title: vehicle_replicate3_SR

city: PASADENA

first: Jevgenij

middle: A.

last: Raskatov

state: California

address: 1200 EAST CALIFORNIA BOULEVARD

department: CCE

institute: CalTech

description:
A549-luc-C8
processed_DESeq

data_processing: Bowtie mapping to hg19+mm9 transcriptome, then eXpress, then DESeq

growth_protocol: RPMI medium supplemented with 10%FBS and Pen-Strep

extract_protocol: Experiments were performed in female SCID-beige mice (Charles River) between 8 and 12 weeks of age. Cells were injected into the left flank area of the animals as suspensions of 25 x 106 mL-1 in RPMI, 200 µL per injection. Treatment and tumor proliferation monitoring. Mice were treated following the schedule delineated in Supporting Information (Table S1). Tumor proliferation was monitored using the XENOGEN imaging device. The animals were anesthetized with 2 5 % isoflurane and subsequently transferred to the imaging chamber, whereupon the isoflurane levels were reduced to 1-2.5 %. The floor of the imager was heated to +37 ºC to avoid hypothermia. Breathing frequency was monitored and not allowed to drop below 1 s-1, adjusting the isoflurane levels accordingly at all times. Endpoint criteria and euthanasia. Animal endpoint criteria encompassed weight loss of over 15 %, restriction of motor function by the engrafted tumor, dehydration of over 10 % and moribund behavior. Where appropriate, the animals were euthanized by asphyxiation in a CO2 chamber. Tumor tissue harvest. Animals were resected and tumors excised using standard forceps, scissors and surgical blades. The tumors were combined into one sample per condition and mechanically sheared in TRIZOL, employing a specialized device (tissue tearer, model 985370). Total RNA workup was performed following the standard TRIZOL procedure, followed by a DNAse digest, double poly-A select; libraries prepared using standard Illumina reagents and protocols

treatment_protocol: Animals were weighed and engrafted (day 0). Treatment was conducted on days 0,2,4,7,9. Injections of 120 nmol Py-Im polyamide in 200 uL PBS/DMSO (4:1) were performed subcutaneously. Animals were weighed again on day 6, typically not exhibiting weight loss of more then 10 %, imaged on day 10, sacrificed and tumors harvested.0

tag: grafting

tag: strain

value: SCID-beige

tag: gender

value: female


title: K279 dHfq Exp plus TEX

status: Public on Oct 02 2012

type: SRA

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

library_source: transcriptomic

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.1.2
Genome_build: AM743169.1
Supplementary_files_format_and_content: wiggle
Normalized (by total number of mapped reads) read coverages in wiggle format

molecule: total RNA

organism: Stenotrophomonas maltophilia

source_name: bacterial

extract_protocol: Sample processing, library construction and deep sequencing analysis were performed as previously described (Sharma 2010). Briefly, total RNA was extracted from K279a and Delta-hfq cultures in exponential growth, and primary transcripts were enriched by a selective degradation of RNAs containing a 5’ mono-phosphate (5’P) by treatment with 5’P-dependent terminator exonuclease (Epicentre). Specifically, equal amounts of RNA were incubated for 60 min at 30°C with terminator exonuclease (TEX treated library) or in buffer alone (untreated library). Following phenol/chloroform extraction, the RNA was precipitated, and treated with 1 unit TAP (tobacco acid pyrophosphatase; Epicentre) for 1 h at 37°C to generate 5’ mono-phosphates for linker ligation, and again purified by organic extraction and precipitation as above. cDNA libraries for Illumina GAIIx sequencing were constructed by vertis Biotechnology AG, Germany (http://www.vertisbiotech.com/). First, -/+TEX treated RNA samples were poly(A)-tailed using poly(A) polymerase, followed by ligation of an RNA adapter to the 5´ P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV RNase H- reverse transcriptase. The resulting cDNAs were PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. Incubation temperatures were 42°C for 20 min, ramp to 55°C, followed by 55°C for 5 min. Each library contains a specific barcode sequence, which is attached to the 5’ end of the cDNAs. The primers used for PCR amplification were designed for amplicon sequencing according to the instructions of Illumina/Solexa.

treatment_protocol: RNA was isolated from S. maltophilia wild-type and Δhfq cultures at different growth phases. Culture aliquots were removed and mixed with 0.2 vol of stop-mix (5% water-saturated phenol, 95% ethanol), snap-frozen in liquid nitrogen and stored at –80°C until RNA isolation. After thawing on ice, bacteria were centrifuged, and RNA was isolated using the TRIzol method followed by treatment with DNase I (Sittka 2008).

tag: genetic background

tag: genotype

value: delta hfq

tag: treatment

value: plus TEX


title: K279 WT Exp minus TEX

growth_protocol: RNA was isolated from S. maltophilia wild-type and Δhfq cultures at different growth phases.

value: wt

value: minus TEX


title: treated_replicate3_SR

country: USA

description:
A549-luc-C8
processed_DESeq

organism: Mus musculus

treatment_protocol: Animals were weighed and engrafted (day 0). Treatment was conducted on days 0,2,4,7,9. Injections of 120 nmol Py-Im polyamide in 200 uL PBS/DMSO (4:1) were performed subcutaneously. Animals were weighed again on day 6, typically not exhibiting weight loss of more then 10 %, imaged on day 10, sacrificed and tumors harvested.


title: genomic_DNA

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

library_source: genomic

data_processing:
MNase-seq reads were aligned to the S.pombe (EF2) genome assembly using the Bowtie alignment program (Langmead et al., 2009).
The center of fragments was calcualted from paired-end reads and the fragment size was set to 140 bp.
The fragments were normalized and processed by the nucleR program (Flores & Orozco, 2011).
Genome_build: EF2
Supplementary_files_format_and_content: wig files were generated using the nucleR program.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: Grow up cells in  YES medium at 30°C

extract_protocol: Cells were suspended in 200 ml of culture medium at a density of 2x107 cells/ml, and then cross-linked with formaldehyde (final concentration of 1% v/v) for 15 minutes at room temperature. The fixed cells were subjected to chromatin isolation and MNase digestion as described above(Bernardi et al., 1991). Pelleted nuclei were digested with 600 U of micrococcal nuclease (NEB) at 37°C for 20 min, and samples were subjected to proteinase K treatment followed by overnight de-cross-linking at 65°C. Naked DNA was prepared from genomic DNA digested with 100 U of micrococcal nuclease. Mono-nucleosomal fragments were gel purified from 1.5% agarose gels run in TAE, and DNA was extracted with QIAGEN gel extraction kits and subject to paired end sequencing using the Illumina platform.


title: treated_replicate2_SR

description:
A549-luc-C8
processed_DESeq


title: treated_replicate1_SR

description:
A549-luc-C8
processed_DESeq


title: vehicle_replicate2_SR

description:
A549-luc-C8
processed_DESeq


title: vehicle_replicate1_SR

description:
A549-luc-C8
processed_DESeq


title: C42B input

city: St. Louis

first: Keith

middle: F

last: Decker

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Internal Medicine

institute: Washington University School of Medicine

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_INPUT.325.1.s_3_345.1.s_2_349_s_4.ATCT.bedGraph: hg18

organism: Homo sapiens

source_name: prostate cancer cells

growth_protocol: Cells were maintained in RPMI 1640 medium with 5% fetal bovine serum (FBS).

extract_protocol: The ChIP-seq library was prepared according to the Illumina Protocol (www. illumina.com). Briefly, 10ng of ChIP DNA was end-repaired, ligated to barcoded adaptors, size selected on agrose gel (300-500 bp) and PCR amplified for 16 cycles using Phusion polymerase (Finnzymes). Ligation of 4 base adapters resulted in fragments consisting of the 4 base barcode followed by the sequence.     The libraries were sequenced in the Illumina HiSeq2000 or Genome Analyzer IIx system according to the manufacturer’s instruction.

treatment_protocol: Cells were cultured in phenol red-free RPMI 1640 supplemented with 5% charcoal/dextran-stripped FBS (CSS) for 3 days. Cells were then treated with EtOH vehicle or 10nM DHT for additional 4 hr or 16 hr.  For siRNA experiments cells were grown in phenol red-free RPMI 1640 containing 5% CSS for 2 days, and then transfected with siRNA duplexes as indicated at a final concentration of 15nM using Lipofectamine RNAiMAX Transfection Reagent according to the manufacturer’s instructions. After transfection, cells were grown in phenol red-free RPMI 1640 containing 5% CSS for 48 hr and then treated with 10nM DHT or vehicle for additional 16 hr.

