title: ccg1-clr2-mC-4A-34


title: MB052_6

status: Public on Sep 01 2015

type: SRA

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
Raw reads aligned using lifescope to hg19 reference genome containing IUPAC ambiguity codes for SNPs listed in dbSNP 135.
Whole gene and isoform expression generated by cufflinks version 2.1.1 using multiread correction and without effective length correction.  Whole gene expression estimated by summation of isoform expression of measurments with status "OK".
SNP calling was performed through samtools mpileup specifically for known heterozygous SNP locations confirmed by SNP chip genotyping generating allele counts.  These allele counts are used to make allelic expression ratio calculations.
Genome_build: hg19 with IUPAC codes for dbSNP 135

molecule: total RNA

organism: Homo sapiens

source_name: hippocampus

extract_protocol:
Frozen brain tissue was homogenized in Trizol (Invitrogen/Life Technologies, Carlsbad, CA), and then phase separated with chloroform. The RNA containing aqueous layer was diluted in binding buffer and applied to Qiagen (Venlo, Limburg, Netherlands) or Denville (South Plainfield, NJ) RNA isolation columns. The bound RNA was DNAse treated and eluted according to kit procedures. Fifty nanograms of total RNA was converted to cDNA and isothermally amplified using the NuGen Ovation RNA-Seq kit procedures (NuGen, San Carlos, CA).
The NuGen brain cDNA was sheared to approximately 150 bp fragments using the Covaris S (Woburn, MA). After shearing, fragments were recovered by centrifuging over an YM-30 spin filter (Amicon, Merck Millipore, Billerica, MA). Fragments greater than 100 bp were retained and eluted from the membrane, with ~ 90% recovery. Bar-coded paired-end SOLiD sequencing libraries were prepared using either SOLiD (Applied Biosystems/Life Technologies, Carlsbad, CA) or NEB (New England Biolab, Ipswich, MA) DNA library preparation kits. The cDNA was end repaired, and then barcoded SOLiD DNA sequencing adaptors were ligated to 1 microgram of input cDNA according to kit instructions. Ligated library product was size selected using a Pippin gel electrophoresis system (Sage Biosciences, Beverly, MA). The prepared library was enriched for correctly adapted product using 5-8 cycles of PCR.

tag: individual

tag: smoker

value: nonsmoker

tag: Sex

value: male


title: MB052_9

source_name: raphae nuclei


title: ccg1-clr2-mC-4A-26

city: Berkeley

first: James

last: Craig

state: CA

address: 341A Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

description:
chromatin immuno precipitated DNA
2015_04_14_SD2_MACS_output_&_Nearby_genes.xlsx

library_source: genomic

data_processing:
reads were aligned with Bowtie2
MACS
genes surrounding the identified peaks were annotated
Genome_build: aligned to Neurospora crassa genome version 12 mitochondria version 10
Supplementary_files_format_and_content: tab delimited spreadsheet of the MACS output with the nearest genes surrounding the peak annotated

molecule: genomic DNA

organism: Neurospora crassa

source_name: whole tissue

growth_protocol: Neurospora crassa was grown on Vogel's Mininal Media for 16 hrs with Sucrose as the carbon source

extract_protocol:
Cells were ground in liquid nitrogen and DNA sheared by sonication, the chromatin was immunoprecipitated by antibody to epitope-tagged transcription factors
Libraries were prepared according to Illumina's instructions for the Genomic DNA Prep Kit, adapters were diluted 1:20, and PCR amplification was carried out to 24 cycles.

