title: WCE_Day5-seq

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: WCE control

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm8) using Bowtie (Langmead et al Genome Biology 2009) version 0.9.9.2 with options -k 2 --best. Only uniquely mapping reads were analyzed further. Multiple hits aligning to the same nucleotide position are discarded above the level expected at a 10^-7 probability from a per-base Poisson model of the uniquely mappable portion of the mouse genome. In practice, this caps the number of hits that start at the same nucleotide to 3 in the RAR ChIP-seq experiments.
Peaks: Binding event detection is carried out using a customized methodology named SEEDS (Sequencing Experiment Event Detection Statistics) that uses statistical significance testing to find regions producing an over-abundance of sequenced reads in the signal experiments compared with the control. The algorithm is run twice across the data. The first pass estimates a scaling factor for control sequencing read depth and a model of the distribution of sequencing read alignment hits around binding events. The second pass applies these parameters to predict a final set of significant events. Before the first pass, the scaling factor is initialized to be the ratio of total hit counts between the signal and control channels. The binding distribution model is initialized to be an empirical distribution estimated around predicted binding events in Oct4 ChIP-seq data (Marson, et al. Cell 2008). All alignment hits are extended in both 3’ and 5’ directions, mirroring the observed distribution of hits around binding events. The extension magnitudes are set equal to the positions where the binding model distribution intersects a uniform distribution over the same area. Control channel hit counts are scaled using the signal-control scaling factor. A sliding window of bin width 50bp and offset 25bp is run over the genome. Overlapping extended hit counts are calculated for both the signal and (scaled) control channels. The background distribution of ChIP-seq hits is modeled as a non-homogenous Poisson process with parameters estimated from the scaled control hit counts. Specifically, the Poisson parameter is chosen as the maximum mean overlapping hit count in 50bp windows of those observed from i) the entire genome, ii) a 5Kbp window centered on the current location, and iii) a 10Kbp window centered on the current location. The use of this dynamic background model is motivated by the desire to correct local ChIP-seq enrichment biases that appear in the signal and control channels, and is similar to the model employed by MACS (Zhang, et al. Genome Biol 2008). A given bin is denoted as potentially enriched if the overlapping hit count exceeds that expected from the background model at a p-value of 10^-9. P-values for each potentially enriched bin’s over-representation in the signal channel over the control are calculated using the binomial distribution CDF (see Rozowsky, et al. Nature Biotech 2009). Neighboring regions in the set of potentially enriched regions are merged, and the maximal p-value observed for the constituent bins is attached to the resulting merged region. The p-values are corrected for multiple hypothesis testing using Benjamini & Hochberg’s method, and all regions with corrected p-values above 0.001 are discarded. False-discovery rates are estimated by repeating the event discovery procedures after swapping the scaled control channel and the signal channel. After the first pass, the scaling factor is estimated by carrying out linear regression on the hit counts observed in 10,000 bp windows that are devoid of potentially significant events in both the signal and control channels. The binding model is estimated from enriched regions with p-values < 10^-7 and signal/control hit count enrichment greater than 10. These regions are aligned around the 'peak' location, defined as the position of maximum probability when scanning the current binding model over the region's hit landscape.

source_name: Day5 motor neurons

growth_protocol: ES cells were differentiated as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized and seeded at 5x10e5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10e7 cells on Day 0. An inducible Cdx2-V5 line was made by inserting the appropriate coding sequence followed by a his-V5 tag peptide in the LoxP of the Ainv15 cell line (ATCC SCRC-1029). Induction of the transgenes was done by adding 2ug/ml of Doxycycline for ~30 hours

extract_protocol: ChIP protocols were adapted from http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html.  Descriptions of these protocol modifications have been previously published (Guenther, et al., Genes Dev 2008). Briefly, approximately 6x10e7 cells taken from each developmental time point were cross-linked using formaldehyde and snap-frozen in liquid nitrogen.  Cells were thawed on ice, resuspended in 5ml lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and mixed on a rotating platform at 4°C for 5 minutes.  Samples were spun down for 3 minutes at 3000rpm, resuspended in 5ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and mixed on a rotating platform for 5 minutes at room temperature.  Samples were spun down once more, resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp.  Triton X-100 was added to the lysate after sonication to final concentrations of 1% and the lysate spun down to pellet cell debris.  The resulting whole-cell extract supernatant was incubated on a rotating mixer overnight at 4°C with 100 µL of Dynal Protein G magnetic beads that had been preincubated for 24 hours with 10 µg of the appropriate antibody in a PBS/BSA solution. Pol2-S5P (Abcam, ab5131), Olig2 (Millipore, ab9610), and anti-V5 (Abcam, ab15828) antibodies were used for ChIP experiments. After approximately 16 hours of bead-lysate incubation, beads were collected with a Dynal magnet.  ChIP samples probing for transcription factor binding were washed with the following regimen, mixing on a rotating mixer at 4°C for 5 minutes per buffer: low-salt buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high-salt buffer (20 mM Tris at pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris at pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40), and TE containing 50 mM NaCl.  ChIP samples probing for histone and chromatin marks were washed 4 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and then once with TE containing 50 mM NaCl, again mixing on a rotating mixer at 4°C for 5 minutes per buffer.  After the final bead wash, samples were spun down to collect and discard excess wash solution, and bound antibody-protein-DNA fragment complexes were eluted from the beads by incubation in elution buffer at 65°C with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C.  Samples were digested with RNase A and Proteinase K to remove proteins and contaminating nucleic acids, and the DNA fragments precipitated with cold EtOH. Purified DNA fragments were processed according to a modified version of the Illumina/Solexa sequencing protocol (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Ectopic exposure to retinoic acid and hedgehog agonist at day 2 during the differentiation protocol. FGF signalling treatment for Cdx2 experiments

value: Ainv15 (ATCC SCRC-1029)

tag: cell stage

tag: chip-antibody

value: WCE


title: 0-1 hr embryo

status: Public on Aug 15 2012

type: SRA

city: Blacksburg

first: Zhijian

last: Tu

state: VA

address: 309 Engel Hall

department: Biochemistry

country: USA

institute: Virginia Tech

library_source: transcriptomic

data_processing:
sam09_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

molecule: total RNA

organism: Aedes aegypti

source_name: embryo, Liverpool strain

growth_protocol: Mosquitoes were reared in a 28 degree C incubator.

extract_protocol: RNA-Seq

treatment_protocol: Female mosquitoes were both blood fed or nonbloodfed depending on the sample

tag: strain

value: Liverpool

tag: tissue

value: embryo

tag: developmental stage

value: 0-1 hr embryo


title: ovaries from 24 hr post blood fed mosquitoes

data_processing:
sam10_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

source_name: 24 hr post blood meal mosquitoes, Liverpool strain

value: ovaries

value: adult

tag: treatment

value: blood fed mosquitoes


title: carcass from 24 hr post blood fed mosquitoes (ovaries extirpated)

data_processing:
sam11_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

value: carcass w/o ovaries


title: ovaries from 0-1 day old mosquitoes

data_processing:
sam08_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

source_name: ovaries, Liverpool strain

value: 0-1 day old females


title: 9 DPA Al

city: Lismore

first: Susan

middle: Alana

last: Gillies

state: NSW

address: Miliatary  Rd

department: Plant Science

country: Australia

institute: Southern Cross University

data_processing:
Sequenicng performed on Illumina Genome Analyzer IIx
Approximately 25—55 million reads were obtained per tissue. Sequences were initially trimmed using default quality parameters of the CLC Genomics Workbench Version 4.0. (CLC bio, Aarhus, Denmark).
Remaining contaminating sequences were removed using an editing package (010 Editor, http:// www.sweetscape.com/010editor/) and the reads returned to CLC for a further round of trimming based on quality scores
Trimmed sequences were sent through the RNA-Seq analysis program of the CLC platform, mapping against the unannotated reference sequences derived from the DFCI Wheat Gene Index, Release 12.0 (The Computational Biology and Functional Genomics Laboratory, Dana Farber Cancer Institute and Harvard School of Public Health) using default parameters. The minimum length fraction was 0.9 and the minimum similarity fraction was 0.8. RPKM was selected as the normalized expression value.
Genome_build: DFCI Wheat Gene Index, Release 12.0

organism: Triticum aestivum

source_name: Seed

extract_protocol:
Total RNA was prepared using a Trizol (Invitrogen, Carlsbad, CA) protocol and purified using an RNeasy Plant Kit (Qiagen, Hilden, Germany).
Tissues were microdissected on ice and snap frozen. Total RNA was isolated and cDNA prepared using MessageAmpII (Invitrogen) using a modified first strand primer including a BpuE1 site which was used to remove the polyA tail.  Libraries were prepared according to Illumina's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 +/- 45 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

value: Aleurone

value: 9 DPA

tag: cultivar

value: Banks


title: pupae

data_processing:
sam06_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

source_name: pupae, Liverpool strain

value: pupae


title: larvae

data_processing:
sam05_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

source_name: larvae, Liverpool strain

value: larvae


title: 6 DPA Al

value: 6 DPA


title: Vegetative Drought Rep 2

status: Public on Aug 14 2012

first: Akshay

last: Kakumanu

state: Virginia

address: 101H Price Hall, Virginia Tech

department: PPWS

description:
Sample 8
processed data file: leaf-cntrl-treated-fpkm.mat.txt

data_processing:
Illumina CASAVA 1.8 used for Base calling
Illumina reads were trimmed for adapter sequences and low quality bases. All reads with final length less than 25 were discarded. The reads were mapped to the masked maize B73 genome using Tophat 1.2.0 using default parameters.
The transcriptome was assembled using Cufflinks 1.0.2 using default parameters. The abundance of each transcript and gene is measured in terms of FPKM.
Genome_build: http://ftp.maizesequence.org/current/assembly/masked/
Supplementary_files_format_and_content: Tab-delimited file with FPKM values for each sample.

