.hg19.level.2.tag.release6
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12574
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,424,189
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 44.69
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817251_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.smRNA-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01583-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin01 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12571
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-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 6
BROWSER_TRACK_NAME: PFM smRNA 01 83
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin01 Library M01583 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,424,189
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 44.69
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Penis

tag: histological type

value: Melanocyte

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: foreskin melanocyte


title: Snyder_EOR-1_Input_L3_rep2 extraction2_seq1 aliquote 1

description: input DNA

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. The sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

tag: strain

value: unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG]


title: Snyder_GEI-11_Input_L2_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: OP179(official name :OP179 genotype :unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by :R. Waterston )


title: Snyder_EOR-1_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_GEI-11_GFP_L2_rep2 extraction2_seq1 aliquote 1


title: HEK293 HSV-1 infected

city: Albany

first: April

middle: D

last: Burch

state: NY

address: 120 New Scotlant Ave

department: Infectious Diseases

institute: Wadsworth Center/ SUNY Albany/ Berkshire School

data_processing:
The sequence data was uploaded to the Galaxy server (https://main.g2.bx.psu.edu/) and manipulations performed therein.
Linker regions were trimmed from the data leaving the purified sequence only.  The resulting sequences were aligned to the human and HSV-1 viral genomes using Bowtie.  2 mismatches were allowed for the viral alignment since the fully sequenced genome available on NCBI is strain 17.  No mismatches were allowed for the human alignment.
Sequences which aligned to the viral genome were assigned a numerical identifier corresponding to the location in the viral genome which the first nucleotide of the sequence aligned to.  These were then organized according to position on the genome and multiple hits stacked.
Where multiple hits grouped, either in a single location or varying by 1-3 nt positions, manual screening was done to extract and compile a full sequence and to eliminate mononucleotide runs.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is in pdf files which have the position and number of hits in each position of the virally encoded RNAs.  Highlighted sections indicate novel species which were sequenced 3+ times.  Also indicated are the known HSV-1 miRNAs which we recovered.

source_name: HEK293 cells infected with HSV-1

growth_protocol: HEK293 cells were grown to 75% confluency and infected with 10 pfu HSV-1 strain KOS/cell.  The infection was allowed to progress 24 hrs, with samples collected every 2 hrs using the miRVANA kit.  Small RNAs were purified as per manufacturers instructions

extract_protocol: The library was constructed by pooling 1 ug of small RNAs from each time point and running the pooled RNAs on a 15% polyacrylamide gel containing 8 M urea.  The region corresponding to the nt range of 15-35 nt was excised and eluted in 0.4 M NaCl.  RNAs were ligated with an RNA linker on the 5' end and a RNA/DNA linker on the 3' end.  RT was performed followed by linker specific PCR to create the final library which was purified on a 4% agarose gel and sent to the Albert Einstein College genomics facillity for Illumina adapter ligation and sequencing. All RNAs from 15-35 nt were purified in order to capture differences in human and viral miRNA production.

treatment_protocol: Infection with 10 pfu HSV-1 strain KOS/cell

tag: cell line

tag: virus strain

value: KOS


title: Snyder_GEI-11_GFP_L2_rep1 extraction1_seq1 aliquote 1


description:
design description: miRNA-Seq analysis of foreskin keratinocyte from skin01 (m01585) using Illumina Genome Analyzer IIx
library name: m01585
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 8
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 3.168 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM817253_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01585-1.hg19.level.1.release6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12570
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,342,320
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 47.7
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817253_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin01.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01585-1.hg19.level.2.tag.release6
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12576
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,342,320
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 47.7
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817253_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01585-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12573
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-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 6
BROWSER_TRACK_NAME: PFK smRNA 01 85
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin01 Library M01585 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,342,320
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 47.7
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Keratinocyte

value: foreskin keratinocyte


title: Snyder_F16B12.6_GFP_L1_rep2 extraction2_seq1 aliquote 1

value: OP114(official name :OP114 genotype :unc119(ed3);wgIs114(F16B12.6::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F16B12.6::EGFP fusion protein is expressed in the correct F16B12.6 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F16B12.6 transcription factor. made_by :R Waterston )

value: fed L1


title: Snyder_GEI-11_Input_L2_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: mRNA-seq of wild-type protonema, dark-grown, time 0 control

city: Taipei

first: Shih-Long

last: Tu

address: 128, Sec 2, Academia Rd,Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica

description: Sample 1

data_processing:
Sequence reads were mapped to the Physcomitrella patens genome V1.6 (http://cosmoss.org/, data also can found in JGI, http://www.phytozome.net/physcomitrella.php) using the BLAT program. RPKM computation was performed by using RACKJ package (http://rackj.sourceforge.net/) with similar algorithm. Data were analyzed in Excel (Microsoft, Redmond, WA, USA).
Genome Build:
WT_R0_Counts_RPKM_all.txt: Physcomitrella patens genome V1.6