treatment_protocol: The filamentous fungus was washed and transferred to fewsh Vogel's Media with Avicel, Xylan, or Sucrose as the carbon source

tag: strain

value: Neurospora crassa OR74A (FGSC2489)

tag: genotype

tag: chip antibody

value: mCherry


title: 93-11-3D endosperm

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

data_processing:
MeDIP-seq reads were aligned to the japonica genome (version 7.0, http://rice.plantbiology.msu.edu/) using BOWTIE2 with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
Enriched regions of DNA methylation were identified using MACS14.
Genome_build: the japonica genome (version 7.0, http://rice.plantbiology.msu.edu/)
Supplementary_files_format_and_content: peak files

organism: Oryza sativa

source_name: Oryza sativa endosperm

growth_protocol: Rice variety Zhonghua11 (Oryza sativa spp. Japonica) and 93-11 (Oryza sativa spp. indica) were cultivated in a phytotron with a light (12h, 28℃)/dark(12h, 22℃) cycle.

extract_protocol:
DNA was extracted from the embryo and endosperm of rice seeds. Methylated DNA was isolated with  anti 5-mc antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq2000 following the manufacturer's protocols.

treatment_protocol: Embryo of 3,6,9 days after pollination (DAP) and endosperm of 2,3,6,9 DAP were manually selected under the dissecting scope. Selected embryo and endosperm were transferred to the eppendorf tube, rinsed with ethanol and placed on ice in the 100% ethanol.

tag: tissue

value: endosperm

tag: developmental stage

value: 3 DAP

tag: cultivar


title: MB052_7

source_name: posterior putamen


title: ccg1-clr2-mC-24A-7


title: ccg1-xlr1-gfp-4X-65

value: GFP


title: MB052_3


title: MB151_5

source_name: amygdala


title: ccg1-clr1-gfp-input-24A-2


title: ccg1-clr1-gfp-ab-24A-2


title: MB052_2


title: human ts 1 RT-

city: Berlin

first: Jorge

last: Ruiz-Orera

state: Berlin

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbruck Center for Molecular Medicine

description:
DNA control, no reverse transcriptase, dUTP stranded protocol, paired-end reads
Strand-specific and paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences using Condetri with the following settings (-hq=30 –lq=10). Adapters were trimmed from filtered reads if at least 5 nucleotides of the adaptor sequence matched the end of each read. In all experiments, reads below 50 nucleotides or with only one member of the pair were not considered.
We aligned the reads to the correspondent reference species genome with Tophat (v. 2.0.8) with parameters –N 3, -a 5 and –m 1, and including the correspondent parameters for paired-end and strand-specific reads whenever necessary. Multiple mapping to several locations in the genome was allowed unless otherwise stated.
Genome_build: hg19, panTro4, rheMac2 (Mmul_051212), mm10
Supplementary_files_format_and_content: Cufflinks output (isoforms.fpkm_tracking) containing abundance measurements and transcript assembly coordinates

molecule: polyA RNA

source_name: Testis

extract_protocol:
Total RNA was extracted using a miRNeasy Mini kit.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer’s protocol.  Poly (A)-positive RNA was purified from 250-500 mg of total RNA using streptavidin-coated magnetic beads (AMPure XP) and subsequently fragmented to ~300 bp. cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen) and random primers. The strand-specific RNA-Seq library preparation was based on the incorporation of dUTP in place of dTTP in the second strand of the cDNA. Double-stranded DNA was further used for library preparation. Such dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and they were quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems). Sequencing was done with a Illumina HiSeq 2000 sequencer in a paired-end design according to the manufacturer’s instructions.

value: Testis

value: Male

tag: age

value: 41 weeks

tag: protocol


title: ccg1-clr1-gfp-4S-5


title: ccg1-clr1-gfp-4S-38


title: MB052_1


title: human lv 1

description:
dUTP stranded protocol, paired-end reads
Strand-specific and paired-end RNA-seq

