title: MCF10A RAS-transormed (8d)

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description: Illumina GA-II, HiSeq 2000

data_processing: Reads were aligned to the human genome (hg18) using bowtie. Wig files which summarize read coverage at each genomic ccordinate (hg18) were generated using a perl script and transcripts' genomic coordinates downloaded from the USCS browser related Tables.

organism: Homo sapiens

source_name: MCF10A breast epithelial cells

growth_protocol: Primary BJ foreskin fibroblasts containing expression constructs for the ecotropic receptor and the human telomerase gene (hTERT), BJ-EHT, were either maintained in a cycling state or contact inhibited by growing them to confluence in DMEM (Gibco) supplemented with 10% FCS and antibiotics. Non-transformed mammary epithelial MCF10A cells were either cultured in DMEM:F12 Ham's medium (Sigma) 1:1, supplemented with 10% fetal calf serum (Gibco), insulin (10 μg ml−1; Sigma), hydrocortisone (0.5 μg ml−1) and epidermal growth factor (20 ng ml−1; Peprotech) or serum starved with DMEM:F12 containing no supplements for 48 hours.

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit from Qiagen. mRNA was isolated with the Oligotex mRNA Kit from Qiagen.
Total RNA was extracted from cells.  mRNA was then isolated, heat fragmented and the fragmented mRNA was converted to single-stranded cDNA using SuperScript III reverse transcriptase and P7-t25-vn oligo-dT primer. This was followed by second-strand cDNA synthesis and end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. After purification, a P5-splinkerette was ligated and the splikerette-ligated cDNA was size-selected for approximately 220 bp long cDNA fragments using the E-Gel iBase Power System from Invitrogen. The final 3'Seq libraries were then generated by PCR amplification of the linker-ligated cDNA with P5 and P7 primers.

treatment_protocol: BJ-EHT/p53kd/p16kd/RASGV12ER cells expressing short hairpin (sh)RNA constructs targeting p53 and p16INK4A and 4-hydroxy-tamoxifen (4-OHT) inducible oncogenic HRASG12V were cultured for 3 days in the presence of 100 nM 4-OHT to transform the cells. To transform the MCF10A cells we transduced them with a retroviral vector expressing RASG12VER, and cultured them for 2 and 8 days in the presence of 100 nM 4-OHT

value: MCF10A breast epithelial cells

tag: growth stage

value: RAS-transformed

tag: rna subtype

value: polyA RNA


title: SMEU37Fe02MP1

status: Public on Jun 18 2012

type: SRA

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

country: USA

institute: University of California Los Angeles

description: Chlamydomonas reinhardtii 2137 - Fe-limited - Replicate #1

library_source: transcriptomic

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe02MP1_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe02MP1_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

molecule: total RNA

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii 2137 - Fe-limited (Minimal media)

growth_protocol: Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium or minimal media.

extract_protocol: Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina by whole transcriptome analysis.

treatment_protocol: To generate Fe-deficient and Fe-limited cultures, cells in the pretransfer culture are grown under Fe-replete conditions to mid to late log phase (10e6-10e7 cells/ml) and diluted to 10e4 cells/ml into fresh Fe-deficient or Fe-limited medium. Two sequential transfers (from 10e6-10e7 cells/ml into fresh Fe-deficient medium) are performed to ensure that residual iron in the Fe-deficient or Fe-limited cultures is reduced.

tag: strain

tag: medium

value: Minimal media


title: MCF10A RAS-transormed (0)

department: Human Genetics

description: Illumina GA-II, HiSeq 2000

tag: cell type


title: SMEU37Fe20TP1

description: Chlamydomonas reinhardtii 2137 - Fe replete - Replicate #1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20TP1_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe20TP1_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe replete (TAP)

value: TAP


title: MCF10A serum-starved

description: Illumina GA-II, HiSeq 2000

value: serum-starved


title: MCF10A proliferative

description: Illumina GA-II, HiSeq 2000

value: proliferative


title: BJ proliferative (reads len 100)

description: Illumina GA-II, HiSeq 2000

source_name: BJ fibroblast cells

value: BJ fibroblast cells


title: MCF10A RAS-transormed (2d)

description: Illumina GA-II, HiSeq 2000

tag: time


title: SMEU37Fe1TP3

description: Chlamydomonas reinhardtii 2137 - Fe-deficient - Replicate #3

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe1TP3_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe1TP3_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe-deficient (TAP)


title: Oocyte litter 3

city: La Jolla

first: Todd

last: Macfarlan

state: CA

address: 10010 North Torrey Pines

institute: The Salk Institute

description: RNA amplified using SPIA

data_processing:
Oocyte_3.wig; genome build: mm9
Bowtie alignments, allowing 3 mismatches per read, allowing up to 20 alignments per read

organism: Mus musculus

source_name: oocyte

growth_protocol: Females were superovulated using standard conditions

extract_protocol: Nugen Ovation RNA-Seq kit(for amplifying RNA) followed by library construction using Illumina mRNA sample prep kit starting with end repair

treatment_protocol: Oocytes were collected by E0.5 and lysed in Prelude Direct Lysis Buffer

tag: genetic background

value: mixed strain oocytes

value: oocyte

tag: crosses

value: LSD1 FL/FL mice (From Wang et al, Nature 446, 2007 ) were crossed with ZP3::Cre mice (Jax labs strain 003651) and backcrossed again to generate LSD1 FL/FL, ZP3Cre+ and - mice. FOr this study, only LSD1 FL/FL, ZP3::Cre negative females were used to produce oocytes.  For 2C embryos, these females were crossed with wild type CB6 males


title: SMEU37Fe20TP2

description: Chlamydomonas reinhardtii 2137 - Fe replete - Replicate #2

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20TP2_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe20TP2_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly


title: Oocyte litter 2

description: RNA amplified using SPIA

data_processing:
Oocyte_2.wig; genome build: mm9
Bowtie alignments, allowing 3 mismatches per read, allowing up to 20 alignments per read


title: Oocyte litter 1

description: RNA amplified using SPIA

data_processing:
Oocyte_1.wig; genome build: mm9
Bowtie alignments, allowing 3 mismatches per read, allowing up to 20 alignments per read


title: 2C::tomato+

data_processing:
2C_tomato_+.wig; genome build: mm9
Bowtie was used to align reads, allowing 2 bp mismatchs and allowing up to 40 alignments per read

source_name: ES cells sorted by FACS

growth_protocol: ES cells grown on gelatin in ES-KOSR media containing 150ug/ml hygromycin

extract_protocol: mRNA-Deq sample prep kit (Illumina)

treatment_protocol: Cells subject to flow cytometry to collect 2C::tomato+ and - cells

value: mixed strain

value: ES background Kdm1a FL/FL, CreERT

tag: genotype


title: G9A knockout

data_processing:
Paired end alignments with Tophat allowing 4 mismatches per 100 bp
Genome Build:
G9a_KO.bed: mm9

source_name: G9A TT2 ES cells

growth_protocol: Stadard ES cell conditions with Lif

extract_protocol: TruSeq RNA sample prep kit

treatment_protocol: RNA prepared by RiboPure (ambion)