tag: cell line

tag: chip antibody

tag: chip antibody manufacturer

tag: chip antibody lot #

tag: chip antibody catalog #


title: treated_replicate1_PE

description:
A549-luc-C8
processed_DESeq


title: 22RV1 input

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.22RV1_INPUT.325.1.s_3_345.1.s_2_349_s_4.TCAT.bedGraph: hg18


title: vehicle_replicate1_PE

description:
A549-luc-C8
processed_DESeq


title: control_SCIDbg_spleen

description:
Mouse total spleen RNA
processed data file: NA

tag: cell type

value: spleen


title: LNCAP input

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_INPUT.325.1.s_3_345.1.s_2_349_s_4.AGTT.bedGraph: hg18

value: LNCaP


title: LNCAP ACH3 treated

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_ACH3_TREATED.0293.s_7.NOBAR.bedGraph: hg18

value: Millipore

value: DHT treated (4h)


title: C42B H3K4ME3 vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_H3K4ME3_VEHICLE.384.s_1.CAGT.bedGraph: hg18

value: EtOH vehicle treated


title: C42B ACH3 vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_ACH3_VEHICLE.337.s_1_337.s_2.TCAT.bedGraph: hg18


title: LNCAP ACH3 vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_ACH3_VEHICLE.328.1.s_7_328.1.s_8.AGTT.bedGraph: hg18


title: C42B ACH3 treated

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_ACH3_TREATED.0293.s_8.NOBAR.bedGraph: hg18


title: C42B FOXA1 treated

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_FOXA1_TREATED.337.s_2_306.s_6.AGTT.bedGraph: hg18

value: Abcam


title: 22RV1 AR treated

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.22RV1_AR_TREATED.337.s_1_306.s_5_442.1.s_5.ATCT.bedGraph: hg18

value: AR


title: LNCAP AR treated 2

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_AR_TREATED_2.692.s_1_710.s_6.TACATGG.bedGraph: hg18


title: 22RV1 AR vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.22RV1_AR_VEHICLE.306.s_5_442.1.s_5.TCAT.bedGraph: hg18


title: C42B FOXA1 vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_FOXA1_VEHICLE.337.s_2_331.1.s_1.ATCT.bedGraph: hg18


title: LNCAP AR vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_AR_VEHICLE.306.s_6_349_s_2_349_s_3.ATCT.bedGraph: hg18


title: C42B AR treated 1

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_AR_TREATED_1.465.s_4.AGTT.bedGraph: hg18

value: DHT treated (16h)


title: C42B siAR 2

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_siAR_2.324.s_7.CAGT.bedGraph: hg18

extract_protocol: For RNA-seq, 10 ug of total RNA was oligo(dT) selected using the Dynabeads mRNA purification kit (Invitrogen) or depleted of ribosomal RNA (rRNA) using the RiboMinus kit (Invitrogen), and subsequently fragmented using RNA Fragmentation Reagents (Ambion). The fragmented RNA was randomly primed with hexamers and reverse-transcribed using the Just cDNA Double-stranded cDNA Synthesis kit (Stratagene). After second-strand synthesis, the cDNA was end-repaired, ligated to barcoded adaptors, size selected on agrose gel (150-300 bp) and PCR amplified for 14 cycles using Phusion polymerase (Finnzymes). Ligation of 4 base adapters resulted in fragments consisting of the 4 base barcode followed by the sequence.   The libraries were sequenced in the Genome Analyzer IIx system according to the manufacturer’s instruction.

value: AR siRNA


title: C42B siAR 1

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_siAR_1.324.s_7.ATCT.bedGraph: hg18


title: C42B AR vehicle 1

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_AR_VEHICLE_1.301.s_7.NOBAR.bedGraph: hg18


title: LNCAP treated 2

description: ribosomal depleted RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.3.3. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.LNCAP_TREATED_2.0267.s_2.CAGT.bedGraph: hg18

value: DHT treated (16hh)


title: LNCAP treated 1

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.LNCAP_TREATED_1.0293.s_5.TCAT.bedGraph: hg18


title: Bisulfite-Seq analysis of RRBS_Lib 270 derived from human inferior temporal lobe cells; RRBS_Lib 270

status: Public on Oct 03 2012

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 270
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11775
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM916080_BI.Brain_Inferior_Temporal_Lobe.RRBS.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 270.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Inferior Temporal Lobe RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Inferior Temporal Lobe, Donor 149 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13911
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: BITL RRBS 49 70
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,891,905
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.4
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 270

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

tag: sample alias

tag: sample common name

value: Brain, Inferior Temporal Lobe

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

tag: disease

value: Inferior Temporal Lobe

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: 2x5hrs Epitect Kit

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina TruSeq adapter

value: Illumina TruSeq primer

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Illumina TruSeq primer pair

value: Pfu Turbo Cx hot start


title: C42B vehicle 1

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_VEHICLE_1.0293.s_5.ATCT.bedGraph: hg18

value: EtOH vehicle treated


title: C42B siNS 2

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_siNS_2.324.s_7.TCAT.bedGraph: hg18

value: non-specific siRNA


title: C42B siNS 1

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_siNS_1.324.s_8.AGTT.bedGraph: hg18


title: LNCAP H3K4ME3 vehicle

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_H3K4ME3_VEHICLE.344.s_8_345.1.s_1.CAGT.bedGraph: hg18

value: LNCaP

value: Millipore


title: LNCAP AR treated 1

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_AR_TREATED_1.216.s_5.NOBAR.bedGraph: hg18

value: AR

value: Abcam

value: DHT treated (4h)


title: C42B treated 1

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_TREATED_1.0293.s_5.CAGT.bedGraph: hg18

value: DHT treated (16h)


title: control_A549

description:
A549 nonsmall lung cancer cell line
processed data file: NA

data_processing: Bowtie mapping to hg19+mm9 transcriptome, then eXpress, then DESeq


title: C42B AR vehicle 3

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_AR_VEHICLE_3.692.s_1_710.s_6.GTTCTCA.bedGraph: hg18


title: C42B vehicle 2

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.3.3. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_VEHICLE_2.692.s_2.TGTTTGT.bedGraph: hg18


title: UW_DnaseSeq_TReg_adult-8wks_C57BL/6

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: TReg

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

tag: lab

value: UW-m

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: cell

value: TReg

tag: cell organism

value: mouse

tag: cell description

value: Regulatory T cells CD4+,CD25+

tag: cell sex

value: M

tag: age

tag: age description

value: Adult 8 weeks

tag: strain description

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

tag: labexpid

tag: labversion

tag: replicate


title: C42B treated 2

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.3.3. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_TREATED_2.692.s_2.TACATGG.bedGraph: hg18

tag: cell line

tag: chip antibody

tag: chip antibody manufacturer

tag: chip antibody lot #

tag: chip antibody catalog #

tag: treatment


title: C42B H3K4ME3 treated

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_H3K4ME3_TREATED.384.s_1.TCAT.bedGraph: hg18


title: IgG- S0

city: Columbus

first: Jeffrey

last: Parvin

state: OH

address: 904 Biomedical Research Tower

department: Biomedical Informatics

institute: the Ohio State University

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
ChIP_IgG_S0.sorted.txt.gz: hg18

source_name: HeLa Cells

growth_protocol: HeLa cells were routinely maintained by replating (typically 2–3 × 10^6 cells into a 10cm plate) in DMEM media+ 10% Bovine serum (Invitrogen, USA)

extract_protocol: Lysates were sheared from sonication, nuclei and histone-DNA complexes were isolated either with affinity purifcation by Ni-NTA and streptoavidin beads (Invitrogen), or by SUMO-1 antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 11257047). Briefly, DNA was end-repaired; dA overhangs were then added and Illumina adapters ligated. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was then captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II for 36bp sequencing following the manufacturer's protocols.

treatment_protocol: HeLa and HeLa-SUMO cells were treated with 2 mM thymidine (Sigma) for 17 h, then removed for 9 h and added at the same concentration for 18 h, and released for the indicated times to synchronize cells in early S, mid-S, late S, and G1 phases, respectively. Mitotic phase cells were obtained by treating with 2 mM thymidine for 15 h and released for 3 h, then treated with 100 ng/ml nocodazole for 15 h.

