title: shLuc.rep2

description: biological replicate 2 (shLuc control)

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw data was filtered to retain only read pairs for which both mates have average base quality score >20.
Reads were mapped against hg19 reference genome with Bowtie (v0.12.8) with the following parameters:  -m 1 --best --strata --chunkmbs 1024 -I 0 -X 1000
Multiple sequencing lanes from the same library were merged with MergeSamFiles.jar from the Picard suite (v1.86).
Duplicate mapped read pairs were removed with MarkDuplicates.jar from the Picard suite (v1.86).
Mapped data filtered to retain only fragments of size 120-180 bases.
Replicate samples were merged with MergeSamFiles.jar from the Picard suite (v1.86).
Each fragment was converted to a single point at the fragment midpoint.
Mapped (midpoint) data converted to bedGraph format.
Genome_build: hg19
Supplementary_files_format_and_content: Genomic distribution of midpoint of fragments storted as bedGraph files (generated via BEDtools v2.17.0).

source_name: MCF-7 cells

extract_protocol:
Nuclei was prepared from 5x105 cells and digested with MNase (1.25, 2.5, or 5 units) for 5 min at 37 °C. Mononucleosomal DNA were collected and pooled.
Library was constructed from 1ug of pooled mononucleosomeal DNA using TruSeq DNA Sample Preparation Kit.

value: shLuc


title: shMBD3.rep1

status: Public on Oct 31 2013

type: SRA

city: RTP

first: Takashi

last: Shimbo

address: 111 TW Alexander Dr.

country: USA

institute: NIH/NIEHS

description: biological replicate 1 (shMBD3)

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: genotype


title: Adelman_Dmel_S2_Rrp40-dep+FP_3prRNA

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: short capped RNA isolated from Drosophila S2 nuclei

library_source: transcriptomic

data_processing:
26 nt scRNA reads were aligned to the Drosophila dm3 genome with Bowtie, requiring unique alignment and allowing 2 mismatches (-m1 -v2).
The genomic location and strand of mapped reads were compiled using custom scripts and visually examined using the UCSC genome browser in .bedgraph format. RNA sequences came from discrete locations and were not binned for further analyses, allowing the hits to be examined at nucleotide resolution.
Normalization: to account for differential sequencing depth, all samples were normalized to 15 million reads. To enable accurate cross-sample comparisons of short capped RNA data sets, the following procedures were implemented. Seventeen synthetic short-capped RNA spikes (length 48-54 nt) were designed to align to non-TSS regions of the Drosophila genome that were systematically devoid of scRNA reads. RNAs were generated by in vitro reverse-transcription and capping. Each spike was added individually to each sample at the Trizol extraction stage at a constant ratio of either 1 or 10 spikes per genome (as determined by cellular or nuclear DNA yield). Counts for each spike scRNA were determined by summing the number of reads aligned in 100-nt strand-specific bins surrounding the genomic sequence complementary to the spike. Cross-sample comparisons were performed by calculating the ratio (aligned read count spiken sample 1)/(aligned read count spiken sample 2) for each of the 17 spikes. The spike normalization factor was calculated as the median of these ratios. For all scRNA samples except flavopiridol-treated samples, the spike normalization factor was ~1 and no spike-based normalization was performed. For three flavopiridol treatment experiments, the spike normalization factor ranged from ~0.6 to ~0.7, reflecting an increase in scRNA species in response to flavopiridol and a corresponding decrease in spike recovery. Flavopiridol-treated samples were normalized by dividing read counts by the respective normalization factors derived from median spike abundance.
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files with unbinned normalized counts representing 3' ends of uniquely aligned scRNAs.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila S2 Cells short capped RNA

growth_protocol: Drosophila S2 cells from the DGRC were grown in M3 media supplemented with bactopeptone, yeast extract and 10% FBS. For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.

extract_protocol:
Total RNA was extracted from nuclei, whole cells, or fractionated cells as indicated using Trizol reagent (Invitrogen).
Liibraries were prepared for 3’ scRNA-sequencing as described in (Nechaev et al., Science 2010).

treatment_protocol: RNAi was performed as described previously (Gilchrist et al. Genes Dev 2008). Cells were harvested 72 hours after addition of dsRNA. To block P-TEFb-mediated pause release, cells were treated with 500 nM Flavopiridol (Sigma) or DMSO vehicle for 10 minutes.

tag: cell line


title: Adelman_Dmel_S2_soluble_3prRNA

description: short capped RNA isolated from soluble fraction of Drosophila S2 cells

treatment_protocol: Cell fractionation was performed as described previously {Wysocka et al., Mol Cell Biol 2001) with modifications. In brief, approximately 5x107 Drosophila S2 cells were collected by centrifugation and, after washing with ice-cold 1xPBS, were lysed in 1 ml of Buffer A (10 mM HEPES [pH 7.9], 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1 mM dithiothreitol, 0.1% Triton-X-100 and Superase-in RNAse inhibitor (Ambion)) by incubating for 10 minutes on ice followed by a 5-minute spin at 1500 g. The pellet was resuspended in 1 ml of buffer B (3 mM EDTA, 0.2 mM EGTA, 1 mM dithiothreitol, Superase-in RNAse inhibitor), processed as above and resuspended in 1 ml buffer B to generate the chromatin fraction. Samples analyzed by scRNA-seq were: whole cells in Buffer A, the two combined supernatants representing the detergent-soluble fraction, and the chromatin-associated pellet, using a uniform cell equivalent portion of each fraction.


title: Adelman_Dmel_S2_chromatin_3prRNA

description: short capped RNA isolated from chromatin fraction of Drosophila S2 cells


title: Adelman_Dmel_S2_cells_3prRNA

description: short capped RNA isolated from intact Drosophila S2 cells


title: Adelman_Dmel_S2_Rrp40-dep__3prRNA

treatment_protocol: RNAi was performed as described previously (Gilchrist et al. Genes Dev 2008). Cells were harvested 72 hours after addition of dsRNA.


title: Adelman_Dmel_S2_FP__3prRNA

treatment_protocol: To block P-TEFb-mediated pause release, cells were treated with 500 nM Flavopiridol (Sigma) or DMSO vehicle for 10 minutes.


title: Adelman_Dmel_S2_Mock-tr__3prRNA


title: Day 12 non-pregnant control, biological replicate 3

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description:
D12C_007
Pool of RNAs from endometrial tissue samples collected from the distal, medial and proximal part of one uterine horn

data_processing:
Basecalls performed using CASAVA version 1.6
Trimming: 3' ends were trimmed using Galaxy FASTQ Quality Trimmer, window size: 5, step size: 1, maximum number of bases to exclude from the window during aggregation: 0, aggregate action for window: min. score, trim until aggregate score is: >=30
Trimmed sequences were filtered according to a minimal length of 30 bp with Galaxy Filter FASTQ
Mapping to genome assembly Sscrofa10.2 with Tophat 1.4, tophat parameters provided in the 'data_processing_parameters.txt' file.
Cuffmerge for generation of a GTF file for transcript annotation
RPKM calculator; calculates RPKM (reads per kilobase per exon model) and number of reads mapped for each gene/transcript from a BAM file based on a given GTF annotation file. GTF from Cuffmerge was used as annotation file. Read counts were subsequently used for statistical analysis with DESeq.
Genome_build: Sscrofa10.2/susScr3
Supplementary_files_format_and_content: txt files, containing columns for transcript consensus ID, Entrez Gene ID, original transcript ID (Refseq ID or Cufflinks ID), nearest Refseq ID, number of mapped reads

organism: Sus scrofa

source_name: non-pregnant control_endometrial tissue

growth_protocol: Prepuberal gilts (crossbreeds of German Landrace and Piétrain) obtained a single injection of 750 IU PMSG (Intergonan®, MSD Animal Health Innovation GmbH, Schwabenheim, Germany) and 72 h later 750 IU hCG (Ovogest®, MSD Animal Health Innovation GmbH) to synchronize ovulation. Gilts of the “pregnant” group were inseminated twice (24 h and 36 h after hCG) with a standard dose of German Landrace semen whereas gilts of the “non-pregnant” control group were inseminated with the supernatant of centrifuged (10 min, 3,000 rpm) semen of the same boar. Gilts were slaughtered on day 12 after insemination.

extract_protocol:
Total RNA was isolated from endometrium using TRIzol® (Invitrogen, Carlsbad, CA, USA) according to the manufacturers recommendations. Purity (based on 260nm:280nm and 260nm:230nm ratios) and quantity of the obtained total RNA was measured by use of a NanoDrop ND-1000 (PEQLAB Biotechnologie GmbH, Erlangen, Germany). Integrity of the RNA was assessed by analysis on Agilent RNA Nano 6000 microfluidic chips with an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). RNA integrity numbers (RIN) of individual samples ranged from 7.9 to 9.5.
Equal amounts of total RNA from samples derived from proximal, medial and distal endometrial sections of one uterine horn were pooled for each animal. The mRNA-Seq sample preparation kit (Illumina, San Diego, USA) was used for preparation of RNA-Seq libraries. Library preparation followed the manufacturers instructions. Briefly, poly(A)-containing RNA was purified with oligo-dT-coated magnetic beads starting from 5 µg total RNA and fragmented under elevated temperature using divalent cations. The obtained cleaved RNA fragments were reverse transcribed to first strand cDNA using Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany) and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments underwent an end-repair process with T4 DNA polymerase, Klenow DNA polymerase and T4 Polynucleotide kinase, addition of a single ´A´-base, and ligation of adapters. Ligation products were subsequently separated on a 2% agarose gel (Biozym Phor Agarose, Biozym Scientific GmbH, Hess. Oldendorf, Germany) and a gel slice was cut out (X-Tracta, Biozym Scientific GmbH) in the 200 bp (±25 bp) range. After isolation of the DNA from the gel slice (QIAquick Gel Extraction Kit, Qiagen, Hilden, Germany), cDNA fragments were amplified through 15 cycles of PCR (Phusion DNA polymerase, New England Biolabs GmbH, Frankfurt a. Main, Germany) to generate the final sequencing libraries. Concentration of the cDNA fragments was estimated on an Agilent DNA 1000 chip (Agilent Technologies) and with the Qubit Fluorometer (Invitrogen).

treatment_protocol: The uteri were removed and each uterine horn was subsequently flushed first with 10 ml and a second time with 50 ml PBS buffer to collect conceptuses and uterine fluid. After flushing, uterine horns were opened longitudinally at the anti-mesometrial side. In pregnant and non-pregnant gilts, samples of the endometrium (containing the lamina epithelialis, lamina propria and tela submucosa, but not tunica muscularis) were taken from three locations of each uterine horn, proximal (the end, close to the ovaries), medial, and distal (next to the corpus uteri). Tissue samples for isolation of RNA were immediately transferred to RNAlater™ (Ambion, Huntingdon, Cambridgeshire, UK), incubated overnight at 4°C and stored at -80°C until further use.