value: G9A KO

tag: treatment

value: 4OHT treated

value: embryonic stem cells


title: 2C litter 2

description: RNA amplified using SPIA

data_processing:
2C_2.wig; genome build: mm9
Bowtie alignments, 3 mismatches per alignment, up to 20 alignments per read, for comparison with oocytes single-end (left side reads) trimmed on 3' end to 72bp

source_name: 2C stage embryos

growth_protocol: Mixed strain female mice were fertilized with C57/Bl6J mice

extract_protocol: Nugen Ovation RNA-Seq kit VII (for amplifying RNA) followed by Covaris fragmentation of cDNA, and library construction using Illumina mRNA sample prep kit starting with end repair

treatment_protocol: Litters of 2C embryos were collected at E1.5 and lysed in Prelude direct lysis buffer

value: mixed strain with C57/Bl6J

tag: developmental stage

value: 2-cell embryo

tag: tissue

value: embryo


title: 2C::tomato-

data_processing:
2C_tomato_-.wig; genome build: mm9
Bowtie was used to align reads, allowing 2 bp mismatchs and allowing up to 40 alignments per read


title: 2C litter 3

description: RNA amplified using SPIA

data_processing:
2C_3.wig; genome build: mm9
Bowtie alignments, 3 mismatches per alignment, up to 20 alignments per read, for comparison with oocytes single-end (left side reads) trimmed on 3' end to 72bp


title: WT

data_processing:
Paired end alignments with Tophat allowing 4 mismatches per 100 bp
Genome Build:
WT.bed: mm9

value: wild type

value: Vehicle treated


title: 2C litter 1

description: RNA amplified using SPIA

data_processing:
2C_1.wig; genome build: mm9
Bowtie alignments, 3 mismatches per alignment, up to 20 alignments per read, for comparison with oocytes single-end (left side reads) trimmed on 3' end to 72bp


title: BJ RAS-transformed (reads len 35)

description: Illumina GA-II, HiSeq 2000

value: RAS-transformed

value: polyA RNA


title: BJ proliferative (reads len 35)

description: Illumina GA-II, HiSeq 2000

value: proliferative


title: IgG ChIP vehicle treated

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations
Uniquely mapped reads with mis-match <= 2 were used for peak detection
Peaks were called using QuEST (version 2.4) using the “Transcription factor binding site” setting (bandwidth of 30 bp, region size of 300 bp) and the “stringent peak calling” parameters (corresponding to 50-fold ChIP to input enrichment for seeding the regions, and 3-fold ChIP enrichment for extending the regions).
Peaks with FDR q <= 0.05 and tags >= 5 were kept for further analysis
Genome_build: hg18
Supplementary_files_format_and_content: The wig files were generated using QuEST, and scores represent combined kernel density for forward and reverse reads at any position.

molecule: genomic DNA

source_name: IgG ChIP vehicle treated

growth_protocol: human lymphoblastoid cells were grown as recommended by Coriell

extract_protocol: Lysates were clarified from sonicated nuclei and NRF2-DNA complexes were isolated with antibody (Epitomics, Clone ID EP1808Y).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 10 μM D,L-sulforaphane (Calbiochem) or 0.1% (v/v) DMSO as a vehicle control for 5 hours

value: lymphoblastoid

tag: cell line

tag: chip antibody

value: rabbit IgG antibody (Invitrogen)


title: BJ confluent (reads len 35)

description: Illumina GA-II, HiSeq 2000

value: BJ fibroblast cells

value: confluent


title: BJ confluent (reads len 100)

description: Illumina GA-II, HiSeq 2000


title: NRF2 ChIP vehicle treated rep3

source_name: NRF2 ChIP vehicle treated

value: rabbit monoclonal anti-NRF2 (Epitomics, Clone ID EP1808Y)


title: input SFN treated

source_name: input SFN treated


title: IgG ChIP SFN treated

source_name: IgG ChIP SFN treated


title: input vehicle treated

source_name: input vehicle treated


title: longissimus muscle_pooled 3 Landrace 63 day fetals

city: College Station

first: Jason

last: Karpac

state: Texas

address: Reynolds Medical Building

department: Molecular and Cellular Medicine

institute: Texas A&M University Health Sciences Center

data_processing:
Data processed by the Beijing Genomics Institute (BGI, commercial service). Clean tags were obtained by filtering raw data to remove adaptor tags, low quality tags and tags of copy number = 1. The clean tags were classified according their copy number in the library and the proportion of each category in relation to total clean tags was determined. Similar analyses were carried out for clean distinct tags.
All possible CATG+17-nt tag sequences were created from the sus scrofa RefSeq and UniGene (NCBI36.1, 20090827) databases and used as reference sequences to align and identify the sequencing tags. All clean tags were aligned to the reference database, and then unambiguous tags were annotated. One mismatch in each alignment was allowed to tolerate polymorphisms across samples. Mismatch could be caused by a sequencing error, but the frequency is very low (1 or 2 per million).
Software/programs used in our analysis:
1. BLAST v2.2.21. (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.21/)
2. BLAT v.34, (http://genome.ucsc.edu/FAQ/FAQblat)
3. SOAP v1.11. . http://soap.genomics.org.cn/#down2.
4. Bowtie v0.12.3. http://bowtie-bio.sourceforge.net/index.shtml
5. Cluster v1.47. http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/
6. Java TreeView v1.1.4r3. http://sourceforge.net/projects/jtreeview/
7. Medusa v1.5.1. http://coot.embl.de/medusa/ Applet. http://coot.embl.de/medusa/Stringlet2Applet.shtml
8. Blast2GO Blast2GO. v2.3.5. http://www.blast2go.org/

organism: Sus scrofa

source_name: pooled longissimus muscle of three fetals (prenatal day 63)

growth_protocol: All animal procedures were performed according to guidelines developed by the China Council on Animal Care and protocol approved by Animal Care and Use Committee of Guangdong Province, P.R. China.

extract_protocol: The RNA library was constructed and deep sequencing preformed by the Beijing Genomics Institute (BGI, commercial service). Total RNA was extracted from frozen muscles using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufactures's protocols. RNA integrity and concentration were evaluated by Agolent 2100 Bioanalyzer (Agilent Technologies). For RNA library construction and deep sequencing, equal quantities of RNA samples from three individual pigs were pooled at every time points. Approximately 6 ug of RNA representing each group were submitted to Solexa (now Illumina Inc.) for sequencing. Sequence tag preparation was done with Illumina's Digital Gene Expression Tag Profiling Kit according to the manufacturer's protocol. In brief, mRNA was isolated from 6ug total RNA by binding the mRNA to a magnetic oligo bead. First-and second-strand cDNA were synthesized while the mRNA was attached to the beads. The double 14 stranded cDNA were digested with NlaIII to wash away all fragmens other than the 3? CATG fragment attached to the oligo bead. Then GEX NlaIII Adapter 1 was ligated at the site of NlaIII cleavage. In addition, GEX NlaIII Adapter 1 contains the sequence for the restriction enzyme MmeI, subsequently, we applied the restriction enzyme MmeI to create the 17 bp tag. The GEX Adapter 2 was ligated at the site of MmeI cleavage. A PCR with 12 cycles was performed with two primers that anneal to the ends of the adapters to enrich the adapter-ligated cDNA construct. The resulting 85 bp fragments were purified from 6% Novex TBE PAGE gel. Subsequently, the purified cDNA tags were sequenced on the Illumina Cluster Station and Genome Analyzer. Image recognition and base calling were performed using the Illumina Pipeline.