molecule: polyA RNA

organism: Zea mays

source_name: Vegetative Drought

growth_protocol: Maize (Zea mays) plants of inbred line B73 were grown in the green house under well watered and drought stress conditions until they reached the reproductive stage (at the onset of silk emergence).

extract_protocol: Two biological replicates were used for all RNA-seq experiments from each tissue type (MLC/MCC and MCD/MLD). The Poly (A) RNA was isolated from purified total RNA using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature, and the cleaved RNA fragments copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was done using DNA Polymerase I and RNaseH, the cDNA fragments processed for end repair, an addition of a single ‘A’ base, and ligation of the adapters. These products were then purified and enriched by PCR to create the final cDNA library and sequenced on the Illumina Genome Analyser IIx system facilitated in Core lab facility at Virginia Bioinformatics Institute.

treatment_protocol: For the drought stress two to three days after irrigation was withheld, the plants were hand pollinated, and 24 hours after pollination measurements and samples were collected for transcriptome analysis. At the end of the drought period (1DAP) the basal leaf meristem of the three youngest leaves and the ovary tissues were sampled for Illumina deep sequencing

value: inbred line B73

value: Basal Leaf Meristem

tag: age

value: 1 DAP (Days after Pollination)

tag: growth condition

value: drought stress


title: 1-5 day old males

data_processing:
sam07_fq_bowtie.bed; genome build: AaegL1
a. NGS transcriptome raw data were alinged to the Ae. aegypti        supercontigs genome (AaegL1 by http://www.vectorbase.org)        using Bowtie (Ver. 0.12.7 - http://bowtie-bio.sourceforge.net)        alignment program.               Options: default quality policy (-n 2 -l 28 -e 70) with       --best option. See the Bowtie manual at        http://bowtie-bio.sourceforge.net/manual.shtml      b. Bowtie outputs (.map) were converted to the SAM format by        SAMtools (http://samtools.sourceforge.net/).      c. SAM files were converted to the BAM binary format by       SAMtools.      d. BAM binary format were converted to the BED format by       bedtools (http://code.google.com/p/bedtools/).

source_name: adult males, Liverpool strain

value: Liverpool

value: whole organism

value: 1-5 day old males


title: Vegetative Control Rep 1

description:
Sample 5
processed data file: leaf-cntrl-treated-fpkm.mat.txt

source_name: Vegetative Control

value: well watered


title: 14 DPA En

value: Starchy endosperm

value: 14 DPA


title: 6 DPA En


title: Vegetative Drought Rep 1

description:
Sample 7
processed data file: leaf-cntrl-treated-fpkm.mat.txt


title: Vegetative Control Rep 2

description:
Sample 6
processed data file: leaf-cntrl-treated-fpkm.mat.txt


title: Reproductive Control Rep 2

description:
Sample 2
processed data file: cob-cntrl-treated-fpkm.mat.txt

source_name: Reproductive Control

value: Ovaries


title: 14 DPA Al

value: Aleurone


title: 9 DPA En

value: 9 DPA


title: Reproductive Control Rep 1

description:
Sample 1
processed data file: cob-cntrl-treated-fpkm.mat.txt


title: Reproductive Drought Rep 1

description:
Sample 3
processed data file: cob-cntrl-treated-fpkm.mat.txt

source_name: Reproductive Drought


title: Reproductive Drought Rep 2

description:
Sample 4
processed data file: cob-cntrl-treated-fpkm.mat.txt


title: CSHL_RnaSeq_HMEpC_cell_total (superseded by GSE78616)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
****************************
GSM984621 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78616
****************************

organism: Homo sapiens

source_name: HMEpC

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 101 nt directed reads

tag: replicate

tag: spikeinpool

tag: localization description

value: Whole cell


title: CSHL_RnaSeq_HAoEC_cell_total (superseded by GSE78613)

description:
****************************
GSM984618 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78613
****************************

source_name: HAoEC


title: CSHL_RnaSeq_HWP_cell_total (superseded by GSE78615)

description:
****************************
GSM984620 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78615
****************************

source_name: HWP


title: CSHL_RnaSeq_HVMF_cell_total (superseded by GSE78614)

description:
****************************
GSM984619 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78614
****************************

source_name: HVMF


title: CSHL_RnaSeq_NHEM.f_M2_cell_total (superseded by GSE78618)

description:
****************************
GSM984616 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78618
****************************


title: CSHL_RnaSeq_SkMC_cell_total (superseded by GSE78611)

description:
****************************
GSM984615 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78611
****************************

source_name: SkMC


title: CSHL_RnaSeq_HSaVEC_cell_total (superseded by GSE78609)

description:
****************************
GSM984613 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78609
****************************

source_name: HSaVEC


title: CSHL_RnaSeq_HAoAF_cell_total (superseded by GSE78612)

description:
****************************
GSM984614 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78612
****************************

source_name: HAoAF


title: CSHL_RnaSeq_NHDF_cell_total (superseded by GSE78610)

description:
****************************
GSM984612 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78610
****************************

source_name: NHDF


title: CSHL_RnaSeq_hMSC-UC_cell_total (superseded by GSE90274)

description:
****************************
GSM984607 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90274
****************************

source_name: hMSC-UC


title: LNCaP_R1881_B3

city: Durham

first: Alok

last: Tewari

address: 101 Science Drive

institute: Duke University

data_processing:
LNCaP_R1881_B3_RPKM.txt; genome build: hg19
Each technical replicate was aligned to the hg19 human genome using BWA and then TopHat.  Appropriate resulting bam files were merged into biological replicates, resulting in three biological replicates of LNCaP mRNA +/- R1881.  Sequence tags mapping within hg19 RefSeq exon and gene models were counted, and RPKM values were calculated for each RefSeq gene.  Number of sequence tags within each gene was input into the edgeR algorithm to identify genes with differential tag counts before and after R1881 treatment.

source_name: LNCaP prostate cancer cells

extract_protocol:
RNA was extracted using the Ambion mirVANA miRNA isolation kit.
mRNA-seq libraries were constructed from RNA with an RNA Integrity Number > 9.0 following Illumina mRNA-seq library preparation instructions

tag: cell line

value: LNCaP

tag: drug treatment


title: CSHL_RnaSeq_hMNC-PB_cell_total (superseded by GSE90275)

description:
****************************
GSM984606 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90275
****************************

source_name: hMNC-PB


title: CSHL_RnaSeq_GM12878_nucleolus_total (superseded by GSE90276)

description:
****************************
GSM984605 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90276
****************************

molecule: nuclear RNA

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: degradome sequencing of O.rufipogon

status: Public on Aug 10 2012

city: Hangzhou

first: Yan

last: chenghai

address: Yuhangtang Road 866

country: China

institute: Zhejiang University

description: Sample 1

data_processing:
Basecalls performed using CASAVA 1.4
Remove adaptors, low quality tags as well as contaminants to get clean reads
Genome_build: de no assembled O.furipogon draft genome
Supplementary_files_format_and_content: FASTA format with title in one line (sequence id, size and reads numbers),followed by sequence in another line

organism: Oryza rufipogon

source_name: 4-leaf stage seedlings

extract_protocol: Total RNA was extracted from leaves of 4-leaf stage seedlings (about 20 days).Libraries were prepared according to Illumina's instructions

tag: tissue

value: leaf

tag: strain

value: dongxiang

tag: developmental stage

value: 4-leaf stage


title: CSHL_RnaSeq_HCH_cell_total (superseded by GSE78607)

description:
****************************
GSM984611 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78607
****************************

source_name: HCH

tag: datatype


title: LNCaP_NoDrug_B2

data_processing:
LNCaP_NoDrug_B2_RPKM.txt; genome build: hg19
Each technical replicate was aligned to the hg19 human genome using BWA and then TopHat.  Appropriate resulting bam files were merged into biological replicates, resulting in three biological replicates of LNCaP mRNA +/- R1881.  Sequence tags mapping within hg19 RefSeq exon and gene models were counted, and RPKM values were calculated for each RefSeq gene.  Number of sequence tags within each gene was input into the edgeR algorithm to identify genes with differential tag counts before and after R1881 treatment.

value: vehicle


title: LNCaP_R1881_B2

data_processing:
LNCaP_R1881_B2_RPKM.txt; genome build: hg19
Each technical replicate was aligned to the hg19 human genome using BWA and then TopHat.  Appropriate resulting bam files were merged into biological replicates, resulting in three biological replicates of LNCaP mRNA +/- R1881.  Sequence tags mapping within hg19 RefSeq exon and gene models were counted, and RPKM values were calculated for each RefSeq gene.  Number of sequence tags within each gene was input into the edgeR algorithm to identify genes with differential tag counts before and after R1881 treatment.