tag: gender

value: female

tag: Stage

value: Day 12 of estrous cycle

tag: organ/tissue

value: uterus/endometrium


title: Day 12 pregnant, biological replicate 1

description:
D12P_003
Pool of RNAs from endometrial tissue samples collected from implantation zones located in the distal, medial and proximal part of one uterine horn

source_name: pregnant_endometrial tissue

value: Day 12 of pregnancy


title: Day 12 pregnant, biological replicate 3

description:
D12P_010
Pool of RNAs from endometrial tissue samples collected from implantation zones located in the distal, medial and proximal part of one uterine horn


title: Day 12 pregnant, biological replicate 4

description:
D12P_012
Pool of RNAs from endometrial tissue samples collected from implantation zones located in the distal, medial and proximal part of one uterine horn


title: Day 12 pregnant, biological replicate 2

description:
D12P_008
Pool of RNAs from endometrial tissue samples collected from implantation zones located in the distal, medial and proximal part of one uterine horn


title: nascentRNA_ICRF_(20130118_8_4)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: S2 cells treated with ICRF-193 were biochemically fractionated to enrich for chromatin bound nascent RNA. Nascent RNA were then fragmented and reverse transcribed.

data_processing:
library strategy: RNA-seq (modified: PMID 22025700)
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: Nascent RNA

extract_protocol: As described in PMID 11340173

tag: cell type

tag: treated with

value: topoisomerase inhibitor ICRF-193


title: Day 12 non-pregnant control, biological replicate 1

description:
D12C_004
Pool of RNAs from endometrial tissue samples collected from the distal, medial and proximal part of one uterine horn


title: Day 12 non-pregnant control, biological replicate 2

description:
D12C_006
Pool of RNAs from endometrial tissue samples collected from the distal, medial and proximal part of one uterine horn


title: TMPseq_ICRF_(20130118_4_2)

description: S2 cells treated with ICRF-193 were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.

data_processing:
library strategy: TMPseq library preparation method (TMPseq.rtf)
1. We used cutadapt (1.1) to trim all leading Cs off of 25bp reads (raw files). 2. We used Novoalign (2.08.01 - Mar 14 2012) to map the clipped reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random. 3. We extracted mapped reads (Supplementary file .txt). 4. We fit a Gaussian kernel density function with bandwidth=20 and wordsize=10 around the end of each mapped read and accumlated resulting counts into base pair intervals (PMID 19520961, supplementary material). 5. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) .

source_name: Crosslinked genomic DNA

extract_protocol: As described in PMID 20685815

tag: exposed to

value: DNA cross-linker TMP


title: Adelman_Dmel_S2_DMSO__3prRNA


title: nascentRNA_Camp_(20130118_8_3)

description: S2 cells treated with Camptothecin were biochemically fractionated to enrich for chromatin bound nascent RNA. Nascent RNA were then fragmented and reverse transcribed.

value: topoisomerase inhibitor Camptothecin

tag: molecule subtype

value: Reverse-transcribed nascent RNA


title: shMBD3.rep2

description: biological replicate 2 (shMBD3)


title: nascentRNA_Ctl_(20130118_8_1)

description: S2 cells were biochemically fractionated to enrich for chromatin bound nascent RNA. Nascent RNA were then fragmented and reverse transcribed.


title: TMPseq_DNA_(20130118_3_1)

description: Purified genomic DNA from S2 were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.


title: nascentRNA_HS_(20130118_8_2)

description: S2 cells heat-shocked at 37degC were biochemically fractionated to enrich for chromatin bound nascent RNA. Nascent RNA were then fragmented and reverse transcribed.


title: TMPseq_Ctl_(20130118_3_2)

description: S2 cells were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.


title: TMPseq_Camp_(20130118_4_1)

description: S2 cells treated with Camptothecin were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.


title: Pol2ChIP_Ctl_(20121019_6_4)

description: Nuclei from S2 cells were MNase-digested and the 80 mM salt soluble fraction was extracted. Pol II antibody (8WG16) was used for ChIP.

data_processing:
library strategy: ChIP-seq (modified; PMID 22025700)
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: Pol II ChIP

extract_protocol: As described in PMID 22085965

tag: chip antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS antibody [8WG16]

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: Pol2ChIP_ICRF_(20121019_6_7)

description: Nuclei from S2 cells treated with ICRF-193 (Topo II inhibitor) were MNase-digested and the 80 mM salt soluble fraction was extracted. Pol II antibody (8WG16) was used for ChIP.


title: Pol2ChIP_Camp_(20121019_6_5)

description: Nuclei from S2 cells treated with Camptothecin (Topo I inhibitor) were MNase-digested and the 80 mM salt soluble fraction was extracted. Pol II antibody (8WG16) was used for ChIP.


title: LowSalt_ICRF_(20121019_7_12)

description: Nuclei from S2 cells treated with ICRF-193 (Topo II inhibitor) were MNase-digested and the 80 mM salt soluble fraction was extracted.

data_processing:
library strategy: MNase-seq (modified; PMID 22025700)
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: Salt fractionation


title: Adelman_Dmel_S2_Mock-tr+FP_3prRNA

description: short capped RNA isolated from Drosophila S2 nuclei


title: shLuc.rep1

description: biological replicate 1 (shLuc control)


title: Day 12 non-pregnant control, biological replicate 4

description:
D12C_011
Pool of RNAs from endometrial tissue samples collected from the distal, medial and proximal part of one uterine horn


title: LowSalt_Camp_(20121019_7_7)

description: Nuclei from S2 cells treated with Camptothecin (Topo I inhibitor) were MNase-digested and the 80 mM salt soluble fraction was extracted.


title: CATCHIT_Ctl_(20120817_8_5)

description: S2 cells were used to measure nucleosome turnover by CATCH-IT

source_name: CATCH-IT Strep pulldown

extract_protocol: As described in PMID 20508129


title: CATCHIT_Camp_(20120817_8_4)

description: S2 cells treated with Camptothecin (Topo I inhibitor) were used to measure nucleosome turnover by CATCH-IT


title: P.M2.3

city: Durham

first: Devjanee

last: Swain Lenz

state: NC

address: 130 Bioscience Drive

institute: Duke University

description: S. paradoxus, developmental stage M2, replicate 3

data_processing:
original base-calling,quality control and trimming of indexes was performed by GTAC at Washington University
aligned sequencing reads using Bowtie v 0.12.7 with parameters -v 1 -m 0
used lab perl script to map alignments to ORFs that are shared between S. cerevisiae and S. paradoxus
used lab perl script to filter out ORFs in which all samples had 0 reads
For allele specific variance stabiliting, use DESeq v1.8.3 with command estimateDispersions(cds, method="pooled-CR", modelFormula=count~stage*allele*species)
For allele non-specific variance stabiliting, use DESeq v1.8.3 with command estimateDispersions(cds, method="pooled-CR", modelFormula=count~stage*species)
Genome_build: parental and hybrid indexes created from S. cerevisiae S288c (SGD) and S. paradoxus N17 (SGRP) genomes
Supplementary_files_format_and_content: 2013.02.06.1.mm.0.MA.all.species.high.counts.allele.non: read counts for all samples, hybrid counts are allele-nonspecific, this is count data for DESeq
Supplementary_files_format_and_content: 2013.02.06.1.mm.0.MA.all.species.high.counts.allele.sp: read counts for all samples, hybrid counts are allele-specific in which "c" designates S. cerevisiae allele and "p" designates S. paradoxus allele, this is count data for DESeq
Supplementary_files_format_and_content: 2013.02.06.allele.non.vsd: variance stabilized data for all samples derived from DESeq, hybrid data is allele-nonspecific
Supplementary_files_format_and_content: 2013.02.07.allele.specific.hybrid.high.counts.vsd: variance stabilized data for all samples derived from DESeq, hybrid counts are allele-specific in which "c" designates S. cerevisiae allele and "p" designates S. paradoxus allele

organism: Saccharomyces paradoxus

source_name: yeast culture

growth_protocol: We inoculated 100 ml of YPD (1% BactoTM yeast extract, 2% BactoTM peptone and 2% dextrose) in 250 ml Erlenmeyer flasks, and incubated the culture at 30ºC and 340 rpm for 15 hours. To sporulate cells we washed cells with water and resuspended the cells in 250 ml of SPO (1% potassium acetate, 0.1% BactoTM yeast extract, 0.05% dextrose) for a final concentration of 107 cells/ml. We incubated the cultures in 1 L baffled flasks at 30ºC at 340 rpm for 24 hours. We used distilled water for all media.

extract_protocol:
We extracted total RNA from samples using Ambion RiboPure-Yeast Kit. We purified mRNA from total RNA using Ambion Micro PolyPurist Kit, and reversed transcribed mRNA into cDNA using polyA primers.
We used T4 DNA Polymerase (NEB), T4 Polynucleotide Kinase (NEB), and Taq Polymerase (NEB) for end repair of the sheered cDNA.  We used T4 ligase (NEB) to ligate index adapters to the cDNA . We pooled each sample to an equal concentration and gel extracted 250 – 350 bp of ligated cDNA and used PCR to amplify the selected fragment to a final concentration of 1 nM.  We submitted our final cDNA library to GTAC at Washington University for sequencing on two Illumina HiSeq lanes. At a run concentration of 6 pM

treatment_protocol: We sampled, washed with distilled water and snap-froze 10 ml cultures prior to RNA extraction.

