title: mock ChIP control 4d

city: Wageningen

first: Alice

last: Pajoro

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

description: 1 biological replicate

data_processing:
Basecalls was performed using CASAVA version 1.7  for AP1_4d_1, AP1_4d_2, AP1_8d_1 and  AP1_8d_2 while CASAVA version 1.8 was used for all the other files
Reads were aligned to the Arabidopsis thaliana genome (TAIR10, http://www.arabidopsis.org/) using Bowtie (Langmead et al., Genome Biology 2009) version 0.12.7, allowing up to 3 mismatches.
From the aligned reads reported, uniquely mapped reads were processed according to the procedure described in (Bardet et al., Nature protocols 2012).
Target genes for genomic regions of interest were retrieved using the function 'distance2Genes' in the Bioconductor package CSAR (Muino et al., Plant Methods 2011) for genes annotated in TAIR10
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited .txt file containing peak definitions: Peak_name, chromosome, peak start, peak end, peak summit, -log10(p-value), fold enrichment, -log10(q-value) and genes with a peak in a region 3kb upstream to 1kb downstream the peak.

source_name: plant inflorescences

growth_protocol: All plants were grown at 20 °C under long day condition (16 h light, 8 h dark) on rockwool.

extract_protocol:
ChIP experiments were performed following a previously published protocol  (Kaufmann et al., Nature Protocols, 2010) using an anti-GR antibody (Glucocorticoid Receptor alpha Polyclonal antibody (PA1-516, Thermo Scientific), to precipitate AP1-GR),  or a peptide SEP3 antibody. 0.75 g of plant material were used for each biological replicate. ChIP experiments performed using pre-immuneserum were used as negative control for each time point.
Libraries were prepared using the Illumina protocol for preparation of ChIP-SEQ libraries with modifications described in Kaufmann et al., Nature Protocols 2010

treatment_protocol: pAP1:AP1-GR ap1-1 cal-1 plants were induced daily with DEX- induction solution (2 mM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Inflorescences where harvested 2, 4 and 8 days after induction.

value: Landsberg

tag: genotype/variation

value: pAP1::AP1-GR ap1 cal

tag: agent

value: DEX

tag: tissue

value: inflorescences

value: pre-immune serum


title: mock ChIP control 8d

status: Public on Feb 03 2014

type: SRA

description: 1 biological replicate

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

tag: ecotype

tag: time

value: 8 days

tag: antibody


title: AP1 ChIP-seq 8d biological reps 1 and 2

description: 2 biological replicates

value: anti-GR antibody (Glucocorticoid Receptor alpha Polyclonal antibody (Thermo Scientific, cat# PA1-516, lot# MD153967; to precipitate AP1-GR)


title: AP1 ChIP-seq 4d biological reps 1 and 2

description: 2 biological replicates

value: 4 days


title: mock ChIP control 2d

description: 1 biological replicate

value: 2 days


title: SEP3 ChIP-seq 8d biological reps 1 and 2

description: 2 biological replicates

value: anti-SEP3 antibody (Eurogentec, custom-made, peptide antibody)


title: h9ESC long 2

city: Taipei

first: Chan-Shuo

last: Wu

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description:
Oligo-dT selected, oligo-dT primered.
F5AGPVJ.psl
GRCh37
BLAT alignment

library_source: transcriptomic

data_processing: All h9ESC 454 reads and the h1ESC 454 reads (downloaded from GEO with accession number: GSE20301) are first aligned against the human reference genome (GRCh37) using BLAT. In the BLAT alignment result, a read is discarded if it shows at least one alignment with an unmapped sequence <= 20 bases in length to the human genome. Each extracted non-co-linear alignment is composed of two topologically distinct mapping parts, with a piece of overlap or gap. Both of the non-overlapping regions of mapping parts are restricted to being longer than 50 bp in length and showing greater than or equal to 95% alignment to the reference genome. The junction site between two topologically distinct genomic loci is designated as a non-co-linear junction site. For each non-co-linear alignment, two BLAT-aligned blocks, with a non-co-linear junction site, are regarded as a non-co-linear junction region. A considered non-co-linear junction region must satisfy both of the following two rules: (1) the non-co-linear junction region must show the highest level of coverage of the corresponding read in the BLAT alignment result; and (2) since the minimal length of the BLAT alignments is 20 bases, the coverage length of (1) must be at least 20 bases longer than that of all possible co-linear-fashion alignments (if they exist) in the BLAT alignment result. After that, 8,822 non-co-linear RNA candidates are extracted, which are supported by 10,135 Roche 454 reads. The BLAT alignments with two topologically distinct mapping parts are also provided (i.e., F5AGPVJ.psl).

molecule: polyA RNA

organism: Homo sapiens

source_name: Embryonic stem cells

growth_protocol: The hESC H9 was grown on MEF feeders (2 Ã 104 cells/cm2) in DMEM/F12 medium plus 20% Knockout Serum Replacement (Invitrogen, Carlsbad, CA) and bFGF (4 ng/ml, Sigma-Aldrich, St. Louis, MO).

extract_protocol: 10ug hESC H9 total RNA was extracted by Tri-reagent (Ambion). The mRNA was purified from total RNA by Poly(A)Purist MAG kit (Ambion) according to manufacturerâs instruction. One ug mRNA was used to synthesize first strand cDNA with oligo-dT primer by Creator SMART cDNA library Construction Kit (Clonetech). The double strand cDNA was generated from first strand cDNA solution by PCR with primers provided in the same kit.

tag: developmental stage

value: Embryonic stem cells

tag: cell line


title: AP1 ChIP-seq 2d biological replicate 1

description: biological replicate of GSM1279837


title: SEP3 ChIP-seq 4d biological reps 1 and 2

description: 2 biological replicates


title: h9ESC long 1


title: T6

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads.
Alignment was performed within Lifescope 2.5.1 software smallRNAs pipeline using default parameters.
Annotation process has been performed within home made pipeline. Alignment bam files with primary alignments (lowest MAPQV) were annotated with .GFF files with genomic coordinates of smallRNAs such as miRNAs (mirbase release 18), tRNAs (UCSC tracks), yRNAs, snoRNAs and piRNAs (fRNAdb) and ensembl ncRNAs tracks (release 69).
Processed data file submitted is a matrix file containning counts for each sample without normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Tabular text-file with feature name, feature type, feature description, feature genomic coordinates and counts associated within each samples, ordered by expression decreasing

molecule: total RNA

organism: Mus musculus

source_name: cutaneaous Squamous Cell Carcinoma

extract_protocol:
Qiagen miRNeasy mini kit
NEBNext Small RNA Library Prep Set for SOLiD
Libraries were size selected on acrylamide gels (Library size: 110 to 150 nt)

value: skin

tag: background strain

value: FVB/N

tag: disease state

value: cutaneaous Squamous Cell Carcinoma


title: T2


title: T4


title: T3


title: DNaseI-seq control

description: control

data_processing:
Basecalls was performed using CASAVA version 1.8
Reads were aligned to the Arabidopsis thaliana genome (TAIR10, http://www.arabidopsis.org/) using Bowtie (Langmead et al., Genome Biology 2009) version 0.12.7, allowing up to 3 mismatches.
From the aligned reads reported, uniquely mapped reads were processed according to the procedure described in (Bardet et al., Nature protocols 2012).
Target genes for genomic regions of interest were retrieved using the function 'distance2Genes' in the Bioconductor package CSAR (Muino et al., Plant Methods 2011) for genes annotated in TAIR10
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited .txt file containing peak definitions: Peak_name, chromosome, peak start, peak end, peak summit, -log10(p-value), fold enrichment, -log10(q-value) and list of genes with the peak at located at 3kb upstream to 1kb downstream of the gene.

extract_protocol:
Nuclei isolation from 0.2 g of plant material was performed according to (Zhang et al., 2007) and DNA digestion was performed according (Hesselberth et al., 2009). Two biological replicates for each time point were sequenced on Illumina HighSeq2000.
Libraries were prepared using the Illumina according to manufacture's instructions of the sample prep kit from Illumina

treatment_protocol: pAP1:AP1-GR ap1-1 cal-1 plants were induced daily with DEX- induction solution (2 mM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Inflorescences were harvested before treatment and 2, 4 and 8 days after induction.

value: pAP1:AP1:GR ap1 cal

value: control


title: T1


title: shControl_rep3

city: San Diego

first: xiayu

last: huang

state: CA

address: 3010 Science Park Road

country: USA

institute: Sanford|Burnham Medical Research Institute

data_processing:
Reads which did not pass the internal Illumina QC were removed.
The rest reads were mapped to mm9 genome using BWA and result bam files were quantified and normalized with the method DESeq in Avadis NGS.
The raw counts after applying the normalization on them are called the `normalized counts'.
The normalized counts are log-transformed to result in what are called `normalized signal values'.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited txt file with log transformed data

source_name: CCE mouse embryonic stem cells

growth_protocol: mES media consisting of DMEM supplemented with 15% FBS, 1% L-glutamine, 1% MEM NEAA, 0.00086% 1-Thioglycerol and 0.01% LIF

extract_protocol:
Total RNA from transduced cells were extracted by Trizol reagent on days 2, 4 and 6 post-transduction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CCE mES cells were transduced with pLKO.1-puro lentivirus expression shRNA. After 24hr, the media was removed and replaced with media containing 1µg/ml puromycin. The media was changed every other day with fresh media with 1µg/ml puromycin.

tag: cell type

value: Mouse embryonic stem cells

value: CCE

tag: treatment

value: Lentiviral control shRNA transduction


title: shControl_rep2


title: DNaseI-seq 8d biological reps 1 and 2

description: 2 biological replicates

value: Landsberg

value: DEX


title: DNaseI-seq 0d biological reps 1 and 2

description: 2 biological replicates

value: not treated

value: 0 days

value: inflorescences


title: S5

source_name: Healthy skin

value: healthy


title: S2


title: S4


title: DNaseI-seq 4d biological reps 1 and 2

description: 2 biological replicates

value: 4 days


title: DNaseI-seq 2d biological reps 1 and 2

description: 2 biological replicates

value: 2 days


title: S7


title: P5

source_name: papilloma

value: papilloma


title: P6

value: skin


title: P1

value: FVB/N


title: H8

source_name: Hyperplastic skin

value: Hyperplastic skin


title: H7


title: H5


title: P4


title: H2


title: H1


title: SOD1 +/+ -3

city: Cambridge

last: Eggan

state: MA

address: 7 Divinity Avenue, Sherman Fairchild 258A

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the genome using the split read aligner TopHat (v2.0.7) and Bowtie2 (v2.0.5) using default parameters. Reference files of the human genome build hg19/ GRCh37, as well as ensembl transcript annotations, were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn, accessed January 2012).
Aligned reads were sorted by coordinate using Picard Tools (v1.44) SortSam, SORT_ORDER=coordinate
Duplicate reads were removed using Picard Tools (v1.44) MarkDuplicates, VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true
Resulting bam files were converted to sam format using samtools view (v0.1.12.a)
Reads in features were counted using the htseq-count python script (v0.5.4) in Python 2.7.3 using default settins except for --stranded=no
Count data was analyzed using the R software package DESeq using methods documented by the package authors. Data was independently filtered to include only features with greater than 2 counts per million in at least two replicates from any condition.
Genome_build: human genome build hg19/ GRCh37, as well as ensembl transcript annotations, were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn, accessed January 2012).
Supplementary_files_format_and_content: Counts mapping to each feature were normalized to library size using the methods implemented in the DESeq software package. Each file contains the number of normalized reads mapping to a feature for that given sample replicate. An additional file provides a matrix of mean counts averaged over all replicates per condition.