title: CSHL_RnaSeq_HPIEpC_cell_total (superseded by GSE78617)

description:
****************************
GSM984604 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78617
****************************

source_name: HPIEpC

tag: datatype description


title: CSHL_RnaSeq_hMSC-BM_cell_total (superseded by GSE90273)

description:
****************************
GSM984608 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90273
****************************

source_name: hMSC-BM

tag: rnaextract


title: LNCaP_NoDrug_B3

data_processing:
LNCaP_NoDrug_B3_RPKM.txt; genome build: hg19
Each technical replicate was aligned to the hg19 human genome using BWA and then TopHat.  Appropriate resulting bam files were merged into biological replicates, resulting in three biological replicates of LNCaP mRNA +/- R1881.  Sequence tags mapping within hg19 RefSeq exon and gene models were counted, and RPKM values were calculated for each RefSeq gene.  Number of sequence tags within each gene was input into the edgeR algorithm to identify genes with differential tag counts before and after R1881 treatment.


title: CSHL_RnaSeq_Monocytes-CD14+_cell_longPolyA (superseded by GSE90272)

description:
****************************
GSM984609 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90272
****************************

value: longPolyA

tag: rnaextract description

value: Poly(A)+ RNA longer than 200 nt

value: Paired 76 nt directed reads


title: CSHL_RnaSeq_NHEM_M2_cell_total (superseded by GSE78619)

description:
****************************
GSM984617 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78619
****************************

tag: biorep


title: LNCaP_R1881_B1

data_processing:
LNCaP_R1881_B1_RPKM.txt; genome build: hg19
Each technical replicate was aligned to the hg19 human genome using BWA and then TopHat.  Appropriate resulting bam files were merged into biological replicates, resulting in three biological replicates of LNCaP mRNA +/- R1881.  Sequence tags mapping within hg19 RefSeq exon and gene models were counted, and RPKM values were calculated for each RefSeq gene.  Number of sequence tags within each gene was input into the edgeR algorithm to identify genes with differential tag counts before and after R1881 treatment.


title: CSHL_RnaSeq_HOB_cell_total (superseded by GSE78608)

description:
****************************
GSM984610 record metadata submitted on Aug 13 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78608
****************************

source_name: HOB

tag: labexpid


title: LNCaP_NoDrug_B1

data_processing:
LNCaP_NoDrug_B1_RPKM.txt; genome build: hg19
Each technical replicate was aligned to the hg19 human genome using BWA and then TopHat.  Appropriate resulting bam files were merged into biological replicates, resulting in three biological replicates of LNCaP mRNA +/- R1881.  Sequence tags mapping within hg19 RefSeq exon and gene models were counted, and RPKM values were calculated for each RefSeq gene.  Number of sequence tags within each gene was input into the edgeR algorithm to identify genes with differential tag counts before and after R1881 treatment.


title: Cyanase 4U

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Bed: Areas of enrichment were identified using a newly developed hotspot algorithm
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: Bed

molecule: genomic DNA

organism: Mus musculus

source_name: intact frozen liver tissue

extract_protocol: The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue.

tag: restriction enzyme

value: Cyanase 4U

value: Liver

tag: age

value: 8 week

tag: gender

value: male


title: Cyanase 1U

value: Cyanase 1U


title: Cyanase 0.25U

value: Cyanase 0.25U


title: Benzonase  0.25U

value: Benzonase  0.25U


title: Dnase I

source_name: fresh liver tissue

value: Dnase I


title: rufi_seed_unique

description: Sample 3

data_processing:
Basecalls performed using CASAVA 1.4
Remove adaptors, low quality tags as well as contaminants to get clean reads
The clean reads were compressed into unique reads with reads numbers
Genome_build: de novo assembled O.furipogon draft genome
Supplementary_files_format_and_content: FASTA format with title in one line (sequence id, size and reads numbers), followed by sequence in another line

source_name: seed

extract_protocol: Total RNA was extracted from leaves and roots of 4-leaf stage seedlings (about 20days), and de-husked 5-10 DPA (days-post-anthesis) developing grains collected from O. rufipogon. Libraries were prepared according to Illumina's instructions

value: seed


title: Benzonase 1U

value: Benzonase 1U


title: Benzonase 4U

value: Benzonase 4U


title: rufi_root_unique

description: Sample 2

value: root

value: dongxiang


title: TT-BDF1-CAST-1a

city: San Francisco

first: Michelle

middle: M

last: Chan

institute: UCSF

description:
Msp1 digested bisulfite converted genomic DNA
RRBS

data_processing:
Alignment using Maq with the following params: maq map -D -s 0 -M c -e 100
Count the number methylated vs unmethylated CpGs (C vs T; G vs A on reverse)
Join the cpg files together
Add the CpG density column (#CpGs +/- 50bp)
Tile the cpg file
Average technical replicates
Genome_build: mm9
Supplementary_files_format_and_content: .cpgs: (chromosome,position,seenCount,methylatedCount);mouseNT100bpMe.txt: (position,100bp methylation value,CpG density)

source_name: TT

growth_protocol: Fibroblasts were isolated from the tail tips of adult male mice, trypsinized, passaged and cultured to confluence in 10% Fetal Bovine Serum supplemented medium before either Nuclear Transfer (NT) or collection for analysis.  Oocytes from gonadotropin primed female mice were isolated in hyaluronidase supplemented M2 medium and NT-reconstructed embryos were cultured in C02 buffered KSOM after activation with 1 mM SrCl2.

extract_protocol:
Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries
Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale

treatment_protocol: Nuclear transfer (NT) embryos were generated by enucleating C57/B6 oocytes in HCZB medium supplemented with 5 ug/ml cytochalasinB followed by transfer of the donor fibroblast nucleus and biopsy of the Meiosis I polar body.  Reconstructed embryos were activated for 1 hour with 1 mM ScCl2, 5 ug/mL cytochalasinB supplemented MZCB medium followed by an additional 5 hrs in cytochalasinB supplemented media alone.  NT-reconstructed embryos were then washed through serial CO2 buffered KSOM drops to remove residual cytochalasin and cultured in this medium before final washing and zona removal using Acidic Tyrode's solution.

value: TT


title: TT-BDF1-CAST-1


title: TT-BDF1-CAST-2


title: NTZy14-BDF1-CAST-2


title: NTZy14-X1-4


title: NTZy14-X1-3


title: NTZy14-BDF1-CAST-1


title: TT-X1-3


title: rufi_leaf_unique

description: Sample 1

value: leaf

value: 4-leaf stage


title: Chlamydomonas reinhardtii cia5 mutant L-CO2

city: Ames

first: Martin

middle: H.

last: Spalding

state: IA

address: 1210 Molecular Biology Building

department: Department of Genetics, Development and Cell Biology

institute: Iowa State University

description:
Illumina's RNA-Seq whole transcriptome analysis
single-end
poly-A purification, random fragmentation

library_source: non-genomic

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.4 assembly of the Chlamydomonas genome. The gmap alignment program (Wu et al., 2005) was used to map the short reads. Alignments were filtered to keep only unique/high similarity hits to the genome.
Alignments were required to completely overlap gene models (Augustus5 annotation). For differential expression analysis, filtered hits from both strands were pooled and summed across the genome to obtain gene counts. Additional normalization was performed to estimate gene expression levels.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Liquid cultures were grown under H-CO2 (5% v/v CO2) in CO2 minimum medium under continuous illumination (50 μmol photons m-2 s-1). Culturing tempreture was controlled at 24ºC concentration of 1.0 million cells per ml

extract_protocol:
Crude RNA samples were isolated according to the standard protocal and then cleaned by DNase I and RNeasy MinElute Cleanup kit (Qiagen Company; Catalog number 79254 and 74204)
Crude RNA samples were isolated according to the standard protocal and then cleaned by DNase I and RNeasy MinElute Cleanup kit (Qiagen Company; Catalog number 79254 and 74204). Cleaned RNA samples were provided to the DNA facility at Iowa State University, where the RNA was processed, the library prepared and 75 cycle single read sequences generated (one sample per lane on the flow cell) on a Genome Analyzer II system (Illumina).

treatment_protocol: After cell culture reach 1.0 to 2.0 million cells per ml concentration, it was seperately connected to H-CO2 (5%), L-CO2 (300~500 ppm), and VL-CO2 (100~200 ppm) gas flow systems. Cell samples were collected after 4 hours induction time under each CO2 condition.

tag: genetic background

tag: genotype

tag: treatment


title: Chlamydomonas reinhardtii cia5 mutant H-CO2


title: TT-X1-4


title: Chlamydomonas reinhardtii cia5 mutant VL-CO2


title: Chlamydomonas reinhardtii 137c wild-type VL-CO2

value: wt


title: Chlamydomonas reinhardtii 137c wild-type H-CO2


title: Adult Female Head (Replicate 2) extraction2_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

description: Small RNA data.