tag: developmental stage

tag: replicate

tag: index 1

value: CTATGGA


title: Ve2

city: Davis

first: Venkatesan

last: Sundaresan

state: CA

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

description: Transcriptional profiling

data_processing:
Illumina CASAVA_v1.8.0 software used for basecalling.
The barcoded Fastq files of the reads were mapped to rice RGAP 7.0 genomic reference sequences using Tophat version 2.0.5 with the default settings except that the 'microexon' search option was switched on, and minimum and maximum intron sizes were set at 20 bases and 15000 bases, respectively.  The mapped reads in the resulting accepted_hits.bam files were assigned to gene exons of the different isoforms of the RGAP 7.0 gene models GFF3 file, using an in-house Perl script.
For gene analysis only uniquely mapped read counts that were assigned to gene exons were used.  Additionally, where more than one isoform is present, the one with the highest number of reads across the three cell types assessed was analyzed further.
To determine differentially expressed genes between the three cell types, the Bioconductor R package edgeR (Robinson et al. 2010) was used.  However, the default normalization method, TMM, assumes that most genes are not differentially expressed between conditions, which was clearly not the case with the three cell types, and so the upper quartile method (75th percentile) was used.  A glm was fitted to the data with tag-wise dispersion.  The following contrasts were created:- EC vs Sp, Sp vs Ve, Ve vs EV, EC vs (Sp + Ve)/2, Sp vs (Ve + EC)/2 and Ve vs (EC + Sp)/2.  Likelihood ratio tests were performed to determine differential expression for each contrast.
Genome_build: RGAP rice vs 7.0
Supplementary_files_format_and_content: The comma separated values (csv) file contains count data for reads mapping to exons for alternative transcript isoforms for Oryza sativa rice gene models for LOC_ loci from RGAP version 7.0

organism: Oryza sativa Japonica Group

source_name: wild type

growth_protocol: Egg cells were isolated using flowers harvested at anthesis from rice plants (Oryza sativa L. ssp. japonica, cultivar “Kitaake”) grown in greenhouses under ambient light during the summer. Sperm and pollen vegetative cells were isolated from near anthesis anthers of vigorous visibly disease-free field grown rice at Dale Bumpers National Rice Research Center in Stuttgart, AR, USA.

extract_protocol:
For egg cell processing, ovaries were mechanically dissected from emasculated flowers under a dissecting scope, moved to fresh 0.3M mannitol (Sigma) prepared using DEPC-treated water (Sigma) and bisected using a double-edged Merkur (Solingen, Germany) razor blades in 3μL drops of 0.3M mannitol. Using an insect pin, the base of the ovary was gently pushed towards the cut surface until the egg cell became visible. Egg cell protoplasts were then immediately transferred to 1.5mL Eppendorf tubes in liquid nitrogen and stored at -80°C.  For sperm cell and vegetative cell cytoplasm sample processing, a differential centrifugation isolation method was used to separate the sperm cells and vegetative cells from whole anthers (Gou et al. 1999, Russell et al. 2012).  Briefly, collected anthers were gently ground in cold 45% (w/v) sucrose solution to release mature pollen grains, filtered through 100 μm nylon mesh, resuspended in a 10× volume of 15% (w/v) sucrose solution for 20 min to release the sperm cells, filtered through a 30μm nylon mesh and layered on a Percoll density gradient, centrifuged and recovered as described previously (Russell et al. 2012). The precipitate consisting of vegetative cell materials was treated as a sperm depleted sample and collected in concert with each sperm cell isolation. Therefore, the sperm and vegetative samples represent paired samples, but these were treated as independent when analyzed in conjunction with the egg cell samples.  Samples collected were immediately transferred and stored in -80°C until use.
RNA from the sperm and vegetative cells was extracted using the QIAGEN RNeasy Plant Mini Kit (QIAGEN) following manufacturer’s instructions including the optional on-column DNAse treatment. For the egg cell samples, RNA was extracted using the RNAqueous-Micro Kit (Applied Biosystems). The protocol was modified to add an on-column DNAse treatment (QIAGEN) after the first wash step. RNA quality for all samples was assessed and concentrations measured using the Agilent Bioanalyzer (Agilent), and samples had an RNA Integrity Number (RIN) ranging from 7.7 – 9. cDNA synthesis was performed using the NuGEN RNA-seq system V2 (NuGEN) with an input of 1.5 – 10 ng of RNA. cDNA was quantified on the ND 1000 Nanodrop Spectrophotometer (Thermo Fisher Scientific, Inc.) and then sheared on the Covaris S220 system (Covaris) using manufacturer’s recommended settings for 200 bp fragments. 170 ng of sheared cDNA was purified using the MinElute Reaction Cleanup Kit (QIAGEN), and libraries were prepared using the NuGEN Ovation Ultralow DR Multiplex Systems 1-8. Samples were multiplexed and run with 6 samples per lane on the Illumina HiSeq 2000 DNA sequencer (Illumina).

tag: cultivar

value: Nipponbare x HEG4 RI line

tag: tissue

value: pollen minus sperm cells

value: wild type


title: P.M2.2

description: S. paradoxus, developmental stage M2, replicate 2

value: GAGACCA


title: Ve3

description: Transcriptional profiling

tag: genotype


title: P.M2.1

description: S. paradoxus, developmental stage M2, replicate 1

value: TAGTATT


title: Ve1

description: Transcriptional profiling


title: P.M1M2.3

description: S. paradoxus, developmental stage M1M2, replicate 3

value: TCGAGAT


title: P.M1M2.2

description: S. paradoxus, developmental stage M1M2, replicate 2

value: TAGGTAA


title: Sp3

description: Transcriptional profiling

value: sperm cells


title: P.M1M2.1

description: S. paradoxus, developmental stage M1M2, replicate 1

value: GCCGTTT


title: EC3

description: Transcriptional profiling

value: Kitaake

value: egg cells x 50


title: Sp2

description: Transcriptional profiling


title: HESC

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

country: China

institute: Beijing Institute of Genomics

description: ribosomal RNA-depleted RNAs from HESCs

data_processing: Reads were mapped to human reference sequence (release hg18, Mar. 2006) from University of California - Santa Cruz (UCSC). Ribosome RNA reads filtering was executed at the beginning of reads mapping with full length of 50bp. The remaining reads were mapped to the reference with the length of 50bp, 45bp and 40bp respectively. Five mismatches were allowed at each mapping step. Reads mapped to unique loci and a fraction of those mapped to multiple loci (2-10) were used for further analysis.To calculate gene expression intensity, the read counts were normalized to reads per kilobase of exon model per million mapped reads (RPKM) according to the gene length and total mapped reads.

source_name: H1 cell line

growth_protocol: ES and peripheral blood (PB) CD34+ cells were cultured in the erythroid-inducing medium to generate ESER and PBER cells respectively.

extract_protocol: SOLiD RNA-seq with invitrogen ribominus kit

treatment_protocol: Normal

value: Undifferentiated HESC


title: P.M1.3

description: S. paradoxus, developmental stage M1, replicate 3

value: TGTGCCA


title: Sp1

description: Transcriptional profiling


title: PBER

description: ribosomal RNA-depleted RNAs from PBER cells

source_name: peripheral blood (PB) CD34+ cells treatment

value: PBER (adult stage)

value: peripheral blood (PB) CD34+-derived erythroid cells


title: ESER

description: ribosomal RNA-depleted RNAs from ESER cells

source_name: H1 cell line treatment

value: ESER (embryonic stage)

value: ES-derived erythroid cells


title: P.M1.1

description: S. paradoxus, developmental stage M1, replicate 1

value: TTGCCCC


title: EC1

description: Transcriptional profiling


title: EC2

description: Transcriptional profiling


title: C.M2.3

description: S. cerevisiae, developmental stage M2, replicate 3

organism: Saccharomyces cerevisiae

value: GGTGAAT


title: C.M2.2

description: S. cerevisiae, developmental stage M2, replicate 2

value: GAGATGC


title: P.C.3

description: S. paradoxus, developmental stage T0, replicate 3

value: TCTTCCT


title: P.M1.2

description: S. paradoxus, developmental stage M1, replicate 2

value: ACTCCAA


title: CATCHIT_ICRF_(20120817_8_6)

description: S2 cells treated with ICRF-193 (Topo II inhibitor) were used to measure nucleosome turnover by CATCH-IT

value: topoisomerase inhibitor:ICRF-193


title: FLER

description: ribosomal RNA-depleted RNAs from FLER cells

source_name: fetal livers cells

value: FLER (fetal stage)

value: fetal liver cells


title: P.C.2

description: S. paradoxus, developmental stage T0, replicate 2

value: AAATGCA


title: C.M2.1

description: S. cerevisiae, developmental stage M2, replicate 1

value: ATGTTCT


title: Prdm5 ab1 lacz/lacz

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
ChIP-Seq data were mapped over the assembly mm9 using Bowtie and peak finding and filtering were performed using MACS software setting a lower "mfold" parameter for the model building to 5.
For each antibody, the data from Prdm5(LacZ/LacZ) cells was used as the background to define peaks. Only peaks sharing overlaps between the two antibodies were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited table containing absolute genomic location of all peaks that passed the filtering and the annotation of the nearest gene available in the reference genome

organism: Mus musculus

source_name: mouse embryo fibroblasts (MEF)

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size. Plolyclonal custom-made PRDM5 antibodies were used for Immunoprecipitation. Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen)
Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's reccomendations

value: mouse embryonic fibroblast

tag: strain

tag: genotype/variation

value: Prdm5 ab1 lacz/lacz


title: Prdm5 ab2 lacz/lacz

value: Prdm5 ab2 lacz/lacz


title: P.C.1

description: S. paradoxus, developmental stage T0, replicate 1

value: ACAGATA


title: Prdm5 ab2 wt

value: Prdm5 ab2 wt


title: C.M1M2.3

description: S. cerevisiae, developmental stage M1M2, replicate 3

value: GTACGGC

tag: index 2

value: GTATTTG


title: C.M1M2.2

description: S. cerevisiae, developmental stage M1M2, replicate 2

value: TTCGCTG


title: Prdm5 ab1 wt

tag: cell type

value: Prdm5 ab1 wt


title: ATRA+ Prdm5 KO rep3

data_processing:
The quality of RNA-seq was evaluated with fastQC software. RNA-Seq data were analyzed using a pipeline based on the use of TopHat and Cufflinks.
The reference genome used for alignment was mm9 and uses UCSC annotation. Differentially expressed genes were detected using the Bioconductor package Cummerbund
Genome_build: mm9

source_name: mouse embryonic stem cells (mES)

extract_protocol:
Total RNA was extracted from cell pellets using the Rneasy plus minikit (Qiagen) according to the manufacturer's instructions
cDNA was sinthetized using TaqMan reverse transcription reagents (Applied Biosystems) and quantitative reverse transcription-PCR (qRT-PCR) was performed with the One Step plus sequence detection system (Applied Biosystems)

value: Prdm5 KO

tag: condition

value: ATRA-induced differentiation


title: TMPseq_DNA2_(20130304_1_1)

description: Purified genomic DNA from S2 were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.


title: C.M1M2.1

description: S. cerevisiae, developmental stage M1M2, replicate 1

value: AACGGAG


title: TMPseq_Ctl2_(20130304_1_3)

description: S2 cells were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.