source_name: motor neurons derived from iPSCs

growth_protocol: iPSCs were grown in mTeSR/matrigel conditions. Motor neuron cultures were generated in an EB-based protocol as described on the relevant manuscripts (Kiskinis et al., 2014, Cell Stem Cell). Motor neurons were purified by FACS based on Hb9::RFP after 15 days of co-culture with primary glial cultures

extract_protocol:
RNA was harvested using Trizol (Invitrogen) according to the manufacturers’ directions. RNA quality was determined using BioAnalyzer (Aligent). RNA integrity numbers above 7.5 were deemed sufficiently high quality to proceed with library preparation.
RNA sequencing libraries were generated from ~250 ng total RNA using the illumina TruSeq RNA kit v2, according to the manufacturers' directions. Libraries were sequenced at the Broad Institute genomics platform on a HiSeq 2500 or at the Harvard Northwest labs sequencing facility on a HiSeq 2000.

treatment_protocol: No treatment was done

tag: genotype

value: SOD1 WT


title: SOD1 +/+ -2


title: TMAR 7-MMSDK analysis

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

description:
TAMR 7 is high-dosage tamoxifen selected resistant sublines
MMSDK-tag

data_processing:
Basecalling was performed in BGI-Shenzhen.
A command line tool FASTX-Toolkit implemented in Perl was used to trim the adaptor sequence. The trimmed tags were subjected to quality filtering, so that only tags with sequencing quality higher than 30 for more than 80% of the nucleotides were used for subsequent analysis. For MMSDK tag mapping, we generated a simulated reference library, i.e., BssHII reference library, by in silico enzyme digestion of the human genome (hg19, UCSC) regardless of the methylation state. This library was used as reference for subsequent mapping of the tags in the MMSDK analysis. In the DGE analysis, refMrna (hg19, UCSC) was used as reference for mapping cDNA tags. Subsequently, the Burrows–Wheeler Aligner (BWA) procedure for aligning the MMSDK and DGE tags to the simulated BssHII reference library and refMrna reference library, respectively, was applied.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text files (linked as supplementary files on the Series record) include gene expression values (normalized tag number) and DNA unmethylation values (normalized tag number) for each Sample .

source_name: Breast cancer cell line

growth_protocol: The human breast cancer cell line MCF-7 was originally received from The Breast Cancer Task Force Cell Culture Bank, Mason Research Institute.  The MCF-7 cells were gradually adapted to grow in low serum concentration. The tamoxifen-sensitive sub-line MCF-7/S0.5 was used to establish tamoxifen-resistant (TAMR) cell lines by long term treatment with 10-6 M tamoxifen. The 4 TAMR cell lines:  MCF-7/TAMR-1 (TAMR-1), MCF-7/TAMR-4 (TAMR-4), MCF-7/TAMR-7 (TAMR-7) and MCF-7/TAMR-8 (TAMR-8) were derived from distinct colonies that emerged in cultures of MCF-7/S0.5 cells treated with tamoxifen. The cells were kept within 10 passages throughout the experiments to reduce a possible variability between experimental results

extract_protocol:
DNA was isolated from the cell lines using DNeasy® Blood & Tissue Kit (Qiagen) according to manufacturer’s protocol. Genomic DNA was digested with BssHII followed by ligation to biotinylated linkers and fragmented by NlaIII (New England BioLabs) cleavage. Because BssHII only cuts unmethylated regions, binding of DNA fragments to streptavidin-conjugated magnetic beads allow separation of the unmethylated and methylated fragments. Bound DNA was ligated to another linker (N) containing the MmeI restriction enzyme recognition site, and then digested with MmeI (New England Biolabs) that generates short sequence tags (20-21 bp, due to enzyme cut floating). The resulting tags were ligated with another linker P7 and amplified by PCR with primers N and P7 for 18 cycles.
Total RNA was extracted from the cell lines with TRI Reagent (Sigma) according to the manufacturer’s protocol. The integrity of the extracted RNA was checked by agarose gel electrophoresis, and the concentration of RNA was estimated by spectrophotometry. Then, mRNA is separated from total RNA by poly-T coated beads and converted to cDNA. The cDNA is isolated and subjected to NlaIII digestion followed by N-ligation, MmeI digestion P7-ligation and PCR to prepare a DEG library in a way analogous to that in MMSDK.

value: breast cancer cell line MCF-7/TAMR-7

value: tamoxifen resistant


title: TMAR 4-MMSDK analysis

description:
TAMR 4 is high-dosage tamoxifen selected resistant sublines
MMSDK-tag

value: breast cancer cell line MCF-7/TAMR-4


title: TMAR 8-MMSDK analysis

value: breast cancer cell line MCF-7/TAMR-8


title: TMAR 1-MMSDK analysis

description:
TAMR 1 is high-dosage tamoxifen selected resistant sublines
MMSDK-tag

value: breast cancer cell line MCF-7/TAMR-1


title: SOD1 A4V/+ -2

value: SOD1 A4V


title: S3


title: MCF-7/S0.5-MMSDK analysis

description:
MCF-7/S0.5 cell line is tamoxifen sensitive and it is parental cell lines for the rest four resistant cell lines
MMSDK-tag

value: breast cancer cell line MCF-7/S0.5

value: tamoxifen sensitive


title: TMAR 7-DGE analysis

description:
TAMR 7 is high-dosage tamoxifen selected resistant sublines
DGE-tag


title: TMAR 8-DGE analysis

description:
TAMR 4 is high-dosage tamoxifen selected resistant sublines
DGE-tag


title: TMAR 1-DGE analysis

description:
TAMR 1 is high-dosage tamoxifen selected resistant sublines
DGE-tag


title: P3


title: TMAR 4-DGE analysis


title: SEP3 ChIP-seq 2d biological replicate 2

data_processing:
Basecalls was performed using CASAVA version 1.7  for AP1_4d_1, AP1_4d_2, AP1_8d_1 and  AP1_8d_2_FC2_lane4.txt.bz2 while CASAVA version 1.8 was used for all the other files
Reads were aligned to the Arabidopsis thaliana genome (TAIR10, http://www.arabidopsis.org/) using Bowtie (Langmead et al., Genome Biology 2009) version 0.12.7, allowing up to 3 mismatches.
From the aligned reads reported, uniquely mapped reads were processed according to the procedure described in (Bardet et al., Nature protocols 2012).
Target genes for genomic regions of interest were retrieved using the function 'distance2Genes' in the Bioconductor package CSAR (Muino et al., Plant Methods 2011) for genes annotated in TAIR10
Genome_build: TAIR10
Supplementary_files_format_and_content: file containing peak definitions: chromosome, peak start, peak end, peak summit, -log10(p-value), fold enrichment, -log10(q-value) and genes with a peak in a region 3kb upstream to 1kb downstream the peak.

source_name: pAP1::AP1-GR ap1 cal inflorescences

value: Landsberg

value: SEP3 antibody

value: inflorescences 4 days after DEX treatment


title: AP1 ChIP-seq 2d biological replicate 2

description:
biological replicate of GSM1142626
AP1_2days.txt

value: GR antibody

value: inflorescences 2 days after DEX treatment


title: MCF-7/S0.5-DGE analysis

description:
MCF-7/S0.5 cell line is tamoxifen sensitive and it is parental cell lines for the rest four resistant cell lines
DGE-tag


title: D. shibae 5 h in the light after 12 days in co-culture with the dinoflagellate P. minimum, replicate 1

status: Public on Feb 01 2014

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

description: mRNA

data_processing:
Sequencing was done on the Genome Analyzer IIx (Illumina, San Diego, CA, USA) following a standard protocol. The fluorescent images were processed to sequences and transformed to FastQ format using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina, San Diego, CA, USA).
The sequencing output (36 bp single end short reads) of the Genome Analyzer IIx was controlled for general quality features using the fastq-mcf tool of ea-utils (http://code.google.com/p/ea-utils) and was mapped against the genome sequence of D. shibae (NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1) using BWA v 0.5.9-r16.
Genome_build: NC_009952.1, NC_009955.1, NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1.
Supplementary_files_format_and_content: Tab-delimited text files include unique and total mapped reads and RPKM values for each gene of one sample.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: D. shibae co-cultured with P. minimum, 5 h in the light

extract_protocol:
RNA isolation: For RNA extraction, the sample was thawed at room temperature and then transferred to a cryotube filled with 0.3 g acid-washed glass beads. The cells were homogenized using the FastPrep-24 instrument (MP Biomedicals, California, USA) at 6.0 m/s for 3 min and then incubated for 5 min at room temperature. Samples were centrifuged at 12,000 g for 10 min at 4°C and the supernatants were transferred to fresh tubes, followed by the addition of 100 µl of 1-bromo-3-chloropropane (BCP, Sigma, Germany) and incubation for 10 min at room temperature. Samples were centrifuged at 12,000 g for 10 min at 4°C, after which the aqueous phase was transferred to new tubes and mixed with 500 µl of absolute ethanol. Extracts were applied to RNeasy spin columns (RNeasy mini kit, Qiagen, Hilden, Germany) and processed according to the manufacturer's instructions. In addition, samples were treated with DNAae I (Qiagen, Hilden, Germany). Removal of genomic DNA was verified via PCR using total RNA as template. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA).
Ribosomal RNA depletion: The Oligotex mRNA kit (Qiagen, Hilden, Germany) was used to isolate the algal mRNA. For isolation of D. shibae mRNA, the MICROBEnrich kit (Ambion, Life Technologies, Darmstadt, Germany) was used to remove the eukaryotic rRNA and MICROBExpress kit (Ambion, Life Technologies, Darmstadt, Germany) to remove the prokaryotic rRNA, according to the manufacturer's instructions.
Libraries of 300 bp for RNA sequencing were prepared using the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. Quality control of the prepared libraries was validated using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, USA). Cluster generation was performed using the Illumina cluster station.