data_processing: raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt

organism: Drosophila melanogaster

source_name: Drosophila melanogaster adult female head

extract_protocol: total RNA from adult female head, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: female head


title: HS gamergater replicate 2 (HiSeq)

status: Public on Aug 09 2012

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator gamergates after removal of gut and poison glands.
HS_gamergate.v3.5.Cdepth

data_processing: BS-Seq reads were aligned onto the corresponding v3.5 reference genomes using SOAP2 allowing two mismatches for 44 or 49 bp paired-end reads and four mismatches for 75 bp paired-end reads.

organism: Harpegnathos saltator

source_name: whole individuals

extract_protocol: Up to 20 µg of total genomic DNA were isolated from embryos, larvae, males, virgin queens and queens for both species, as well as major and minor workers for C. floridanus, and workers and gamergates for H. saltator. DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 150 bp, followed by end-repair, 3'-end addition of dA, and adapter ligation. Methylated adapters were used according to the manufacturer's instructions (Illumina). The bisulfite conversion of sample DNA was carried out using a modified NH4SO4-based protocol and amplified by 9 cycles of PCR. Pair-end sequencing was carried out using Illumina Genome Analyzers.

treatment_protocol: The bisulfite conversion of sample DNA was carried out using a modified NH4SO4-based protocol.

tag: colony

value: HS gamergater


title: HS worker replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator workers after removal of gut and poison glands.
HS_worker.v3.5.Cdepth

value: HS worker


title: HS virginQueen replicate 1 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator virgin queens after removal of gut and poison glands.
HS_VQ.v3.5.Cdepth

value: HS virginQueen


title: HS egg replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator eggs.
HS_egg.v3.5.Cdepth

value: HS egg


title: 3rd Instar Larvae (Replicate 2) extraction2_seq1 aliquote 1

description: Small RNA data.

source_name: Drosophila melanogaster 3rd instar larvae

extract_protocol: total RNA from 3rd instar larvae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Stage

value: 3rd instar larvae


title: HS Larva replicate 1 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator larvae.
HS_Larva.v3.5.Cdepth

value: HS Larva


title: HS_VQ (smRNA-seq)

description: Sequenced reads were generated from whole individuals of Harpegnathos saltator virgin queens after removal of gut and poison glands.

data_processing: smRNA-Seq reads were aligned onto the corresponding v3.5 reference genomes using SOAP2 without allowing any mismatch.

extract_protocol: For smRNA-seq, we gel-purified 18-30 nts RNAs from the samples utilized for RNA-seq. Illumina 5' and 3' RNA adapter were sequentially ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina HiSeq 2000.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: tissue

value: whole body

tag: sample type

value: virgin queen


title: HS_Q (RNA-seq)

description: Sequenced reads were generated from whole individuals of Harpegnathos saltator queens after removal of gut and poison glands.

data_processing: RNA-Seq reads were aligned onto the corresponding v3.5 reference genomes using TopHat v1.0.12 with default parameters.

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 ug total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3'overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

value: queen


title: HS Queen replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator queens after removal of gut and poison glands.
HS_Q.v3.5.Cdepth

value: HS Queen


title: HS_VQ (RNA-seq)


title: CF male replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus males after removal of gut and poison glands.
CF_male.v3.5.Cdepth

organism: Camponotus floridanus

value: CF male


title: Adult Female Head (Replicate 1) extraction1_seq1 aliquote 1

description: Quality scores in the supplementary file for GSM240749 are undefined.  Quality of the bases assessed by (1) identifying for the sequenced linker, which is a known sequence, and (2) mapping the clipped sequence to the genome and taking only perfect hits.

source_name: Drosophila melanogaster female heads

extract_protocol: total RNA from female head, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: female heads


title: CF virginQueen replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus virgin queens after removal of gut and poison glands.
CF_VQ.v3.5.Cdepth

value: CF virginQueen


title: CF larva replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus larvae.
CF_larva.v3.5.Cdepth

value: CF larva


title: Pupae 2-4d (Replicate 2) extraction2_seq1 aliquote 1

description: Small RNA data.

source_name: Drosophila melanogaster 2-4 day old pupae

extract_protocol: total RNA from 2-4 day old pupae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: 2-4 day old pupae


title: Adult Male Head (Replicate 1) extraction1_seq1 aliquote 1

description: small RNAs

source_name: Drosophila melanogaster male heads

extract_protocol: total RNA from male head, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: male heads


title: CF Egg replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus eggs.
CF_Egg.v3.5.Cdepth

value: CF Egg


title: Chlamydomonas reinhardtii 137c wild-type L-CO2

value: wt


title: CF_VQ (smRNA-seq)

description: Sequenced reads were generated from whole individuals of Camponotus floridanus virgin queens after removal of gut and poison glands.


title: CF Major replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus major workers after removal of gut and poison glands.
CF_Major.v3.5.Cdepth

value: CF Major


title: CF Minor replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus minor workers after removal of gut and poison glands.
CF_Minor.v3.5.Cdepth

value: CF Minor


title: CF_VQ (RNA-seq)


title: Pupae 2-4d (Replicate 1) extraction1_seq1 aliquote 1

description: Small RNA data.

extract_protocol: total RNA from  2-4 day old pupae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH


title: CF Queen replicate 2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Camponotus floridanus queens after removal of gut and poison glands.
CF_Q.v3.5.Cdepth

value: CF Queen


title: HS Queen replicate 1 (HiSeq)


title: CF_Q (RNA-seq)

description: Sequenced reads were generated from whole individuals of Camponotus floridanus queens after removal of gut and poison glands.


title: HS_Q (smRNA-seq)


title: HS Larva replicate 2 (HiSeq)


title: HS virginQueen replicate2 (HiSeq)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator queens after removal of gut and poison glands.
HS_VQ.v3.5.Cdepth

value: HS virginQueen


title: CF larva replicate 1 (GA)


title: CF male replicate 2 (GA)


title: CF virginQueen replicate 1 (GA)


title: CF Minor replicate 1 (GA)


title: CF Minor replicate 2 (GA)


title: CF male replicate 1 (GA)


title: CF_Q (smRNA-seq)


title: CF Major replicate 1 (GA)


title: Adult Male Body (Replicate 1) extraction1_seq1 aliquote 1

description: small RNAs

source_name: Drosophila melanogaster male body

extract_protocol: total RNA from male body, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: male body


title: CF control (GA)

description:
Sequenced reads were generated from PCR-amplified genomic DNA of Camponotus floridanus.
CF_control.v3.5.Cdepth

value: CF control


title: CF Egg replicate 2 (GA)


title: CF Egg replicate 1 (GA)


title: CF Queen replicate 1 (GA)


title: CF Major replicate 2 (GA)


title: HS worker replicate 2 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator workers after removal of gut and poison glands.
HS_worker.v3.5.Cdepth

value: HS worker


title: HS worker replicate1 (GA)


title: HS male replicate 1 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator males after removal of gut and poison glands.
HS_male.v3.5.Cdepth

value: HS male


title: 6-10hr Embryo (Replicate 1) extraction1_seq1 aliquote 1

description: small RNAs

source_name: Drosophila melanogaster 6-10hr embryo

extract_protocol: total RNA from 6-10hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: 6-10hr embryo


title: HS gamergater replicate 1 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator gamergates after removal of gut and poison glands.
HS_gamergate.v3.5.Cdepth

value: HS gamergater


title: 6-10hr Embryo (Replicate 2) extraction2_seq1 aliquote 1

description: small RNAs


title: HS egg replicate 1 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator eggs.
HS_egg.v3.5.Cdepth

value: HS egg


title: HS control (GA)

description:
Sequenced reads were generated from PCR-amplified genomic DNA of Harpegnathos saltator.
HS_control.v3.5.Cdepth

value: HS control


title: HS virginQueen replicate 1 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator virgin queens after removal of gut and poison glands.
HS_VQ.v3.5.Cdepth


title: Mof_ChIPSeq 1

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: Rm 5215A, MS I, 1301 Catherine Rd,

department: Department of Pathology, Department of Biological Chemistry

institute: University of Michigan

data_processing:
Short read sequences were mapped to mouse genome version mm9 with ELAND.
HPeak 2.2 with default settings was used to call peaks.
Genome_build: mm9
Supplementary_files_format_and_content: eland file gives mapping results in tab-delimited text format. Peak file give peak calling results in tab-delimited text format.

source_name: Embryonic stem cells

growth_protocol: ES cells were derived from day 3.5dpc mice and were maintained on MEF feed cells in the presence of LIF, typically in 60mm plates.

extract_protocol: Lysates were clarified from sonicated nuclei and MOF-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.

treatment_protocol: Before the ChIP experiments, ES cells were seeded in plates without feeder cells for two passages to remove MEF cells.

tag: cell type

value: wild type ES cells

tag: passage

tag: strain

tag: antibody

value: Mof

tag: antibody vendor

value: Santa Cruz


title: Mof_ChIPSeq 2


title: Input DNA, rep2

status: Public on Aug 08 2012

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Basecalls were performed using GAP Pipeline version 1.7.
Reads were aligned to the Mus musculus genome (assembly NCBI37/mm9) using Bowtie.
Reads with more than four matches were excluded.
Peak calling was performed by using the ChIP-Seq Web Server (http://ccg.vital-it.ch/chipseq/).
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files were produced using the online analysis tools on the Chip-Seq Web Server (http://ccg.vital-it.ch/chipseq/).