tag: exposed to

value: DNA cross-linker TMP


title: ATRA+ Prdm5 KO rep2


title: C.M1.3

description: S. cerevisiae, developmental stage M1, replicate 3

value: AAACCTT


title: ATRA+ Prdm5 KO rep1


title: ATRA+ Prdm5 wt rep2

value: Prdm5 wt


title: C.C.3

description: S. cerevisiae, developmental stage T0, replicate 3

value: GATAGTT


title: TMPseq_Camp2_(20130304_1_8)

description: S2 cells treated with Camptothecin were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.

tag: treated with

value: topoisomerase inhibitor Camptothecin


title: ATRA+ Prdm5 wt rep1


title: C.M1.1

description: S. cerevisiae, developmental stage M1, replicate 1

value: GAGGCGT

value: ACCATAC


title: ATRA+ Prdm5 wt rep3


title: C.C.1

description: S. cerevisiae, developmental stage T0, replicate 1

value: TACATGG


title: C.C.2

description: S. cerevisiae, developmental stage T0, replicate 2

value: TGCCCAT


title: LIF- Prdm5 KO rep2

value: LIF cytokine deprivation


title: MDA231_H3K4_me3

description: The ChIP-seq libraries were prepared from 10ng of both Input and ChIP DNA samples using a ChIP-seq sample preparation kit (Illumina) according to the manufacturer’s protocol.

data_processing:
Basecalls performed using CASAVA version 1.7
Raw data from the replicates were merged.
Raw data was filtered by the following steps:  reads were filtered if the average base quality score <20 and duplicate reads removed (based on identical sequences)
Reads were mapped against hg19 reference genome (excluding haplotype chromosomes) with Bowtie (v0.12.8 using the following parameters:  -v 2 -m 1); HeK4 data were mapped against hg18 reference genome with ELAND program
Mapped data was filtered to remove hits with >2 mismatches to the reference genome.
Genome_build: hg19; hg18 for H3K4 data
Supplementary_files_format_and_content: bigwig file per sample per strand showing mapped read coverage; generated by BEDtools genomeCoverageBed and bedGraphToBigWig.
Supplementary_files_format_and_content: MBD3 bed files were generated by SICER v1.1 (redundancy threshold=1, window size=200, gap size=600, fragment size=300, FDR=0.001)
Supplementary_files_format_and_content: H3k4 wig files were generated by MACS-1.3.3 with default parameters.

extract_protocol: ChIP experiments were carried out using a Magna ChIP kit (Millipore) following the manufacturer’s suggested protocols. For each ChIP experiment, 5×106 MDA-MB-231 cells were crosslinked with 10% formaldehyde at 37°C for 10 minutes. The anti-trimethyl-H3K4 (Upstate, no. 04-745) antibody was used.

tag: cell line

tag: antibody


title: LIF- Prdm5 KO rep3


title: LIF- Prdm5 KO rep1


title: LIF- Prdm5 wt rep3


title: MDA231_H3K4_input

value: none, input


title: LIF- Prdm5 wt replicate 2


title: TMPseq_ICRF2_(20130304_1_5)

description: S2 cells treated with ICRF-193 were exposed to trimethylpsoralen (TMP) and cross linked with UV light. Genomic DNA was extracted, sonicated, and cross linked fragments were enriched by sequential denaturation and Exo I digestion.

value: topoisomerase inhibitor ICRF-193


title: LIF- Prdm5 wt replicate 1


title: MCF-7_MBD3

description: Library was prepared by Nextera XT kit

growth_protocol: Human breast cancer cell lines (MCF-7 and MDA-MB-231) were grown under standard conditions in DMEM/F12 supplemented with 10% fetal bovine serum and pen-strep.

extract_protocol:
Cells were fixed with DSG (Disuccinimidyl glutarate) followed by formaldehyde.  Chromatin was sonicated with Bioruptor to an average size of 0.3-0.6 kb. Chromatin was incubated with anti-MBD3 antibody (Abcam; ab91458) for 16hr followed by incubation with dynabeads A/G (Invitrogen). ChIP DNA was reverse-crosslinked and purified with Minelute PCR purification kit (Qiagen).
Library was prepared by TruSeq DNA Sample Prep kit (Illumina) or Nextera XT DNA sample prep kit (Illumina) according to the manufacturer's protocol.

value: anti-MBD3 antibody (Abcam; ab91458)


title: WT-control-Chromatin pull down

city: La Jolla

first: James

middle: W

last: Golden

department: Biology

institute: UCSD

data_processing:
Sequence reads were demultiplexed based on index sequences and saved as FASTA files for analysis in CLC Genomics Workbench 5.
Sequencing reads from the experimental HetR-6xHis sample were randomly assigned to three files and the full Chromatin pull down analysis was performed on each sample as a technical replicate.
Genome_build: Chromatin pull down reads from the three HetR-6xHis samples and the WT sample were aligned to NCBI’s current build of the Anabaena genome (ASM970v1) with CLC Genomics Workbench 5.
Supplementary_files_format_and_content: CLC Chromatin pull down analysis, peak

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: Anabaena filaments

growth_protocol: 100-ml or 2-ml liquid cultures were grown to an OD750 of 0.05 in BG-11(NH4) medium, which lacked sodium nitrate and contained 2.5 mM ammonium chloride and 5 mM MOPS (pH 8.0).

extract_protocol:
Cells were cross linked with disuccinimidyl glutarate (DSG) and ethylene glycol bis(succinimidyl succinate) (EGS), followed by formaldehyde. Cells were broken by bead beating and DNA was sheared via sonication. His-tagged HetR was bound to Dynabeads, crosslinks were reversed, proteins were digested, DNA was column purified.
DNA was prepared for sequencing with the Illumina Chromatin pull down Sample prep kit by the Next Generation Sequencing Core at The Scripps Research Institute (La Jolla, CA) following the manufacturer’s protocol. Sequencing was performed on the Illumina HiSeq platform with 4 samples multiplexed on one cell, yielding approximately 40 million 40-bp reads per sample.

treatment_protocol: For nitrogen deprivation, cultures were spun down at 4,000 x g for 5 minutes and washed three times in BG-110 media by centrifugation and decanting of the supernatant. Cells were then resuspended in 100 ml or 2 ml BG-110 at a final OD750 of between 0.02 and 0.05. Cells were grown for 6 hours in BG-110 shaking at 100 μmol photons m-2 s-1.

tag: treatment

value: nitrogen deprivation

tag: time

value: 8 h post nitrogen deprivation

value: Wild type

tag: strain background


title: MCF-7_MBD3_input

description: Library was prepared by Nextera XT kit


title: HetrBC2-Chromatin pull down

value: 6 h post nitrogen deprivation

value: hetR mutant strain UHM103 carrying pAM4375 that expresses HetR-6His


title: C.M1.2

description: S. cerevisiae, developmental stage M1, replicate 2

tag: developmental stage

tag: replicate

value: AATACGC


title: Laublab_BglII_HiC_NA1000_swarmer_cell_empty_pMT675_van_locus

status: Public on Oct 30 2013

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
Library strategy: Hi-C-Seq
Paired-end sequencing reads were mapped independently to the genome of Caulobacter crescentus CB15N (NCBI Reference Sequence: NC_011916.1) using Bowtie 2.1.0 and an algorithm which iteratively increases truncation length to maximize yield of valid Hi-C interactions (Imakaev et al., 2012. PMID: 22941365). Only read pairs with both reads that were uniquely aligned to the genome were considered for subsequent steps.
The Caulobacter CB15N genome was then divided into restriction fragments (700 BglII fragments and 2025 NcoI fragments). Each read of a read pair was sorted into its corresponding restriction fragment. Read pairs were classified as valid Hi-C products, non-ligation, or self-ligation products; only valid Hi-C products were considered below.
To create interaction matrices, the Caulobacter genome was first divided into 405 10-kb bins. We then assigned valid Hi-C products to the bins as follows. Recall that each valid Hi-C product involves the ligation of two restriction fragments. If both restriction fragments are contained entirely within bins (e.g. suppose fragment 1 is contained within bin A and fragment 2 is contained within bin B), we incremented the count of interactions between bins A and B by one. If one of the restriction fragments spanned two bins (e.g. suppose fragment 1 is contained within bin A but fragment 2 spans bins B and C) then we incremented the count of interactions between bin A and B by an amount proportional to the fraction of fragment 2 that overlaps bin B (and similarly for the count of interactions between A and C). Thus, each read contributes a count of one to the interaction map, but it can be split between bins. This means of assigning reads to bins was necessary to analyze data at a high 10-kb resolution. Interactions of a bin with itself, and with neighboring bins were discarded, as in Imakaev et al., 2012. For the presentation of the matrices, three discarded diagonals were later given the maximal cut-off value of 0.035.
Raw Hi-C contact maps can be biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We therefore normalized raw contact maps using an iterative normalization procedure, implemented using the hiclib library for Python (https://bitbucket.org/mirnylab/hiclib). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle: mij =mij * (total reads) / (total reads in bin i * total reads in bin j). Iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 1e-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using Python and R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .txt: tab-delimited text files of Hi-C contact maps/matrices before and after normalization by iterative correction. Files ending with .RPKPM.txt: tab-delimited text file of reads per kilobases per million mapped reads of genomic DNA for synchronous population of Caulobacter at 0, 10, 30, 45, 60 and 75 min after synchronization.

organism: Caulobacter vibrioides CB15

source_name: Caulobacter crecentus CB15N

growth_protocol: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290). After synchronization, swarmer cells were released into PYE for 0, 10, 30, 60, 75 or 150 minutes before fixing with formadehyde for chromosome conformation capture and Hi-C analysis. For antibiotic treatments, swarmer cells were incubated with 25 ug/mL or 50 ug/mL novobiocin (final concentration) or 25 ug/ml rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

extract_protocol:
Hi-C experiments were performed using either BglII or NcoI according to previous publications (Umbarger MA. 2012. Chromosome conformation capture assays in bacteria. PMID: 22776362 and Lieberman-Aiden, E. et al., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. PMID: 19815776).
Standard library construction for Illumina Hiseq2000 sequencing platform

treatment_protocol:
Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE and fixed immediately by 1% formadehyde.
None

value: swarmer cells (0 min after synchronization)

value: rsaA knock-out empty pMT675 at van locus

tag: restriction enzyme

value: BglII


title: Laublab_BglII_HiC_NA1000_swarmer_cell_rsaA_relocation_xyl_locus

value: rsaA knock-out PrsaA_rsaA at xyl locus


title: Laublab_gDNA_sequencing_NA1000_cellcycle_75min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE  and shaked  for 75 min at 30 degree C before fixing immediately by 1% formadehyde.

value: 75 min fter synchronization

value: wild type


title: Laublab_gDNA_sequencing_NA1000_cellcycle_10min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE  and shaked  for 10 min at 30 degree C before fixing immediately by 1% formadehyde.