tag: strain/background

tag: light/dark condition

value: 5 h light

tag: single/co-culture

value: co-culture

tag: days in co-culture with p. minimum


title: D. shibae 5 h in the light after 12 days in co-culture with the dinoflagellate P. minimum, replicate 2

description: mRNA

data_processing:
Sequencing was done on the Genome Analyzer IIx (Illumina, San Diego, CA, USA) following a standard protocol. The fluorescent images were processed to sequences and transformed to FastQ format using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina, San Diego, CA, USA).
The sequencing output (36 bp single end short reads) of the Genome Analyzer IIx was controlled for general quality features using the fastq-mcf tool of ea-utils (http://code.google.com/p/ea-utils) and was mapped against the genome sequence of D. shibae (NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1) using BWA v 0.5.9-r16.
Genome_build: NC_009952.1, NC_009955.1, NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1
Supplementary_files_format_and_content: Tab-delimited text files include unique and total mapped reads and RPKM values for each gene of one sample.


title: SOD1 +/+ -1


title: Pitx2-flag ChIP-Seq

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

data_processing:
Basecalling performed on Torrent Suit 2.2
ChIP-Seq reads were aligned to mm9 genome assembly using ion-alignment 2.2.4-1
The ChIP-seq signal was normalized to a 10 million read total. Bedgraph file was generated using Homer version 4.1, makeUCSCfile (-o auto) function.
Enriched peaks were called using Homer v4.1 findPeaks function with following parameters: findPeaks -style factor -o auto -fdr 0.01. Poisson p-value threshold 1.00e-04.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using Homer-v4.1; Y-axis scale represents normalized read number. Bed files include genomic intervals of enriched peaks.

source_name: postnatal heart

extract_protocol:
Chromatin immunoprecipitation was performed as described previously using EZ ChIPTM kit (Millipore) and Anti-FLAG M2 Affinity Gel (Sigma)
For the construction of library for sequencing, 10-50 ng of purified ChIP DNA was end-repaired using Ion Plus Fragment Library Kit (Part no. 4471252, Life Technologies) and purified with two rounds of AMPure®  XP beads (Beckman Coulter, Brea, CA) capture to size select fragments approximately 100–250 bp in length. The end-repaired DNA was ligated to Ion Torrent compatible adapters. Followed by 15 cycles of PCR amplification before downstream template preparation. DNA fragments of the completed library ranged from approximately 170–220 bp in length.

tag: developmenta stage

value: 12-week postnatal

value: whole heart

tag: chip-seq antibody

value: Anti-FLAG M2 Affinity Gel (Sigma)


title: KO-Lin-

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Reads were aligned to mm10 using TopHat (v2.0.7) using default parameters except -p 8 and -G.  The reference genome and GTF file for mm10 were obtained from http://tophat.cbcb.umd.edu/igenomes.html
Transcripts were assembled and quantified using Cufflinks (v2.0.2) with default parameters except -p 8 and -G.
The transcript assemblies from each sample were merged using cuffmerge in Cufflinks (v2.0.2) using default parameters.
Differential expression was performed between samples
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files from Cufflinks that include FPKM values for each sample.

source_name: Bone Marrow

extract_protocol:
Bone marrows from 4 mice in each genotype were pooled and were used to positively select Gr1/Mac1 double positive cells by magnetic beads, which were lyzed and total RNA isolated from them using Trizol method. The remaining cells were negatively selected for uncommitted progenitor cells and subjected to RNA isolation as above.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lin- bone marrow hematopoietic progenitor

tag: strain

tag: age

value: 12 weeks

value: Diap1 -/-


title: Het-Lin-

value: Diap1 +/-


title: WT-Lin-

value: Wild type


title: KO-Gr1+Mac1+

value: Gr1+Mac1+ myeloid cells


title: WT-Gr1+Mac1+


title: SOD1 A4V/+ -1

value: SOD1 A4V


title: CBX4 C-terminal pull-down

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

data_processing:
Illumina base-calling pipeline; Heclios base-calling pipeline
for Illumina data: aligned to dm3 using bowtie (-t 1 -k 1); Helicos data was aligned using helisphere pipeline with default parameters, and uniquely aligned reads only.
conservative estimates of enrichment calculated using SPP (http://compbio.med.harvard.edu/Supplements/ChIP-seq/), using window size of 5Kb.
Genome_build: hg18
Supplementary_files_format_and_content: TDF files (for IGV browser) containing conservative estimates of  smoothed enrichment

source_name: 293T Rex cell line

growth_protocol: Human 293 T-REx cells were grown in 150mm x 25mm dishes in DMEM (Invitrogen Cat #11965), supplemented with 10% FBS, 1% penicillin/streptomycin. 1.5 × 109 cells were harvested. Cell cultures were split in half by adding an equal volume of HyClone CCM3 serum-free medium (Thermo Scientific, Cat No.SH30065) and grown in eight T-flasks (225 cm2) to a density of ~5x106 cells/ml. Cells were transferred into four 2.8L Fernbach glass flasks (Bellco, Glass Inc.).

extract_protocol:
Soluble chromatin was incubated with IgG agarose beads (Sigma, Cat # A2909). For every 10 ml of sonicated chromatin, 0.5-1 ml beads were added. The mixture was rotated end-over end in the 15 ml Falcon tubes for 12-16 h at +4°C. Beads were then washed 3 times for 10 min at +4°C with 15 bead volumes of RIPA buffer and spun down for 5 min at 1000g, +4°C between washes. Beads were then washed for 10 min with 15 bead volumes of buffer TEN 140 buffer with 0.1% Triton X-100 at +25°C and spun down for 5 min at 1000 g, +25°C. In order to elute the complexes (protein-DNA-RNA), 12-15 bead volumes of IgG Elution buffer were added to the beads. The slurry was mixed by inversion for 1 hour at +25°C. This elution step was repeated one more time. In order to eliminate urea from the samples, the eluates were first concentrated  in 10K Amicon Ultra-15 columns (3000g, 15min at +25°C) and then washed/buffer exchanged 3 times with 15 ml of TEN 140 buffer with 0.1% Triton X100 (3000g, 5-15min at +25°C) in a fresh Amicon column. The resulting 0.5 ml concentrate was diluted with 2500 ul of RIPA buffer and transferred into two Eppendorf tubes.  Biotin-Streptavidin affinity purification 150-300 ul of Streptavidin Agarose beads (Thermo Scientific, cat # 20349) were added to each tube.  The mixture was rotated end-over-end for 12-16 hours at +16°C. Beads from both tubes were pooled into one 15 ml Falcon tube washed once with RIPA buffer, once with TEN 140 buffer with 0.1% Triton X100, twice with IgG Elution buffer and twice with IgG Elution buffer without SDS. For each washing step, beads were mixed with 12 ml of a given buffer on a rotating wheel for 10 min at +25°C and spun down for 5 min at 1000 g, +25°C. Beads were re-suspended in 10 ml of TEN 140 buffer and divided into three tubes: 6 ml for protein work, 2 ml for DNA and 2 ml for RNA analysis.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments from 300-700 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's

treatment_protocol: Harvested 293 T-REx cells were homogenized by using a 100 ml Dounce homogenizer (Bellco, Glass Inc.), 10 strokes of each of A and B pestles. For every 4-5 ml of cell pellet volume 100 ml of NEB buffer+0.1 mM PMSF pre-chilled on ice were added. Without delay, 100 ml of cell/nuclear homogenate was poured into a T-225 flask containing a room-temperature mixture of 360 ml of PBS and 40 ml of 37% formaldehyde and incubated for 30 min at 25°C on a orbital shaker platform with vigorous shaking (100rpm). Fixed nuclei were pelleted by spinning for 10 min at 4000 g, +4°C. The supernatant was carefully decanted and the nuclear pellet was washed four times with 100 ml of ice-cold PBS with 0.1 mM PMSF. Nuclei were pelleted between washes for 10 min at 4000g, +4°C. Nuclei were resuspended in glycerol buffer and snap-frozen in liquid N2 prior to further processing. Frozen nuclear extracts from human 293 T-Rex cells were thawed and spun down for 10 min at 4000 g, +4°C. Pellets were washed with 10-20 volumes of TE buffer with 0.1 mM PMSF and spun down for 10 min at 4000g, +4°C. Pellets were again re-suspended with 10 volumes of TE buffer with 0.1 mM PMSF by pipetting up and down. SDS was added to the mixture to a final concentration of 1%. The mixture was inverted in the tube 10 times and spun down for10 min at 4000 g, +4°C. The supernatant was carefully removed (Note: the pellet may be quite loose) and the pellet was re-suspended with 10 volumes of TE buffer with 0.1 mM PMSF by pipetting and further spun down for 10 min at 4000 g, +4°C. This washing step was repeated twice. The pellet was re-suspended with 1.5 volumes of TE buffer with 0.1 mM PMSF by pipetting up and down. SDS was added to a mixture to a final concentration of 0.1%. The resulting viscous mixture was sonicated in 4.5 ml aliquots using a Misonix Sonicator 3000 with Microtip power output level 7 and total sonication processing time of 5 min (human sample), 15 sec pulse “on” and 45 sec “off” time to generate DNA fragments in the range of 300-2000 bp.   Triton X-100 (1% final) and NaCl (140 mM final) were added to the sonicated samples. Samples were mixed on a rotating wheel for 5 min  at +4C and spun down for 10 min at 10000 g, +4°C. The supernatant containing the soluble chromatin was collected. Note: In order to control for chromatin input composition and quality (for protein, DNA and RNA), a 1 ml aliquot is reserved before proceeding with the next step.

tag: pull-down biotap

value: CBX4 C-terminal BioTAP


title: CBX4 C-terminal input


title: S2 Terminator only

city: Durham

first: Colin

middle: Scott

last: Maxwell

state: NC

address: 4314 FFSC

department: Biology

institute: Duke University

data_processing:
Library strategy: scRNA-Seq
Mapped to WS210 or Flybase v 5.30 using Bowtie v0.12.7. Required one unique mapping position. Reads that did not map during this step were stripped of the first 22 nt, then remapped. If the read mapped and the first 22 nt matched the sequence of either SL1 or SL2, the read was counted as trans-spliced.
Created bedgraphs using HTSeq, only the 5'-most base of the read was recorded. Each bedgraph was then converted to reads per million, where the number of reads is the total uniquely mapped reads present in the lirbary. Note that 3' libraries map to the opposite strand.
Genome_build: WS210 or Flybase v5.30
Supplementary_files_format_and_content: bedgraphs