organism: Physcomitrium patens

source_name: wild-type_dark-grown_time 0 control

growth_protocol: 10-day-old wild-type and pubs hy2 protonema were grown in the dark for 3 days

extract_protocol: Total RNA was extracted by using the Plant Total RNA Miniprep Purification Kit (GeneMark, Taiwan). MID-mRNA sequencing was carried out as suggested by Illumina, Inc. The method was adopted from mRNA-seq library prep protocol with addition of MID barcodes to the ds cDNA fragments and volume adjustment. Using the mRNA-seq kit, poly-A RNA were purified from 10-15 mg of total RNA by oligo-dT beads and subjected to cation-catalyzed fragmentation for four minutes at 94˚C. The mRNA fragments were then converted into ds cDNA by random priming, and the ends were repaired and A-tailed. Multiplexing barcodes were then added to the DNA fragment ends with modifications from the paired-end gDNA library prep kit (Illumina, USA). The ligation products were size-selected on agarose gel (200-400 bp), subjected to 18 cycles of PCR and cleaned up by Ampure beads (Beckman Agencourt, USA). The libraries were quantified fluorometrically by Qubit (Invitrogen, USA) and BioAnalyzer High Sensitivity DNA chip (Agilent, USA). Mixing of the differentially barcoded samples for each lane was based on qPCR-derived relative concentration for amplifiable fraction of each library.

treatment_protocol: 1 hour red light treatment (660 nm LED, 5 μmol m-2 s-1) at growth temperature (25 °C)

tag: ecotype

tag: genotype/variation

value: wild type

tag: age

value: protonema

tag: tissue

value: chloronema


title: mRNA-seq of wild-type protonema, 1 hr red light

description: Sample 2

data_processing:
Sequence reads were mapped to the Physcomitrella patens genome V1.6 (http://cosmoss.org/, data also can found in JGI, http://www.phytozome.net/physcomitrella.php) using the BLAT program. RPKM computation was performed by using RACKJ package (http://rackj.sourceforge.net/) with similar algorithm. Data were analyzed in Excel (Microsoft, Redmond, WA, USA).
Genome Build:
WT_R1_Counts_RPKM_all.txt: Physcomitrella patens genome V1.6

source_name: wild-type_1 hr red light


title: mRNA-seq of pubs hy2 protonema, dark-grown, time 0 control

description: Sample 3

data_processing:
Sequence reads were mapped to the Physcomitrella patens genome V1.6 (http://cosmoss.org/, data also can found in JGI, http://www.phytozome.net/physcomitrella.php) using the BLAT program. RPKM computation was performed by using RACKJ package (http://rackj.sourceforge.net/) with similar algorithm. Data were analyzed in Excel (Microsoft, Redmond, WA, USA).
Genome Build:
pubshy2_R0_Counts_RPKM_all.txt: Physcomitrella patens genome V1.6

source_name: pubs hy2 mutant_dark-grown_time 0 control

value: pubs hy2 double mutant (phytochrome-deficient mutant)


title: mRNA-seq of pubs hy2 protonema, 1 hr red light

description: Sample 4

data_processing:
Sequence reads were mapped to the Physcomitrella patens genome V1.6 (http://cosmoss.org/, data also can found in JGI, http://www.phytozome.net/physcomitrella.php) using the BLAT program. RPKM computation was performed by using RACKJ package (http://rackj.sourceforge.net/) with similar algorithm. Data were analyzed in Excel (Microsoft, Redmond, WA, USA).
Genome Build:
pubshy2_R1_Counts_RPKM_all.txt: Physcomitrella patens genome V1.6

source_name: pubs hy2 mutant_1 hr red light


title: Snyder_F16B12.6_Input_L1_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: Hermaphrodite


title: Snyder_F16B12.6_GFP_L1_rep1 extraction1_seq1 aliquote 1

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180


title: Snyder_F16B12.6_Input_L1_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_DAF12_GFP_L3_rep1 extraction1_seq1 aliquote 1

value: OP167(official name :OP167 genotype :unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by :S Kim )


title: Snyder_DAF12_GFP_L3_rep2 extraction2_seq1 aliquote 1


title: Snyder_SEA2_GFP_L3_rep1 extraction1_seq1 aliquote 1

value: OP193(official name :OP193 genotype :unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by : )


title: Snyder_NHR11_GFP_L2_rep2 extraction2_seq1 aliquote 1

value: OP305(official name :OP305 genotype :unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by :R Waterston )


title: Snyder_NHR11_GFP_L2_rep1 extraction1_seq1 aliquote 1


title: Snyder_SEA2_GFP_L3_rep2 extraction2_seq1 aliquote 1

value: unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119)


title: Snyder_NHR11_Input_L2_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_CES1_GFP_L1_rep2 extraction2_seq1 aliquote 1

value: OP174(official name :OP174 genotype :unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by :S. Kim )


title: Snyder_LIN15B_Input_L4_rep1 extraction1_seq1 aliquote 1

description: input DNA

value: OP184(official name :OP184 genotype :unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by :S Kim )