treatment_protocol: Purebred 15 Lantang (LT) and 15 Landrace (Lde) sows which have the same genetic background were artificially inseminated with semen from same purebred boars respectively.

tag: breed

value: Landrace

value: longissimus muscle

value: prenatal day 63


title: NRF2 ChIP vehicle treated rep1


title: NRF2 ChIP SFN treated rep2

source_name: NRF2 ChIP SFN treated


title: Col0_methyl-Seq_rep2

status: Public on Jun 17 2012

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing: Each raw read was first trimmed to the longest contiguous read segment with Phred quality score>=20 (using DynamicTrim from the SolexaQA software, Cox et al, 2010) and then trimmed for the adaptor sequence if exists using an inhouse perl script. We mapped paired reads and singleton reads (when read from the other end was discarded due to low quality) to the Arabidopsis genome (TAIR10) using BRAT (Harris et al. 2009, doi:10.1093/bioinformatics/btp706). Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ). The wig files give methylation level for all Cs covered by at least 4 reads (*PlusStrand.wig for Watson strand and *MinusStrand.wig for Crick strand).

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis seedlings were grown on Murashige-Skoog (MS) nutrient agar plates at 23℃ with 16 h light and 8 h of darkness for 2 weeks.

extract_protocol: Libraries were prepared according to a published protocol (Lister et al., 2008). Briefly, sonicated DNA was end-repaired by using End Repair Enzyme Mix (NEB, #E6041A). The blunt end DNA were treated with Klenow fragment (NEB, #E6044A) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Unmethylated cytosine residues were converted to uracil by EpiTect bisulfite Kit (Qiagen, 59104) after adaptor ligation. After bisufite treated DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 250~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx/HiSeq 2000 following the manufacturer's protocols.

tag: genotype/variation

value: WT

tag: ecotype


title: NRF2 ChIP vehicle treated pilot


title: NRF2 ChIP SFN treated pilot


title: NRF2 ChIP SFN treated rep1


title: SMEU37Fe20MP1

data_processing:
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates. Processed files correpond to the bowtie standar output format.
Genome Build:
SMEU37Fe20MP1_1.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly
SMEU37Fe20MP1_2.bowtie: Augustus 10.2 gene models - Chlamydomonas V4 genome assembly

source_name: Chlamydomonas reinhardtii 2137 - Fe replete (Minimal media)

value: Minimal media


title: 3P_Seq_4hpf

city: Cambridge

first: Igor

last: Ulitsky

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: 3P-Seq 4 hpf

data_processing:
For 3P-Seq: Reads were reverse complemented and aligned to the D. rerio genome (Zv9/danRer7) using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their 3' end within a terminal adenylate-run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. (GSE24924)
For 3P-PE-Seq: In each read pair, read #1 captured the 3' end of the poly(A) tail in the antisense orientation, and read #2 captured a portion of the 3' region of the transcript, and occasionally, the beginning of the poly(A) tail, in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing.  A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. After leading Ts and terminal As were removed from reads #1 and #2, respectively, they were mapped to the genome using Bowtie, allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non-A base in read #2. The length of the poly(A) tail at that position was estimated using the corresponding read #1, and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers.
Genome_build: danRer7
Supplementary_files_format_and_content: The .bed files contain the positions where 3P-Seq reads were mapped, and the name of each track is the number of reads mapping to that position.
Supplementary_files_format_and_content: The bigWig (.bw) files contain a summary of the number of reads whose 3' ends mapped to each position in the genome.
Supplementary_files_format_and_content: For the paired-end sequencing for mapping poly(A) tail lengths, the text files contain the following columns : chromosome, position, strand, number of poly(A) length reads, followed by the individual measurements (lower bounds on poly(A) tail length)

molecule: polyA RNA

organism: Danio rerio

source_name: whole embryo at 4 hours post fertilization

growth_protocol: Zebrafish embryos or adults grown under standard condition

treatment_protocol: Anesthetized decorioneted embryos were washed three times in PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HP04, pH 7.4) and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer, dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at-80C.

value: whole embryo

value: 4 hours post fertilization


title: 3P_PE_Seq_PreMZT

description: 3P-PE-Seq 1.5-2 hpf

source_name: whole embryo at 1.5-2 hours post fertilization

extract_protocol: 3P-PE-Seq:  To selectively capture polyadenylated ends for paired-end sequencing, 2.5 µg of total RNA from 2–2.2 or 6 hpf zebrafish embryos was splint ligated to a 3' biotinylated adapter (p-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGACACATAC-biotin, IDT) in the presence of bridge oligo (TTCCGATCTTTTTTTTT, IDT) using T4 Rnl2 (NEB) in an overnight reaction at 18°C. Following partial digestion with RNase T1 (Ambion), 115–750-nt RNAs were isolated from a denaturing polyacrylamide gel and ligation products were captured on streptavidin M-280 Dynabeads (Invitrogen). RNAs were phosphorylated at the 5' end on beads using PNK (NEB) and subsequently ligated to an adapter (C3.spacer-GTTCAGAGTTCTAcaguccgacgauc, uppercase, DNA; lowercase, RNA; IDT) using T4 Rnl1 (NEB) in an overnight reaction at room temperature. Complementary DNA was synthesized on beads using SuperScript II (Invitrogen) primed with AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACG (IDT), liberated from the beads by base hydrolysis, size selected (155–790 nt) on a denaturing polyacrylamide gel, and amplified by PCR for 15 cycles. 180–750-nt products were isolated from a formamide gel and amplified for four additional cycles using primers that contain the Illumina paired-end sequencing primer binding sites. After a final formamide gel purification and size selection (220–800-nt), 80x80 paired-end sequencing was performed on the Illumina Hi-Seq platform.

value: wild type

value: 1.5-2 hours post fertilization


title: 3P_Seq_1cell

description: 3P-Seq 1 cell

source_name: whole embryo at 1 cell stage

value: 1 cell stage


title: NRF2 ChIP vehicle treated rep2


title: 3P_Seq_PostMZT

description: 3P-Seq 6 hpf

source_name: whole embryo at 6 hours post fertilization

value: 6 hours post fertilization


title: 3P_Seq_Adult

description: 3P-Seq Adult

source_name: mixed gender adults

treatment_protocol: For adult fish, anesthetized fish were homogenized in the TissueRuptor (Qiagen). Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at-80C.

value: whole adult

value: adult


title: 3P_Seq_72hpf

description: 3P-Seq 72 hpf

source_name: whole embryo at 72 hours post fertilization

value: 72 hours post fertilization


title: 3P_Seq_PreMZT

description: 3P-Seq 1.5-2 hpf


title: 3P_Seq_Testis

description: 3P-Seq Testis

source_name: male adults

treatment_protocol: Ovaries and testes were obtained as described  in Gupta and Mullins 2010.