source_name: Liver

value: Liver

value: dUTP stranded protocol


title: MB011_9

value: smoker


title: ccg1-clr1-gfp-4A-4


title: human ht 2

source_name: Heart

value: Heart

value: 56 weeks


title: MB052_5


title: ccg1-clr1-gfp-4A-37


title: MB011_7


title: human ht 1


title: human br 2

source_name: Brain

value: Brain

value: 67 weeks


title: MB011_6


title: MB052_4

source_name: insula

value: nonsmoker


title: ccg1-clr1-gfp-4A-27


title: MB011_5

value: male


title: human ts 2

value: 25 weeks


title: 6971_4X_Vogels3

data_processing:
alignment was performed by Tophat (v2.04)
Raw Gene counts was performed by Htseq (0.6)
Gene counts were normalized by Cufflinks (v2.02)
Differential expression was performed with Cuffdiff (v2.02)
Genome_build: aligned to Neurospora crassa genome version 12 mitochondria version 10 (BROAD)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, raw gene counts, and differential expression analysis comparing 2 or more libraries

source_name: whole fungus

extract_protocol:
Total RNA was extracted using Phenol Chlorophorm, ethanol  precipitated, and DNAsed and cleaned on a Qiagen column
Libraries were prepared using standard Illumina protocols

treatment_protocol: The filamentous fungus was washed and transferred to fresh Vogel's Media with Xylan or Sucrose as the carbon source or Vogel's without a carbon source.

value: Neurospora crassa OR74A (FGSC2489)

value: FGSC2489; deltaxlr-1::HygR


title: 6971_4X_Vogels4


title: human br 1

value: 24 weeks


title: human ts 1

value: 71 weeks


title: MB011_4


title: mRNA-seq from M cells, pretreated with cycloheximide_2

city: San Francisco

first: Marvin

last: Tanenbaum

state: ca

address: Genentech Hall, MC 2200, Room N316,   600 16th street

department: CMP

institute: UCSF

description:
mRNA-seq
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
M_exp2_mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3’ ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the human genome hg19
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions
wig files were then generated by summing the numbers of reads obtained from each position in the human genome. For this each read was counted once, for the mRNA samples the 5' end of each read was used, for the ribosome footprints samples the caculated postion of the ribosome P-site was used.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.
Supplementary_files_format_and_content: [Supplemental_table_S1_mRNA_analysis.txt] A list of genes for which at least one of the samples (G2, M or G1) had at least a sum of 200 reads in the mRNA sample.
Supplementary_files_format_and_content: [Supplemental_table_S2_TE_analysis.txt] A list of genes for which all three samples had at least a sum of 200 reads in the mRNA sample, and at least one sample had at least 200 reads in the ribosome footprint sample.

source_name: Human Retinal pigment epithelial cells immortalized with hTERT

extract_protocol:
RNA was extracted by lysing cells with Trizol
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.

tag: cell type

value: RPE-1 cells immortalized with hTERT

tag: cell synchronization

value: Cells were treated with 6 micromolar RO-3306 for 18 hr. RO-3306 was then removed and mitotic cells were harvested 45 min later through mitotic shake-off

tag: cell cycle timepoint

value: M

tag: drug pre-treatment

value: cells were pretreated with cycloheximide


title: MB011_3


title: 6971_4X_Vogels1


title: MB011_2


title: 6971_4X_Vogels2


title: human lv 2

value: Liver

value: Male

value: 64 weeks

value: dUTP stranded protocol


title: MB011_8

source_name: cerebellum

value: smoker


title: xlr-1-A828V_4S_Vogels

value: FGSC2489; his-3::p_ccg1::xlr-1-A828V, deltaxlr-1::HygR, mat a


title: MB011_1


title: xlr-1-A828V_4NC_Vogels2


title: xlr-1-A828V_4NC_Vogels3


title: mRNA-seq from G1 cells, pretreated with cycloheximide_2

description:
mRNA-seq
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
G1_exp2_mRNA

value: Cells were treated with 6 micromolar RO-3306 for 18 hr. RO-3306 was then removed and mitotic cells were collected 45 min later through mitotic shake-off and replated to allow normal mitotic exit. 3hr later G1 cells were harvested.