title: Snyder_CES1_Input_L1_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119)


title: Snyder_CES1_GFP_L1_rep1 extraction1_seq1 aliquote 1


title: Snyder_CES1_Input_L1_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_LIN15B_GFP_L4_rep2 extraction2_seq1 aliquote 1


title: Snyder_LIN15B_GFP_L4_rep1 extraction1_seq1 aliquote 1


title: Snyder_Pdpl1_DPL1_GFP_L1_rep2 extraction2_seq1 aliquote 1

value: YL425(official name :YL425 genotype :unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG:DPL-1 3?UTR genotype :unc-119 (+)] outcross :3 mutagen :Bombard tags :GFP::3xFlag description : made_by : )


title: Snyder_Pdpl1_DPL1_GFP_L1_rep1 extraction1_seq1 aliquote 1

value: unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG:DPL-1 3?UTR


title: Snyder_NHR11_Input_L2_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_Pdpl1_DPL1_Input_L1_rep2 extraction2_seq1 aliquote 1

description: input DNA


description:
design description: miRNA-Seq analysis of foreskin fibroblast from skin01 (m01584) using Illumina Genome Analyzer IIx
library name: m01584
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 8.8
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.264 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM817252_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.smRNA-Seq.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01584-1.hg19.level.1.release6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.12569
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,199,206
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 50.12
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817252_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.smRNA-Seq.skin01.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01584-1.hg19.level.2.tag.release6
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Fibroblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin01 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12575
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,199,206
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 50.12
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817252_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.smRNA-Seq.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01584-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin01 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12572
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-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 6
BROWSER_TRACK_NAME: PFF smRNA 01 84
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin01 Library M01584 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,199,206
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 50.12
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Penis

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


title: Snyder_Pdpl1_DPL1_Input_L1_rep1 extraction1_seq1 aliquote 1

description: input DNA

value: fed L1


title: Snyder_DAF12_Input_L3_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: Hermaphrodite


title: Snyder_SEA2_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_SEA2_Input_L3_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_DAF12_Input_L3_rep1 extraction1_seq1 aliquote 1

description: input DNA

value: OP167(official name :OP167 genotype :unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by :S Kim )


title: Snyder_LIN15B_Input_L4_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_Pefl1_EFL1_GFP_L1_rep1 extraction1_seq1 aliquote 1

value: YL424(official name :YL424 genotype :unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG:EFL-1 3?UTR genotype :unc-119 (+)] outcross :3 mutagen :Bombard tags :GFP::3xFlag description : made_by : )


title: Snyder_Pefl1_EFL1_Input_L1_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG:EFL-1 3?UTR


title: Snyder_Pefl1_EFL1_Input_L1_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_Ppie1_DPL1_Input_YA_rep2 extraction2_seq1 aliquote 1

description: input DNA

value: YL390(official name :YL390 genotype :unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG:DPL-1 3?UTR genotype :unc-119 (+)] outcross :3 mutagen :Bombard tags :GFP::3xFlag description : made_by : )

value: Young Adult


title: Snyder_Ppie1_DPL1_GFP_YA_rep2 extraction2_seq1 aliquote 1

value: unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG:DPL-1 3?UTR


title: Snyder_Ppie1_DPL1_GFP_YA_rep1 extraction1_seq1 aliquote 1


title: Snyder_Ppie1_DPL1_Input_YA_rep1 extraction1_seq1 aliquote 1

description: input DNA


title: Snyder_Ppie1_EFL1_GFP_YA_rep2 extraction2_seq1 aliquote 1

value: YL445(official name :YL445 genotype :unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG:EFL-1 3?UTR genotype :unc-119 (+)] outcross :3 mutagen :Bombard tags :GFP::3xFlag description : made_by : )


title: Snyder_Ppie1_EFL1_Input_YA_rep1 extraction1_seq1 aliquote 1

description: input DNA

value: unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG:EFL-1 3?UTR


title: Snyder_Ppie1_EFL1_Input_YA_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_CEH-26_GFP_LE_rep2 extraction2_seq1 aliquote 1

value: OP500(official name :OP500 genotype :unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by :R. Waterston )

value: late embryo


title: Snyder_CEH-26_Input_LE_rep2 extraction2_seq1 aliquote 1

description: input DNA


title: Snyder_Ppie1_EFL1_GFP_YA_rep1 extraction1_seq1 aliquote 1


title: Snyder_Pefl1_EFL1_GFP_L1_rep2 extraction2_seq1 aliquote 1


title: H3.1 non-dividing rep1

value: Columbia HTR13-GFP

tag: chip antibody

value: GFP

tag: genetic background

value: Columbia

value: Oldest 4 to 6 leaves

tag: chip antibody manufacturer

value: Invitrogen

tag: chip antibody catalog #


title: Snyder_CEH-26_GFP_LE_rep1 extraction1_seq1 aliquote 1

tag: developmental stage

tag: genotype

tag: Sex