tag: affinity tag in derived hela cells

value: IgG

tag: growth phase

value: HeLa Cells


title: C42B AR treated 2

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_AR_TREATED_3.710.s_6.TGTTTGT.bedGraph: hg18


title: SUMO1- S0

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
ChIP_SUMO1_S0.sorted.txt.gz: hg18


title: LNCAP vehicle 2

description: ribosomal depleted RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.3.3. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.LNCAP_VEHICLE_2.0267.s_2.AGTT.bedGraph: hg18

value: LNCaP

value: EtOH vehicle treated


title: ChAP HeLa Input

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
HeLa_Input_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-M rep2

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
M_rep2_min10_triangle_subpeaks.wig.gz: hg18

value: His6-biotin-tagged SUMO-1


title: C42B AR vehicle 2

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_AR_VEHICLE_2.692.s_1_710.s_6.CGTCGCT.bedGraph: hg18

value: AR

value: Abcam


title: ChAP SUMO1-M rep1

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
M_rep1_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-S6 rep3

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S6_rep3_min10_triangle_subpeaks.wig.gz: hg18


title: LNCAP vehicle 1

description: polyA RNA

data_processing:
bedGraph file:   wigples were split according to barcode and barcodes were removed from fastq files.  RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table:  Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).  Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.LNCAP_VEHICLE_1.0293.s_5.AGTT.bedGraph: hg18


title: LNCAP H3K4ME3 treated

description: genomic DNA

data_processing:
bedgraph file:  Samples were split according to barcode and barcodes were removed from fastq files.  ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1.  Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.LNCAP_H3K4ME3_TREATED.344.s_8_345.1.s_1.TCAT.bedGraph: hg18

value: Millipore

value: DHT treated (4h)


title: ChAP SUMO1-S6 rep2

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S6_rep2_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-S3 rep3

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S3_rep3_min10_triangle_subpeaks.wig.gz: hg18


title: Halictid

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

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

department: Bioinformatics

country: China

institute: BGI-SHENZHEN

data_processing: use the halictid genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -p 4 -r 20 --mate-std-dev 10 -m 2 -I 100000 --solexa1.3-quals

organism: Lasioglossum albipes

source_name: pooled RNA samles

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg 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’ dA 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.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: tissue

value: whole body


title: ChAP SUMO1-S0 rep3

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S0_rep3_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-S0 rep2

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S0_rep2_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-S0 rep1

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S0_rep1_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-G1 rep3

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
G1_rep3_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-G1 rep1

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
G1_rep1_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-M rep3

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
M_rep3_min10_triangle_subpeaks.wig.gz: hg18


title: ChAP SUMO1-S3 rep1

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S3_rep1_min10_triangle_subpeaks.wig.gz: hg18


title: direct RNA sequencing (DRS) of control HeLa cells

status: Public on Oct 01 2012

city: Irvine

first: Yongsheng

last: Shi

address: B228 Med Sci I

department: Microbiology and Molecular Genetics

institute: University of California, Irvine

data_processing:
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie
iCLIP-seq reads were mapped to hg19 using Bowtie
Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com)
Genome_build: hg19
Supplementary_files_format_and_content: bed format

source_name: HeLa

growth_protocol: DMEM + 10% fetal bovine serum

extract_protocol:
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)
iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A301-092A; lot #: A301-092A-1)
iCLIP-seq library strategy was the same as by Konig et al, NSMB (2010) 17: 909.

treatment_protocol: HeLa cells were transfected with shRNA construct and/or siRNAs using Lipofectamine 2000 (Invitrogen)

tag: strategy

value: RNA-Seq

value: HeLa

tag: genotype/variation

value: control


title: ChIPseq mES Input

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: Input control for mouse ES cell

data_processing:
The sequenced tags were aligned to mouse genome (mm8) and the peak detection was done using MACS.
Genome Build:
CME213-ES-input.bed: mm8

source_name: E14 mouse embryonic stem cells

growth_protocol: Mouse E14Tg2A ES cells were cultured on 0.1% gelatin-coated plates and maintained in GMEM supplemented with 10% FCS (Hyclone), MEM non-essential amino acids, beta-mercaptoethanol, L-glutamine, sodium pyruvate, sodium bicarbonate, penicillin/streptomycin and LIF (home-produced).

extract_protocol: Standard Illumina single end read library was prepared as per as manufacturer's instruction to be sequenced on a GAII sequencer (14 round amplification cycle was used)


title: ChIPseq mES NcoA3

description: ChIP-seq of NcoA3 in mouse ES cell

data_processing:
The sequenced tags were aligned to mouse genome (mm8) and the peak detection was done using MACS.
Genome Build:
CME214-mES-NcoA3.bed: mm8


title: direct RNA sequencing (DRS) of CstF64-RNAi cells

source_name: Stable HeLa cell line


title: direct RNA sequencing (DRS) of CstF64&t-RNAi cells

source_name: Stable HeLa cell line transfected with siRNAs


title: Susceptible

first: Mariangela

last: Bonizzoni

address: Hewitt Hall, Rm 3501B

institute: Univ of California Irvine

description:
Sample 2
average insert size for paired end reads: 80 (each side)

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the UC Davis Genome Center using the pipeline Cassava 1.7.
Reads were aligned to the An. gambiae genome using TopHat (Trapnel et al., 2009. Bioinformatics 25: 1105-1111). Paramenters were as default. We used the An. gambiae genome as strict reference guide for transcript annotation.
Differential transcript accumulation levels between sample 1 and sample 2 were assessed by the Cuffdiff program within Cufflinks (Trapnell et al., 2010. Nat Biotechnology 28: 511). Cuffdiff was run requiring a minimum alignment count of 10 and the upper-quartile-norm option.
Genome_build: Ensembl AgamP3
Supplementary_files_format_and_content: cuffDiff_deltamethrin.xls (linked as supplementary file on Series record):reports CuffDiff results

organism: Anopheles gambiae

source_name: whole body

extract_protocol: First strand synthesis by oligo-dT enriches for poly-A RNA. Standard Illumina RNA-seq protocol.

treatment_protocol: WHO bioassay test for deltamethrin resistance

tag: geographic origin

value: Emutete, Kenya

tag: status

value: early knock-down after exposure to deltamethrin


title: br_mml_bra

city: Lausanne

first: Henrik

last: Kaessmann

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Base calling was performed using the standard Illumina software used on the Illumina Genome Analyzer Iix. Quality score in the raw fastq files are encoded using Phred 64.
Read were trimmed using a standard in-house procedure, removing the following adpater sequence: ATCTCGTATGCCGTCTTCTGCTTG
Reads of length 15-23 nucleotides were then selected to perform miRNA detection (see Methods in the related paper) and then to estimate expression level of detected miRNAs. To compute expression levels, we mapped 15-23 nt reads on the miRNA mature sequences (+/- 3base pair flanks) using bowtie (allowing for multiple mappings but no mismatch: bowtie -v 0 -a. ). We also mapped the reads on their respective genome, masking the miRNA precursor sequences, to identify reads mapping to genomic location other than miRNAs and excluded from the dataset miRNAs for which more than 10% of the mapped reads mapped also to other genomic locations.
For each mature miRNA, reads were then counted. When two (or more) miRNA genes shared more than 10% of their reads, a single joint expression value was computed for them, thus only counting once every single read (i.e., the two miRNAs are considered as one in the relevant analyses). If two (or more) miRNA genes shared less than 10% of their reads, then shared reads were equally distributed across the miRNA genes. Thus, in all cases, multiple mapping reads are never counted more than once for expression values.
Normalization across tissues was performed using edgeR (Robinson et al. 2010), which takes into account variable library sizes and corrects for biases in expression level estimates caused by highly expressed genes in a subset of tissues.
Genome_build: Ensembl Release 57
Supplementary_files_format_and_content: For each species, a processed data file is available containing a normalized expression matrix (mir.id denoted the miRNA gene ID as used in Supplementary Table 1).

organism: Macaca mulatta

source_name: Frontal Cortex

extract_protocol: We extracted high-quality RNA from the 38 samples described above using standard protocols. We then prepared small RNA-seq libraries for each of these samples using Illumina Small RNA v1.5 Sample Preparation protocol with the following optimizations. We first purified small RNAs (18-30 nucleotides) from total RNA using denaturing PAGE gel electrophoresis. We used 10% Novex TBE PAGE gel instead of the 6% described in the protocol to ensure a better separation of the cDNA constructs during the purification step.