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Nematodes were maintained on standard NGM plates with E. coli OP50 as food (Lewis 1995), but liquid culture was used to prepare RNA-seq samples.  A starved 5 cm plate was used to inoculate 25 mL of liquid culture (S-complete plus 40 mg/mL E. coli HB101)(Lewis 1995).  The culture was incubated at 20°C and 180 rpm for 65 hr and then bleached to produce a clean preparation of embryos.  Embryos were suspended in S-complete at 5 eggs/mL and incubated at 20°C and 180 rpm for 24 hr so that they hatch and enter L1 arrest.  After 24 hr, cultures were fed with 40 mg/mL HB101 to initiate synchronous development and they were incubated at 20°C and 180 rpm for 57 hr.  In these conditions, the first eggs are fertilized at about 53 hr, and when bleached at 57 hr the yield is typically about 10 eggs per worm.  After 57 hr the cultures were bleached, and the eggs were suspended in S-complete at 10 eggs/mL. Animals were incubated at 20°C and 180 rpm for 24 hr so that they hatch and enter L1 arrest, corresponding to approximately 12 hr starvation. Arrested larvae were collected by centrifugation and washed 3 times in S-basal before being flash frozen. Drosophila S2-DRSC cells were cultured in 150-mm plates in Schneider's Insect Cell Medium (Invitrogen) supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine (Invitrogen) at 25°C. Independent biological replicates were used for each sequenced library, and they are summarized in Supp. Tables 1 and 2.

extract_protocol: 100 ng size selected RNA was used to make each library. Size selected RNA was treated sequentially with RNA 5’ Polyphosphatase (Epicentre), Terminator 5’-Phosphate Dependent Exonuclease (Epicentre) and Tobacco Acid Pyrophosphatase (TAP; Epicentre), except in controls where only one or two enzymes were used. Enzymatic reactions were performed according to the manufacturer’s protocol. RNA was purified with phenol/chloroform and precipitated with 1/10th volume sodium acetate, 1.5 μl Glycoblue and ethanol after each reaction. The remaining RNA was used to prepare sequencing libraries using the SOLID Total RNA-seq Kit (Applied Biosystems) with a modified version of the Whole Transcriptome Library Protocol. The fragmentation step was omitted since RNA was size selected. Adaptor A was ligated to size selected RNA for sequencing 5’ ends and Adaptor B was used for sequencing 3’ ends. Reverse transcription and cDNA purification were performed according to the manufacturer’s protocol. cDNA was gel purified on a 6% TBE-urea polyacrylamide gel (Invitrogen) and excised at 75 – 145 nt. Gel slices were shredded and cDNA eluted in 300 mM NaCl, 10 mM Tris-Cl (pH 8.0) and 1 mM EDTA. Eluate was cleared of gel with a Corning Costar Spin-X column (0.22 μm). 1 μl of GlycoBlue (15 mg/mL) was added, and cDNA was precipitated with isopropanol at -80°C, washed with 80% ethanol and resuspended in 8 μl water. 2 μl gel purified cDNA was used as template in a 15 cycle PCR reaction according the manufacturer’s protocol. PCR products were purified with the Purelink PCR Micro Kit (Invitrogen) and eluted in 20 μl water. PCR products were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent). PCR products were size selected by running them on an 8% TBE (native) polyacrylamide gel and excising 115-200 bp specifically avoiding the primer dimer band around 100 bp. Gel purified libraries were precipitated as described for cDNA and resuspended in 15 μl water. DNA concentration was determined with the Qubit High Sensitivity DNA Kit (Invitrogen). Libraries were sequenced on the SOLID 5500 platform (Applied Biosystems) with single end 50 bp reads according to the manufacturer’s protocol in the Duke IGSP Genome Sequencing and Analysis Core Resource facility. 5’ mRNA-seq libraries were made by the same protocol as scRNA-seq libraries, except fragmented mRNA was used as starting material. Polyadenylated mRNA was selected from total RNA using Dynal oligo(dT) beads (Invitrogen) according to the manufacturer’s instructions. Two sequential rounds of selection were performed. 200 ng polyadenylated mRNA was fragmented with RNAse III by the same protocol used to fragment mRNA for making mRNA-seq libraries with the SOLiD Total RNA-seq Kit (Applied Biosystems).  Fragmentation reactions were incubated for 10 min at 37°C. Fragmented mRNA was purified with phenol/chloroform and precipitated with 1/10th volume sodium acetate, 1.5 μl Glycoblue and ethanol before being treated with Terminator 5’-Phosphate Dependent Exonuclease (Epicentre) and Tobacco Acid Pyrophosphatase (TAP; Epicentre) as described above for scRNA-seq libraries. Samples were subsequently processed the same way as scRNA-seq libraries, using Adaptor A to sequence the 5’ ends of the RNA.

value: S2 cells

tag: sequencing direction

tag: enzymes used

value: Terminator exonuclease


title: S2 TAP only

value: Tobacco acid pyrophosphatase


title: C17orf96 N-temrinal pull-down

value: C17orf96 N-terminal BioTAP


title: S2 Terminator and TAP only

value: Terminator exonuclease, Tobacco acid pyrophosphatase


title: S2 no enzymes


title: C17orf96 N-terminal input


title: SEP3 ChIP-seq 2d biological replicate 1

tag: ecotype

value: Landsberg

tag: antibody

value: SEP3 antibody

tag: tissue

value: inflorescences 4 days after DEX treatment


title: C17orf96 C-terminal input


title: Pitx2-flag input

value: 12-week postnatal

value: whole heart

value: none (input)


title: C10orf12 r2 input


title: C10orf12 r2 pull-down

value: C10orf12 C-termianl BioTAP


title: C10orf12 r1 input


title: C17orf96 C-terminal pull-down

value: C17orf96 C-terminal BioTAP


title: Ezh2 C-terminal input


title: C10orf12 r1 pull-down


title: Ezh2 N-terminal pull-down

value: Ezh2 N-terminal BioTAP


title: Pol II ChIP-Seq in HeLa

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
base-calling was performed by the University of Iowa DNA Facility
paired-end ChIP-Seq reads were filtered for fragments between 50-500 bp and aligned to hg19 using Bowtie 2.0.5 and the following parameters: --minins 50 --maxins 500 --no-mixed --no-discordant
alignment output was converted from sam to bampe format using Samtools 0.1.18
bedGraph files for visualizing ChIP-Seq reads were generated using MACS 2.0.10 "callpeak" function and the following parameters:  --format BAMPE --bdg
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated as described above using MACS 2.0.10; scores represent the sum of overlapping ChIP fragments over hg19

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in suspension at 5% CO2 and 37°C in Minimum Essential Medium Eagle Spinner Modification (S-MEM) (Gibco, 11380-037) supplemented with 2 mM L-glutamine and 10% FBS.

extract_protocol:
HeLa cells were grown to 0.5 million cells/ml and crosslinked with 1% formaldehyde in media for 10 minutes before glycine addition to 125 mM. After washing and lysis, cells were sonicated in RIPA buffer (50 mM Tris, pH 7.6; 150 mM NaCl; 1 mM EDTA; 0.25% sodium deoxycholate; 1% IGEPAL CA-630) on ice using a Fisher Model 550 Sonic Dismembrator. For each ChIP, sonicated supernatant from 5 million cells was incubated at 4°C overnight with 10 µg of Pol II (Santa Cruz, sc-899), NELF (sc-23599), or DSIF (sc-28678) antibody, and then 1 hr with 50 µl Protein G-Sepharose bead slurry (Sigma, P3296). Beads were washed in columns with 15 ml ice cold RIPA buffer and rinsed with 10 ml ice cold PBS. Immunocomplexes were eluted, incubated at 65°C overnight to reverse crosslinks, and treated with RNase A and Proteinase K. DNA was isolated by MinElute PCR purification kit (QIAGEN, 28004).
Library preparation was performed by the University of Iowa DNA Facility using the Ovation SP Ultralow DR Multiplex System (Nugen, 8033-32) for Mondrian.

tag: cell line

value: HeLa

value: Pol II (N-20) (Santa Cruz, sc-899)


title: Ezh2 N-terminal input


title: DSIF ChIP-Seq in HeLa


title: NELF ChIP-Seq in HeLa

value: NELF-A (A-20) (Santa Cruz, sc-23599)


title: XZ8015_Rep1B_ERY

city: Baltimore

first: Hervé

last: Tettelin

state: MD

address: 801 W Baltimore St

department: Institute for Genome Sciences

institute: University of Maryland

data_processing:
Reads were aligned to reference genomes using bowtie version 0.9.9.2, with parameters -v 2 -k 1
RPKMs were calculated using in-house scripts
Genome_build: AIKI00000000 (GA02254), AILS00000000 (GA17457), AFGA00000000 (GA17545), AGPO00000000 (GA41565)
Supplementary_files_format_and_content: Tab-separated tables of RPKM values

organism: Streptococcus pneumoniae

source_name: culture

extract_protocol:
Total RNA from bacterial samples was extracted using the QIAGEN RNeasy Mini Kit (Qiagen Sciences, Germantown, MD) followed by DNase treatment in solution and rRNA depletion with the Epicentre Ribo-Zero kit (Epicentre, Madison, WI).
Illumina RNAseq libraries were prepared with the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) with a variation of the manufacturer’s protocol. Actinomycin D was added to the first strand synthesis reaction. Between first and second strand cDNA synthesis, the primers and nucleotides were removed from the samples with NucAway spin columns (Ambion, Austin, TX). The second strand was synthesized with a dNTP mix containing dUTP. Adapters containing 6 nucleotide indexes were ligated to the double-stranded cDNA. After adapter ligation, the second strand cDNA was digested with 2 units of Uracil-N-Glycosylase (Applied Biosystems, Carlsbad, CA). The DNA was purified between enzymatic reactions and the size selection of the library was performed with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA). The quantity and size of the libraries were assessed on the LabChip GX (Perkin Elmer, Waltham, MA) and with the Library Quantification Kit for Illumina (Kapa Biosciences, Woburn, MA).