value: testis


title: 3P_Seq_PreMZT_2

description: 3P-Seq 1.5-2 hpf lane 2


title: NRF2 ChIP SFN treated rep3

value: lymphoblastoid


title: 3P_Seq_Brain

description: 3P-Seq Brain

value: brain


title: 3P_Seq_Ovary

description: 3P-Seq Ovary

source_name: female adults

value: ovary


title: rdd_methyl-Seq_rep2

description: treated with bisulfite

value: rdd triple mutant


title: 3P_Seq_PreMZT_3

description: 3P-Seq 1.5-2 hpf HiSeq


title: rdd_methyl-Seq_rep1

description: treated with bisulfite


title: dcp2D_xrn1D_rep3

city: Boulder

first: Yuriko

last: Harigaya

state: Colorado

address: 3415 Colorado Ave, UCB 596

institute: University of Colorado at Boulder

data_processing:
Read sequences composed of 20- or 21-nucleotide-long captured RNA sequences followed by the 3' Illumina adaptor sequence were selected using fastx_barcode_splitter.pl in FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/download.html).
The file of the barcode-matched reads was converted to a fasta file containing reads from which the adaptor sequences were removed using Perl.
Identical sequences were collapsed and counted using fastx_collapser in FASTX-Toolkit to generate a file of distinct sequences and occurrence counts.
The distinct sequences were aligned to reference sequences using Bowtie 0.12.7 with parameters -f -m 1. In this setting, two mismatches were allowed (default), and alignments were required to be unique.
The abundance of each sequence read was plotted as a function of its position in 6,603 yeast mRNA using Perl. In this process, sequence reads that were aligned to the reference with no mismatch were used. ORF annotations were downloaded from SGD (http://downloads.yeastgenome.org/chromosomal_feature/ SGD_features.tab) on May 11, 2012. UTR lengths were taken from Nagalakshmi et al. (2008) Science, 320:1344. Where UTR annotation was not available, the ORF start/end was considered to be the transcript start/end. For each sample, read counts were normalized to the total reads mapping to all mRNAs.
Genome_build: S288C_reference_genome_R64-1-1_20120203, A364A 2 micron plasmid sequence (NCBI accession number NC_001398), dsRNA virus genome (killer virus M1, virus L-A and L-BC, single stranded viruses 20S and 23S; NCBI accession numbers NC_001782, NC_003745, NC_001641, NC_004051 and NC_004050, respectively), and the sequence of the kanMX6 cassette (Longtine et al., 1998, Yeast, 14:953)
Supplementary_files_format_and_content: transcript profiles: The tab-delimited files contain read counts at all nucleotide positions in 6,603 protein-coding transcripts in Saccharomyces cerevisiae. Each line represents one transcript. The first element of each line represents the gene name. The UTR annotations were taken from Nagalakshmi et al. (2008) Science, 320:1344. When UTR annotation was not available, the ORF start/end was considered to be the transcript start/end.

organism: Saccharomyces cerevisiae

source_name: dcp2D::HIS3 xrn1D::kanMX

growth_protocol: Cells were grown to mid-log phase (OD600 = 0.3) in YPD media at 30˚C.

extract_protocol: RNA was extracted from frozen cells by a hot phenol method. Polyadenylated RNA was selected using Oligo (dT) DynaBeads (Invitrogen). A 5' RNA adaptor that includes a recognition site for the MmeI restriction enzyme was selectively ligated to 5' monophosphorylated species using T4 RNA ligase (Ambion). The ligated RNA was reverse-transcribed using oligo(dT) linked to a 3' adaptor sequence, PCR-amplified for 10 cycles and treated with MmeI, which cleaves 20 or 21 nucleotides 3' of the recognition site. The digestion products were gel-purified, ligated to a 3' double-strand DNA adaptor and again gel-purified. The resultant material was PCR-amplified, gel-purified and subject to high-throughput Illumina sequencing.

value: dcp2D::HIS3 xrn1D::kanMX


title: ros1-4_methyl-Seq_rep2

description: treated with bisulfite

value: ros1-4 mutant


title: 3P_Seq_24hpf

description: 3P-Seq 24 hpf

source_name: whole embryo at 24 hours post fertilization

treatment_protocol: Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS (137 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8 mM Na2HP04, pH 7.4) and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer, dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at -80C.

value: 24 hours post fertilization


title: ros1-4_methyl-Seq_rep1

description: treated with bisulfite


title: WT_rep2

source_name: wild type


title: 11-15 DPA small RNA

status: Public on Jun 16 2012

city: Canberra

first: Jennifer

last: Taylor

address: Clunies Ross St

department: Plant Industry

country: Australia

institute: CSIRO

data_processing: Analysis of small RNA sequencing included trimming of 3' adapter sequences and creation of a non-redundant sequences or signatures list. Sequences that were over 50% homopolymer or dinucleotide repeat were removed and read counts for each unique sequence were normalised to reads per million of total sequenced reads. Only signatures that were 18 to 25 nucleotides in length and with minimum expression of 1 RPM were considered. Exact matches, in sequence and length, to a known miRNA in miRBase were annotated. Processed data from the three samples were combined in a single file and a readme provided as SmRNA-unique.readme.txt.

organism: Hordeum vulgare

source_name: 11-15 day post anthesis grains

growth_protocol: Barley (Hordeum vulgare) plants were grown in naturally lit phytotron glasshouses with air temperature set at 17°C/9°C day/night cycle. The plants were grown from October to December where the time of anthesis was determined for each heads based on the dissection of the middle spikelet.

extract_protocol: small RNA libraries were prepared from total RNA following the Illumina small RNA protocol

treatment_protocol: RNA was extracted using a phenol/chloroform based method from grain harvested on each day after anthesis and equal RNA amounts pooled to make 1-5, 6-10 and 11-15 day samples

tag: cultivar

value: 'Golden Promise'

value: 11-15 day post anthesis grains


title: 6-10 DPA degradome

data_processing: Analysis of PARE RNA sequencing included trimming of 3' adapter sequences and creation of a non-redundant sequence set. Sequences that were over 50% homopolymer or dinucleotide repeat were removed and reads were trimmed to 20 nt. Read counts for each unique sequence were normalised to reads per million of total sequenced reads.  Processed data from the three samples were combined in a single file and a readme provided as PARE-unique.readme.txt.

source_name: 6-10 day post anthesis grains

extract_protocol: degradome libraries were constructed from purified mRNA according to the method of German et al (Nature Protocols 2009, 4:356-362)

value: 6-10 day post anthesis grains


title: 3P_PE_Seq_PostMZT

description: 3P-PE-Seq 6 hpf

value: wild type

value: whole embryo


title: 1-5 DPA small RNA

source_name: 1-5 day post anthesis grains

value: 1-5 day post anthesis grains


title: idm1-1_methyl-Seq_rep2

description: treated with bisulfite

value: idm1-1 mutant


title: THC3710.1

status: Public on Jun 15 2012

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Theca.C.HEIFER.THC3710.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

organism: Bos taurus

source_name: Theca cells of dominant follicle

growth_protocol: The estrous cycles of 16 Holstein-Friesian lactating cows  and 17 nulliparous Holstein-Friesian dairy heifers (1.6 years ± 0.06; kept on the same farm) were pre-synchronized by insertion of a controlled intravaginal drug releasing device (CIDR) (containing 1.38g of progesterone) and a 2 ml intramuscular injection of a prostaglandin F2α anologue. Subsequent to detection of estrus, animals were treated with a used CIDR on Day 8 (Day 0 = observed estrus).