tag: tissue/cell

value: Frontal Cortex

tag: age

value: 8 Years

tag: gender

value: Female


title: TFAP2C ChIP A375

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

data_processing:
Basecalls done at Iowa State University genome center with CASAVA 1.3
Reads alligned to hg18 using bowtie version 0.12.7
BedTools version 2.11.2 genomeCoverageBed was used to generate bedgraph files
bedGraphToBigWig followed by bigWigtoWig was used to generate depth of coverage plots
Genome_build: hg18
Supplementary_files_format_and_content: wig files generated by genomeCoverageBed and represent number of reads covering a region

growth_protocol: Melanoma cell line A375 were maintained in RPMI-1640 (with 10% Fetal Bovine Serum (FBS), penicillin,100U/ml and Streptomycin 100mg/ml) and incubated at 370C in a humidified atmosphere (5% CO2).

extract_protocol:
One hundred million cells were cross-linked for 10 min at 37°C using 0.7% formaldehyde, 0.125 M glycine. Cells were washed twice with PBS, resuspended in lysis buffer [50 mmol/L HEPES (pH 8.0), 85 mmol/L KCl, 0.5% IPEGAL CA-630 + Roche complete protease inhibitors (Indianapolis, IN)] and incubated for 5 min. Cells were collected by centrifugation and cell pellets were frozen in liquid nitrogen and stored at minus 80°C. Cell pellets were thawed in lysis buffer, collected by centrifugation and cell nuclei were resuspended in RIPA buffer [1xPBS, 1% IPEGAL CA-630, 0.5% sodium deoxycholate, 0.1% SDS + Roche Complete protease inhibitors]. Chromatin was sonicated using conditions determined empirically for A375 cells to achieve an optimal fragment length between 400 to 100 bp. After sonication, samples were centrifuged at 20,000 × g for 10 min at 4°C. The supernatant containing cross-linked DNA/histones was diluted with IP dilution buffer to 2 mg/ml [0.01% SDS, 1.1% Triton-X 100, 1.2 mmol/L EDTA, 16.7 mmol/L Tris-Cl, pH 8.1, 167 mmol/L NaCl] plus protease inhibitors]. The sample was immunoprecipitated with 10 μg of TFAP2C monoclonal antibody SC-12762X (Santa Cruz Biotechnology, Santa Cruz, CA; cat number sc-12762 clone 6E4/4), with the addition of Dynal sheep anti-mouse Dynabeads and allowed to recognize their antigens overnight at 4°C with rotation. Protein/antibody/DNA complexes were collected magnetically followed by washing and elution. Protein/DNA cross-links were reversed using 200 mmol/L NaCl at 65°C overnight. DNA was treated with Proteinase K and RNase A and was recovered with Qia Quick PCR Kit (Qiagen) according to manufacturer's suggested protocol. Purified DNA was quantified by using a NanoDrop ND-1000 (NanoDrop, Wilmington, DE).
ChIP-Seq libraries were prepared by repairing the DNA fragment ends, adding an “A” to the 3′ end of the repaired fragments, and ligating adapters using Illumina's ChIP-Seq sample prep kit. Libraries were enriched by 15 cycles of PCR amplification and size selected (200–300 bp) on a 2% agarose gel. The library was quantified and the sizes checked on a Bioanalyzer 2100 using the DNA 1000 and high sensitivity DNA chips. The library was clustered on the flow cell using the v.2 cluster generation kit (Illumina). The flowcell was loaded onto a Genome Analyzer II and subjected to single sequencing using v.3 36 cycle sequencing kit (Illumina). Image analysis, base calling and alignment were performed using Pipeline v.1.3 software.

tag: cell type

value: pigmented melanoma

tag: antibody

value: TFAP2C monoclonal antibody SC-12762X (Santa Cruz Biotechnology, Santa Cruz, CA)


title: br_mml_tes

source_name: Testis

value: Testis

value: 9 Years

value: Male


title: main_mml_tes


title: br_mml_kid

source_name: Kidney

value: Kidney


title: ChAP SUMO1-G1 rep2

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
G1_rep2_min10_triangle_subpeaks.wig.gz: hg18

value: His6-biotin-tagged SUMO-1

tag: chip antibody

tag: cell line

value: HeLa Cells


title: Dark sample RNA-Seq

city: Qingdao

first: Yun

middle: Yan

last: Deng

address: Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

data_processing: Raw reads were cleaned by removing adaptor sequences, empty reads and filtering reads containing unknown nucleotides (Ns) >5. The remaining clean reads were assembled into unigenes using SOAPdenovo. TGICL was used to process unigenes from different samples to acquire a single set of non-redundant unigenes.

organism: Saccharina japonica

source_name: healthy thalli of  S. japonica

growth_protocol: Fresh materials of S. japonica were rinsed with sterilized seawater and cultured in darkness for 4 h

extract_protocol: The total RNA of every sample (BL and dark treatment respectively) was extracted and treated with RNase-free DNase I (TaKaRa) for 45 min according to the manufacturer’s protocols. Beads with Oligo(dT) are used to isolate poly(A) mRNA. Fragmentation buffer is added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primer is used to synthesize the first-strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. Short fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly (A). After that, the short fragments are connected with sequencing adapters. And, after the agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates. At last, the library could be sequenced using Illumina HiSeq™ 2000.

treatment_protocol: Samples were immersed in sterilized seawater under blue light and in darkness respectively for 2h

tag: development stage

value: sporophyte

value: vegetative tissue

tag: sample type

value: mature thalli

value: dark


title: main_mml_kid


title: ChAP SUMO1-S6 rep1

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S6_rep1_min10_triangle_subpeaks.wig.gz: hg18


title: main_mml_hea

source_name: Heart

value: Heart


title: ChAP SUMO1-S3 rep2

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes (Hg18) using the Illumina Genome Analyzer II Pipeline. Only sequence with uniquely mapped were used for analysis.
Peaks: Peak detection was performed with FindPeaks 4.0.10 package (http://www.bcgsc.ca/platform/bioinfo/software/findpeaks)
Genome Build:
S3_rep2_min10_triangle_subpeaks.wig.gz: hg18


title: main_mml_cer

source_name: Cerebellum

value: Cerebellum


title: main_mml_bra

value: Frontal Cortex


title: main_oan_tes

organism: Ornithorhynchus anatinus

value: Adult


title: main_oan_kid


title: main_oan_hea


title: main_oan_cer


title: Resistant

description:
Sample 1
average insert size for paired end reads: 80 (each side)

value: Emutete, Kenya

value: resistant to deltamethrin


title: main_oan_bra

source_name: Brain

value: Brain


title: Blue light sample RNA-Seq

tag: treatment

value: blue light


title: main_hsa_tes

value: Testis

value: 51 years


title: main_hsa_kid

value: Kidney

value: 26 years

value: Male


title: main_hsa_cer

value: 68 years


title: shYAP (YAP knockdown)

city: La Jolla

first: Karen

last: Tumaneng

address: 2880 Torrey Pines Scenic Drive

institute: UCSD-SCRM

data_processing:
The purified cDNA library was used for cluster generation on Illumina's Cluster Station and then sequenced on Illumina GAIIx following vendor's instruction for running the instrument.
Raw sequencing reads were obtained using Illumina's Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module.
A proprieettary software package, ACGT101-miR v3.2 (LC Sciences) was used for standard data analysis
A series of digital filters (LC Sciences) were employed to remove various un-mappable reads.
Filtering by length. Default = 15 nt. For microRNA discovery.
Data further sorted by copy number.
Unique sequence mapped to mRNA was removed.
Genome_build: hg18
Supplementary_files_format_and_content: text files generated. Files include RAW data, Filtered Data, Mapped Data and the summary.

source_name: shYAP (YAP knockdown)

growth_protocol: Stable MCF10A cell lines with YAP overexpression, YAP knockdown, or control vector were cultured in DMEM/F12 media supplemented with 5% horse serum, 20ng/mL EGF, 0.5ug/mL, 10ug/mL insulin, 100ng/mL cholera toxin, and 50ug/mL penicillin/streptomycin.

extract_protocol:
MicroRNA-enriched RNA was isolated from stable MCF10A cell lines using miRNeasy Mini Kit (Qiagen).
A small RNA library was generated from RNA samples according to Illumina's sample preparation instruction.  Briefly, RNA sample was size fractionated, and 15-20 nt RNA was isolated and purified. Then 5' and 3' Adaptor ligation was done using T4 RNA ligase (Promega), then reverse transcribed, and PCR amplified, and the amplified product was purified for sequencing.