value: 10 min fter synchronization


title: MDA231_MBD3_input

description: Library was prepared by TruSeq DNA Sample Prep kit or Nextera XT kit.


title: Laublab_gDNA_sequencing_NA1000_cellcycle_30min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE  and shaked  for 30 min at 30 degree C before fixing immediately by 1% formadehyde.

value: 30 min fter synchronization


title: Laublab_gDNA_sequencing_NA1000_cellcycle_0min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE and fixed immediately by 1% formadehyde.

value: 0min after synchronization


title: Laublab_gDNA_sequencing_NA1000_cellcycle_60min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE  and shaked  for 60 min at 30 degree C before fixing immediately by 1% formadehyde.

value: 60 min fter synchronization


title: Laublab_BglII_HiC_NA1000_cellcycle_0min

value: 0 min after synchronization


title: Laublab_gDNA_sequencing_NA1000_cellcycle_45min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE  and shaked  for 45 min at 30 degree C before fixing immediately by 1% formadehyde.

value: 45 min fter synchronization


title: Laublab_BglII_HiC_NA1000_cellcycle_10min


title: Laublab_BglII_HiC_NA1000_swarmer_cell_hup1hup2_knockout

value: hup1hup2 knock-out


title: Laublab_BglII_HiC_NA1000_cellcycle_75min


title: Laublab_BglII_HiC_NA1000_cellcycle_60min


title: Laublab_BglII_HiC_NA1000_swarmer_cell_smc_knockout

value: smc knock-out


title: Laublab_BglII_HiC_NA1000_swarmer_cell_Rifampicin_25ug_per_ml_30min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE containing 25 ug/ml Rifampicin and were incubated for 30 min before fixation by 1% formadehyde.


title: Laublab_BglII_HiC_NA1000_swarmer_cell_Novobiocin_25ug_per_ml_30min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE containing 25 ug/ml Novobiocin and were incubated for 30 min before fixation by 1% formadehyde.


title: Laublab_NcoI_HiC_NA1000_swarmer_cell_untreated

value: NcoI


title: Laublab_BglII_HiC_NA1000_swarmer_cell_untreated_replicate2


title: Laublab_HiC_NA1000_swarmer_cell_rsaA_relocation_van_locus

value: rsaA knock-out PrsaA_rsaA at van locus


title: Laublab_BglII_HiC_NA1000_swarmer_cell_Novobiocin_50ug_per_ml_30min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE containing 50 ug/ml Novobiocin and were incubated for 30 min before fixation by 1% formadehyde.


title: Laublab_BglII_HiC_NA1000_swarmer_cell_untreated_replicate1


title: Laublab_BglII_HiC_NA1000_cellcycle_45min


title: Laublab_BglII_HiC_NA1000_cellcycle_30min


title: edm2-4 BS-seq

status: Public on Oct 29 2013

city: Shanghai

first: Lan

last: Yang

address: 300 Fenglin Road

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences

description: Sample 2

data_processing:
For data analysis, adapter and low quality sequences were trimmed and clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP but allowing up to 2 mismatches.
Identification of differentially methylated regions (DMRs) was conducted according to reference (1) (Ausin et al., 2012) with modifications. In brief, only cytosines with a depth of at least 4 in libraries were retained for further analysis.
DNA methylation levels in every 200-bp windows with a step size of 50 bp were compared between wild-type and mutant plants using Fisher’s exact test with a p-value cutoff of 0.05. The p-values were then adjusted using the Benjamini-Hochberg method to control for FDRs.
Windows with ≥7DMCs (differentially methylated cytosines, defined as C with p<0.01 in Fisher’s exact test) and ≥1.5 fold change in DNA methylation levels were retained and combined if gap size is not more than 200 bp to generate DMRs.
Finally, the lengths of DMRs were adjusted to be from the first mC to the last mC.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files report methylation ratios

organism: Arabidopsis thaliana

source_name: 14-d-old entire seedlings

growth_protocol: Seeds are sown on MS media, and then treated at 4C overnight. Afterwards, plates are placed under light for germination and growth for 14 days.

extract_protocol:
Genomic DNA was extracted with CTAB method from 14-d Arabidopsis seedlings. Then RNA is eliminated by RNaseI.
Five micrograms of genomic DNA was fragmented into 100-300bp by sonication approach.  The fragments were blunt‐ended and phosphorylated, and a single ʹAʹ nucleotide was added to the 3ʹ ends of the fragments. Then the fragments were ligated to adaptors. The resulting DNAs were treated with ZYMO EZ DNA Methylation-Gold kit to finish bisulfite conversion. After DNAs were recovered from gel, PCR amplifications were performed to enrich those DNAs with proper sizes. Finally, the final purified products were quantitated prior to cluster generation.

treatment_protocol: no special treatment

value: edm2-4 mutant

tag: tissue

value: 14-d-old entire seedlings


title: col RNA-seq

description: Sample 1

data_processing:
Clean sequenceing reads of edm2 and wild type samples which filter the adapter and low quality were mapped to TAIR10 genome by TopHat 2.0.6 individually . Up to two mismatchs and maximum intron length is 10kb as the threshold, then the unique mapped reads were choosen for subsequent analysis.
Reads number were counted in 5' part and 3' part respectively for each gene which be separated by intronic TE or long methylation intron(length more than 500bp and methylation ratio more than 20%) ,then the 3'/5' expression ratio was compared in edm2 and wild type to look for the 3' down-regulation genes in edm2.
Significantly different degrees given by fisher's exact test.Genes which FDR value less than 0.05 and expression ratio reduced at least two times in edm2 mutant were choosen as candidate.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph format and normalized by library size

extract_protocol:
RNA was extracted with Trizol reagent from 14-d Arabidopsis leaves, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
The extracted RNA was sent to BGI (Shenzhen, China) for RNA-seq library preparation and whole transcriptome sequencing. Briefly, The total RNA was treated with DNaseI and then subjected for mRNA enrichment. The derived mRNA was used as the template for first strand cDNA synthesis by using oligo dT primer. The adaptor was added to the 5’ end of the first strand cDNA and then the second strand cDNA was synthesized by using the primer pairing to the adaptor. The double strand cDNA was sonicated into 300-500 bp fragments for pair-ended sequencing with HiSeq 2000.

value: wild-type


title: col BS-seq

description: Sample 1


title: csbCPT30m1

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: Cockayne syndrome group B fibroblasts

growth_protocol: Cells were hTERT immortalized and grown as monolayers in MEM supplied with 10% fetal bovine serum and antibiotics.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: In the CPT treatment samples, the cells were treated with 20 µM camptothecin (Sigma) for 60 minutes. After the 60 minutes, the CPT was washed out. Depending on the treatment, the bromouridine was added 15 minutes before the washout, immediately after the washout or 15 minutes after the washout. The control samples were not exposed to CPT. Bromouridine (Aldrich) was added to the media to a final concentration of 2 mM and cells were incubated at 37°C for 15 min in the treament samples and 30 minutes in the control samples. Cells were then washed 3 times in PBS and either collected directly (nascent RNA, Bru-Seq) or chased in conditioned media containing 20 mM uridine for 6 hours at 37°C (6-hour old RNA, BruChase-Seq).

value: Cockayne syndrome group B fibroblasts

tag: camptothecin exposure time

value: 60 minutes

tag: bromouridine labeling start

value: 15 minutes after washout

tag: bromouridine labeling time

value: 15 minutes

value: CPT exposure

tag: stranded

value: TRUE


title: csbCPT15m1

tag: cell type

value: Immediately after washout


title: csbCPT0m1

value: 15 minutes prior to washout


title: csb0h1

value: 0 minutes

value: 30 minutes

value: Control


title: nfCPT30m1

source_name: Foreskin fibroblasts

value: Foreskin fibroblasts


title: nfCPT0m1


title: nfCPT15m1


title: nf0h3a


title: C7

city: Lanzhou

first: Min-jun

last: Xu

state: Gansu

address: 1 Xujiaping, Yanchangbu

department: State Key Laboratory of Veterinary Etiological Biology

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

description: Sample 1

data_processing:
Illumina Casava1.7 software used for basecalling;Remove low qulity reads strictly;Trim adaptor sequence;Remove too small and polyA
Non-coding RNA, such as rRNA, tRNA, snRNA, snoRNA, and other ncRNAs were removed by searching against the GenBank and Rfam databases (http://rfam.sanger.ac.uk/). Repetitive sequences were removed using RepeatMasker (http://www.repeatmasker.org). Filtered reads were then mapped onto the genome of T. gondii (http://www.ncbi.nlm.nih.gov/assembly/GCF_000006565.1/) using the Short Oligo nucleotide Analysis Package (SOAP). Novel miRNAs were predicted with Mfold (http://www.bioinfo.rpi.edu/applications/mfold) and evaluated by MirCheck.
The miRNAs of each sample were then compared with each other.
Genome_build: ME49 at: http://www.ncbi.nlm.nih.gov/assembly/GCF_000006565.1/
Supplementary_files_format_and_content: Excel file with 10 spreadsheets containing miRNA compared results of each two samples.

organism: Toxoplasma gondii

source_name: Toxoplasma gondii

growth_protocol: Tachyzoites of each genotype were intraperitoneally inoculated into specific-pathogen-free (SPF) grade Kunming mice of 8 weeks old (from the Animal Center of Sun Yat-Sen University) and passaged for 3 generations to recover their activity and virulence.

extract_protocol:
The prepared tachyzoites were ground into a fine powder in a mortar and pestle with liquid nitrogen. Total RNA was then extracted from the powder using TRIzol Reagent according to the manufacturer’s protocol
Briefly, 10 μg total RNA were used for the isolation of RNA fragments of 20-40 bases long using a Novex 15% TBE-Urea gel. The fragments were ligated to 5´ and 3´ adaptors (Illumina), reverse transcribed with an RT-PCR kit and purified using a 6% TBE PAGE gel.

treatment_protocol: The mice were euthanased and the body cavity washed with PBS solution (pH7.2). The washing solution containing tachyzoites was collected and centrifuged for 15 min at 3000 rpm and the pellet washed 3 times. The pellet was digested with 10 ml of 0.25% trypsin at 37 ºC for 20 min to remove host cells, and then centrifuged as previously. Finally, the pellet was suspended in PBS, pipetted into 1.5 ml Eppendorf tubes, centrifuged and then the parasite pellet was preserved at -80 ºC until use for total RNA preparation.