extract_protocol: The standard Illumina protocol for generating single read RNAseq data was followed. Version 2 illumina sequencing kits were used.

treatment_protocol: Selection group had their used CIDRs removed on the morning of Day 14 and were slaughtered. On the last ultrasound scan before slaughter all animals had a newly selected dominant follicle and a corpus luteum present. Animals assigned to the Differentiation and Luteinization groups received a luteolytic dose of PG on Day 13 and the CIDR was removed on the morning of Day 15 to accurately synchronise the follicular phase differentiation of selected dominant follicles. Animals assigned to the Differentiation group were then slaughtered on Day 16 between 24 and 30 h after CIDR removal and before any animals displayed estrus indicating the onset of the gonadotrophin surge. Animals assigned to the Luteinization group  received an intramuscular injection of 5 ml GnRH  30 h post CIDR removal which induces a synchronised gondotrophin surge, and were slaughtered 18-22 h after the administration of GnRH (day 17) timed to occur before ovulation but after the onset of luteinisation.

value: Theca

tag: Stage

value: Luteinized

tag: animaltype

value: Heifer

tag: animalid


title: THC3704.1

data_processing:
Theca.C.HEIFER.THC3704.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THC3702

data_processing:
Theca.C.HEIFER.THC3702.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THC3751.1

data_processing:
Theca.C.HEIFER.THC3751.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THC3597.1

data_processing:
Theca.C.HEIFER.THC3597.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: RNASeq of pro-B cell fraction B, wt

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: Illumina RTA 1.12.4.2
fastq extraction:  Illumina CASAVA 1.8.2 configureBclToFastq.pl
alignment: tophat v1.3.3 [--splice-mismatches=1 --min-anchor-length=8 --min-isoform-fraction=0.15  --max-multihits=5 --coverage-search -G refseq_genes.gtf –segment-length=18]
Genome_build: mm9
Supplementary_files_format_and_content: coverage in bedgraph format [normalized by library size] as generated by bedtools 2.15.0 genomecov  -bg -split. Only uniquely aligned reads were included in coverage output.

source_name: Hardy pro-B cell fraction B, wt

growth_protocol: Bone marrow cells from FNIP1+/+  and FNIP1-/-  mice were stained with CD24(HSA)-FITC, CD43-PE, B220-PerCP-Cy5.5, and BP-1-APC. Fraction B (B220lowCD43+CD24+BP-1-) and Fraction C-C’ (B220lowCD43+CD24+BP-1+) pro-B cells were sorted

extract_protocol: RNA was isolated with Trizol and libraries were generated with TrueSeq kits according to manufacturer's instructions.

tag: strain

value: wt

tag: cell

value: Hardy pro-B cell fraction B


title: THC3576.1

data_processing:
Theca.C.HEIFER.THC3576.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: RNASeq of pro-B cell fraction B, Fnip1-/-

source_name: Hardy pro-B cell fraction B, Fnip1-/-

value: Hardy pro-B cell fraction CC'


title: Mock

city: Strasbourg

first: Anamika

last: Krishanpal

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

description: Chromatin IP against yeast specific Antibody

data_processing:
Mock_MCF7.bed; genome build: hg19
ChIP-seq data were mapped using the ELAND software (Illumina) allowing one mismatch.

growth_protocol: MCF-7 cells plated in 15cm Petri-dishes.(medium: DMEM, 1g/l glucose + 10%FCS + Gentamicin + Insulin 0,6µg/ml)

extract_protocol: Lysates were clarified from sonicated nuclei and RNA PolII-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: human breast adenocarcinoma

tag: passages

value: No Antibody


title: Col0_methyl-Seq_rep1

description: treated with bisulfite

source_name: seedling

value: WT


title: RNASeq of pro-B cell fraction CC', Fnip1-/-

source_name: Hardy pro-B cell fraction CC', Fnip1-/-

tag: genotype


title: Pol II Chip-seq

description: Chromatin IP against RNA Pol II

data_processing:
PolII_MCF7.bed; genome build: hg19
ChIP-seq data were mapped using the ELAND software (Illumina) allowing one mismatch.

source_name: Chromatin IP against RNA Pol II

value: RNAPol II (H-224) X


title: TCC726.1

data_processing:
Theca.C.COW.TCC726.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

value: Cow


title: 6-10 DPA small RNA

value: 'Golden Promise'


title: TCC718.1

data_processing:
Theca.C.COW.TCC718.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: dcp2D_xrn1D_rep2

value: dcp2D::HIS3 xrn1D::kanMX


title: idm1-1_methyl-Seq_rep1

description: treated with bisulfite

data_processing: Each raw read was first trimmed to the longest contiguous read segment with Phred quality score>=20 (using DynamicTrim from the SolexaQA software, Cox et al, 2010) and then trimmed for the adaptor sequence if exists using an inhouse perl script. We mapped paired reads and singleton reads (when read from the other end was discarded due to low quality) to the Arabidopsis genome (TAIR10) using BRAT (Harris et al. 2009, doi:10.1093/bioinformatics/btp706). Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ). The wig files give methylation level for all Cs covered by at least 4 reads (*PlusStrand.wig for Watson strand and *MinusStrand.wig for Crick strand).


title: WT_rep1

value: wild type


title: dcp2D_xrn1D_rep1


title: TCC681.1

data_processing:
Theca.C.COW.TCC681.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCC623.1

data_processing:
Theca.C.COW.TCC623.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: 11-15 DPA degradome

value: 11-15 day post anthesis grains


title: THB3711

data_processing:
Theca.B.HEIFER.THB3711.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

value: Differentiated


title: THB3701.1

data_processing:
Theca.B.HEIFER.THB3701.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THB3587.1

data_processing:
Theca.B.HEIFER.THB3587.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THB3566.1

data_processing:
Theca.B.HEIFER.THB3566.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: 1-5 DPA degradome

data_processing: Analysis of PARE RNA sequencing included trimming of 3' adapter sequences and creation of a non-redundant sequence set. Sequences that were over 50% homopolymer or dinucleotide repeat were removed and reads were trimmed to 20 nt. Read counts for each unique sequence were normalised to reads per million of total sequenced reads.  Processed data from the three samples were combined in a single file and a readme provided as PARE-unique.readme.txt.

value: 1-5 day post anthesis grains


title: THB3562.2

data_processing:
Theca.B.HEIFER.THB3562.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

value: Theca


title: TCB740.1

data_processing:
Theca.B.COW.TCB740.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCB682.2

data_processing:
Theca.B.COW.TCB682.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCB578.2

data_processing:
Theca.B.COW.TCB578.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCB575.1

data_processing:
Theca.B.COW.TCB575.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THA3757.1

data_processing:
Theca.A.HEIFER.THA3757.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

value: Selected


title: TCB678.1

data_processing:
Theca.B.COW.TCB678.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THA3563.1

data_processing:
Theca.A.HEIFER.THA3563.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

value: Heifer


title: TCB666.1

data_processing:
Theca.B.COW.TCB666.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THA3568

data_processing:
Theca.A.HEIFER.THA3568.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCA710.1

data_processing:
Theca.A.COW.TCA710.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THA3585.2

data_processing:
Theca.A.HEIFER.THA3585.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCA677.1

data_processing:
Theca.A.COW.TCA677.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCA566.1

data_processing:
Theca.A.COW.TCA566.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCA656.2

data_processing:
Theca.A.COW.TCA656.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCB699.1

data_processing:
Theca.B.COW.TCB699.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHC3704.1

data_processing:
Granulosa.C.HEIFER.GHC3704.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.