value: Mammary epithelial cell

tag: passage

value: 3 to 4


title: main_hsa_hea

value: 29 years


title: wtCtrl (control)

source_name: wtCtrl (control)


title: main_hsa_bra

value: 63 years


title: RRBS_K562_rep1

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

description: Reduced Representation Bisulfite Sequencing of HL60

data_processing: Sequencing reads were mapped to the reference genome hg18 using RRBSmap allowing 2 mismatches and methylation scoring was performed using the GBSA software.

source_name: k562 Cell lines

growth_protocol:
hES, LiPS 1 and LiPS3 cells were grown in ES KO DMEM supplemented with 15% KSR serumn in presence of 5ng/ml FGF, at 37 °C in a humidified atmosphere with 5% CO2
K562 cells were grown in  DMEM supplemented with 10% FBS , at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol: DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C’CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5’-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected before subjecting to sequencing.

treatment_protocol: Genomic DNA was isolated from the cell lines. DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C’CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5’-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected, and sequenced on the Illumina GA IIxat a reading length of 36 bp.

tag: digestion

value: MspI

value: bisulfite


title: wtYAP (YAP overexpression)

source_name: wtYAP (YAP overexpression)


title: RRBS_hES_H1_p37_rep1

source_name: hES Cell lines

value: hES


title: RRBS_hES_H1_p37_rep2


title: RRBS_K562_rep2


title: RRBS_Lips3_p13

source_name: Lips3 Cell lines


title: RRBS_Lips1_p3

source_name: Lips1 Cell lines


title: RRBS_Lips1_p13


title: RRBS_Lips3_p3


title: Sordaria_macrospora_SM9

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

description: RNA amplification (linear)

data_processing:
BAM files were generated as follows: Raw reads from fastq files were quality cleaned (removal of reads with "N" and trimming from 3'end of bases with quality scores <10, only reads with >20 bases after trimming were kept) and afterwards, sequencing adapters were removed (library preparation was done using a concatenation step after adapter ligation) using custom-made Per scripts. Reads were mapped to the Sordaria macrospora genome (version 2, CABT02000000) with Tophat (Trapnell et al. 2009, Bioinf 25: 1105)
Tab-delimited text file (Sordaria_macrospora_quantification.txt) was generated as follows: Based on the mapping data from the BAM files, reads >34 bases mapping to each annotated locus tag were counted using custom-made Perl scripts. Then, two different quantification strategies were used, one named "classic", the other using LOX (Zhang et al. 2010, Bioinf 26: 1918). (Due to great morphological differences in the analyzed samples, many genes seemed to be differentially expressed, and this type of data cannot be analyzed with statistical models as, for example, used in DESeq of baySeq which are based on the assumption that the majority of genes is not differentially expressed, these quantification method were tested but did not give realistic results with the data). The "classic" analysis was done as follows: Read counts were normalized to total counts for each experiment (columns "SM1 (veg) normalized read counts" etc.), then, for each expression to be tested (e.g. veg/sex), the ratios for the four possible combination of experiments (in this case e.g. SM1/SM2, SM1/SM7, SM6/SM2, SM6/SM7) was calculated and the average ratio was calculated (columns "veg/sex ratio classic" etc.). Also, ratios were classified into 5 groups (columns "veg/sex group classic"): group 4, all ratios <= 0.25 or >= 5; group 3: mean ratio <= 0.25 or >=4 and coefficient of variance <0.5; group 2: all ratio <= 0.5 or >= 2; group 1: mean ratio <= 0.5 or >=2 and coefficient of variance <= 0.5; group 0: all other ratios. The LOX analysis was done as described by Zhang et al. (2009), ratios in columns "veg/sex ratio lox" etc., Bayesian probability in columns "veg/sex Bayesian prob lox" etc. Columns 2-5 of the file contain a summary of the classic and LOX analysis for differential expression with each gene indicated as downregulated (-1), upregulated (1) or not differentially expressed according to the following criteria: for veg/sex and for pro1 proto / wt proto, a gene is up- or downregulated if ratio >4 or <0.25 and gene in groups 1-4 of classic analysis and Bayesian probability of LOX analysis = 1; for wt proto / sex and pro1 proto / sex, a gene is up- or downregulated if ratio >8 or <0.125 and gene in group 1-4 for classic analysis and Bayesian probability of LOX analysis = 1

organism: Sordaria macrospora

source_name: pro1 protoperithecia

growth_protocol: Strains were grown on BMM (fructification medium) for 3-5 days. For total mycelium samples, strains were grown in liquid medium, for protoperithecia samples, strains were grown on microscopic slides for laser capture microdissection that were coated with a thin layer of BMM agar.

extract_protocol: Libraries were constructed at GATC (Konstanz, Germany) with the SMART cDNA kit (Clontech) using oligo-dT primers for first strand synthesis. The kit protocol selects for full-length cDNAs)

treatment_protocol: For total mycelium samples, mycelia were filtered and frozen in liquid nitrogen, ground in liquid nitrogen, and RNA was extracted with standard phenol/chloroform treatment. For laser capture microdissection, samples were fixated in Ethanol at 4°C for 24 h prior to microdissection. Laser capture microdissection was carried out with a MMI laser (UV laser) mounted on an Olympus microscope. Total RNA from microdissection samples was isolated with the PicoPure Kit (Arcturus) with a freezing/thawing step prior to extraction to break cell walls. RNA was amplified (two rounds) with the EpiCentre TargetAmp 2.0 kit.

tag: strain

tag: tissue

value: protoperithecia


title: Sordaria_macrospora_SM5

description: RNA amplification (linear)

source_name: wild type protoperithecia

value: wild type


title: Sordaria_macrospora_SM4

description: RNA amplification (linear)


title: Sordaria_macrospora_SM6

source_name: wild type vegetative mycelium

value: total vegetative mycelium


title: Sordaria_macrospora_SM1


title: Sordaria_macrospora_SM7

source_name: wild type sexual mycelium

value: total sexual mycelium


title: Sordaria_macrospora_SM2


title: mmu_spermatid

source_name: Spermatids

value: Spermatids

value: pool of individuals


title: mmu_sertoli

source_name: Sertoli cells

value: Sertoli cells


title: main_mmu_tes

source_name: Testis

value: Testis

value: Adult


title: main_mmu_hea

source_name: Heart

value: Heart

value: Male


title: main_mmu_kid

source_name: Kidney

value: Kidney


title: main_mmu_cer

source_name: Cerebellum

value: Cerebellum


title: main_mmu_bra

source_name: Brain

value: Brain


title: CstF64-iCLIP rep3

source_name: HeLa

tag: strategy

value: iCLIP-Seq

value: HeLa

tag: clip antibody


title: CstF64-iCLIP rep2


title: main_mdo_kid

organism: Monodelphis domestica

value: 6 months


title: Sordaria_macrospora_SM8

description: RNA amplification (linear)

value: protoperithecia


title: main_mdo_tes

value: 8 months


title: CstF64-iCLIP rep1


title: main_mdo_hea


title: main_mdo_bra


title: main_gga_tes

organism: Gallus gallus

value: ~1 year, adult


title: main_mdo_cer

value: 19.5 months


title: M2_2

city: Bonn

first: Andrea

last: Nino Castro

state: NRW

address: Carl Troll str. 31

institute: Life and Medical Sciences institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then mapped to hg19 whole genome using Casava1.8.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Casava1.8. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
All analysis concerning differential expression of total transcripts were calculated using the values from Casava 1.8.
We only used TopHat/Cufflinks for analyzing the transcript variants, etc. and these tables/results are part of the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM.txt file includes RPKM values for each Sample.