tag: strain

tag: genotype

value: A genotype between I and II

tag: host

value: 8 wks old SPF-grade Kunming mice

value: Tachyzoites

tag: molecule subtype

value: microRNA


title: K562/ADM

city: Canberra

first: Stephen

middle: John

last: Ohms

state: Australian Capital Territory

address: Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Basecalls performed using CASAVA version 1.7.0
The Illumina small RNA read files (in fastq format) were first processed with the groupGAreads.pl Perl script (downloaded from the miRanalyzer web site) to condense the read files for upload. Singleton reads (i.e. reads with only one count) were omitted.
The condensed read files were then submitted to the miRanalyzer web server (http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php) and mapped (with Bowtie) to miRBase 16 and other libraries of transcribed sequences (listed on the miRanalyzer web site) using default parameters
Following mapping, normalization of the reads and analysis of differential expression was carried out with the R/Bioconductor DESeq package built-in to miRanalyzer
Genome_build: hg18
Supplementary_files_format_and_content: The edited miRanalyzer output Series supplementary file GSE51774_processed_data.txt contains differentially-regulated known microRNAs. The fields are: miRbase ID, Normalized read count K562, Normalized read count K562/ADM, Fold Change (K562:K562/ADM), log2(Fold Change (K562:K562/ADM)), Unadjusted p-value, Benjamini-Hochberg adjusted p-value

source_name: K562/ADM cell line

extract_protocol:
Total RNA was  isolated from K562 and K562/ADM cells and enriched using PEG to precipitate HMW RNAs. [Reference: Lu C, Meyers BC, Green PJ (2007) Construction of small RNA cDNA libraries for deep sequencing. Methods 43: 110-117.]
Small RNA libraries for sequencing were prepared based on Illumina’s alternative v1.5 protocol and a published method. [Reference: Lu C, Meyers BC, Green PJ (2007) Construction of small RNA cDNA libraries for deep sequencing. Methods 43: 110-117.]

treatment_protocol: A stable adriamycin (ADM,  Sigma)-resistant  cell line  variant (K562/ADM) was established from K562 by continuous exposure of the cells  to  increasing concentrations  of ADM up to 1000  ng/mL. Subsequently,  K562/ADM  cells  were cultured in the presence of 1000  ng/mL  of ADM to  maintain  the drug-resistant phenotype.

tag: cell line

value: stable adriamycin-resistant  cell line  variant (K562/ADM)


title: Pru

description: Sample 2

value: Pru

value: Type II


title: Cap_acid_metatranscriptome

first: Mallory

last: Embree

address: PFBH/EBU3a, 9500 Gilman Drive Rm. 414

department: Bioengineering

institute: University of California, San Diego

description:
processed data file: smith_cap_vs_hex_deseq.txt
smith_cap_vs_hex_cufflinks.txt
mconcilii_cap_vs_hex_cufflinks.txt
mconcilii_but_vs_hex_cufflinks.txt

data_processing:
Illumina RTA v1.13 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Smithella and Methanosaeta genomess using bowtie v0.12.8, 64 bit with parameters -X 400 -S -q -n 2 -m 1 -y -p 8. Data was mapped as single end data to increase mapping efficiency to the single cell genome. For the Butyric Acid and Caprylic Acid samples, the same libraries were sequenced 3 times on the Miseq to increase read count. All 6 files were then used for mapping.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks; Count data was generated and analyzed using HTSeq and Deseq
Genome_build: NC_015416 (Methanosaeta concilii), Smithella genome is pending in submission
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, as well as Deseq output if applicable.

organism: mixed culture KAZ_0815

source_name: Microbial community enrichment

growth_protocol: The consortium was propagated in the laboratory on anoxic medium containing 0.3 g NH4Cl, 0.5 g MgSO4•7H2O, 2.5 g NaHCO3, 0.5 g K2HPO4, 0.05 g KBr, 0.02 g H3BO3, 0.02 g KI, 0.003 g Na2WO2•2H2O, 0.002 g NiCl2•6H2O, trace elements and trace minerals as previously described (Zengler et al 1999). The medium was sparged with a mixture of N2/CO2 (80:20 v/v) and the pH was adjusted to 7.0. After autoclaving, anoxic CaCl2 (final concentration 0.25 g/L) and filter-sterilized vitamin solution were added. Cells were supplemented with 1.7 mmol anoxic hexadecane, 5 mM butyric acid, or 2 mM caprylic acid and incubated at 30 °C. Bottles were degassed as necessary to relieve over-pressurization. Cells from the hexadecane culture were used as innocula for the butyric acid and caprylic acid samples

extract_protocol:
Total RNA was extracted using a modified version of the Nuclespin RNA XS protocol. mRNA was purified using a modified version of the RiboZero Metabacteria protocol.
cDNA was generated from purified mRNA. Sequencing libraries were generated using a modified Nextera protocol.

treatment_protocol: The consortium was cultured on hexadecane, butyric acid, and caprylic acid.

tag: sample info

value: Undefined community:Includes Smithella sp, Methanosaeta concilii, Methanoculleus

tag: incubation time (days) before harvest

tag: carbon source

value: 2 mM caprylic acid

value: Archaea and Bacteria


title: QHO

description: Sample 3

value: QHO


title: XD

description: Sample 5

value: XD

value: Type I


title: nucleosome J1

first: Yong

last: Zhang

address: 1239 Siping Road

institute: Tongji University

description: Sample 1

data_processing:
All sequenced reads were aligned using bowtie version 4.1.2.
Uniquely mapped reads with a maximum of two mismatches were kept.
All mapped reads were extended to 147 bp in their 3’ direction, and the middle 73 bp were piled up to generate wig files.
Genome_build: mm9
Supplementary_files_format_and_content: wig format

source_name: embryonic stem cells

growth_protocol: ES cells were cultured in DMEM with 15% FBS and LIF.

extract_protocol: Collect 10ml cells in a 15ml BD tube, and fix in 1% formaldehyde for 1 minute at room temperature. Formaldehyde was quenched by adding 1ml 1.25M glycine. Cells were rinsed 3 times in ice-cold PBS, immediately resuspended in cell lysis buffer (10mM Tris-HCl pH7.5/10mM NaCl/0.5%NP40) and lysed for 5 min on ice. Nuclei were collected by centrifugation, washed with ice-cold PBS, collected by centrifugation again and resuspended in digestion buffer (50mM Tris-HCl pH7.5/1mM CaCl2/0.2%Triton X-100). Samples were divided into 200μl aliquots, prewarmed to 37°C and incubated with MNase (stored in MNase storage buffer (10mM HEPES pH7.5/100mM NaCl/1mM CaCl2/50% glycerol) and diluted in MNase dilution buffer (50mM Tris-HCl pH8/10mM NaCl/126mM CaCl2/5% glycerol)). Concentration of MNase and time of incubation were optimized to obtain 80% mononucleosomes as determined by Agilent 2100 BioAnalyzer analysis. Library were prepared using the Illumina sequencing library preparation protocol.

value: embryonic stem cells


title: But_acid_metatranscriptome

description:
processed data file: smith_but_vs_hex_deseq.txt
smith_but_vs_hex_cufflinks.txt

value: 5 mM butyric acid


title: RH

description: Sample 4

value: RH


title: K562

source_name: K562 cell line

treatment_protocol: Human chronic myelogenous leukemia  K562  cells  bought from ECACC (Sigma)  were cultured in complete RPMI 1640 medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2.


title: Dscam control mixture 2

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

country: Germany

institute: Technische Hochschule MIttelhessen

description: in vitro transcribed Dscam mRNA

data_processing:
Library strategy: Circularization-Assisted Multi-Segment Sequencing
The bases were called from the raw images using the offline base caller OLB-1.9.0. Note that due to our special multiple-segment sequencing protocol, the control lane produced output only for the first segment which contained the barcodes. Therefore the quality values of the produced fastq files are not reliable.
The read files were demultiplexed according to the barcodes. The barcodes consist of two parts which are ligated during the circularization step and then sequenced as one segment. A read was only retained if both parts of the barcode matched to the same reference sequence with at most one mismatch.
The three exonic segments of each read were aligned separately to the drosophila melanogaster dscam exon sequences using bowtie2 (parameters: --very-sensitive-local -5 3). Only the reads for which all three segments could uniquely be mapped to exons from the respective cluster were retained.
Genome_build: dm3
Supplementary_files_format_and_content: The processed data files contain the number of reads for each combination of exon 4 (1..12), exon 6 (1..48) and exon 9 (1..33).

source_name: in vitro transcribed Dscam mRNA

extract_protocol:
total RNAs were extracted using Trizol reagent following manufacturer's protocol.
Libraries were prepared using customized pipeline for our Circularization-Assisted Multi-Segment Sequencing. In brief, first, using RT-PCR with the barcode-indexed primers targeting constitutive exon 3 and exon 10, Dscam mRNA was reverse-transcribed and amplified. After circularization of the 2kb RT-PCR products and another round of PCR with the primers targeting constitutive exon 7 and exon 8, the amplification product of approximately 1kb in length was then sequenced.

tag: sample type

value: eight Dscam mRNAs with known concentrations by in vitro transcribing cloned Dscam cDNAs containing different combinations of exons 4, 6, and 9

tag: gene

value: Dscam


title: Dscam isoforms Profiling for S2 (2nd replicate)

source_name: S2 cell line

value: cell line derived from embryonic hemocytes


title: Hexadecane_metatranscriptome

description:
processed data file: smith_cap_vs_hex_deseq.txt
smith_cap_vs_hex_cufflinks.txt
smith_but_vs_hex_deseq.txt
smith_but_vs_hex_cufflinks.txt
mconcilii_cap_vs_hex_cufflinks.txt
mconcilii_but_vs_hex_cufflinks.txt

value: 1.7 mmol hexadecane


title: hESC_H1_Illumina

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

institute: Stanford

data_processing:
Illumina reads were aligned to reference genome hg19 by SpliceMap
PacBio reads were corrected by LSC
Gene isoforms were identified by IDP
Gene/transcript abundance was estimated by rSeq (optimized and integrated into IDP)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each transcript

molecule: polyA RNA

source_name: Human embryonic stem cell, H1

growth_protocol: Male human Embryonic Stem cells (H1) were used for our study. The cells were routinely cultured in feeder free conditions on Matrigel (BD) and in mTeSR1 (Stem Cell technologies). RNA seq was performed on cells between passage 50 and 55. The undifferentiated state of the hESCs was assayed by immunofluorescence for transcription factors OCT4 and NANOG and for the surface markers SSEA4, TRA-1-60 and TRA-1-81 (Figure S9). Pluripotency, assessed by teratoma assay, revealed the capacity of hESCs to form in vivo derivatives of the three germ layers