source_name: Total thymocytes, input

growth_protocol: Freshly isolated cells.

extract_protocol: 10^7 cells/sample were crosslinked by 1% formaldehyde and sonicated by a Branson sonicator. Chromatin was immunoprecipitated by using an affinity-purified rabbit polyclonal antibody raised against KAP1 amino acids 20–418 (RBCC) (Schultz DC Gen Dev 2001 (PMID 11230151), kindly provided by Dr. Rauscher) or polyclonal H3K9me3 antibody (Diagenode). Detailed protocol for chromatin immunoprecipitation is described elsewhere (Meylan S. et al. BMC Genomics 2011 (PMID 21791101)). After de-crosslinking of both IP and total input, DNA was quantified with the Qubit fluorometer (Invitrogen) and 10 ng were used to prepare libraries for sequencing, following the ChIP-Seq library preparation protocol (including end repair for blunted end fragments, addition of "A" base to the 3' end and ligation of adapters to DNA fragments) (Illumina kit IP-102-1001). Ligation products were then purified on 2% E Gels Size Select (Invitrogen, fragments of 200 bp recovered), followed by enrichment of DNA fragments by PCR (18 cycles). No more than two libraries were loaded per gel to avoid cross contamination. Libraries were purified on AMP XP beads (Agencourt), quantified with a Qubit fluorometer and size distribution determined on the Agilent Bioanalyzer (High Sensitivity DNA chip).

treatment_protocol: Total thymocytes were treated with ammonium chloride solution to lyse red cells, and live cells were separated by density gradient.

tag: strain/background

value: T cell progenitors

tag: chip antibody


title: Heart Tissue Infected

city: San Marcos

first: DENISE

last: GARCIA

address: 333 S. Twin Oaks Valley Rd.

department: Biological Sciences

institute: California State University, San Marcos

description: Specific Pathogen Free

data_processing:
DeepSAGE analyses were carried out using multiple software pacakages specific to SAGE analysis
The primary raw sequence data produced by the SAGE technique and 454 sequencing was extracted using the PERL script DeepSAGE_extract.pl (www.bio.auc.dk/en/biotechnology/software_applications/) accessed July 8, 2009. Duplicate ditags were included and the minimum length of each ditag was increased from 35 to 36 base pairs. To determine digital gene expression differences, two sets of libraries from heart and muscle tissue were compared and visualized using the scatter plot function in the Discovery Space 4 program available at: http://www.bcgsc.ca/discoveryspace/primer. Significantly differentially expressed DeepSAGE tags were mapped to eight cDNA derived reference databases; litopenaeid contigs, litopenaeid singletons, penaeus contigs, penaeus singletons, Marsupenaeus japonicas and Fenneropenaeus chinensis contigs and Marsupenaeus japonicas and Fenneropenaeus chinensis singletons. Gene ontology was performed using a program named Blast2GO (http://www.blast2go.org/).

organism: Penaeus stylirostris

source_name: Specific Pathogen Free

growth_protocol: Animals where kept in environmentally controlled tanks

extract_protocol: Libraries of sequence tags were generated via the Long-SAGE kit (Invitrogen®, Carlsbad, CA) until the ditag PCR preparation step and directly pyrosequenced by 454 Roche.

treatment_protocol: Shrimp were injected with either saline (30 ul; control) between the second and third tergal plates of the lateral side of the tail using a 1 ml tuberculin syringe.  Infected individuals were inoculated with homogenate created from IHHNV infected shrimp tissue.  After 24 hours, the shrimp were sacrificed and tissue was collected

value: Heart

tag: infection

value: Infected

tag: animals

value: Live post-larval shrimp


title: input DNA


title: HS Larva replicate 2 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator larvae.
HS_Larva.v3.5.Cdepth

value: HS Larva


title: HS Queen replicate 1 (GA)

description:
Sequenced reads were generated from whole individuals of Harpegnathos saltator queens after removal of gut and poison glands.
HS_Q.v3.5.Cdepth

value: HS Queen


title: Lateolabrax japonicus_RNA-Seq1

city: HangZhou

first: Ding

last: He

state: ZheJiang

address: YuHangTang road

department: College of Life Science

institute: ZheJiang University

data_processing: These raw reads were then assembled into non-redundant consensuses using grape, tgicl and CAP3 software.

organism: Lateolabrax japonicus

source_name: head kidney and spleen tissues

growth_protocol: The fish were kept in running aerated seawater (salinity 30) at 25°C and fed with commercial pellet food at a daily ration of 0.7% of their body weight.

extract_protocol: After RNA extraction, the poly-A containing mRNAs were purified using oligo-dT attached magnetic beads, and fragmented into small pieces using divalent cations under elevated temperature. Then, the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA polymerase I and RNase H. These cDNA fragments were underwent an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products were subsequently purified and enriched with PCR to create the final cDNA libraries. The transcriptome sequencing was conducted by the Solexa/Illumina RNA-seq. For this, four fluorescently labeled nucleotides and a specialized polymerase were used to determine the tens of millions of clusters base by base in parallel. The 75 bp raw Pair End (PE) reads were generated by Illumina Genome Analyzer II system.

treatment_protocol: The fish in experimental groups were inoculated intraperitoneally with 0.2 ml of Vibrio harveyi at dosage of 1×108 CFU per fish. In parallel, the fish in control groups were administrated with 0.2 ml of mock PBS.

value: head, kidney and spleen

value: mock and challenged combined


title: Gill Tissue Infected

description: Specific Pathogen Free

value: Gill


title: Adult Female Body (Replicate 2) extraction2_seq1 aliquote 1

description: small RNAs

source_name: female body

extract_protocol: total RNA from female body, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: female body


title: Gill Tissue Control

description: Specific Pathogen Free

value: Control


title: H3K9me3_KAP1-KO_ChIPSeq

source_name: Total thymocytes, KAP1 KO, H3K9me3 ChIP

value: T cell-specific Kap1 knockout

value: Diagenode

tag: antibody catalog #


title: Adult Male Body (Replicate 2) extraction2_seq1 aliquote 1

source_name: male body

extract_protocol: total RNA from adult bodies, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

value: male body


title: Heart Tissue Control

description: Specific Pathogen Free

source_name: Libraries of sequence tags were generated via the Long-SAGE kit (Invitrogen®, Carlsbad, CA) until the ditag PCR preparation step and directly pyrosequenced by 454 Roche.


title: H3K9me3_WT_ChIPSeq

source_name: Total thymocytes, WT, H3K9me3 ChIP

value: wild type


title: HS male replicate 2 (HiSeq)

value: HS male


title: KAP1_KAP1-KO_ChIPSeq

description: RBCC antibody: Schultz et al. Genes Dev. 2001 (PMID 11230151).

source_name: Total thymocytes, KAP1 KO, KAP1 ChIP

value: RBCC (KAP1 amino acids 20–418)


title: Input DNA, rep1

value: T cell progenitors


title: KAP1_WT_ChIPSeq

source_name: Total thymocytes, WT, KAP1 ChIP


title: Muscle Tissue Infected

description: Specific Pathogen Free

value: Muscle


title: ZK2_RNA-seq

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

data_processing:
After reads containing sequencing adapters and reads of low quality (those in which the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed, the clear reads were aligned to the S. cerevisiae S288c genes (the sequences and the annotations of S. cerevisiae genes were downloaded form SGD database) with SOAPAligner. Mismatches no more than 2 bases were allowed in the alignment. The gene expression level was normalized by per kilobase of exon region per million mapped reads (RPKM). Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of the base number in a gene covered by unique mapping reads to the total bases number of that gene.
Genome_build: sacCer2

organism: Saccharomyces cerevisiae

source_name: Yeast S. cerevisiae strain ZK2

growth_protocol: Yeast cells were cultured in 25mL YPD medium (10g/L yeast extract, 20g/L peptone, and 20g/L glucose) with an initial OD600 of 0.05.

extract_protocol: The total RNA was extracted at early-stationary phase by the hot phenol method and then treated with RNase-free DNase I (TaKaRa) for 30 min according to the manufacturer’s protocols.  The poly (A) containing mRNA molecules were puriﬁed and the cDNA libraries were prepared according to the manufacturer’s instructions (Illumina). The cDNA library products were sequenced on the Illumina HiSeq™ 2000.

tag: application

value: Bioethanol strain


title: Lai S2 cells Sample S2-GMR1 (Replicate 1) extraction1_seq1 aliquote 1

description: small RNAs

source_name: D. melanogaster S2 cells from Gerard Rubin's lab

extract_protocol: total RNA from S2 cell, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: cell line


title: THP-1_puro_rep#1

city: Kiel

first: Mario

last: Brosch

address: Schittenhelmstr. 12

department: 1. Medical Department

country: Germany

institute: University Hospital Kiel

description:
ribosomal footprint
THP-1_puro_minus-strand.bedGraph
THP-1_puro_plus-strand.bedGraph

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, rRNA contamination was eliminated, then mapped to hg19 whole genome using novoalign v2.1 with parameters
Reads of triplicates were combined
Peaks describe position of ribosomal footprint, which was determined by adding 12 nt to the 5'-end of the read
Genome_build: hg19
Supplementary_files_format_and_content: UCSC bedGraph files

source_name: human monocyte cell line

extract_protocol: Rnase I footprinting, sucrose density gradient, RNA extraction, RNA size fractionation, polyadenylation, reverse transcription, cDNA circularization, PCR amplification. The material to be sequenced was exactly prepared as described in: Ingolia NT, Ghaemmaghami S, Newman JRS, and Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223.