source_name: human monocyte derived macrophages

extract_protocol:
Macrophages were harvested and directly lyzed using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
instrument name: Illumina HiScanSQ

tag: donor

value: M2 macrophages (alternatively activated)


title: mmu_spermatocyte

source_name: Spermatocytes

tag: tissue/cell

value: Spermatocytes

value: pool of individuals


title: M2_3


title: M1_2

value: M1 macrophages (classically activated)


title: M2_1


title: M1_3


title: M1_1


title: main_gga_bra

tag: age


title: TWI1_KO_nonOx

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed. To study the base composition and thermodynamic stability of small RNAs, reads containing any bases other than A, C, G or T were excluded and the remaining reads were collapsed to non-redundant datasets. To study thermodynamic stability, 29 nt RNA sequences were mapped to the LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html) without allowing any mismatches. Then, the passenger strand scnRNA sequences were estimated. The local thermodynamic stabilities (kcal/mol) of 4 base pairs at the ends of the guide and passenger duplexes were calculated using the free energy parameters at 37ºC in 1 M NaCl (Freier et al. 1986) without including the initiation value. To study potential trimming and tailing reactions on small RNAs, 24-32 nt RNA sequences were mapped to the LMR genomic region by allowing two mismatches, and the mismatched positions in the scnRNAs were analyzed.
The processed data files linked below represent base composition of 24-32 nt small RNAs from TWI1 cells at 3 h post-mixing, prepared with no oxidation process
The Mismatch data file represents 24-32 nt RNA from TWI1 cells  at 3 h post-mixing, prepered with no oxidation process, were mapped to the LMR genomic region by allowing two mismatches, and the percentage of mismatches at each position was calculated

organism: Tetrahymena thermophila

source_name: mating TWI1 KO cells at 3h post-mixing

growth_protocol: Wild-type Tetrahymena thermophila strains B2086 and CU428, and the complete (germ plus soma) TWI1 KO (Mochizuki and Gorovsky 2004) strains 20-1 and 20-4 were used for total RNA preparation. Mating of cells was induced as described (Gorovsky et al. 1975), and asynchronous mating initiation was limited by adding quarter of the total volume of 4x SPP at ~3 hr post-mixing.

extract_protocol: RNA was isolated from 2.5 x 106 mating cells at the indicated times post-mixing using the mirVana miRNA isolation kit (Ambion). For periodate oxidation of small RNAs (Akbergenov et al. 2006), the RNA pellet was dried and resuspended in 17.5 µl borax buffer (4.375 mM borax, 50 mM boric acid; pH 8.6). Next, 2.5 µl 0.2 M sodium periodate was added, and the reaction was incubated for 10 min at RT in the dark. Then, 2 µl of glycerol was added, the reaction was incubated for another 10 min at RT in the dark, and the small RNAs were purified by ethanol precipitation.   The cDNA library of small RNAs was constructed as described (Hafner et al. 2008) with some modifications. In brief, approximately one-tenth of the purified RNA (with or without periodate oxidation) was mixed with radiolabeled 26- and 32-nt oligoribonucleotides (5’-GUC GUA CGC GGA AUA GUU UAA ACU GU-3’ and 5'-AUC UUG GUC GUA CGC GGA AUA GUU UAA ACU GU-3’, respectively; the PmeI restriction site is underlined), fractionated in a sequencing gel, and the gel region containing the two radiolabeled markers and a few bases on each side were excised. RNA was recovered from the gel and ligated to a 5'-adenylated 3' adapter oligonucleotide (5’-App-TCG TAT GCC GTC TTC TGC TTG-L-3’; L = 3'OH blocking group; a gift from Markus Landthaler from the Tuschl lab) using truncated T4 Rnl2tr (NEB). After gel fractionation and purification as above, the product was ligated to the 5' adapter oligoribonucleotide (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3') using T4 RNA ligase (Ambion). The gel-purified final ligation product was then reverse-transcribed using the primer 5’-CAA GCA GAA GAC GGC ATA CGA-3’ and PCR-amplified using that reverse transcription primer and the primer 5’-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3’. After phenol-chloroform extraction followed by ethanol precipitation, the PCR product was digested with PmeI (to cut the size markers) and fractionated by agarose gel electrophoresis, and the uncut PCR product was purified from the gel. The amplified cDNA libraries were mixed with phiX174 phage DNA at one-tenth of the amount of DNA, and single-read 36-base sequences were generated on the Illumina GAII platform obtaining 2-30 million reads.

value: Whole RNAs

tag: genotype/variation

value: TWI1 KO

tag: post-mixing time


title: main_gga_cer

tag: gender

value: Male


title: WT_6h_nonOx

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed. To study the base composition and thermodynamic stability of small RNAs, reads containing any bases other than A, C, G or T were excluded and the remaining reads were collapsed to non-redundant datasets. To study thermodynamic stability, 29 nt RNA sequences were mapped to the LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html) without allowing any mismatches. Then, the passenger strand scnRNA sequences were estimated. The local thermodynamic stabilities (kcal/mol) of 4 base pairs at the ends of the guide and passenger duplexes were calculated using the free energy parameters at 37ºC in 1 M NaCl (Freier et al. 1986) without including the initiation value. To study potential trimming and tailing reactions on small RNAs, 24-32 nt RNA sequences were mapped to the LMR genomic region by allowing two mismatches, and the mismatched positions in the scnRNAs were analyzed.
The processed data file linked below represents base composition of 29 nt small RNAs from wild-type cells at 6 h post-mixing, prepared with no oxidation process

source_name: mating wild-type cells at 6h post-mixing

value: wild type

tag: strains


title: Hfq coIP OD2+9h

city: Cologne

first: Konrad

last: Förstner

address: Gleueler Str. 60

institute: ZB MED - Information Centre for Life Sciences

description: RNA coimmunoprecipitated with anti-FLAG antibody

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences
Size filtering: discarding reads shorter than 12 nt
Read mapping using segemehl version 0.9.4
Genome_build: SL1344 complete genome: FQ312003.1
Genome_build: SL1344_plasmid1 (pSLT_SL1344): NC_017720.1
Genome_build: SL1344_plasmid2 (pCol1B9_SL1344): NC_017718.1
Genome_build: SL1344_plasmid3 (pRSF1010_SL1344): NC_017719.1
Supplementary_files_format_and_content: Unnormalized read coverages in wiggle format (*_plus.wig = plus strand; *_minus_= _minus_strand.wig)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Hfq coIP OD2+9h

growth_protocol: Wild-type and Hfq-3xFLAG Salmonella strains were grown in LB. During growth, Equal amount of culture samples were withdrawn at OD600 of 0.15, 0.5, 2.0 and 3h, 6h, 9h after reaching OD2, and overnight culture for coimmunoprecipitation analysis.

extract_protocol: RNA was co-immunoprecipitated by anti-FLAG monoclonal antibody from bacterial lysate, treated with DNase I

tag: genetic variation

value: SL1344 hfq-3xFLAG

tag: antibody

value: anti-FLAG


title: Hfq coIP overnight

source_name: Hfq coIP overnight


title: WT_3h_Ox

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed. To study the base composition and thermodynamic stability of small RNAs, reads containing any bases other than A, C, G or T were excluded and the remaining reads were collapsed to non-redundant datasets. To study thermodynamic stability, 29 nt RNA sequences were mapped to the LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html) without allowing any mismatches. Then, the passenger strand scnRNA sequences were estimated. The local thermodynamic stabilities (kcal/mol) of 4 base pairs at the ends of the guide and passenger duplexes were calculated using the free energy parameters at 37ºC in 1 M NaCl (Freier et al. 1986) without including the initiation value. To study potential trimming and tailing reactions on small RNAs, 24-32 nt RNA sequences were mapped to the LMR genomic region by allowing two mismatches, and the mismatched positions in the scnRNAs were analyzed.
The processed data files linked below represent base composition of oxidation-resistant 24-32 nt small RNAs from wild-type cells at 3 h post-mixing
The processed data file ddG represents thermodynamic stability differences between the two ends of the individul oxidation-resistant 29 nt small RNAs from wild-type cells  at 3 h post-mixing

source_name: mating wild-type cells at 3h post-mixing

tag: sample type

value: Oxidation-resistant RNAs


title: Hfq coIP OD2+6h

source_name: Hfq coIP OD2+6h


title: main_gga_kid

value: Kidney


title: Hfq coIP OD0.5

source_name: Hfq coIP OD0.5


title: Hfq coIP OD2+3h

source_name: Hfq coIP OD2+3h


title: Hfq coIP OD0.15

source_name: Hfq coIP OD0.15


title: Hfq coIP OD2.0

source_name: Hfq coIP OD2.0


title: Control coIP overnight

source_name: Control coIP overnight

value: SL1344 wild-type


title: Control coIP OD2+9h

source_name: Control coIP OD2+9h


title: Control coIP OD2+6h

source_name: Control coIP OD2+6h


title: main_gga_hea

source_name: Heart

value: Heart


title: Control coIP OD2+3h

source_name: Control coIP OD2+3h


title: WT_3h_nonOx

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed. To study the base composition and thermodynamic stability of small RNAs, reads containing any bases other than A, C, G or T were excluded and the remaining reads were collapsed to non-redundant datasets. To study thermodynamic stability, 29 nt RNA sequences were mapped to the LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html) without allowing any mismatches. Then, the passenger strand scnRNA sequences were estimated. The local thermodynamic stabilities (kcal/mol) of 4 base pairs at the ends of the guide and passenger duplexes were calculated using the free energy parameters at 37ºC in 1 M NaCl (Freier et al. 1986) without including the initiation value. To study potential trimming and tailing reactions on small RNAs, 24-32 nt RNA sequences were mapped to the LMR genomic region by allowing two mismatches, and the mismatched positions in the scnRNAs were analyzed.
The processed data file linked below represents base composition of 29 nt small RNAs from wild-type cells at 3 h post-mixing, prepared with no oxidation process