extract_protocol:
Total RNA was prepared by TRIzol extraction (Ambion; http://www.ncbi.nlm.nih.gov/pubmed/2440339) and treated with RNase-free DNase I to degrade contaminating gDNA. This was followed by a second extraction with acid-phenol-chloroform and the RNA was precipitated in 0.5M ammonium acetate and 2.5 volumes of ethanol. The integrity of the RNA was tested by a Bioanalyzer RNA Nano assay (Agilent). PolyA RNA was purified from the total RNA (>100 µg) using magnetic oligo-dT beads (Dynal) according to the manufacturer’s recommended protocol.
Two different manufacturer’s kits and accompanying protocols for generating full-length cDNAs were employed; Clontech SMARTer PCR and Invitrogen Superscript Full-Length cDNA kit. Each utilizes a retroviral reverse transcriptase to initiate cDNA synthesis at the 3’ polyA tail, but the two kits use different mechanisms to capture the 5’ end information. The Clontech method relies upon template-switching to an exogenous tag oligonucleotide when the reverse transcriptase reaches the 5’ end of the molecule. The Invitrogen method employs an RNase I digestion and subsequent 7-methyl-guanosine affinity step to purify the RNA-DNA hybrids that represent a full copy of the transcript. This is followed by an RNA ligase step to add a defined sequence to the 5’ ends of the polyA RNAs, prior to reverse transcription. For each method, 1 µg of polyA RNA served as the input material into the recommended protocol and the manufacturer methods were followed up through second strand cDNA synthesis. At this point, PCR (12-15 cycles; Phusion DNA polymerase. New England Biolabs) was used to amplify the double-stranded cDNA by using specific primers directed to the defined sequences present at the 5’ and 3’ ends of the cDNAs. Long extension times of 3.5 minutes ensure that longer molecules can be captured as well. The cDNA libraries were assayed by fluorimetry and Bioanalyzer assays. Both of Clontech and Invitrogen kits are reproducible. For example, housekeeping genes at different sizes (ACTB, 1808bp; GADPH, 1310bp; SARS 2291bp; IARS, NM_002161, 4406bp and NM_013417, 4510bp) are detected by full length long reads from the two preps .

value: Human embryonic stem cells

tag: passage


title: K15-CrePR/ KrasG12D/ Ptenff/LSL YFP; Telogen; Dorsal skin; YFP+ cells

status: Public on Oct 28 2013

city: Boulder

first: Zhaojie

state: CO

address: 2300 Arapahoe Ave

institute: University of Colorado at Boulder

description:
sample1
smallRNA profiling

data_processing:
adaptor removal with self-written python scripts
miRNA mapping with BLAST, parameters: -m 8
BLAST results parsing and miRNA counts with self-written python scripts
Genome_build: Mouse miRNA sequences from Mirbase.org (Release 17)
Supplementary_files_format_and_content: .txt file containing counts assigned to each miRNA

source_name: mouse skin

growth_protocol: Mice were housed in the Mouse Facility under standard conditions.

extract_protocol:
RNA was extracted from cells with the use of Trizol according to the Trizol manufacturer's instructions.
Ligation-based small RNA cloning protocol. Two adaptors (3' adaptor and 5' adaptor) were ligated to small RNAs followed by RT-PCR and gel-purification. Then purified PCR products were sent out for sequencing.
3' barcode('TGAGTC') after a miRNAs' read and IDT DNA linker1 sequence

value: mixed background (C57bl/6 and FVB)

tag: genotype/variation

value: K15-CrePR/ KrasG12D/ Ptenff/LSL YFP

tag: hair growth phase

value: Telogen

tag: tissue

value: Dorsal skin


title: Kidney_EC_translatome_2

city: Solna

first: Jan

middle: M

last: Stenman

address: Box 240

country: Sweden

institute: Ludwig Institute for Cancer Research Ltd

description:
Sample 20
ribosome bound RNA (TRAP RNA)

data_processing:
All reads were aligned to the mouse (mm10) genome using RNA-Seq unified mapper (RUM; Grant et al., 2011).
Non-uniquely mapped reads were removed.
Rpkgforgenes (available at http:sandberg.cmb.ki.se/rnaseq/), options  -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bamu, was used to generate RPKM values and read counts. Gene annotiations used were transcripts in RefSeq (January 2013).
Genome_build: UCSC version mm10 (Genome Reference Consortium GRCm38)
Supplementary_files_format_and_content: Gene expression values and read counts (tab-delimited text file).

source_name: kidney endothelial cells

extract_protocol:
Organ was dissected and homogenized in TRAP lysis buffer (Heiman et al., 2008, Cell). Extract was cleared by centrifugation. Ribosome-bound RNA was immunoprecipitated. RNA was eluted and purified using RNeasy® Micro Kit (Qiagen).
TruSeq RNA Sample Preparation Kits v2

tag: age

value: embryonic day 14.5

value: kidney endothelial cells


title: Kidney_EC_translatome_3

description:
Sample 21
ribosome bound RNA (TRAP RNA)


title: Kidney_EC_translatome_1

description:
Sample 19
ribosome bound RNA (TRAP RNA)


title: Kidney_translatome_3

description:
Sample 18
ribosome bound RNA (TRAP RNA)

source_name: kidney

value: kidney


title: edm2-4 RNA-seq

description: Sample 2

value: edm2-4 mutant

value: 14-d-old entire seedlings


title: Kidney_translatome_2

description:
Sample 17
ribosome bound RNA (TRAP RNA)


title: nf0h3b

value: Foreskin fibroblasts

tag: camptothecin exposure time

value: 0 minutes

tag: bromouridine labeling start

tag: bromouridine labeling time

value: 30 minutes

tag: treatment

value: Control

tag: stranded

value: TRUE


title: K15-CrePR/ LSL YFP (WT Control); Telogen; Ventral Skin; YFP+ cells

description:
sample3
smallRNA profiling

extract_protocol:
RNA was extracted from cells with the use of Trizol according to the Trizol manufacturer's instructions.
Ligation-based small RNA cloning protocol. Two adaptors (3' adaptor and 5' adaptor) were ligated to small RNAs followed by RT-PCR and gel-purification. Then purified PCR products were sent out for sequencing.
3' barcode('ACATGC') after a miRNAs' read and IDT DNA linker1 sequence

tag: strain

value: K15-CrePR/ LSL YFP (WT Control)

value: Ventral Skin


title: Kidney_translatome_1

description:
Sample 16
ribosome bound RNA (TRAP RNA)

tag: genotype


title: Dscam control mixture 1

description: in vitro transcribed Dscam mRNA

value: eight Dscam mRNAs with known concentrations by in vitro transcribing cloned Dscam cDNAs containing different combinations of exons 4, 6, and 9

value: Dscam


title: K15-CrePR/ LSL YFP (WT Control); Anagen; Dorsal skin; YFP+ cells

description:
sample2
smallRNA profiling

extract_protocol:
RNA was extracted from cells with the use of Trizol according to the Trizol manufacturer's instructions.
Ligation-based small RNA cloning protocol. Two adaptors (3' adaptor and 5' adaptor) were ligated to small RNAs followed by RT-PCR and gel-purification. Then purified PCR products were sent out for sequencing.
3' barcode('GTGTAC') after a miRNAs' read and IDT DNA linker1 sequence

value: mixed background (C57bl/6 and FVB)

value: Anagen


title: Kidney_transcriptome_2

description: Sample 14

extract_protocol:
Organ was dissected and homogenized in TRAP lysis buffer (Heiman et al., 2008, Cell). Extract was cleared by centrifugation. RNA was purified using RNeasy® Micro Kit (Qiagen).
TruSeq RNA Sample Preparation Kits v2


title: Kidney_transcriptome_1

description: Sample 13


title: Brain_Emx1_translatome_3

description:
Sample 12
ribosome bound RNA (TRAP RNA)

source_name: forebrain emx1-lineage

value: forebrain (emx1-lineage)


title: Brain_Emx1_translatome_1

description:
Sample 10
ribosome bound RNA (TRAP RNA)

value: embryonic day 14.5


title: Brain_Emx1_translatome_2

description:
Sample 11
ribosome bound RNA (TRAP RNA)


title: Brain_translatome_1

description:
Sample 4
ribosome bound RNA (TRAP RNA)

source_name: forebrain

value: forebrain


title: Brain_EC_translatome_2

description:
Sample 8
ribosome bound RNA (TRAP RNA)

source_name: forebrain endothelial cells

tag: cell type

value: forebrain endothelial cells


title: Brain_EC_translatome_1

description:
Sample 7
ribosome bound RNA (TRAP RNA)


title: Brain_translatome_3

description:
Sample 6
ribosome bound RNA (TRAP RNA)


title: Brain_transcriptome_2

description: Sample 2


title: Brain_transcriptome_3

description: Sample 3


title: Brain_transcriptome_1

description: Sample 1


title: Brain_EC_translatome_3

description:
Sample 9
ribosome bound RNA (TRAP RNA)


title: RNA-Seq_Smc2_R2

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: RNA-Seq from mES cells after knockdown of Smc2.

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all RNA-Seq samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 2 -n 2 --best --sam. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq RPKM expression values were computed for each gene using RPKM_count.py 2.3.5.