title: mRNA-seq from G2 cells, pretreated with cycloheximide_1

description:
mRNA-seq
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
G2_exp1_mRNA

value: Cells were treated with 6 micromolar RO-3306 for 18 hr and harvested


title: mRNA-seq from G1 cells, pretreated with cycloheximide_1

description:
mRNA-seq
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
G1_exp1_mRNA


title: xlr-1-A828V_4NC_Vogels1


title: Ribosome footprints from M cells, pretreated with cycloheximide_2

description:
Ribosome profiling of ribosome-protected mRNA
library strategy: Ribosome profiling
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
Supplemental table S2_TE analysis.txt
M_exp2_FP

extract_protocol:
Cells were lysed with 0.5% triton, the lysate was cleard by centirifugation, treated with RNaseI for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using acid:Phenol extraction method
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.


title: 2489_4X_Vogels2


title: Ribosome footprints from M cells, pretreated with cycloheximide_1

description:
Ribosome profiling of ribosome-protected mRNA
library strategy: Ribosome profiling
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
Supplemental table S2_TE analysis.txt
M_exp1_FP


title: Ribosome footprints from G2 cells, pretreated with cycloheximide_2

description:
Ribosome profiling of ribosome-protected mRNA
library strategy: Ribosome profiling
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
Supplemental table S2_TE analysis.txt
G2_exp2_FP


title: Ribosome footprints from G2 cells, pretreated with cycloheximide_1

description:
Ribosome profiling of ribosome-protected mRNA
library strategy: Ribosome profiling
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
Supplemental table S2_TE analysis.txt
G2_exp1_FP


title: 2489_4X_Vogels3


title: 2489_4X_Vogels1


title: Ribosome footprints from G1 cells, pretreated with cycloheximide_2

description:
Ribosome profiling of ribosome-protected mRNA
library strategy: Ribosome profiling
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
Supplemental table S2_TE analysis.txt
G1_exp2_FP


title: Hi-C, SK-N-SH, Replicate 1

city: La Jolla

first: David

last: Gorkin

state: California

address: 9500 Gilman Dr. CMM-East 2071

institute: Ludwig Institute for Cancer Research

data_processing:
Hi-C reads were mapped to hg19 using BWA-MEM. Reads were aligned as single ends, and read pairs are then re-constructed after mapping.
Unmapped reads were filtered out and PCR duplicate reads were removed with PicardTools MarkDuplicates.
Contact matrices were constructed at 40kb resolution and normalized with HiCNorm (Hu, M. et al., Bioinformatics. 2012. PMID: 23023982).
Topologically associated domains (“TADs”) were identified based on Directionality Index (“DI”) as described previously (Dixon et al., Nature. 2012. PMID: 22495300), with one exception: DI was calculated using a sliding window of 300 kb upstream/downstream of the view point.
Genome_build: hg19

source_name: SK-N-SH

growth_protocol: Cells cultured in RPMI media supplemented with 10% FBS

extract_protocol: Hi-C and library prep were performed as previously described (Dixon et al., Nature. 2012. PMID:22495300).

treatment_protocol: Cells crosslinked for 10 minutes at room temperature with 1% formadehyde. Quencing was performed with 0.125M glycine for 5 minutes are room temperature

tag: cell line

value: SK-N-SH


title: Ribosome footprints from G1 cells, pretreated with cycloheximide_1

description:
Ribosome profiling of ribosome-protected mRNA
library strategy: Ribosome profiling
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
Supplemental table S2_TE analysis.txt
G1_exp1_FP


title: 293 PTBP1 and PTBP2 double knockdown with exon-excluded PTBP1 overexpression_rep1