tag: treatment

value: ERY


title: XZ8015_Rep2B_ERY


title: XZ8009_Rep2A_uninduced

value: uninduced


title: XZ8015_Rep1B_SPR

value: SPR


title: XZ8015_Rep2B_uninduced


title: XZ8009_Rep2A_LL37


title: XZ8015_Rep1B_uninduced


title: XZ8009_Rep2A_ERY


title: XZ8009_Rep1A_uninduced


title: XZ8009_Rep1A_SPR


title: XZ8009_Rep1A_ERY


title: XZ7022_Rep2_LL37


title: XZ7022_Rep2_uninduced


title: XZ7022_Rep1_uninduced


title: Ezh2 C-terminal pull-down

value: Ezh2 C-terminal BioTAP


title: XZ7022_Rep2_ERY


title: XZ8009_Rep1A_LL37


title: XZ7022_Rep1_SPR


title: XZ7022_Rep1_ERY


title: GA41565_Rep2_uninduced


title: XZ7022_Rep1_LL37


title: GA41565_Rep2_ERY


title: GA41565_Rep2_LL37


title: GA41565_Rep1_uninduced


title: GA41565_Rep1_SPR


title: GA41565_Rep1_ERY


title: GA17545_Rep2_SPR


title: Het-Gr1+Mac1+

tag: cell type

value: Gr1+Mac1+ myeloid cells

value: 12 weeks

tag: genotype

value: Diap1 +/-


title: GA17545_Rep1_uninduced


title: GA17457_Rep3_LL37


title: GA17545_Rep2_ERY


title: GA17545_Rep1_ERY


title: GA17457_Rep1_LL37


title: GA17457_Rep1_SPR


title: GA17457_Rep1_ERY


title: GA17457_Rep3_SPR


title: GA17457_Rep1_uninduced


title: GA02254_Rep2_uninduced


title: GA17457_Rep0_ERY


title: GA02254_Rep2_LL37


title: GA02254_Rep2_ERY


title: GA02254_Rep1_uninduced


title: GA02254_Rep1_LL37


title: GA02254_Rep1_SPR


title: GA17457_Rep0_uninduced


title: Purine-Repleted sample

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.3
Quality of the reads in fastq files were determined using fastqc and internal tools
SL RNA-Seq reads were aligned against Leishmania infantum genome Version 4.1 downloaded from www.TriTrypDB.org
Samtools v0.1.19 was used to convert alignment files from one format to another
Internal tools were used to estimate splice leader counts against each gene
Genome_build: LinJ V4.1
Supplementary_files_format_and_content: Gene level splice leader read count data generated using custom scripts. The read counts are median normalized within each library

organism: Leishmania donovani

source_name: laboratory culture, whole cell lysate

growth_protocol: L. donovani strain 1S2D [124] of the visceralizing clonal derivative LdBob [125] were employed in these studies. Wild type LdBob promastigotes were routinely cultured at 26 °C in 5 % CO2 in modified Dulbecco's Modified Eagle-Leishmania (DME-L) medium [126] that lacked bovine serum albumin and was supplemented with 5% serum plus (Sigma-Aldrich), 1 mM glutamine, 1X RPMI 1640 vitamin mix, 10 μM folate, hemin (2 ml from a 500x stock containing 2.5 g l-1), and 100 μM hypoxanthine as a purine source. To elicit purine starvation conditions, cells were grown in DME-L lacking hypoxanthine but with all other media components present. Early log phase L. donovani promastigotes were cultivated in purine-replete and purine-deplete media for 24 h.

extract_protocol:
1 X 10^8 cells at early log phase were removed from each condition, harvested by centrifugation and washed twice in D-PBS to remove all media components.  Total RNA from the purine-replete and purine-deplete cells was isolated using an RNeasy kit (Qiagen Inc., Valencia, CA) according to the manufacturer's protocol.
Next Generation Sequencing (NGS) libraries were constructed by priming ~1 µg of total RNA from either the purine-starved or purine-replete sample with a random hexamer primer (TCCGATCTCTNNNNNNN) for first strand cDNA synthesis and an oligonucleotide primer (TCAGTTTCTGTA) derived from the Leishmania splice leader (SL) sequence for second-strand cDNA synthesis.  The resultant cDNA was amplified by PCR for 12-15 cycles using the oligonucleotides that overlapped with the initial primers and containing adapters for subsequent cluster generation and sequencing using Solexa sequencing by synthesis (SBS) technology.

tag: lifestage

value: promastigotes

value: wildtype

value: purine-depleted medium

tag: growth phase

value: early log


title: Purine-Depleted sample

value: purine-repleted medium


title: GA41565_Rep1_LL37


title: GA02254_Rep1_ERY


title: GA17545_Rep2_uninduced


title: IgG

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

description: Sample 2

data_processing:
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
ChIP peaks were analyzed using MACS (Feng et al., 2012) with respect to IgG control.
Genome_build: Flybase release 5.41 GCA_000001625.2

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/streptomycin (GIBCO, Invitrogen).

extract_protocol:
Standard chromatin extraction procedures were utilized for  ChIP analysis using anti-Beaf32 or anti-IgG control antibodies. Antibodies were generated in the lab (Affinity purified, rabbit antibodies raised against 18AA-long C-terminal peptides.
ChIP samples were prepared for sequencing using standard Illumina protocols of TruSeq ChIP sample prep kits from 1.2 ng of starting precipitated DNA to generate sequencing libraries

treatment_protocol: S2 cells were treated with formaldehyde followed by standard sonication procedures

value: Late embryonic derived S2 cells

tag: chip antibody

value: anti-IgG control antibody


title: Beaf-32

description: Sample 1


title: N2 Terminator and TAP only

organism: Caenorhabditis elegans

source_name: Starved L1 larvae

value: Starved L1 larvae

value: Terminator, Tobacco acid pyrophosphatase


title: Chimpanzee_MeDIP

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: DNA IP against 5-Methylcytosine

data_processing:
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Aligned fragments were lifted from the host genome to hg19
Wig files were created using the MEDIPS v1.0 bioconductor package
Genome_build: hg19, panTro2.1, mmul1
Supplementary_files_format_and_content: Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC. Scores represent normalised (reads per million) read depth across the genome. Bed files contain lists of differentially methylated regions located in the human genome (hg19). These were defined by comparison of human MeDIP-seq data to chimpanzee (panTro2) and macaque (rheMac2) MeDIP-seq data.

organism: Pan troglodytes

source_name: Blood

extract_protocol:
MagMeDIP kit (Diagenode) for Immunoprecipitation
Pooled DNA from these samples was subjected to AutoMeDIP-seq as previously described (Butcher et al. Methods (2010) 52, 223-31), using the NEBNext DNA Sample Prep Mastermix (New England Biolabs) for the library preparation and the MagMeDIP kit (Diagenode) for the immunoprecipitation. Adequate enrichment of the methylated DNA fraction (compared to input) was quality controlled using qPCR. Following adapter-mediated PCR, the library was subjected to size selection (300-350 bp) from low melting-point agarose gels. The excised fraction was quality controlled by qPCR. Cluster generation and 36 base paired-end sequencing was performed by the UCL Genomics Core Facility according to the manufacturer’s recommendation, using an Illumina GAIIX platform.

value: blood


title: N2 TAP only

value: Tobacco acid pyrophosphatase


title: 3' scRNA-seq TFIIS mutant rep1

value: 5' poly-phosphatase, Terminator exonuclease, Tobacco acid pyrophosphatase


title: 3' scRNA-seq N2 rep1


title: 3' scRNA-seq N2 rep2


title: Macaca_MeDIP

description: DNA IP against 5-Methylcytosine

organism: Macaca mulatta


title: 5' scRNA-seq rep2

value: 5' poly-phosphatase, Terminator exonuclease, Tabacco acid pyrophosphatase


title: CP190-WT2

description: Late embryonic derived S2 cells from Drosophila melanogaster

data_processing:
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
ChIP peaks were analyzed using MACS (Feng et al., 2012) with respect to input control.
Genome_build: Flybase release 5.41 GCA_000001625.2

extract_protocol:
S2 cells were treated with formaldehyde (0.8% final, 15 min) followed by standard sonication and extraction procedures of chromatin for ChIP analysis
ChIP samples were prepared for sequencing using standard Illumina protocols of TruSeq ChIP sample prep kits from 100 ng of starting precipitated DNA to generate sequencing libraries

treatment_protocol: S2 cells were stably transfected after precipitation with calcium of serial vectors (pUWG) carrying the neomycin resistance gene together with mutant-Beaf gene as compared to WT. G418 resistant colonies were taken after about 10 days under selection and then grown under normal conditions.

value: wild type Beaf


title: N2 no enzymes


title: Mutrep1

data_processing:
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
HTseq (default parameters) was used for counting the RNASeq reads for each sample
DEGSeq package (Wang et al., 2010) was then used to identify differentially expressed genes (p-value<0.001)
Genome_build: Flybase release 5.41 GCA_000001625.2
Supplementary_files_format_and_content: abundance measurements tab-delimited text files

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,  Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma)  and 1% penicillin/streptomycin (GIBCO, Invitrogen).

extract_protocol:
S2 cells were frozen on dry ice, and RNA was harvested 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.
RNA libraries were prepared for sequencing using standard Illumina protocols TruSeq RNA sample prep v2 (PN # RS-122-2001 and RS-122-2002). 200 ng total RNA were used to generate sequencing libraries, no poly-A selection was performed.

treatment_protocol: S2 cells were stably transfected after precipitation with calcium of serial vectors (pUWG) carrying the neomycin resistance gene together with mutant-Beaf gene as compared to WT. G418 resistant colonies were taken after about 10 days under selection and then grown under normal conditions. For RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for beaf32 or ctcf  were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 5 days and cells were then harvested.

value: mutant Beaf


title: CP190-input

value: input


title: CP190-WT1


title: WTrep3


title: CP190-mut


title: Mutrep2


title: WTrep1


title: CTCF1

value: CTCF1 control


title: Mutrep3


title: WTrep2


title: CTCF2

value: CTCF1 KD


title: chipD4

status: Public on Jan 31 2014

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

data_processing:
Raw reads were mapped to mm9 with TopHat version 1.4.1
FPKM for each gene as expression value was assigned by cufflinks version 1.3.0
Cuffdiff was used to identify differentially expressed genes
ChIP-seq reads were aligned with SOAP version 2.20 to the mouse genome build mm9
findPeaks software of Homer was used to identify Oct6 binding peaks with 4 fold more normalized tags in experiment group than control
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, bed files includes the tag density

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs (R1 and R1/E) were maintained on feeders in standard medium. ESC serum-free neural differentiation and EB replating were performed as described previously (Watanabe et al, 2005)