source_name: Granulosa cells of dominant follicle

value: Granulosa

value: Luteinized


title: THA3703.1

data_processing:
Theca.A.HEIFER.THA3703.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: TCA610.1

data_processing:
Theca.A.COW.TCA610.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHC3702

data_processing:
Granulosa.C.HEIFER.GHC3702.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHC3597.1

data_processing:
Granulosa.C.HEIFER.GHC3597.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: THA3700

data_processing:
Theca.A.HEIFER.THA3700.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHC3576.1

data_processing:
Granulosa.C.HEIFER.GHC3576.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCC726.1

data_processing:
Granulosa.C.COW.GCC726.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHC3710.1

data_processing:
Granulosa.C.HEIFER.GHC3710.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCC623.1

data_processing:
Granulosa.C.COW.GCC623.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHC3751.1

data_processing:
Granulosa.C.HEIFER.GHC3751.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHB3711

data_processing:
Granulosa.B.HEIFER.GHB3711.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHB3701.1

data_processing:
Granulosa.B.HEIFER.GHB3701.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCC681.1

data_processing:
Granulosa.C.COW.GCC681.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHB3566.1

data_processing:
Granulosa.B.HEIFER.GHB3566.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB740.1

data_processing:
Granulosa.B.COW.GCB740.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB682.2

data_processing:
Granulosa.B.COW.GCB682.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB699.1

data_processing:
Granulosa.B.COW.GCB699.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB578.2

data_processing:
Granulosa.B.COW.GCB578.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB666.1

data_processing:
Granulosa.B.COW.GCB666.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB678.1

data_processing:
Granulosa.B.COW.GCB678.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHB3562.2

data_processing:
Granulosa.B.HEIFER.GHB3562.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHA3703.1

data_processing:
Granulosa.A.HEIFER.GHA3703.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHA3563.1

data_processing:
Granulosa.A.HEIFER.GHA3563.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCC718.1

data_processing:
Granulosa.C.COW.GCC718.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHA3757.1

data_processing:
Granulosa.A.HEIFER.GHA3757.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCA677.1

data_processing:
Granulosa.A.COW.GCA677.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCA656.2

data_processing:
Granulosa.A.COW.GCA656.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCA710.1

data_processing:
Granulosa.A.COW.GCA710.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHB3587.1

data_processing:
Granulosa.B.HEIFER.GHB3587.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHA3585.2

data_processing:
Granulosa.A.HEIFER.GHA3585.2.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GHA3568

data_processing:
Granulosa.A.HEIFER.GHA3568.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCA610.1

data_processing:
Granulosa.A.COW.GCA610.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCB575.1

data_processing:
Granulosa.B.COW.GCB575.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: GCA566.1

data_processing:
Granulosa.A.COW.GCA566.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.


title: koB

city: New Haven

last: Wallace

state: CT

address: Biology - KBT

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

data_processing: Reads were aligned to the B. halodurans C-125 genome (accession number NC_002570.2) with SOAP2 and gene scores called with custom Perl scripts.

organism: Halalkalibacterium halodurans

source_name: bacterial culture

growth_protocol: Cells were grown overnight at 37° in Luria-Bertani broth adjusted to pH ~10.5 with 1% (w/v) Na2CO3. Cells were diluted to OD ~0.02 in fresh media and grown 3 hours, rediluted in pre-warmed media to OD 0.02, and grown to early-mid exponential stage (OD 0.2-0.3)

extract_protocol: Total RNA was treated with an Invitrogen RiboMinus kit for Bacteria to deplete rRNAs and then sent to Otogenetics (Tucker, Georgia, USA) for library preparation and paired-end Illumina sequencing.

treatment_protocol: Cultures were split into 3 ml aliquots and treated with 5% (v/v) aqueous-distilled ethanol for 3 hours in sealed, shaking tubes at 37°C. Three culture tubes were combined and total RNA extracted from pelleted cells.

value: ΔoleΔoap


title: wtA_etoh

value: wild-type

tag: timepoint (hrs)


title: koA_etoh


title: wtB


title: koB_etoh


title: koA


title: wtB_etoh


title: DHS-seq mature B [8630]

status: Public on Jun 14 2012

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

data_processing:
Sequence reads that passed the Illumina quality filtering were considered for alignment. In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNA (BK000964.1) were removed. The remaining reads were aligned against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al., 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard. RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256.
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain all uniquely aligned reads

source_name: Mature B

extract_protocol: About 5 ng of ChIP-precipitated DNA, DNA excised from DHS sites or cDNA prepared from mRNA was used as starting material for generating single-end or paired-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol. DNA fragments of the following sizes were selected for the different experiments: 150–250 bp for DHS site mapping, 200–350 bp for ChIP-seq and 150–700 bp for RNA-seq. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested at 37 C for 30 min in 57 μl of 1x TE buffer pH 8 with 5 units of uracil-N-glycosylase (UDG; New England Biolabs) as described (Parkhomchuk et al., 2009) followed by PCR amplification. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit. Cluster generation and sequencing was carried out by using the Illumina/Solexa Genome Analyzer (GA) IIx systems according to the manufacturer’s guidelines. Sequencing of the paired-end libraries (DHS site mapping) yielded a read length of 76 bp for each end of a DNA fragment, whereas a read length of 36 bp was obtained with single- end libaries (ChIP-seq and RNA-seq).

value: Tcrb E-beta(-/-)

tag: extraction method

value: Ex vivo

value: Lymph Nodes


title: DHS-seq mature B [8440]

tag: tissue


title: DHS-seq pro-B [8335]

source_name: Pro-B

value: 4-5 day culture

value: Bone Marrow


title: DHS-seq Pax5-deleted pro-B [8438]

value: 3-4 week culture


title: DHS-seq Pax5-deleted pro-B [8953]


title: DHS-seq pro-B [8439], 1


title: RA 24h RNASeq

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

description: total RNA

data_processing:
Counts: Sequence reads were obtained and mapped to the Mouse (July, 2007) genomes mm9 using the Illumina Genome Analyzer Pipeline and Bowtie aligner. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: murine embryonic stem cells grown as embryoid bodies for 4 days and treated 24 hours with 5 micromolar all trans retinoic acid

growth_protocol: Murine ES cells were grwon under standard conditions in the presence of LIF and inactivated fibroblast feeder cells. Cells were passaged three times in absence of feeder cells and then transfered to bacterial dishes to initiate embryoid body formation. Embryoid bodies were grwon for 4 days before RA treatement

extract_protocol: For ChIP-seq, lysates were clarified from sonicated nuclei and RAR-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. For RNA-seq, total RNA was isolated with trizol and mRNA-seq libraries were prepared after selection of the polyA containing fraction using the standard Illumina protocol.

treatment_protocol: Embryoid bodies were treated with all trans retinoic acid dissolved in ethanol. Celle were fixed with 0.4 % formaldehyde for 10 minutes before scraping and sonnication.