tag: treatment

value: puromycin 100µg/ml


title: HS Larva replicate 1 (GA)

source_name: whole individuals

extract_protocol: Up to 20 µg of total genomic DNA were isolated from embryos, larvae, males, virgin queens and queens for both species, as well as major and minor workers for C. floridanus, and workers and gamergates for H. saltator. DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 150 bp, followed by end-repair, 3'-end addition of dA, and adapter ligation. Methylated adapters were used according to the manufacturer's instructions (Illumina). The bisulfite conversion of sample DNA was carried out using a modified NH4SO4-based protocol and amplified by 9 cycles of PCR. Pair-end sequencing was carried out using Illumina Genome Analyzers.

tag: colony

value: HS Larva


title: THP-1_cyclo_rep#1

description:
ribosomal footprint
THP-1_cyclo_minus-strand.bedGraph
THP-1_cyclo_plus-strand.bedGraph

value: cycloheximide 100µg/ml


title: RNA-seq of mock (untreated) CD4+ T cells

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

institute: Southern University of Science and Technology

data_processing:
TCD4_mock-junctions.bed; genome build: mm9
Alignment: Sequence reads were aligned to the mm9 mouse genome assembly using the TopHat and Cufflinks combination
Splice Junctions: A bed file containing the splice junctions as determined by the TopHat and Cufflinks combination

source_name: CD4+ T cells_untreated

growth_protocol: CD4+ T cells were purified from 4 pooled mice spleens using the BD IMag CD4+ T cell enrichment kit -DM, according to the manufacturers instructions.

extract_protocol: Library and Sequencing were performed at BGI, China. Library Constuction and Sequencing were performed using standard Illumnina kits and protocols. Insert sizes were 199.014 bp for anti-CD3/CD28 treated CD4+ T cells and 211.79 bp for Mock treated CD4+ T cells

treatment_protocol: Cells were treated with plate-immoblised anti-CD3e (2 ug/ml) and anti-CD28 (2 ug/ml) for 4 hours or were mock treated identically but omitting the antibody. Total RNA was harvested using TRIzol according to the manufacturers protocol

tag: gender

value: male

value: CD4+ T cells

value: Mock treated as below, but omitting the antibodies


title: cmt3atxr56_8C_DNAseq

status: Public on Aug 07 2012

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Sample 7

data_processing:
DNA-Seq reads were were first trimmed to 36mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Reads mapping to identical coordinates were collapsed into one read.
Genome_build: TAIR8
Supplementary_files_format_and_content: DNA-seq data: Column 1 is chromosome. Column 2 is strand read mapped to (+/-). Column 3 is the genomic coordinate.

mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Each RNA-seq  processed file gives 20- or 25-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads. Column 1 is chromosome. Column 2 is the genomic coordinate. Column 3 is the normalized counts.

BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads.  Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR8
Supplementary_files_format_and_content: BS-seq data: Column 1 is chromosome (1..5).  Column 2 is the coordinate of the genomic cytosine. Column 2 is genomic strand (+/-) of the cytosine. Column 3 is context (CG, CHG, or CHH) of the genomic cytosine. Column 4 is the empirical observed fraction of 5'-methylation, calculated as (# read C) / (# read C + # read T).

organism: Arabidopsis thaliana

extract_protocol:
DNA-seq libraries: One gram of mature rosette leaves were collected from 3-4-week-old plants, chopped in 0.5 ml of filtered Galbraith buffer, and stained with propidium iodide. A BD FACS Aria II in the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility was used to sort the nuclei.  For sequencing, 7,000-9,000 8C nuclei of each sample were collected, and purified DNA with Picopure purification kit (Arcturus) following manufacturer instructions.  Libraries were generated and sequenced following manufacturer instructions (Illumina).

RNA-seq libraries: RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol (Invitrogen).  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina).

Bisufite-Seq libraries: 0.5-1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).

tag: ecotype

tag: genotype/variation

tag: tissue

value: 3 wk leaves


title: kypsuvh5suvh6atxr56_8C_DNAseq

description: Sample 8


title: RNA-seq of anti-CD3/anti-CD28 treated CD4+ T cells_4 hours

description: RNA-seq of anti-CD3/anti-CD28 treated CD4+ T cells for 4 hours

data_processing:
TCD4_cd328-RNAseq-junctions.bed; genome build: mm9
Alignment: Sequence reads were aligned to the mm9 mouse genome assembly using the TopHat and Cufflinks combination
Splice Junctions: A bed file containing the splice junctions as determined by the TopHat and Cufflinks combination

source_name: CD4+ T cells_anti-CD3/anti-CD28 treated_4hr

tag: cell type

value: Treated with immoblised anti-CD3/anti-CD28 for 4 hours


title: THP-1_cyclo_rep#3


title: THP-1_cyclo_rep#2


title: WT_8C_DNAseq_rep3

description: Sample 3


title: THP-1_puro_rep#2


title: met1atxr56_8C_DNAseq

description: Sample 6


title: BPE_HS_HSF1_ChIPSeq_3

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline. ChIP-Seq reads were aligned to HG18 using ELAND  software (Illumina).
Identification of enriched genomic regions was performed as described previously (Guenther et al., 2008). Briefly, each ChIP-Seq read (a maximum of two repeat reads were allowed) was extended 100 bp to approximate the middle of the sequenced fragment. The extended fragments were subsequently allocated to 25 bp bins across the genome. Read density for each bin was calculated and enriched bins were identified by comparison to a Poisson background model using a p-value threshold of 10-12. The minimum ChIP-seq read density required to meet this threshold for each dataset is indicated in Table S1. Enriched bins within 200 bp were combined to form enriched regions. Enriched regions less than 100 bp were removed. Because of the non-random nature of background reads, enriched bins and regions were also required to have an eight-fold greater ChIP-seq density versus a nonspecific control IgG immunoprecipitation performed under identical conditions. All RefSeq genes that were within 8 kb of enriched regions were considered to be enriched genes. Enriched genes and regions for all experiments are listed in Table S1.
Genome_build: HG18
Supplementary_files_format_and_content: Processed data is provided as .xls.  It contains enriched regions of HSF1 binding (enriched regions) and the genes that are located within 8 Kb of each region (enriched genes) for each cell line and condition.

source_name: BPE cells

extract_protocol: Nuclear extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Immortalized mammary epithelial cells

value: IGG (Santa Cruz, sc-2027, Lot# C2210)

tag: tumorigenic or nontumorigenic

value: Non-tumorigenic

tag: 42˚ c, 1h heat-shock?

value: YES


title: Muscle Tissue Control

description: Specific Pathogen Free

value: Control

value: Live post-larval shrimp


title: THP-1_puro_rep#3


title: HME_HS_HSF1_ChIPSeq_2

source_name: HME cells

tag: antibody


title: WT_8C_DNAseq_rep2

description: Sample 2

value: wild type


title: atxr56_8C_DNAseq

description: Sample 4


title: 3rd Instar Larvae (Replicate 1) extraction1_seq1 aliquote 1

description: Small RNA data.

source_name: Drosophila melanogaster 3rd instar larvae

extract_protocol: total RNA from 3rd instar larvae, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Stage

value: 3rd instar larvae


title: CSHL_RnaSeq_hMSC-AT_cell_total (superseded by GSE90271)

first: ENCODE

last: DCC

institute: ENCODE DCC

description:
****************************
GSM981260 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90271
****************************

source_name: hMSC-AT

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: total

tag: rnaextract description

value: Total RNA extract (longer than 200 nt)

tag: biorep

tag: labexpid

tag: labversion

value: iIDR

tag: readtype

tag: readtype description

value: Paired 101 nt directed reads

tag: replicate

tag: spikeinpool

tag: localization description

value: Whole cell


title: Seed Coat (100-200 mg)

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing: The raw data were preprocessed to remove low quality reads and clip adapter sequences. Subsequently only 20-21 nt sequences with high quality scores were collected for analysis. The ultrafast Bowtie aligner was used to map soybean degradome reads to the Phytozome Glycine max gene models. The distinct reads that perfectly matched soybean transcript sequences remained. The CleaveLand pipeline was used to find sliced miRNA targets using the Phytozome Glycine max gene models and all Glycine max miRBase, release 17 mature miRNA sequences as input.  All alignments with scores up to 7 and no mismatches at the cleavage site (between the tenth and eleventh nucleotides) were considered candidate targets. This analysis was done for all five libraries separately.

organism: Glycine max

source_name: Seed Coat

growth_protocol: Soybean (Glycine max cv. Williams) plants were grown in a greenhouse.  Seeds were collected at different developmental stages such as early maturation green 25-50 mg, mid maturation yellow-green 100-200 mg and late maturation yellow 300-400 mg fresh weight seed. Immediately, cotyledons and seed coats were separated by dissecting whole seeds and then frozen in liquid nitrogen. Subsequently the tissue was freeze dried and stored at -80˚C.