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (iMEFs). For expression analysis, cells were grown for one passage off of iMEFs, on gelatinized tissue-culture plates.

extract_protocol:
Total RNA extraction was performed using the miRVana miRNA extraction kit (Ambion, AM1560) and the recovered RNA was eluted in 30 μl elution buffer. Cell numbers were counted from proxy plates using C-Chip disposable hemocytometers (Digital Bio).  An amount of RNA that corresponds to 6.52E+05 cells was used for subsequent steps. Total RNA concentrations were measured using the NanoDrop ND-1000.  Synthetic RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added to each sample based on cell number.  For each sample 1.42 ul of a 1:10 dilution of the synthetic RNA Mix 1 was added to each RNA sample.
Libraries were prepared using the TruSeq RNA Kit version 2 (Illumina, RS-122-2001) according to manufacturer's instructions.

treatment_protocol: shRNA plasmids targeting the mouse CapH2, Smc2, Smc1 mRNA and GFP (control) (Open Biosystems, Huntsville) were used. Sample CapH2 R1(also known as #3) used hairpin TRCN0000175785, CapH2 R2 (also known as #4) used TRCN0000175531, Smc2 R1 also known as #1) used TRCN0000108952, Smc2R2 (also known as #2) used TRCN0000108953, Smc1 used TRCN0000109033, and GFP used TRCN0000072201.  Viral media was collected 48 hours after co-transfection and the V6.5 mES cells were directly infected with the viral media 24 hours after initial plating of the mES cells. The infection media was 1:5 viral media:mES cell media with 8ug/ml polybrene. The efficiently infected cells were grown for 24 hours before selection with 0.5ug/ml puromycin for 48hours, then 1ug/ml puromycin for 48 more hours. V6.5 cells were cross-linked 96 hours post selection and frozen for experiments such as RNA-Seq, measuring knockdown efficiency and cell counting.

value: V6.5 embryonic stem cells

tag: cell count

tag: shRNA

tag: barcode (already removed)

value: ATTCCT


title: RNA-Seq_Smc2_R1

value: ACTGAT


title: Kidney_transcriptome_3

description: Sample 15

value: kidney


title: RNA-Seq_CapH2_R2

description: RNA-Seq from mES cells after knockdown of CapH2.

value: GAGTGG


title: RNA-Seq_Smc1

description: RNA-Seq from mES cells after knockdown of Smc1.

value: ATCACG


title: RNA-Seq_CapH2_R1

value: CGTACG


title: Brain_translatome_2

description:
Sample 5
ribosome bound RNA (TRAP RNA)


title: Mg_H3K36Me3

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

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

source_name: mammary gland

extract_protocol: Illumina standard protocol

tag: tissue type

value: mammary gland

tag: developmental stage

value: lactation day 8

tag: gender

value: female

tag: antibody

tag: antibody vendor

value: abcam

tag: antibody catalog #

tag: antibody lot #


title: Mg_H3K27Me3_rep1

value: millipore


title: UNG KO gammaH2AX ChIP-seq, untreated

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: 2109 Adelbert Rd.

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Unique reads were aligned to the hg18 genome assembly using Bowtie, discarding reads with > 1 reportable alignment (-m 1)
Peaks were called using MACS 1.4 using the drug-treated sample as the treatment file and the untreated sample as the control file with a step size of 25 bp
Genome_build: hg18
Supplementary_files_format_and_content: sgr files were created from MACS-generated wig files and give ChIP-seq signal in 25 bp windows across chromosomes 1-22 and X

source_name: Cultured cells

extract_protocol:
ChIP was performed as described (PMID 19275939).
Sequencing libraries were constructed as described (PMID 19275939) with the exception of the library amplification step.  Instead of Phusion DNA polymerase, Expand High Fidelity PLUS (Roche) was used with the following cycling parameters:  The following parameters were used for thermal cycling: 5 min at 94°C, 18  cycles of 30 sec at 94°C, 30 sec at 65°C, and 60 sec at 72°C followed by a 7 min final elongation at 72°C.

tag: cell line

tag: genotype/variation

value: UNG knockout; UNG-/-

tag: treated with

tag: chip antibody

value: Anti-gamma H2A.X (phospho S139) antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Mg_H3K36Me3_input

tag: strain


title: Lvr_H3K36Me3

source_name: liver

value: liver


title: Lvr_H3K36Me3_input


title: Lvr_H3K27Me3_input


title: Mec_H3K35Me3

source_name: mammary epithelial cells

tag: cell type

value: mammary epithelial cell

value: 12 week virgin-diestrus


title: Mg_H3K27Me3_input


title: UNG KO gammaH2AX ChIP-seq, pemetrexed-treated

value: pemetrexed


title: Mg_H3K27Me3_rep2


title: Lvr_H3K27Me3_rep2


title: Lvr_H3K27Me3_rep1


title: UNG WT gammaH2AX ChIP-seq, pemetrexed-treated

value: wild type; UNG+/+


title: UNG KO gammaH2AX ChIP-seq, cisplatin-treated

value: cisplatin


title: UNG WT gammaH2AX ChIP-seq, untreated


title: RNA_Seq_GFP

description: RNA-Seq from mES cells after knockdown of GFP (control).

value: V6.5 embryonic stem cells

tag: cell count

tag: shRNA

value: CGATGT


title: UNG WT gammaH2AX ChIP-seq, cisplatin-treated


title: pre3_NT

status: Public on Oct 27 2013

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

description: extracting total RNA 36h later ater Vc treatment

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9
Supplementary_files_format_and_content: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.

source_name: mouse embryonic fibroblasts (MEFs)

extract_protocol:
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: passage

tag: medium

value: vitamin C (vc)

tag: treatment

value: untreated control


title: pre2-2_NC

description: extracting total RNA 48h later after transfecting Control siRNA(including 36h Vc treatment)

value: control siRNA


title: pre2-2_siTet1

description: extracting total RNA 48h later after transfecting Tet1 siRNA(including 36h Vc treatment)

value: Tet siRNA


title: pre3_NC


title: pre3_siTet1


title: Wildtype parasite sample

status: Public on Oct 26 2013

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 major Friedlin 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: LmjF V4.1
Supplementary_files_format_and_content: Gene level splice leader read count data generated using custom scripts. The read counts are median normalzied within each library

organism: Leishmania major

source_name: laboratory culture, whole cell lysate

growth_protocol: All studies used derivatives of Leishmania major Friedlin V1 (MHOM/JL/81/Friedlin), grown at 26°C in M199 medium (US Biologicals) supplemented with 40 mM 4-(2-hydroxyethyl)-1-piperazineethanesuphonic acid (HEPES) pH 7.4 (Fisher Scientific), 100 uM adenine (Sigma), 1 µg mL-1 biotin (Sigma), 10 µg mL-1 hemin (Sigma), 2 µg mL-1 biopterin (Schircks Laboratories), 50 units/mL penicillin (Gibco), 50 µg/mL streptomycin (Gibco), and 10% (v/v) heat inactivated fetal calf serum (HyClone). Cell density was determined by using a model Z1 Coulter counter (logarithmic phase) or hemocytometer (stationary phase). Metacyclic promastigotes were purified from stationary phase day 4 cultures using a negative peanut agglutination assay [22]. Semisolid M199 medium was prepared using supplemented M199 medium with 1% (w/v) Difco noble agar (BD Diagnostic Systems)

extract_protocol:
Logarithmically-growing promastigotes from WT L. major FV1, one H3V/HYG transfectant, and two Δh3v transfectants were collected and resuspended at a concentration of 5x108 cells/mL in TriZOL (Invitrogen). The aqueous phase was isolated by adding 0.2 mL chloroform (Fisher Scientific) and centrifugation at 12,000 x g for 15 minutes at 4°C. The aqueous phase was isolated and RNA was precipitated by adding 1 volume of 100% isopropanol (Fisher Scientific) and centrifugation at 12,000 x g for 10 minutes at 4°C. The RNA pellet was washed with 75% ethanol (Pharmco) and was resuspended in nuclease-free water (Ambion). Purified RNA was treated with 20 units of DNAse I (Ambion) and was precipitated using 1/10 volumes 3M sodium acetate (Sigma) and 3 volumes 100% ethanol. RNA was pelleted by centrifugation at 15,000 g-1 and the resulting pellet was washed with cold 75% ethanol and resuspended in RNAse-free water (Ambion).
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.

value: Friedlin V1 (MHOM/JL/81/Friedlin)

tag: lifestage

value: promastigotes

tag: genotype

value: wildtype

tag: growthphase

value: early log


title: pre2-2_NT


title: H3V double knockout parasite sample2

value: H3V gene knockout - homozygous


title: H3V double knockout parasite sample1


title: H3V single knockout parasite sample

value: H3V gene knockout - heterozygous


title: Ion_mDC_polII

status: Public on Oct 25 2013

first: Christine

middle: S

last: Cheng

address: 7 Cambridge Center

institute: Broad Institute of MIT and Harvard

data_processing:
alignment were performed using BWA aligner
ChIP-seq peak calling was performed using the contiguous segmentation algorithm as part of the Scripture package (http://www.broadinstitute.org/software/scripture/)
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bed files are output from scripture program, which identify ChIP-seq regions that have enriched peaks

source_name: mouse dendritic cells

growth_protocol: Mouse dendritic cells were isolated from wild type C57BL/6 mice and cultured as previously published. Melanoma tumor derived cell lines were culturedin 10% FCS medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to Illumina or Ion Torrent protocols.

treatment_protocol: mouse dendritic cells were treated with 0.1ug/ml LPS

value: polII

tag: antibody concentration (ug/ml)

value: mouse dendritic cells


title: Ion_mDC_H3K4me3_0.4ng


title: Ion_mDC_H3K4me3_56ng


title: Ion_H3K4me3_melanoma_tumor_5

source_name: Melanoma tumor tissue

value: Melanoma tumor tissue


title: Ion_H3K4me3_melanoma_tumor_4


title: Ion_mDC_H3K4me3_4ng


title: Ion_WM266-4_H3K4me3

source_name: Melanoma derived cell line

tag: cell line

value: Melanoma derived cell line


title: Ion_WM115_H3K4me3


title: RTT2-iPS-32bi

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: gene expression in iPSC

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 human genome by Tophat.
FPKM value was calculated by Cufflinks
Genome_build: hg19

source_name: induced pluripotent stem cell from RTT patient

growth_protocol: ESC and iPSC were cultured in hES medium containing bFGF.

extract_protocol:
Total RNA was isolated using RNeasy kit (QIAGEN) followed by cDNA synthesis usingSuperscript Reverse Transcriptase kit (iScript™ cDNA Synthesis Kit, Bio-rad).
Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Part# RS-100-0801).

treatment_protocol: iPSCs were incubated in the virus supernatant supplemented with protamine sulfate for 24 hr and then the cells were replaced in fresh ES culturing medium added puromycin at a final concentration of 1 µg/ml. iPSC colonies resistant to puromycin were selected for 2 weeks, and used to confirm the knock-down of MeCP2.

value: RTT2 fibroblast

tag: mutation

value: no


title: RTT3-iPS-46bi

description: gene expression in iPSC

value: RTT3 fibroblast


title: Ion_WM115_H3K27me3


title: Ion_H3K4me3_melanoma_tumor_2


title: RTT4-iPS-19bi

description: gene expression in iPSC

value: RTT4 fibroblast


title: Ion_H3K4me3_melanoma_tumor_3


title: PGP1-iPSCs

description: gene expression in iPSC

source_name: induced pluripotent stem cell


title: Ion_H3K4me3_melanoma_tumor_6


title: Ion_H3K4me3_melanoma_tumor_7


title: Detroit551-iPSCs

description: gene expression in iPSC


title: RTT5-iPS-42m

description: gene expression in iPSC

value: RTT5 fibroblast


title: Ion_WM266-4_H3K27me3


title: H1

description: gene expression in ESC

source_name: human embryonic stem cell


title: H7

description: gene expression in ESC