title: br_mdo_kid

organism: Didelphis virginiana

source_name: Kidney

value: 25 months

value: Female


title: Control coIP OD2.0

source_name: Control coIP OD2.0


title: br_mdo_bra

source_name: Brain

value: Brain

value: 11.5 months


title: Control coIP OD0.5

source_name: Control coIP OD0.5


title: Control coIP OD0.15

source_name: Control coIP OD0.15


title: ActivatedBCell_WT_RPA

status: Public on Sep 30 2012

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
Alignment: Standard Illumina image-analysis pipeline with default quality filters is used to determine the short-read sequences and their qualities. The outcome of the pipeline is aligned to mouse mm9 genomes assembly using Bowtie. All reads mapping with no mismatch were retained.
Density of non-redundant alignments was determined in 200nt bins along the genome.
Genome Build:
s8_101108_B3_WT_IL4_RPA-W200.bedGraph: mm9

source_name: Spleen

growth_protocol: B cells were isolated from WT and mutant spleens by immunomagnetic depletion with anti-CD43 beads (Miltenyi Biotech) and stimulated for 72h with LPS (25 μg/ml; Sigma), IL4 (5 ng/ml; GIBCO) or RP105 (2.5 μg/ml; PharMingen).

extract_protocol: After 72h in culture, cells were crosslinked for 10 min at room temperature with 1% (vol/vol) formaldehyde, followed by quenching with 0.125 M glycine (final concentration). Crosslinked cell samples were then sonicated to obtain DNA fragments 200–500 bp in length. Sonicated chromatin from 10 × 106 cells was precleared with 40 μl protein A magnetic beads, followed by incubation overnight at 4 °C in radioimmunoprecipitation assay (RIPA) buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 0.1% (wt/vol) SDS, 0.1% (wt/vol) sodium deoxycholate and 1% (vol/vol) Triton X-100) with 10 μg of RPA antibody (Cat# NA19L, Calbiochem). Beads were washed twice with RIPA buffer alone, then twice with RIPA buffer plus 0.3 M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% (vol/vol) Igepal CA630 and 0.5% (wt/vol) sodium deoxycholate), once with Tris-EDTA buffer (Tris 10 mM, pH 8.0, and 1 mM EDTA) plus 0.2% (vol/vol) Triton X-100, and once with Tris-EDTA buffer alone. ChIP DNA was extracted for 4 h at 65 °C in Tris-EDTA buffer with 0.3% (wt/vol) SDS and proteinase K (1 mg/ml). Samples were sequenced on a Genome Analyzer IIx after being prepared for microsequencing according to the manufacturer's protocol (Illumina). Each genome-wide analysis represents a single immunoprecipitation analyzed in one lane of the Ilumina slide.

tag: genotype

value: wild-type

value: RPA

tag: antibody cat#

tag: antibody vendor

value: Calbiochem


title: mES-H3K14ac-13HH3

city: Strasbourg

first: Krishanpal

last: Karmodiya

email: krish@igbmc.fr, laszlo@igbmc.fr

address: 1 rue Laurent Fries / BP 10142

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

description: Chromatin IP against H3K14ac

data_processing:
ChIP-seq data were mapped using the ELAND software (Illumina) allowing one mismatch.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Embryonic stem cells

growth_protocol: mES cells were grwon using standard protocol.

extract_protocol: ChIP DNA and input DNA were first band-isolated on a 2% agarose to obtain fragments between 150 and 350 base pairs and DNA was extracted using the QIAquick gel extraction kit (Qiagen) and eluted in 34 Î¼L. For input DNA, because DNA amounts are higher than DNA recovered by ChIP, input DNA after gel extraction was diluted 1:5. After end-repair and addition of a single adenosine ("A") nucleotide, adapters were ligated to samples for 15 min at room temperature in the following fashion: the samples eluted from the MinElute column in 10 Î¼L were ligated to 1 Î¼L of adapters using 1.3 Î¼L of LigaFast T4 DNA Ligase (3 Units/Î¼L; Promega) and 12.3 Î¼L Rapid Ligation Buffer (Promega). For DNA libraries, the Illumina genomic DNA adapters were diluted 1:10. After 15 min, samples were purified with the MinElute PCR purification kit (Qiagen).

treatment_protocol: No treatment

tag: cell type

value: mES

tag: cell line

tag: strain

tag: passage

value: Mouse monoclonal, H3K14ac_13HH3_1A5.A1

value: Laszlo Tora


title: mES-H3K9ac

description: Chromatin IP against H3K9ac

value: Rabbit polyclonal, H3K9a

tag: antibody catalog

value: Abcam


title: Human CLIPseq FUS/TLS

first: Gene

last: Yeo

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

institute: UCSD

description: Cross-linking IP against FUS/TLS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 or hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9 and hg18
Supplementary_files_format_and_content: BED format of all reads

source_name: Human brain

extract_protocol: Cells from whole brain of ten mice were pooled; cell suspension was distributed in 10 cm cell culture dishes and irradiated three times at 400 mJ/cm2 on ice with short breaks between each exposure. Irradiated brain cells were precipitated by brief centrifugation at 4oC, resuspended in PBS and distributed in ten 1.6 mL tubes, each containing cells corresponding to one mouse brain. Cells were disrupted on ice using PBS containing 0.1% SDS, 0.5% deoxycholate (Na), 0.5% NP-40, DNase treated and cleared from cell debris. Cell extracts were then incubated with protein G paramagnetic beads (Invitrogen) coupled to a custom-made mouse monoclonal anti-TDP-43 antibody (Ling, 2010) (40mg of antibody per 400 mL of beads per sample).  After 4hrs, beads were washed and associated RNAs were treated with three different concentrations (100U, 0.2U and 0.02U per sample) of micrococcal nuclease (MNase, Roche), while attached on the beads. Samples were then treated with alkaline phosphatase (NEB) and an RNA-linker (5¢P-UCGUAUGCCGUCUUCUGCUUG-Pmm, Thermo Scientific) was attached to the 3¢ end of RNAs. At this step we saved 40ul of each sample for immunoblot analysis before radiolabelling. The remaining samples were then labeled with P32-g-ATP using T4 polynucleotide kinase (NEB). Unlabelled and radiolabeled RNA-protein complexes were then released from the beads by incubating at 70oC in NuPAGE LDS sample buffer without reducing agent (Invitrogen). Samples were then migrated on 10% Bis-Tris NuPAGE gels using MES buffer (Invitrogen) and transferred to nitrocellulose membranes (0.45 mm pore size, Invitrogen). The membrane with unlabelled samples was subjected to immunobloting using a primary antibody rabbit anti-TDP-43 (Aviva system biology; Cat #ARP38942_T100; 1:2,000) (see below for the immunoblot protocol). The membrane with the radiolabelled samples was rinsed with PBS, put in a clean plastic wrap and exposed to an autoradiography film. Using the autoradiogram as a guide, membrane pieces containing complexes with higher molecular weight than the expected protein size were excised. Isolated membrane pieces were then incubated with 4mg/mL Proteinase K (Takara Bio Inc.) at 37oC for 20 min with shaking at 1200 rpm. The reaction was stopped with the addition of 7 M Urea and incubation at 37oC for 20 min with shaking at 1000 rpm. The released RNA were then extracted with phenol:chloroform.  To precipitate the RNA, the aqueous phase was transferred in a separate tube where sodium acetate, linear acrylamide, ethanol and isopropanol were added and the samples were incubated at -20oC overnight. The next day, samples were centrifuged for 10 mins at maximum speed in a microcentrifuge at 4oC. RNA pellets were washed twice with 75% ethanol and dried at room temperature. RNAs were resuspended in an RNA ligation buffer and an RNA-linker (Bi-AAUGAUACGGCGACCACCGA, Thermo Scientific) was attached to their 5¢ end. Samples were treated once more with DNase I and precipitated with Phenol Chloroform as described above. RNAs were then reverse transcribed using SuperScript III (Invitrogen) and amplified by PCR using high fidelity Phusion polymerase (NEB) with the following primers: CAAGCAGAAGACGGCATACGA (P3) and AATGATACGACCACCGA (P5). Amplified libraries were then migrated in a 12% acrylamide gel and 75-200bp DNA fragments were excised and frozen at -20oC overnight. Acrylamide pieces were crushed into smaller pieces and DNA fragments were eluted by incubating overnight at 4oC in 50mM NaCl, 10mM TrisHCl, pH=8.0. Supernatants containing the DNA libraries were incubated with 3M sodium acetate and 100% ethanol with glycogen to facilitate DNA precipitation overnight at -80oC. DNA fragments were precipitated and pellets were resuspended in water and filtered through Spin X Centrifuge tube filter (Costar) to remove acrylamide contaminants. DNA libraries were precipitated and then resuspended in 12-20mL of DEPC-treated water. Libraries were quantified by the Qubit Quantitation Platform (Invitrogen) before loading on an Illumina Genome Analyzer 2 (GA2) flow-cell in a concentration of 8 pM per lane. Sequencing was carried out on the Illumina GA2 according to the manufacturer’s instructions for 36 cycles using the “P5” primer.