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. For ChIP-Seq, cell lysates were clarified from sonicated nuclei and Oct6-DNA complexes were precipitated with antibody, then genomic DNA was recoveried and purified for subsequent library construction
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and inducible Oct6-overexpressing ESCs with Dox-treatment for 6 days

tag: time point

value: ESC neural differentiation day4

value: oct6 overexpressed ESC, ChIP


title: fbs_dox_d2

value: embryonic body day2

value: dox induce oct6 overexpression


title: fbs_dox_d6

value: embryonic body day6


title: fbs_dox_d4

value: embryonic body day4


title: N2 Terminator only

value: Starved L1 larvae

value: Terminator exonuclease


title: inputD4

value: oct6 overexpressed ESC, input


title: 3' scRNA-seq TFIIS mutant rep2


title: fbs_D6

value: control


title: fbs_D2


title: 5' scRNA-seq rep1


title: fbs_D4


title: Human_MeDIP

description: DNA IP against 5-Methylcytosine

value: blood


title: 3WT_RNA-Seq

city: Aurora

first: Lee

last: Niswander

state: Colorado

address: 12801 E. 17th Ave Bld RC1 South 12400

department: Pediatrics

institute: UC Denver Anschutz Medical Campus

data_processing:
The basecalling software was Illumina's Real-Time Analysis (RTA) version 1.12.  The HiSeq 2000 interface software was HiSeq Control Software (HCS) version 1.4.  The software/pipeline tool used to convert the qseq basecall files into fastq files was CASAVA v1.7.
reads were aligned to the MM9 mouse genome using Gsnap, allowing a mismatch of 4% and an indel cost of 2.0. Version 2012-07-20.
Bam files were converted to Bed files, then BedTools were used to create a count of the reads
Genome_build: mm9
Supplementary_files_format_and_content: LDHR_Norm all gene list.xls

extract_protocol:
Three somite matched E9.5 embryos were collected of both Baf155+/+ and Baf155Msp3/Msp3 alleles. Cranial tissue above the pharyngeal arches and otic vesicles was harvested and stored at -80°C until all samples were collected. RNA was isolated using the RNeasy mini kit from Qiagen (74106).
Libraries were according to the instructions using the Illumina TruSeq RNA Sample Preparation Kit V2 (RS-122-2001).

tag: strain background

value: Mixed C57BL/6J and 129/SvImJ

tag: genotype/variation

value: homozygous wildtype

tag: developmental stage

value: 19-21 somites, cranial tissue


title: 3Mut_RNA-Seq

value: NTD mutants with the BAF155^msp3 allele


title: 2Mut_RNA-Seq


title: 2WT_RNA-Seq


title: 1WT_RNA-Seq


title: VitE1

city: Gothenburg

first: Erik

last: Larsson

address: Medicinaregatan 9A

department: Medical Biochemistry

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment with tophat 1.3.3 to the UCSC mm9 assembly
Quantification of UCSC genes with htseq-count, using the intersection-strict option
Normalization of count values using DESeq 1.14.0
Genome_build: mm9
Supplementary_files_format_and_content: normalized_data.tsv: DESeq normalized expression values for all 30 samples

source_name: K-RAS-induced lung tumor

extract_protocol:
RNeasy Plus Mini RNA extraction kit (Qiagen).
TruSeq RNA Sample Preparation v2 kit (Illumina)

value: Vitamin E-treated

tag: animal no


title: VitE2


title: VitD2


title: VitB1


title: VitA2


title: VitC2


title: NacE1

value: NAC-treated


title: NacD2


title: VitB2


title: NacC2


title: NacC1


title: VitA1


title: NacE2


title: NacB2


title: NacB1


title: NacA2


title: 1Mut_RNA-Seq


title: CtrlE2

value: Untreated


title: 0.125% 180min rep1

city: Kgs. Lyngby

first: Gitte

middle: M.

last: Knudsen

state: Not applicable

address: Matematiktorvet, Bldg 301

department: Department of Systems Biology

institute: Technical University of Denmark

data_processing:
The RNA seq data was analyzed using the CLC genomics workbench software (CLC Aarhus, version 6.0). Quality and quantity of RNA sequence data was evaluated by the number of reads, GC%, PHRED-score, nucleotide contribution, quality distribution and enriched 5mers sequences. All reads were trimmed removing the 15 first nucleotides from the 5´end due to non-normal nucleotide distribution. Subsequently, reads were sorted according to their respective adaptor sequences and individually aligned to the reference genome. Reads Per Kilobase per Million (RPKM) was used as expression value.Quality control of the transcriptomic data was evaluated by use of hierarchal clustering and principal component analysis. The gene expression profiles of biological replicates were paired and compared between treated and control samples within the same time point. Baggerlys test was used to evaluate statistical significant gene expression differences with a statistical filter of fold changes above 2, P-value < 0.05 and false discovery rate (FDR) < 0.05
Genome_build: ASM19603v1 [L. monocytogenes EGD-e reference genome (NC_003210.1)]
Supplementary_files_format_and_content: xslx files including total gene reads, RPKM values etc. for each sample

organism: Listeria monocytogenes EGD

growth_protocol: An overnight L. monocytogenes EGD BHI (Brain Heart Infusion) culture was diluted 100-fold in prewarmed BHI and incubated at 37°C with 250 rpm. When the culture reached OD600nm ≈ 0.4, the culture was split into four, diluting the culture four times in prewarmed BHI and reincubated at 37°C with 250 rpm. At OD600nm ≈ 0.4, equal volumes of L. plantarum WHE 92 supernatant or MQ were added each flask to obtain final concentrations of 0% (MQ control), 0.125%, 0.1875% and PT 0.1875% supernatant. Samples for gene expression and bacterial counts were taken at time zero of supernatant addition, at 10 min, 60 min and 180 min with two independent biological replicates.

extract_protocol:
RNA samples were stabilized with RNAprotectTM (Qiagen 76506) and stored at – 80°C prior to RNA purification with RNeasy Mini Kit (Qiagen 74104) including DNase treatment with RNase free DNase (Qiagen 79254) according to the manufacturer’s instructions. Quantity and quality of the purified total RNA was evaluated by Nanodrop and Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit. Five µg total RNA from each sample was ethanol precipitated, dissolved in 15 ul RNase free water and used as input in MICROBExpressTM Kit (Ambion AM1905) to remove of 16S and 23S rRNA. mRNA samples were evaluated on Qubit RNA assay kit (Invitrogen Q32852) and on Agilent 2100 Bioanalyzer with the RNA 6000 Nano kit.
Libraries for RNA Seq were prepared using TruSeq RNA Sample preparation Kit v2 (set A: RS-122-2001 and set B: RS-122-2002) according to the manufactures protocol. In brief, cDNA was generated from mRNA, which had been fragmented to approximately 180 bp. Specific adaptors were ligated to each of the 20 samples. The library was validated by measuring quantity with Qubit dsDNA BR assay kit and quality with Agilent 2100 Bioanalyzer on DNA-1000 chip. Due to a peak at 1500 bp, an E-gel size select (Invitrogen G6610-02) was performed to isolate the cDNA sequences of 200-400 bp. Lastly, each library was normalized to 10 nM and pooled yielding a final concentration of 7.92 nM with an average base pair size of 290.

tag: protocol

value: 0.125% L. plantarum WHE 92 supernatant

tag: strain

value: EGD


title: VitD1


title: VitC1


title: 0.1875% 180min rep2

value: 0.1875% L. plantarum WHE 92 supernatant


title: CtrlE1


title: 0.125% 180min rep2


title: CtrlD2


title: MQ 180min rep2

source_name: MQ 180min rep2

value: MQ water


title: CtrlC2


title: NacD1


title: CtrlC1


title: CtrlB1


title: CtrlB2


title: CtrlD1


title: PT 0.1875% 60min rep1

value: 0.1875% L. plantarum WHE 92 supernatant pretreated with 1 mg/ml Proteinase K


title: 0.125% 60min rep2


title: 0.1875% 60min rep1


title: CtrlA2


title: MQ 60min rep2

source_name: MQ 60min rep2


title: PT 0.1875% 60min rep2


title: MQ 60min rep1

source_name: MQ 60min rep1


title: 0.1875% 10min rep2


title: MQ 10min rep2

source_name: MQ 10min rep2


title: NacA1


title: 0.1875% 10min rep1


title: MQ 10min rep1

source_name: MQ 10min rep1


title: 0.1875% 180min rep1


title: MQ 180min rep1

source_name: MQ 180min rep1


title: CtrlA1


title: 0.125% 60min rep1


title: 0.1875% 60min rep2


title: MQ 0h rep2

source_name: MQ 0h rep2


title: MQ 0h rep1

source_name: MQ 0h rep1


title: nanoCAGE of early promyelocytes 1

city: Copenhagen

first: Johannes

middle: Eichler

last: Waage

address: Ole Maaløesvej 5

department: Biotech Research and Innovation Center

institute: University Of Copenhagen

description: nanoCAGE (cap analysis of gene expression with low input material)

data_processing:
Mapping: Bowtie, v 0.12.8, default parameters
Clustering of neighbouring tags
Genome_build: hg19
Supplementary_files_format_and_content: BED-files containing TSS tag clusters for each sample

source_name: Bone marrow, early promyelocytes

extract_protocol:
BM was aspirated from the posterior iliac crest of healthy donors and patients. Cellular fractions containing mononuclear cells (MNCs) and polymorphonuclear neutrophils (PMNs, only healthy subjects) were purified as described previously. (Helena Mora-Jensen). MNC fractions from APL patients were cryopreserved and stored in liquid nitrogen.BM populations representing successive stages of terminal neutrophil differentiation were prospectively purified by cell-sorting of MNC/PMN fractions stained with cocktail of fluorochrome-conjugated MoAbs as described previously by our group.(Helena-Mora Jensen)   BM populations representing early developmental stages of the hematopoietic hierarchy including hematopoietic stem cells (HSCs), mulitpotent progenitors (MPPs), common myeloid progenitors (CMPs), granulocyte-monocyte progenitors (GMPs), and megakaryocyte-erythroid progenitors (MEPs) were purified by cell sorting of MNC fractions from healthy subjects. Likewise GMP-like blast populations were purified from thawed MNC fractions of APL patients by flow cytometry based cell sorting essentially as described previously. (Manz et al. 2002,  Majeti et al.)
nanoCAGE was performed as described in Salimullah et al,CSH Prot., 2012, with 50 ng total RNA for all samples.

value: early promyelocytes

value: Bone Marrow, Iliac Crest


title: nanoCAGE of purified leukemic blasts 1

source_name: Bone marrow, leukemic blasts

value: leukemic blasts


title: telogen-sample

city: Yangling

first: xiaolong

last: wang

address: Xinong Rd 22

institute: NWAFU

data_processing:
Illumina Casava1.7 software used for base-calling
After getting rid of low quality reads and removing reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, reads with poly (A), reads shorter than 18 nt, the clean reads were obtained.
The clean reads were mapped to the goat genome (http://goat.kiz.ac.cn/GGD/download.htm) by SOAP v1.11 to analyse their expression and distribution in the genome.
Genome_build: Goat genome V1.0 (2012-08-19)
Genome_build:GCA_000317765.1

organism: Capra hircus

source_name: telogen

extract_protocol:
Approximately 1-cm2 skin samples were harvested for distinct hair cycle stages (anagen, catagen and telogen) of the Shanbei White cashmere goat and immediately frozen in liquid nitrogen. Total RNA from the mixed skin tissues of ten adult goats was isolated using the RNAiso plus kit (TaKaRa, Dalian, China) according to the manufacturer’s protocol.The sRNA libraries were constructed for the skin tissue from the anagen, catagen and telogen stages, and were sequenced using an Illumina/Solexa Genome Analyzer at the Beijing  Genomics Institute (BGI), Shenzhen.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: cashmere goat

value: skin

value: telogen


title: nanoCAGE of early promyelocytes 2


title: anagen-sample

source_name: anagen

value: anagen


title: catagen-sample

source_name: catagen

value: catagen


title: RPMI-8402_ZFX_ChIPSeq

status: Public on Jan 30 2014

city: New York

first: Stuart

last: Weisberg

state: NY

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIPSeq reads were aligned to the human hg19 genome using the short read aligner Bowtie (2.0.0)
Significantly enriched ChIP regions were identified using the Model-based analysis of ChIP-Seq (MACS) (1.4.0) using input chromatin as controls
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated by MACS. The 5th column of MACS-generated bed files is the -10*log10pvalue of peak region.