extract_protocol: Total RNA was extracted from freeze dried cotyledons and seed coats using a modified procedure from McCarty DR (1986). Approximately 200 μg of total RNA was used to select poly (A) RNA using the Oligotex mRNA mini kit (Qiagen).The sliced ends possessing 5’ monophosphate were ligated to an RNA adapter consisting MmeI recognition site in its 3’end. After ligation and RT-PCR, the PCR product was digested with MmeI. The digested PCR product was purified and ligated to a double-stranded DNA adapter. After PCR amplification, the final PCR product was gel purified and sequenced using sequencing-by-synthesis (SBS) technology (Illumina).

treatment_protocol: Optimal green house growth conditions

tag: cultivar

value: Williams

tag: tissue

value: Seed Coat

tag: developmental stage

value: mid maturation yellow-green 100-200 mg


title: BPE_HS_HSF1_ChIPSeq_2

tag: cell type

value: Immortalized mammary epithelial cells

tag: antibody

tag: tumorigenic or nontumorigenic

tag: 42˚ c, 1h heat-shock?


title: CSHL_RnaSeq_HFDPC_cell_total (superseded by GSE78606)

address: 300 Pasteur Dr

description:
****************************
GSM981258 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78606
****************************

source_name: HFDPC

tag: datatype

tag: datatype description

tag: rnaextract


title: Seed Coat (25-50 mg)

value: early maturation green 25-50 mg


title: CSHL_RnaSeq_CD34+_Mobilized_cell_total (superseded by GSE78605)

description:
****************************
GSM981257 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78605
****************************

tag: rnaextract description

tag: biorep

tag: labexpid


title: Cotyledon (25-50 mg)

source_name: Cotyledon

value: Cotyledon


title: ddm1atxr56_BS-seq

description: Sample 43

tag: ecotype

tag: genotype/variation

value: 3 wk leaves


title: atxr56_BS-seq

description: Sample 42


title: mom1atxr56_seedling_RNAseq_setC

description: Sample 40

value: 10 day seedlings


title: Cotyledon (300-400 mg)

value: late maturation yellow 300-400 mg


title: CSHL_RnaSeq_HPC-PL_cell_total (superseded by GSE78604)

description:
****************************
GSM981255 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78604
****************************

source_name: HPC-PL

tag: labversion

tag: readtype

tag: readtype description

tag: replicate

tag: spikeinpool


title: mom1atxr56_seedling_RNAseq_setB

description: Sample 39

tag: tissue


title: CSHL_RnaSeq_MCF-7_cytosol_longPolyA (superseded by GSE90267)

description:
****************************
GSM981252 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90267
****************************

value: longPolyA

value: Poly(A)+ RNA longer than 200 nt

tag: localization description

value: The fluid between the cells outer membrane and the nucleus


title: CSHL_RnaSeq_SK-N-SH_cell_longPolyA (superseded by GSE90266)

description:
****************************
GSM981253 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90266
****************************

source_name: SK-N-SH

value: RnaSeq

value: Sequencing analysis of RNA expression


title: CSHL_RnaSeq_IMR90_cell_longPolyA (superseded by GSE90263)

description:
****************************
GSM981249 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90263
****************************

value: iIDR


title: CSHL_RnaSeq_IMR90_nucleus_longPolyA (superseded by GSE90262)

description:
****************************
GSM981248 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90262
****************************

value: Paired 101 nt directed reads

value: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA


title: CSHL_RnaSeq_SK-N-SH_cytosol_longPolyA (superseded by GSE90264)

description:
****************************
GSM981251 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90264
****************************


title: drm12atxr56_seedling_RNAseq_setB

description: Sample 37


title: CSHL_RnaSeq_SK-N-SH_nucleus_longPolyA (superseded by GSE90265)

description:
****************************
GSM981250 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90265
****************************


title: Cotyledon (100-200 mg)

tag: cultivar

value: Williams

tag: developmental stage


title: drm12atxr56_seedling_RNAseq_setC

description: Sample 38


title: Lai S2 cells Sample S2-GMR2 (Replicate 2) extraction2_seq1 aliquote 1

description: Small RNA data.

source_name: Drosophila melanogaster S2 cells from Gerard Rubin's lab

extract_protocol: total RNA from S2R+ cells, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: cell line


title: CSHL_RnaSeq_A549_nucleus_longPolyA (superseded by GSE90259)

description:
****************************
GSM981247 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90259
****************************

tag: datatype

tag: datatype description


title: CSHL_RnaSeq_A549_cytosol_longPolyA (superseded by GSE90258)

description:
****************************
GSM981246 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90258
****************************

tag: rnaextract

tag: rnaextract description


title: 0-1hr Embryo (Replicate 1) extraction1_seq1 aliquote 1

description: small RNAs

source_name: Drosophila melanogaster 0-1hr embryo

extract_protocol: total RNA from 0-1hr embryo, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: Stage

value: 0-1hr embryo


title: kypsuvh5suvh6atxr56_seedling_RNAseq_setC

description: Sample 36

tag: ecotype


title: CSHL_RnaSeq_MCF-7_nucleus_longPolyA (superseded by GSE90261)

description:
****************************
GSM981245 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90261
****************************

tag: biorep

tag: labexpid


title: cmt3atxr56_seedling_RNAseq_setC

description: Sample 34

tag: genotype/variation


title: CSHL_RnaSeq_IMR90_cytosol_longPolyA (superseded by GSE90260)

description:
****************************
GSM981244 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90260
****************************

tag: labversion

tag: readtype

tag: readtype description


title: colon-Tumor-2_IGG_ChIPSeq

source_name: patient colon tumor

tag: cell type

value: Patient Tumor

tag: antibody

value: IGG (Santa Cruz, sc-2027, Lot# C2210)

tag: tumorigenic or nontumorigenic

value: Tumorigenic

tag: 42˚ c, 1h heat-shock?

value: No


title: cmt3atxr56_seedling_RNAseq_setA

description: Sample 33

tag: tissue


title: kypsuvh5suvh6atxr56_seedling_RNAseq_setA

description: Sample 35


title: colon-Tumor-2_HSF1_ChIPSeq_2


title: CSHL_RnaSeq_IMR90_cell_total (superseded by GSE90257)

description:
****************************
GSM981243 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90257
****************************

tag: datatype

value: total

value: Total RNA extract (longer than 200 nt)

tag: replicate

tag: spikeinpool

tag: localization description

value: Whole cell


title: met1atxr56_seedling_RNAseq_setB

description: Sample 31

value: 10 day seedlings


title: colon-Tumor-2_HSF1_ChIPSeq_1


title: colon-Tumor-1_IGG_ChIPSeq


title: ddm1atxr56_seedling_RNAseq_setC

description: Sample 30


title: mom1_seedling_RNAseq_setC

description: Sample 28


title: mom1_seedling_RNAseq_setB

description: Sample 27


title: met1atxr56_seedling_RNAseq_setC

description: Sample 32


title: Breast-Tumor-2_HSF1_ChIPSeq_1

source_name: patient breast tumor


title: Breast-Tumor-2_IGG_ChIPSeq


title: drm12_seedling_RNAseq_setC

description: Sample 26


title: ddm1atxr56_seedling_RNAseq_setA

description: Sample 29


title: drm12_seedling_RNAseq_setB

description: Sample 25


title: Breast-Tumor-2_HSF1_ChIPSeq_2


title: kypsuvh5suvh6_seedling_RNAseq_setC

description: Sample 24


title: Adult Female Body (Replicate 1) extraction1_seq1 aliquote 1

description:
Small RNA data.
library strategy: RNA-Seq
library source: total RNA

source_name: female body

value: female body


title: colon-Tumor-1_HSF1_ChIPSeq_1


title: Breast-Tumor-1_IGG_ChIPSeq


title: Vp-infected group

city: Shantou

first: Zhu

last: Shuo

address: Daxue Road

department: Science

institute: Shantou University

description: small RNA

data_processing:
Illumina Casava software used for basecalling.
using clean-fastq_v1.pl to remove adapters and low quality tags as well as contaminants
aligning these data in the NCBI with all EST sequences from Scylla paramamosain and its closely related species Daphnia pulex.
Genome_build: all EST sequences from Scylla paramamosain and its closely related species Daphnia pulex (v1.0) in NCBI database (May 2012)
Supplementary_files_format_and_content: tab-delimited text files include count values for each read ...

organism: Scylla paramamosain

source_name: 7 different mud crab tissues mixtures (mesenteron, heart, liver, gill, brain, muscle and blood)

extract_protocol: 4 samples respectively from two groups were collected for RNA isolation every 12 hours after challenged. Blood were mixed with anti-coagulant solution and centrifuged at 800g at 4°C for 20 min to collect the haemocytes. This haemocytes and six other tissues(mesenteron, heart, liver, gill, brain and muscle) from normal conditions and the infection group after 24 hours were collected to extracted RNA using TRIzol® (Invitrogen, USA) according to the manufacturer's protocol. the residue DNA were cleaned away by RNase-free DNase I to gain RNA of high quality , which was confirmed though the ratio of 260/280 nm and RIN value. 1 ug of RNA from this seven different tissues of two groups respectively were used to isolate small RNA. We kept 18-30nt fragments for small RNA library costruction by PAGE.