tag: tissue

value: brain

tag: antibody 1

value: Fus

value: catalog #:A300-302A

tag: antibody 2

value: Fus/Tls

value: manufacturer:Santa Cruz

value: catalog #:clone 4H11 sc-47711


title: fetus_4

city: Atlanta

first: Tao

last: Wang

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description: 5hmC-chemical label pull down

data_processing:
Library strategy: 5hmC-capture-seq
Bowtie aligned
remove duplicate reads
To identify fetus- and adult-specific DhMRs in human brain, we employed a Poisson-based peak identification algorithm (MACS) using aligned 5-hmC-enriched tags. DhMRs were determined among all pairs of 5-hmC-enriched samples by directly comparing one sample (this submission) to another (two adult samples previous submitted in GEO with accession number: GSM794671 GSM794674) in each direction.
Genome_build: hg18/NCBI36
Supplementary_files_format_and_content: text files with adult and fetus specific DhMRs

source_name: human cerebellum DNA

extract_protocol: Approximately 50ng (5ul) of each 5hmC enriched DNA was used for Illumina SR library preparation by NEBNext ChIP-Seq Sample Prep Reagent Set 1(NEB) according to the manufacturer’s standard protocol.

treatment_protocol: Genomic DNA was  purified by Proteinase K digestion (0.667g/l Proteinase K in 10 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200mM NaCl, overnight at 55°C) followed by extraction with equal volume 25:24:1 phenol:chloroform:isoamyl  alcohol saturated with 10mM Tris, pH 8.0, 1mM EDTA. Purified genomic DNA was precipitated with an equal volume of isopropanol and resuspended in 10mM Tris-HCl, pH 8.0.

value: cerebellum


title: ActivatedBCell_53BP1KO_RPA

data_processing:
Alignment: Standard Illumina image-analysis pipeline with default quality filters is used to determine the short-read sequences and their qualities. The outcome of the pipeline is aligned to mouse mm9 genomes assembly using Bowtie. All reads mapping with no mismatch were retained.
Density of non-redundant alignments was determined in 200nt bins along the genome.
Genome Build:
s6_101108_B3_53BP1mm_IL4_RPA-W200.bedGraph: mm9

value: 53BP1 knockout


title: ActivatedBCell_Ku70KO_RPA

data_processing:
Alignment: Standard Illumina image-analysis pipeline with default quality filters is used to determine the short-read sequences and their qualities. The outcome of the pipeline is aligned to mouse mm9 genomes assembly using Bowtie. All reads mapping with no mismatch were retained.
Density of non-redundant alignments was determined in 200nt bins along the genome.
Genome Build:
s4_101108_B3_Ku70mm_IL4_RPA-W200.bedGraph: mm9

value: Ku70 knockout


title: Mouse CLIPseq Fus/Tls rep3

description: Cross-linking IP against Fus/Tls

source_name: Whole brain

tag: genetic background

tag: age

value: 8 weeks


title: Mouse CLIPseq Tdp43

description: Cross-linking IP against Tdp43

value: custom Tdp43 rabbit monoclonal against peptides 128-140


title: Mouse CLIPseq Fus/Tls rep1

description: Cross-linking IP against Fus/Tls


title: brain RNAseq Fus/Tls-oligo rep4.2

description: strand-specific RNAseq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 or hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: BED format of all reads

source_name: Striatum

value: brain striatum

value: 8-10 weeks

tag: treatment

value: Fus/Tls anti-sense oligo


title: Mouse CLIPseq Fus/Tls rep2

description: Cross-linking IP against Fus/Tls


title: mES-Input

description: input

value: mES

value: no antibody


title: mES-H3K14ac-7G8

description: Chromatin IP against H3K14ac

value: Mouse monoclonal, H3K14ac_7G8

value: Hiroshi Kimura


title: brain RNAseq Fus/Tls-oligo rep4.1

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep4.2

description: strand-specific RNAseq

value: control anti-sense oligo


title: brain RNAseq Fus/Tls-oligo rep2.1

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep4.3

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep3.3

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep4.1

description: strand-specific RNAseq


title: brain RNAseq Fus/Tls-oligo rep1.1

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep3.2

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep2.1

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep3.1

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep2.3

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep1.2

description: strand-specific RNAseq


title: brain RNAseq control-oligo rep2.2

description: strand-specific RNAseq


title: UNC_FaireSeq_Pancreas_OC

status: Public on Sep 28 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromFaire

tag: datatype

value: FaireSeq

tag: datatype description

value: FAIRE-seq Open Chromatin

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.1

tag: cell

tag: cell organism

value: human

tag: cell description

value: Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2)

tag: cell karyotype

value: normal

tag: cell sex

value: M

tag: replicate


title: UNC_FaireSeq_Small_intestine_OC

value: Primary frozen small intestine tissue from NCTC donor IDs 10-0063A (Rep B1) and 09-0143A (Rep B2)


title: UNC_FaireSeq_MRT_G401

value: Malignant renal rhabdoid tumor line

value: cancer

tag: cell lineage

value: missing


title: UNC_FaireSeq_Colon_OC

value: Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian

value: B


title: brain RNAseq Fus/Tls-oligo rep2.2

description: strand-specific RNAseq

tag: tissue

value: brain striatum

value: 8-10 weeks

value: Fus/Tls anti-sense oligo


title: UNC_FaireSeq_Kidney_OC

value: Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE)


title: UNC_FaireSeq_MCF-7_Estradiol_10nM_30m

value: FaireSeq

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff:0.1

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: ectoderm

value: F

tag: treatment description

value: 30 min with 10nM 7b-Estradiol (Crawford)


title: UNC_FaireSeq_RCC_7860

value: FAIRE-seq Open Chromatin

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.1

value: human

value: renal cell adenocarcinmoma

value: M


title: UW_ChipSeq_AG04450_H3K9me3

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwHistone

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: ChipSeq

value: Chromatin IP Sequencing

value: fetal lung fibroblast

value: normal

value: endoderm

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

tag: antibody targetdescription

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: labexpid


title: UNC_FaireSeq_MRT_TTC549

tag: datatype

value: FaireSeq

tag: datatype description

value: FAIRE-seq Open Chromatin

tag: controlid

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_female,p-value cutoff:0.1

tag: cell

tag: cell organism

tag: cell description

value: Malignant Hepatic Rhabdoid tumor line

value: cancer

value: missing


title: UNC_FaireSeq_Frontal_cortex_OC

value: human

value: Primary ventromedial prefrontal cortex, from KPBBB donor IDs 673 (Rep B1) and 913 (Rep B2)

tag: cell karyotype

tag: cell sex

value: F

tag: replicate


title: brain RNAseq Fus/Tls-oligo rep3.1

description: strand-specific RNAseq

tag: tissue

value: brain striatum

tag: genetic background

tag: age

value: 8-10 weeks

tag: treatment

value: Fus/Tls anti-sense oligo