growth_protocol: Cells were maintained in RPMI 1640 with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and ZFX-DNA complexes were isolated with antibody.
Library construction and sequencing were performed at the Yale Center for Genome Analysis. Briefly, magnetic AMPure XP beads (Beckman Coulter) are used to purify the user-sheared DNA samples and remain with the sample throughout library construction.  Following each process step, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution.  Following fragmentation, T4 DNA polymerase and T4 polynucleotide kinase blunt end and phosphorylate the fragments.  The large Klenow fragment then adds a single adenine residue to the 3' end of each fragment and custom adapters (IDT) are ligated using T4 DNA ligase.  The inserts are size-selected in-solution and adapter-ligated DNA fragments are then PCR amplified using custom-made primers (IDT).  During PCR, a unique 6 base index is inserted at one end of each DNA fragment. Samples were sequenced on a single-end version 3 Illumina flow cell on a HiSeq 2000

value: T-lymphoblastic leukemia (T-ALL)


title: NOMO-1_Input

value: Acute myeloid leukemia (AML)


title: NOMO-1_ZFX_ChIPSeq


title: Dre_155_4hpf_RPF

status: Public on Jan 29 2014

city: Cambridge

first: Stephen

last: Eichhorn

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
cytoplasmically-enriched RNA
processed data file: Dre_155_4hpf.txt

data_processing:
Raw read files were stripped of adaptor and mapped to the appropriate species' genome and/or transcriptome.
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value. Poly(A)-tail length measurements were generated using PAL-seq tags that mapped within the 3' UTR of an annotated gene.
Genome_build: Human: hg18; Mouse: mm9; Zebrafish: danRer7; Drosophila: dm3; Arabidopsis: tair10; S. cerevisiae: sacCer3; S. pombe: Spombe1; Xenopus: Unigene
Supplementary_files_format_and_content: One set of processed data files contains abundance and poly(A)-tail length measurements for each gene. Another set contains raw fluorescence intensities for each base for each cycle of sequencing-by-synthesis and streptavidin flow-in for each sequencing cluster. Another set contains normalized streptavidin fluorescence intensities for each sequencing cluster.

molecule: cytoplasmic RNA

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: Each sample was grown or maintained in accordance with standard protocols.

extract_protocol: Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)

treatment_protocol: RNA-seq: Cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation. Ribosome profiling: Cell extracts were processed as described in Subtelny et al., 2014 (GSE52809).                                 PAL-seq: Polyadenylated ends in total RNA were ligated to a biotinylated adaptor, then partially digested with RNase T1. The resulting fragments were size-selected (104-750 nt), captured on streptavidin beads, and used for library preparation.

value: AB

value: 4 hours post-fertilization


title: Dre_mock_4hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_mock_4hpf.txt


title: Dre_155_2hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_155_2hpf.txt

value: 2 hours post-fertilization


title: RPMI-8402_Input


title: Dre_132_6hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_132_6hpf.txt

value: 6 hours post-fertilization


title: Dre_155_6hpf_RNA

description:
cytoplasmically-enriched RNA
processed data file: Dre_155_6hpf.txt


title: Dre_132_2hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_132_2hpf.txt


title: Dre_mock_6hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_mock_6hpf.txt


title: Dre_132_4hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_132_4hpf.txt


title: Dre_mock_2hpf_RPF

description:
cytoplasmically-enriched RNA
processed data file: Dre_mock_2hpf.txt


title: Dre_mock_6hpf_RNA


title: Dre_132_6hpf_RNA


title: Dre_132_4hpf_RNA


title: Dre_155_4hpf_RNA


title: Dre_mock_4hpf_RNA


title: M9081

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Sequenced reads were aligned to the reference genome NCBI build 37 using TopHat version 1.3.3. We only used mapped reads with less than 3 mismatches.
We used the genes annotated in RefSeq to quantify gene expression levels. The expression level of each exon was obtained by counting the number of reads mapped to that exon and the expression of a gene is the sum of read counts of all exons in a gene.  Reads mapped to multiple exons in a gene were counted only once.
The gene or exon level expression was normalized to the number of reads per kilobase per million mapped reads (RPKM)
Genome_build: NCBI build 37
Supplementary_files_format_and_content: RPKM data matrix

extract_protocol:
RNA was prepared from the frozen biopsies using the Qiagen Allprep kit. Skin punch biopsies were trimmed of visible subcutaneous fat and visible blood was removed by blotting on saline-soaked gauze.  Biopsies were then snap frozen in liquid nitrogen and stored at -80 deg C.  For RNA isolation, frozen skin biopsy samples were wrapped in an aluminum foil pouch pre-frozen in liquid nitrogen, placed in a prechilled steel mortar, and crushed with a hammer. The pulverized frozen tissue was quickly transferred into a 1.5-ml microcentrifuge containing 1 ml of the Allprep buffer and glass grinding beads. The tube was vigorously agitated on a Vortex mixer for 5 minutes to complete the extraction process. From this point on the sample was processed exactly as described in the kit manual. RNA quality and quantity were checked using an Agilent Bioanalyzer.
Libraries for high throughput sequencing were prepared using the Illumina mRNA-Seq kit. Briefly, the process involved isolating polyadenylated RNA, fragmentation by heating at 90°C, random-primed cDNA preparation, ligation of adaptors, and size selection on an agarose gel. A gel slice corresponding to approximately 120 bp insert was isolated, and the DNA was extracted and amplified by 15 cycles of PCR using the adaptor primers. The gel purified final product was checked for quality and quantity on an Agilent Bioanalyzer. The library thus prepared was sequenced one sample per lane in an 8-lane flow cell on the Illumina Genome Analyzer IIx. The raw sequencing output of the 80-base single read sequencing was 2000-3000 Mb per lane corresponding to 25-37.5 million reads.

tag: tissue type

value: lesional psoriatic skin


title: Dre_155_2hpf_RNA


title: Dre_mock_2hpf_RNA


title: M9027

value: normal skin


title: Dre_132_2hpf_RNA


title: Drosophila_PAL_only

description:
PAL-Seq
processed data file: Drosophila.txt
processed data file: Drosophila_PAL_norm_intensities.txt.gz
processed data file: Drosophila_PAL_raw_intensities.txt.gz

source_name: Drosophila melanogaster S2 cells


title: Dre_155_6hpf_RPF


title: M9004


title: M9000


title: M9049


title: M8979


title: M8846


title: M8882


title: M8825


title: M8719


title: M8704


title: M8659


title: M8900


title: M8815


title: nanoCAGE of purified leukemic blasts 2

tag: tissue


title: M8755


title: M8771


title: M8654


title: M8698


title: M8639


title: M8702


title: M8646


title: M9132


title: M8561


title: M856


title: M8610


title: M8530


title: M8554


title: M8868


title: M8883


title: M8487


title: M8485


title: M8492


title: M8483


title: M8490


title: M8481


title: M8470


title: M8424


title: M8376


title: M8298


title: M7912


title: M7972


title: M8282


title: M8280


title: M8221


title: M7834


title: M8065


title: M7838


title: M7825


title: M7786


title: M7874


title: M7832


title: M7807


title: M7768


title: M7772


title: M777


title: M7748


title: M7747


title: M7749


title: M7767


title: M7741


title: M7743


title: M7742


title: M7730


title: M7731


title: M7715


title: M7714


title: M7702


title: M7711


title: M7704


title: M7710


title: M7682


title: M7684


title: M7701


title: M7785


title: M7670


title: M7663


title: M7664


title: M7744


title: M7647


title: M7651


title: M7669


title: M7605


title: M7642


title: M7473


title: M7588


title: M7600


title: M7252


title: M7204


title: M7264


title: M7450


title: M7305


title: M6953


title: M7003


title: M6861


title: M7168


title: M7685


title: M6844


title: M6782


title: M6690


title: M6390


title: M6346


title: M6245


title: M6153


title: M6171


title: M9003


title: M5936


title: M5904


title: M5917


title: M5766


title: M5742


title: M582


title: M5883


title: M5849


title: M5441


title: M5414


title: M5324


title: M5286


title: M5305


title: M5611


title: M5592


title: M5258


title: M5223


title: M5243


title: M6794


title: M6708


title: M5247


title: M5177


title: M5146


title: Xla_st9_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Xla_st9.txt
processed data file: Xla_st9_PAL_norm_intensities.txt.gz
processed data file: Xla_st9_PAL_raw_intensities.txt.gz

organism: Xenopus laevis

source_name: xenopus laevis embryo

value: stage 9


title: Xla_st3_4_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Xla_st3_4.txt
processed data file: Xla_st3_4_PAL_norm_intensities.txt.gz
processed data file: Xla_st3_4_PAL_raw_intensities.txt.gz

value: stage 3-4


title: M5144


title: M5130


title: M5142


title: M5478


title: M5385


title: Pombe_RNA

description:
cytoplasmically-enriched RNA
processed data file: Pombe.txt

organism: Schizosaccharomyces pombe

source_name: schizosaccharomyces pombe cells


title: Pombe_RPF


title: M5079


title: M5063


title: M4977


title: M4981


title: M5030


title: M5219


title: M4874


title: Xla_st12_12.5_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Xla_st12_12.5.txt
processed data file: Xla_st12_12.5_PAL_norm_intensities.txt.gz
processed data file: Xla_st12_12.5_PAL_raw_intensities.txt.gz


title: M4708


title: M4787


title: M4934


title: M4701


title: M4649


title: M4616


title: M4459


title: M4545


title: M4532


title: M4505


title: M4390


title: M4397


title: M4389


title: M4379


title: M4356


title: M4368


title: M4344


title: M4334


title: M4689


title: M4298


title: M4294


title: M4284


title: M4999


title: M4271


title: M4257


title: Xla_st12_12.5_RPF

description:
cytoplasmically-enriched RNA
processed data file: Xla_st12_12.5.txt


title: M4277


title: M3978


title: Xla_st9_RNA

description:
cytoplasmically-enriched RNA
processed data file: Xla_st9.txt


title: Xla_st12_12.5_RNA


title: M4288


title: M4310


title: M3171


title: Xla_st3_4_RNA

description:
cytoplasmically-enriched RNA
processed data file: Xla_st3_4.txt


title: Xla_st9_RPF


title: 3T3_polysome_profile_7.5_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_7.5_ribosomes.txt
processed data file: 3T3_polysome_profile_7.5_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_7.5_PAL_raw_intensities.txt.gz