treatment_protocol: 20 crabs were inoculated in the ventral of their hind legs with 20uL of Vibvia parahaemolyticus each (SAMPLE2) and the other 20 crabs were injected 20uL Saline (0.9%) as the control group (SAMPLE1).

tag: infection

value: infected with Vibrio parahaemolyticus


title: normal group

description: small RNA

value: control

value: 7 different mud crab tissues mixtures (mesenteron, heart, liver, gill, brain, muscle and blood)


title: kypsuvh5suvh6_seedling_RNAseq_setA

description: Sample 23

tag: ecotype


title: Breast-Tumor-1_HSF1_ChIPSeq_1


title: cmt3_seedling_RNAseq_setC

description: Sample 22


title: cmt3_seedling_RNAseq_setA

description: Sample 21


title: BT20_IGG_ChIPSeq

source_name: BT20 cells

value: breast cancer cell line


title: colon-Tumor-1_HSF1_ChIPSeq_2


title: Breast-Tumor-1_HSF1_ChIPSeq_2


title: BT20_HSF1_ChIPSeq_2


title: met1_seedling_RNAseq_setD

description: Sample 20


title: BT20_HSF1_ChIPSeq_1


title: met1_seedling_RNAseq_setC

description: Sample 19


title: ddm1_seedling_RNAseq_setC

description: Sample 18


title: NCIH838_HSF1_ChIPSeq_1

source_name: NCIH838 cells

value: lung cancer cell line


title: BPLER_IGG_ChIPSeq

source_name: BPLER cells

value: Transformed mammary epithelial cells


title: NCIH838_IGG_ChIPSeq


title: ddm1_seedling_RNAseq_setA

description: Sample 17


title: atxr56_seedling_RNAseq_setB

description: Sample 15


title: atxr56_seedling_RNAseq_setC

description: Sample 16


title: NCIH838_HSF1_ChIPSeq_2


title: BPLER_HSF1_ChIPSeq


title: SKBR3_IGG_ChIPSeq

source_name: SKBR3 cells


title: HMLER_IGG_ChIPSeq

source_name: HMLER cells


title: SKBR3_HSF1_ChIPSeq_2


title: BPE_HS_HSF1_ChIPSeq_1

source_name: BPE cells

value: Immortalized mammary epithelial cells

value: Non-tumorigenic

value: YES


title: NCIH441_HSF1_ChIPSeq_2

source_name: NCIH441 cells


title: WT_seedling_RNAseq_setB

description: Sample 12

value: wild type


title: atxr56_seedling_DNAseq

description: Sample 10


title: NCIH441_IGG_ChIPSeq

value: IGG (Santa Cruz, sc-2027, Lot# C2210)

value: Tumorigenic


title: SKBR3_HSF1_ChIPSeq_1

value: No


title: BPE_HS_IGG_ChIPSeq


title: WT_seedling_RNAseq_setD

description: Sample 14


title: WT_seedling_RNAseq_setA

description: Sample 11


title: HME_HS_HSF1_ChIPSeq_1

source_name: HME cells


title: HMLER_HSF1_ChIPSeq


title: HME_HS_IGG_ChIPSeq


title: WT_seedling_RNAseq_setC

description: Sample 13


title: BPE_HSF1_ChIPSeq


title: BPE_IGG_ChIPSeq


title: HME_IGG_ChIPSeq


title: WT_seedling_DNAseq

description: Sample 9


title: HME_HSF1_ChIPSeq


title: MCF7_IGG_ChIPSeq

source_name: MCF7 cells


title: HT29_HSF1_ChIPSeq_2

source_name: HT29 cells

value: colon cancer cell line


title: HCT15_IGG_ChIPSeq

source_name: HCT15 cells


title: HT29_HSF1_ChIPSeq_1


title: HCT15_HSF1_ChIPSeq_2


title: HCT15_HSF1_ChIPSeq_1


title: NCIH441_HSF1_ChIPSeq_1


title: SW620_HSF1_ChIPSeq_2

source_name: SW620 cells


title: ZR751_HSF1_ChIPSeq_1

source_name: ZR751 cells


title: ZR751_HSF1_ChIPSeq_2


title: ZR751_IGG_ChIPSeq


title: NCI1703_IGG_ChIPSeq

source_name: NCI1703 cells


title: NCI1703_HSF1_ChIPSeq_2


title: MCF7_HSF1_ChIPSeq_1


title: HT29_IGG_ChIPSeq


title: NCI1703_HSF1_ChIPSeq_1


title: MCF10A_HS_IGG_ChIPSeq

source_name: MCF10A CELLS


title: MCF7_HSF1_ChIPSeq_2


title: MCF10A_HS_HSF1_ChIPSeq_2


title: CSHL_RnaSeq_Monocytes-CD14+_cell_longNonPolyA (superseded by GSE90270)

city: Stanford

description:
****************************
GSM981259 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90270
****************************

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: rnaextract

value: longNonPolyA

tag: rnaextract description

value: Poly(A)- RNA longer than 200 nt

tag: biorep

value: iIDR

value: Paired 76 nt directed reads

value: Whole cell


title: MOV10 PAR-CLIP

city: Basel

first: Cem

last: Sievers

address: Mattenstrasse

country: Switzerland

institute: ETH Zurich

data_processing:
quality filtering according to the Illumina quality filter
adapter removal. The adapter introduced during the procedure required for sequencing is removed
Bowtie alignment using the following parameter setting:--best --chunkmbs 512 -S -M 100 -p 8 -k 1
Aligned reads were used to compute the relative substitution frequency at positions with coverage of at least 20
Genome_build: hg19
Supplementary_files_format_and_content: The final file contains information about read substitutions with respect to the reference genome at specific genomic positions. Each row specificies one substitution. The columns contain information regarding chromosome, genomic position (zero offset), strand, substitution, coverage at position and number of specified substitions at the position

source_name: MOV10 PAR-CLIP

growth_protocol: HEK293 cells were cultured in DMEM medium with 10% FBS at 37°C

extract_protocol: Using the Invitrogen Flp-In T-REx system, HA-Streptavidin tagged MOV10 was expressed in HEK 293 cells. The PARCLIP protocol by Hafner et al, Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP, 2010, Cell, was modified to allow for a nuclear isolation step prior to the immunoprecipitation as well as the use of the Streptavidin tag. After 365 nm crosslinking the cells were harvested, washed with cold PBS and pelleted at 500 rcf for 5 minutes. The supernatant was removed and every 6x106 cells were resuspended in a cold mixture of 3 mL of PBS, 9 mL of mQ water and 3 mL of Nuclear Isolation Buffer (1.28 M Sucrose, 40 mM Tris-HCl pH 7.5, 20 mM MgCl2, 4 % Triton X-100) with Aprotinin 3.3 μg/mL, Leupeptin 10 μg/mL, Pepstatin 4 μg/mL added. The resulting suspension was rolled for 10 minutes at 4°C and subsequently spun at 2500 rcf for 10 minutes. After aspirating the supernatant, nuclei were resuspended in 1 mL of Lysis Buffer (50 mM HEPES pH 7.5, 150 mM KCl, 1 mM NaF, 1 % NP40, Roche cOmplete Proteinase Inhibitors) for every 6x106 cells. The resuspended nuclei were sonicated in a diagenode Bioruptor for 15 cycles of 30 seconds on and 30 seconds off. Except for minor changes, all subsequent steps followed the protocol in the original protocoll (Hafner et al. see above) library as obtained by the method described above

treatment_protocol: HEK293 cells were incubated with 4-thiouridine over night

tag: cell line


title: CSHL_RnaSeq_CD20+_cell_longNonPolyA (superseded by GSE90269)

description:
****************************
GSM981254 record metadata submitted on Aug 06 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90269
****************************

tag: labexpid

tag: labversion

tag: readtype

tag: readtype description


title: MCF10A_IGG_ChIPSeq

tag: cell type

tag: antibody

tag: tumorigenic or nontumorigenic

tag: 42˚ c, 1h heat-shock?


title: ddm1atxr56_8C_DNAseq

description: Sample 5

tag: genotype/variation

tag: tissue

value: 3 wk leaves


title: MCF10A_HS_HSF1_ChIPSeq_1


title: MCF10A_HSF1_ChIPSeq_2


title: MCF10A_HSF1_ChIPSeq_1


title: WT seed

city: Beijing

first: Mingming

last: Kang

address: No. 2 Yuanmingyuan West Rd,

institute: China Agricultural University

data_processing:
Illumina Casava1.4  for basecalling.
Read-count were generated after filtering of adaptor sequences and removal of low quality reads by Illumina's GA pipeline.
Genome_build: RefGen_v2(5b.60)
Supplementary_files_format_and_content: tab-delimited text files containing length, read count and sequence

source_name: seeds

extract_protocol: Total RNAs were extracted using TRIzol reagent (Invitrogen). 16-30 nt small RNAs were gel purified from 15% PAGE gel, 5' and 3' adaptors were added and followed by RT-PCR using adaptor-specific primers. The PCR products were isolated and purified from agarose gel and used for cluster generation

value: seed

tag: developmental stage

tag: genotype

value: wild type (B73)


title: WT leaf

source_name: leaves

value: leaf

value: 3 weeks after germination


title: SW620_IGG_ChIPSeq


title: SW620_HSF1_ChIPSeq_1