city: Toronto

first: Serge

last: Gueroussov

state: Ontario

address: 160 College Street, Room 1030

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Splicing analysis: Detailed description of the analysis pipeline can be found in [Irimia et al. Cell 159, 1511-1523 (2014)]. A summary of the main steps is provided here. An RNA-Seq dataset is first aliged to the genome using Bowtie. Reads that map to the genome are discarded from further analysis since exon-exon junctions (EEJs) are absent from genomic sequence. Reads that failed to align to the genome are aligned to a custom library of EEJs using Bowtie. To quantify splicing, the combination of EEJs that define each splicing event was created. For the case of single exon skipping events, we generated EEJs for C1A, AC2 and C1C2 (A represents the alternative exon and C1 and C2 represent the neighboring constitutive exons), requiring a minimum of eight positions from each exon. For multi-exon events we generated all possible forward combinations from C1 to C2 exons. If multiple alternative 5’ and/or 3’ splice sites were associated with any alternative, C1 or C2 exons, they were also included in the combinations. Read counts for each EEJ were then used to calculate the Percent Spliced In (PSI) of each event. A  simplified format of the formula is: PSI = 100% * (reads supporting inclusion / total reads).
Genome_build: Homo sapiens, hg19; Gallus gallus, galGal3
Supplementary_files_format_and_content: 293_all_splicing_events.tab: tab delimited text file summarizing the splicing analysis of 293 data, where each row corresponds to a unique splicing event. The table has the following columns: GENE - gene ID, EVENT - unique event ID containing the ENSEMBL gene ID, COORD - genomic coordinates of the alternative exon, LENGTH - nucleotide length of the alternative exon, FullCO - genomic coordinates of alternative exon as well as the coordinates of the last and first basepairs of the upstream and downstream exons, respectively, COMPLEX - refers to type of splicing event (S/C1/C2/C3: alternative cassette exon > 15 nucleotides, ME: mutually exclusive exons, Alt3: alternative 3´ splice site, Alt5: alternative 5´ splice site, MIC: alternative micro cassette exon ≤ 15 nucleotides), siCon+siCon2 - PSI in cells treated with control siRNA (2 replicates), KD+KD2 - PSI in cells treated with PTBP1 + PTBP2 siRNA (2 replicates), Resc_L+Resc_L2  - PSI in cells treated with PTBP1 + PTBP2 siRNA with overexpression of full-length PTBP1 (2 replicates), Resc_S+Resc_S2 - PSI in cells treated with PTBP1 + PTBP2 siRNA with overexpression of exon-skipped PTBP1 (2 replicates), siCon.Q+siCon2.Q+KD.Q+KD2.Q+Resc_L.Q+Resc_L2.Q+Resc_S.Q+Resc_S2.Q - quality scores for the corresponding PSI values, see  [Irimia et al. Cell 159, 1511-1523 (2014)] for details. // dt40_all_splicing_events.tab: tab delimited text file summarizing the splicing analysis of dt40 data, where each row corresponds to a unique splicing event. First 6 columns are the same as in 293_all_splicing_events.tab, WT1 + WT2 - PSI in wildtype cells (2 replicateS), HET34 + HET48 - PSI in cells with PTBP1 exon 8 delted from one allele (2 indepndent clones), HOM3 + HOM7 - PSI in cells with PTBP1 exon 8 deleted from both alleles (2 independent clones), WT1.Q+WT2.Q+HET34.Q+HET48.Q+HOM3.Q+HOM7.Q - quality scores for the corresponding PSI values, see  [Irimia et al. Cell 159, 1511-1523 (2014)] for details.

source_name: Flp-In™ T-REx™ 293 Cell Line

growth_protocol: Monolayer growth in DMEM with 10% FBS

extract_protocol:
Total RNA was extracted from cultured cells using TRI reagent (Sigma).
Standard illumina protocol with DNAse treatment and polyA selection.

treatment_protocol: siRNA transfection with Lipofectamine RNAiMax (Life Technologies)

value: inducible 3xFLAG exon-excluded PTBP1 at Flp-In locus


title: mRNA-seq from M cells, pretreated with cycloheximide_1

description:
mRNA-seq
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
M_exp1_mRNA


title: BicR 5-mC

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.16.
Signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5)
Genome_build: hg18
Supplementary_files_format_and_content: Bed files can be visualized by Integrative genomic viewer ver 2.2 (IGV ver 2.2)

source_name: prostate cancer cells

growth_protocol: LNCaP and BicR cells were cultures in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. For 5-mC and 5-hmC immunoprecipitation, we used methycollector and hydroxymethylcollector (Active motif) to obtain double stranded DNA modified with 5-mC and 5-hmC.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).