value: ES cells grown as embryoid bodies

tag: treatment

value: all trans retinoic acid

tag: time


title: Control RNASeq

description: total RNA

source_name: murine embryonic stem cells grown as embryoid bodies for 4 days with no retinoic acid treatment

value: control


title: DHS-seq pro-B [8439], 2


title: RA 24h ChIPSeq

description: nuclear chromatin

data_processing:
Counts: Sequence reads were obtained and mapped to the Mouse (July, 2007) genomes mm9 using the Illumina Genome Analyzer Pipeline and Bowtie aligner. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
RA_24h_ChIPSeq_reads.bed: mm9

tag: chip antibody

value: anti-RAR

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: RA 2h ChIPSeq

description: nuclear chromatin

data_processing:
Counts: Sequence reads were obtained and mapped to the Mouse (July, 2007) genomes mm9 using the Illumina Genome Analyzer Pipeline and Bowtie aligner. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
RA_2h_ChIPSeq_reads.bed: mm9

source_name: murine embryonic stem cells grown as embryoid bodies for 4 days and treated 2 hours with 5 micromolar all trans retinoic acid

value: 2 h


title: CAGE-seq mature B [8300]

data_processing:
Library strategy: CAGE-Seq
Sequence reads that passed the Illumina quality filtering were considered for alignment. In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNA (BK000964.1) were removed. The remaining reads were aligned against the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (Langmead et al., 2009), allowing up to two mismatches and ignoring any read that would map more than once in the genome. In detail, the alignment was done using the following parameters: –m 1 –v 2 –best –strata –tryhard. RNA-Seq cleaning was performed using the following settings: –v 3 –k 1 --tryhard --chunkmbs 256.
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain all uniquely aligned reads

value: WT


title: wtA


title: H3K4me3 ChIP-seq mature B [8070], 2

tag: antibody

value: H3K4me3 Ab (Abcam ab8580-100)


title: H3K27me3 ChIP-seq mature B [8080], 1

value: H3K27me3 Ab (gift from T.Jenuwein)


title: H3K9ac ChIP-seq mature B [8059], 3

value: H3K9ac Ab (Upstate 07-352, LOT# DAM1394804)


title: H3K27me3 ChIP-seq mature B [8080], 2


title: H3K9ac ChIP-seq mature B [8059], 4


title: H3K9ac ChIP-seq mature B [8086]


title: H3K9ac ChIP-seq mature B [8059], 2


title: H3K9ac ChIP-seq mature B [8059], 1


title: CAGE-seq pro-B [8300]


title: RNASeq of pro-B cell fraction CC', wt

data_processing:
base calling: Illumina RTA 1.12.4.2
fastq extraction:  Illumina CASAVA 1.8.2 configureBclToFastq.pl
alignment: tophat v1.3.3 [--splice-mismatches=1 --min-anchor-length=8 --min-isoform-fraction=0.15  --max-multihits=5 --coverage-search -G refseq_genes.gtf –segment-length=18]
Genome_build: mm9
Supplementary_files_format_and_content: coverage in bedgraph format [normalized by library size] as generated by bedtools 2.15.0 genomecov  -bg -split. Only uniquely aligned reads were included in coverage output.

source_name: Hardy pro-B cell fraction CC', wt

value: wt

value: Hardy pro-B cell fraction B


title: H3K4me3 ChIP-seq mature B [8070], 1

value: Ex vivo


title: H3K4me3 ChIP-seq mature B [8088], 2

value: Lymph Nodes


title: H3K4me3 ChIP-seq mature B [8088], 3


title: H3K4me3 ChIP-seq mature B [8088], 1


title: H3K27me3 ChIP-seq pro-B [8111], 3

value: 4-5 day culture


title: H3K27me3 ChIP-seq pro-B [8116], 2

value: Bone Marrow


title: H3K4me2 ChIP-seq mature B [8069], 2


title: H3K4me2 ChIP-seq mature B [8069], 1


title: H3K27me3 ChIP-seq pro-B [8116], 1


title: H3K9ac ChIP-seq pro-B [8113], 1


title: H3K4me3 ChIP-seq pro-B [8110], 1


title: H3K27me3 ChIP-seq pro-B [8111], 1


title: H3K9ac ChIP-seq pro-B [8108], 1


title: H3K9ac ChIP-seq pro-B [8113], 2


title: H3K9ac ChIP-seq pro-B [8108], 2


title: H3K27me3 ChIP-seq pro-B [8111], 2


title: H3K4me2 ChIP-seq pro-B [8109], 2


title: H3K4me2 ChIP-seq pro-B [8109], 1


title: H3K4me2 ChIP-seq pro-B [8114], 1


title: H3K4me1 ChIP-seq pro-B [8666]

value: H3K4me1 (Abcam ab8895)


title: Control Bio-ChIP-seq mature B input [8095], 2

value: Dynabeads M-280 Streptavidin (Invitrogen)


title: Pax5 Bio-ChIP-seq mature B [8090], 2

value: mix C57BL/6 and 129


title: Control Bio-ChIP-seq mature B input [8095], 1


title: Pax5 Bio-ChIP-seq mature B [8090], 1


title: H3K4me2 ChIP-seq pro-B [8114], 2


title: Pax5 Bio-ChIP-seq mature B [8097], 5


title: Pax5 Bio-ChIP-seq mature B [8097], 4


title: Pax5 Bio-ChIP-seq mature B [8097], 2


title: Pax5 Bio-ChIP-seq mature B [8097], 3


title: Pax5 Bio-ChIP-seq pro-B [8417]

value: Pax5(Bio/Bio) Rag2(-/-)


title: Pax5 Bio-ChIP-seq mature B [8097], 1


title: H3K4me3 ChIP-seq pro-B [8115], 2


title: Pax5 Bio-ChIP-seq pro-B [8093], 1


title: H3K4me3 ChIP-seq pro-B [8115], 1


title: H3K4me3 ChIP-seq pro-B [8110], 2


title: RNA-seq Pax5-deleted mature B [8742],1

value: Pax5(delta/-) = Cd23-Cre Pax5(fl/-)


title: RNA-seq Pax5-deleted mature B [8743]

value: Pax5(delta/delta) = Cd23-Cre Pax5(fl/fl)


title: Pax5 Bio-ChIP-seq pro-B [8093], 3


title: Pax5 Bio-ChIP-seq pro-B [8093], 2


title: RNA-seq pro-B [8404]

value: WT = Pax5(fl/fl)


title: RNA-seq Pax5-deleted pro-B [8402]

value: Pax5(delta/delta) = Vav-Cre Pax5(fl/fl)


title: RNA-seq pro-B [8275], 3


title: RNA-seq pro-B [8403]


title: RNA-seq mature B [8159], 2

value: WT


title: RNA-seq pro-B [8275], 1


title: RNA-seq mature B [8159], 1


title: RNA-seq pro-B [8275], 2


title: RNA-seq mature B [8276], 1


title: RNA-seq mature B [8276], 2


title: RNA-seq pro-B [8818]


title: RNA-seq BLP [8559]

source_name: BLP


title: RNA-seq ALP [8558]

source_name: ALP


title: Kc WT Late S-Phase Repliseq Rep2 extraction6_seq1 aliquote 1

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

data_processing: Illumina_sequencing:DM:1 protocol. Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).  Processed data are obtained using following parameters: read length is 36   Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   Illumina sequencing WIG Generation RPKM:DM:1 protocol. For Repliseq experiments, a bin size of 10000 bp stepping every 2500 bp was used.