source_name: 3T3 cells

tag: cell line


title: 3T3_polysome_profile_11_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_11_ribosomes.txt
processed data file: 3T3_polysome_profile_11_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_11_PAL_raw_intensities.txt.gz


title: CASP1234


title: M3418


title: 3T3_RPF

description:
cytoplasmically-enriched RNA
processed data file: 3T3.txt


title: 3T3_polysome_profile_5.5_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_5.5_ribosomes.txt
processed data file: 3T3_polysome_profile_5.5_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_5.5_PAL_raw_intensities.txt.gz


title: M3059


title: Liver_RPF

description:
cytoplasmically-enriched RNA
processed data file: Liver.txt

source_name: mouse liver

value: 6 week

tag: Sex

value: Male


title: 3T3_RNA


title: 3T3_polysome_profile_3_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_3_ribosomes.txt
processed data file: 3T3_polysome_profile_3_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_3_PAL_raw_intensities.txt.gz


title: M4208


title: 3T3_polysome_profile_4_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_4_ribosomes.txt
processed data file: 3T3_polysome_profile_4_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_4_PAL_raw_intensities.txt.gz


title: 3T3_polysome_profile_0_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_0_ribosomes.txt
processed data file: 3T3_polysome_profile_0_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_0_PAL_raw_intensities.txt.gz


title: Liver_RNA


title: 3T3_polysome_profile_2_ribosomes_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_2_ribosomes.txt
processed data file: 3T3_polysome_profile_2_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_2_PAL_raw_intensities.txt.gz


title: 3T3_contact_inhibited_1_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_contact_inhibited_1.txt
processed data file: 3T3_contact_inhibited_1_PAL_norm_intensities.txt.gz
processed data file: 3T3_contact_inhibited_1_PAL_raw_intensities.txt.gz


title: 3T3_polysome_profile_1_ribosome_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_polysome_profile_1_ribosome.txt
processed data file: 3T3_polysome_profile_1_PAL_norm_intensities.txt.gz
processed data file: 3T3_polysome_profile_1_PAL_raw_intensities.txt.gz


title: HeLa_total_PAL_only

description:
PAL-Seq
processed data file: HeLa_total.txt
processed data file: HeLa_total_PAL_norm_intensities.txt.gz
processed data file: HeLa_total_PAL_raw_intensities.txt.gz

source_name: HeLa cells

value: HeLa


title: 3T3_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3.txt
processed data file: 3T3_PAL_norm_intensities.txt.gz
processed data file: 3T3_PAL_raw_intensities.txt.gz


title: Hek293T_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: HEK293T.txt
processed data file: Hek293T_PAL_norm_intensities.txt.gz
processed data file: Hek293T_PAL_raw_intensities.txt.gz

source_name: HEK293T cells


title: Xla_st3_4_RPF


title: Cerevisiae_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Cerevisiae.txt
processed data file: Cerevisiae_PAL_norm_intensities.txt.gz
processed data file: Cerevisiae_PAL_raw_intensities.txt.gz

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae cells


title: Cerevisiae_total_PAL

description:
PAL-Seq
processed data file: Cerevisiae_total.txt
processed data file: Cerevisiae_total_PAL_norm_intensities.txt.gz
processed data file: Cerevisiae_total_PAL_raw_intensities.txt.gz


title: Liver_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Liver.txt
processed data file: Liver_PAL_norm_intensities.txt.gz
processed data file: Liver_PAL_raw_intensities.txt.gz


title: 13293-100mers-GM12878-247_pool_split

city: Pasadena

first: Diane

middle: E

last: Trout

address: 1200 E California Blvd M/C 156-29

institute: California Institute of Technology

data_processing: Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Reads of length 100 bp were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequence.   Reads were mapped using TopHat 1.4.1 and the GENCODE V13 annotation (using the "--GTF" option in TopHat). Quantification was carried out using Cufflinks 2.0.2

extract_protocol: Single GM12878 cells were picked from a culture dish using a micropipet.  They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument.

tag: labexpid


title: 13294-100mers-GM12878-248_pool_split (superseded by GSE78432)

description:
****************************
GSM1299393 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 13297-100mers-GM12878-251_pool_split (superseded by GSE78432)

description:
****************************
GSM1299396 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 13292-100mers-GM12878-246_pool_split (superseded by GSE78432)

description:
****************************
GSM1299391 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 13296-100mers-GM12878-250_pool_split (superseded by GSE78432)

description:
****************************
GSM1299395 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 13280-100mers-GM12878-232_pool_split (superseded by GSE78432)

description:
****************************
GSM1299389 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 13295-100mers-GM12878-249_pool_split (superseded by GSE78432)

description:
****************************
GSM1299394 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 13273-100mers-GM12878-226_pool_split_10


title: 13299-100mers-GM12878-253_pool_split (superseded by GSE78432)

description:
****************************
GSM1299398 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: Arabidopsis_PAL_only

description:
PAL-Seq
processed data file: Arabidopsis.txt
processed data file: Arabidopsis_PAL_norm_intensities.txt.gz
processed data file: Arabidopsis_PAL_raw_intensities.txt.gz

source_name: arabidopsis thaliana leaves

tag: ecotype

value: Columbia


title: 13271-100mers-GM12878-220_pool_split_4


title: 13272-100mers-GM12878-225_pool_split_9


title: 13270-100mers-GM12878-219_pool_split_3


title: 13269-100mers-GM12878-218_pool_split_2


title: 13281-100mers-GM12878-233_pool_split (superseded by GSE78432)

description:
****************************
GSM1299390 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: HeLa_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: HeLa.txt
processed data file: HeLa_PAL_norm_intensities.txt.gz
processed data file: HeLa_PAL_raw_intensities.txt.gz


title: 12823-100mers-GM12878_pool_split_7


title: 13268-100mers-GM12878-217_pool_split_1


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Right Atrium Tissue; renlab.H3K36me3.STL003RA.02.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Right Atrium Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18856
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: Right Atrium tissue; renlab.H3K36me3.STL003RA.02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sra sample accession

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Right Atrium

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: 12824-100mers-GM12878_pool_split_8


title: Hek293T_RPF

description:
cytoplasmically-enriched RNA
processed data file: HEK293T.txt


title: 3T3_contact_inhibited_2_PAL_only

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: 3T3_contact_inhibited_2.txt
processed data file: 3T3_contact_inhibited_2_PAL_norm_intensities.txt.gz
processed data file: 3T3_contact_inhibited_2_PAL_raw_intensities.txt.gz


title: Hek293T_RNA


title: 13298-100mers-GM12878-252_pool_split (superseded by GSE78432)

description:
****************************
GSM1299397 record metadata submitted on Dec 30 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78432
****************************


title: 12821-100mers-GM12878_pool_split_5


title: Dre_132_6hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_132_6hpf.txt
processed data file: Dre_132_6hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_132_6hpf_PAL_raw_intensities.txt.gz

value: AB

value: 6 hours post-fertilization


title: Dre_mock_6hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_mock_6hpf.txt
processed data file: Dre_mock_6hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_mock_6hpf_PAL_raw_intensities.txt.gz


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Liver Tissue; renlab.H3K27me3.STL011LI.01.01

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY835
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17517
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

tag: sample alias

value: coronary artery disease

value: Liver

value: coronary artery disease. No history of hypertension or diabetes.

value: Male

value: Histone H3K27me3

value: Active Motif


title: Dre_132_2hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_132_2hpf.txt
processed data file: Dre_132_2hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_132_2hpf_PAL_raw_intensities.txt.gz

value: 2 hours post-fertilization


title: Dre_155_2hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_155_2hpf.txt
processed data file: Dre_155_2hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_155_2hpf_PAL_raw_intensities.txt.gz


title: Dre_155_4hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_155_4hpf.txt
processed data file: Dre_155_4hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_155_4hpf_PAL_raw_intensities.txt.gz

value: 4 hours post-fertilization


title: Dre_132_4hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_132_4hpf.txt
processed data file: Dre_132_4hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_132_4hpf_PAL_raw_intensities.txt.gz


title: Pombe_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Pombe.txt
processed data file: Pombe_PAL_norm_intensities.txt.gz
processed data file: Pombe_PAL_raw_intensities.txt.gz


title: Dre_mock_4hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_mock_4hpf.txt
processed data file: Dre_mock_4hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_mock_4hpf_PAL_raw_intensities.txt.gz


title: Dre_mock_2hpf_PAL

description:
PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_mock_2hpf.txt
processed data file: Dre_mock_2hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_mock_2hpf_PAL_raw_intensities.txt.gz


title: 12822-100mers-GM12878_pool_split_6


title: HFSC_Sox9 cKO_RNA-Seq_2

status: Public on Jan 28 2014

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

description:
processed data file: FPKM_RNA_seq_KO_experiments_mm9.txt
Sox9 Knock out replicate 2

data_processing:
ChiP Seq: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program. Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification using software MACS. ChIP-Seq Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm;
RNA-seq:Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the tophat program using tophat2 with default parameters. Transcripts abundance was estimated by cufflinks 1.0.3.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from RNAseq experiement. Bed files lists coordinates of peaks called from ChiP-seq experiment

source_name: HFSC_Sox9 cKO_RNA-Seq

growth_protocol: HFSCs were FACS-purifed from the telogen back skins of indicated ages of mice

extract_protocol: ChIP-Seq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). RNA-Seq: Illumina TruSeq™ RNA kit (Catalog # RS-930-20 01)

treatment_protocol: ChIP-Seq: No treatment;  RNA-Seq: RU486-treatment to activate CrePGR, males P48-P61, females P53-P66

value: C57BL6, mixed

value: Sox9 Knock out

tag: gender

value: female

tag: age

value: back skins

tag: sorting markers

value: integrin α6hi and CD34+  and ScaI- and YFP+

tag: cell type

value: hair follicle stem cells (HFSCs)


title: HFSC_Sox9 cKO_RNA-Seq_1

description:
processed data file: FPKM_RNA_seq_KO_experiments_mm9.txt
Sox9 Knock out replicate 1

tag: strain background

tag: genotype/variation

value: male


title: HFSC_Sox9 Het_RNA-Seq_1

description:
processed data file: FPKM_RNA_seq_KO_experiments_mm9.txt
Control replicate 1

source_name: HFSC_Sox9 Het_RNA-Seq

value: wild type (control)