organism: Drosophila melanogaster

source_name: Kc WT Late S-Phase Repliseq Rep2

growth_protocol:
The general growth protocol for growing Drosophila cell lines in culture.
Cells are pulse labeled with 50ug/ml BrdU for one hour, and washed with 1x PBS.
FACS Protocol.1. Spin cells down and resuspend in 300µl of PBS. (For large pellets increase this volume and increase the EtOH volume proportionally)2. Fix by adding 5ml of 70% EtOH Dropwise while vortexing gently, incubate at -20ºc for at least 30 minutes.3. Spin, remove EtOH and resuspend in 5ml PBS. Allow cells to rehydrate at 4ºc for at least an hour.4. Spin and resuspend the cells in 4ml of PBS with 10µg/ml RNaseA and 10µg/ml PI. Incubate at RT for at least 30min up to several hours (alternatively incubate for 10min at 37ºc)Cells were sorted into early mid and late S-phase fractions using a FACS Vantage SE (BD Biosciences) equipped with the DiVa acquisition system.

extract_protocol: An immunoprecipitation procedure in which anti-BrdU is used to enrich for BrdU labeled DNA. We have a population of cells that have been labeled with BrdU and sorted into different stages of S-phase using FACS for replication timing analysis. To isolate the BrdU-substiluted DNA from these cells, we must immunoprecipitate them with an anti-BrdU antibody. This method was optimized and selected from two papers - Cimbora (MeS,2000) and Hansen (Cell, 1993). Generation of genomic library suitable for Illumina sequencing starts with random shearing of genomic DNA with sonication followed by Illumina-developed sample preparation protocol.

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

value: se/e

tag: Sex

value: Female


title: RNA-seq ALP [8485]

value: Ex vivo


title: Kc WT Mid S-Phase Repliseq Rep2 extraction5_seq1 aliquote 1

source_name: Kc WT Mid S-Phase Repliseq Rep2


title: RNA-seq Pax5-deleted mature B [8742],2

value: Lymph Nodes


title: RNA-seq BLP [8486]


title: 103 year-old male Caucasian

status: Public on Jun 13 2012

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description:
Y103
Whole Genome Bisulphite sequencing : EZ DNA Methylation Gold kit (ZIMO)

data_processing:
Read mapping: Two reference sequences were prepared based on the hg19 human reference; referenceC2T had the C residues replaced by T's, and referenceG2A had the G's replaced by A's. Two sets of reads were generated in the same way; setC2T with the C's replaced by T's, and setG2A with the G's replaced by A's.  Both sets of reads were aligned to each of the two references, producing four sets of mappings. This mapping strategy allowed reads to be aligned irrespective of the methylation status of any C residues.  The alignment was performed using the GEM alignment software allowing up to 4 mismatches in high quality bases (bases with quality scores > 25). Uniquely mapping read pairs were used to generate an empirical distribution of insert sizes of each of the libraries, and this is information was used to select read pairs with unique compatible mappings.
The bisulfite conversion followed by a PCR step generates 4 different strands; the original + and - strands along with their complements.  Reads derived from the original + strand (and its complement) will align to referenceC2T, while reads from the original - strand (and complement) will align to referenceG2A.  Both members of a read pair are derived from the same original strand, and >99% of mapped reads could have the original strand assigned unambiguously. By keeping the information on the original strand origin of each read pair, the methylation status of C residues on either of the two original strands can be inferred along with the underlying genotypes, because any conversion due to the bisulphite treatment will only be seen on read pairs deriving from one of the two original strands.

Methylation call files were generated using Bismark methylation call procedure from the bam aligned files and then processed as a bed files with columns showing : Chromosome, initial and end position of this Cpg and its methylation value

source_name: a centenarian

extract_protocol: For normal BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer. The reads generated by Illumina sequencing were aligned to the reference genome using SOAPaligner2. The alignment and methylation estimation was performed as described before (Li, Y. et al. PLoS Biol 8, e1000533 (2010)).

treatment_protocol: Peripheral blood was obtained from a healthy donor (age 103) and from umbilical cord blood from a newborn. Peripheral blood mononuclear cells (PBMC) were extracted using a Ficoll gradient. To separate CD19 and CD4 positive cells CD19 MicroBeads and CD4+ T cell Isolation kit II (Miltenyi Biotec) was applied following the manufacturerâs instructions.  DNA was extracted using  Phenol:Chloroform:Isoamylalcohol (Sigma), respectively.

tag: racial classification

value: Caucasian

tag: gender

value: male

tag: age

value: 103 years

tag: source tissue

value: Peripheral blood

value: CD4+T Cells


title: RNA-seq Pax5-deleted pro-B [8405]

value: 4-5 day culture

value: Bone Marrow


title: RNA-seq pro-B [8275], 4


title: Kc WT Early S-Phase Repliseq Rep2 extraction4_seq1 aliquote 1

source_name: Kc WT Early S-Phase Repliseq Rep2


title: Kc WT Early S-Phase Repliseq Rep1 extraction1_seq1 aliquote 1

source_name: Kc WT Early S-Phase Repliseq Rep1


title: Kc WT Mid S-Phase Repliseq Rep1 extraction2_seq1 aliquote 1

source_name: Kc WT Repliseq Rep1


title: RNA-seq pro-B [8819]


title: RNA-seq pro-B [8817]


title: ECC1_E2_R1

city: Huntsville

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

data_processing:
To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value

source_name: Endometrial cancer cell line

growth_protocol: Both ECC-1 and T-47D were grown on phenol red-free RPMI-1640 supplemented with 10% dextran/charcoal treated fetal bovine serum for five days.  RNA lysate was harvested from 100 mm dishes

extract_protocol: mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment.  Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41.

treatment_protocol: Cells were treated with either 10 nM 17β-estradiol, 100 nM genistein, 100 nM bisphenol A or 0.02% DMSO (vehicle control) for 8 hours before harvesting.

value: 8 hour 10 nM 17β-estradiol

tag: replicate

tag: cell line


title: ECC1_BPA_R2

value: 8 hour 100 nM bisphenol A


title: ECC1_DMSO_R1

value: 8 hour 0.02% DMSO


title: ECC1_GEN_R2

value: 8 hour 100 nM genistein


title: ECC1_BPA_R1


title: ECC1_E2_R2


title: Kc WT Late S-Phase Repliseq Rep1 extraction3_seq1 aliquote 1

source_name: Kc WT Late S-Phase Repliseq Rep1

value: embryo-derived cell-line

tag: genotype


title: ECC1_DMSO_R2


title: T47D_GEN_R2

source_name: Breast cancer cell line


title: T47D_E2_R2


title: newborn male Caucasian

description:
NB
Whole Genome Bisulphite sequencing : EZ DNA Methylation Gold kit (ZIMO)

source_name: a newborn

value: newborn

value: Umbilical cord blood

tag: cell type


title: T47D_DMSO_R2


title: T47D_BPA_R1


title: T47D_GEN_R1


title: T47D_DMSO_R1