treatment_protocol: LNCaP and BicR cells were treated with vehicle or DHT 10 nM for 24 h or 1h.

value: BicR

value: prostate cancer

tag: treatment

value: anti-negative control miRNA

value: 5-mC (Methylcollector:active motif)


title: 293 PTBP1 and PTBP2 double knockdown with full-length PTBP1 overexpression_rep2

value: inducible 3xFLAG full-length PTBP1 at Flp-In locus


title: anti-miR BicR 5-mC

value: anti-miR-29b treatment


title: 293 PTBP1 and PTBP2 double knockdown with exon-excluded PTBP1 overexpression_rep2


title: Hi-C, SK-N-SH, Replicate 2


title: BicR input

value: input


title: mRNA-seq from G2 cells, pretreated with cycloheximide_2

description:
mRNA-seq
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified.
Supplemental table S1_mRNA analysis.txt
G2_exp2_mRNA

value: RPE-1 cells immortalized with hTERT

value: cells were pretreated with cycloheximide


title: BicR 5-hmC


title: anti-miR BicR 5-hmC


title: 293 PTBP1 and PTBP2 double knockdown_rep2

value: wildtype


title: 293 PTBP1 and PTBP2 double knockdown with full-length PTBP1 overexpression_rep1


title: LNCaP 5-hmC

value: LNCaP

value: no treatment


title: 293 control knockdown_rep1


title: 293 control knockdown_rep2


title: LNCaP 5-mC


title: DS21512

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description:
The following processed data files are pooled  pooled short read data from 2 biological replicates (GSM1824054 [DS19056] and GSM1824055 [DS21512]):
Col-0.Root.Hair.DNase.pooled.6.8M.signal.bw
Col-0.Root.Hair.DNase.pooled.6.8M.peaks.bed

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to A. thaliana reference TAIR10 with bowtie version 0.12.7 with the following parameters: bowtie -p 8  --mm -n 2 -m 1 --best --phred33-quals
Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration except that peak thresholding was set to 95 percentile.
Tissue and cell type DNase I data were subsampled to a uniform lebel of 6.8 million reads (excluding ChrC/ChrM), subsequent processing steps were applied to this subsampled set
4DPA and 7DPA DNase I data were subsampled to a uniform lebel of 6.65 million reads (excluding ChrC/ChrM, and centromeric regions), subsequent processing steps were applied to this subsampled set
Genome_build: TAIR10
Supplementary_files_format_and_content: Dnase bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent per base Dnase cleavages in a 150bp window at 20bp steps across the genome.
Supplementary_files_format_and_content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites

organism: Arabidopsis thaliana

source_name: rood hair cell 7 day

growth_protocol: Root sample seedlings were planted on 1XMS, 0.8% agar, 1% sucrose, and stratified for 2-4 days before being placed vertically in an incubator with LD (16hr light, 22°C; 8hr dark, 20°C) conditions for 7-10 days. See coat samples were obtained by collecting whole siliques 4 or 7 days past anthesis.  For the flower samples, open or unopen flowers were collected and prepped.  Seed coat and flower samples were collected from soil grown plants grown in LD conditions.

extract_protocol:
DNaseI: Nuclei were extracted and isolated with biotin-capture methods. Nuclei were then treated with 30-60u of DNase I for 3 minutes at 25°C. Resulting genomic DNA was size fractionated and small (double cut) fragments were sequenced using Illumina technology.
Illumina  TruSeq v2

tag: intact line

tag: experiment

value: DNaseI-seq


title: DS20132

description:
The following processed data files are pooled short read data from 2 biological replicates (GSM1824052 [DS20131] and GSM1824053 [DS20132]):
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.signal.bw
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.peaks.bed
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.signal.bw
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.peaks.bed

source_name: seed coat cell (4 days past anthesis)


title: DS20131


title: BicR DHT treated

data_processing:
The SOLiD-generated RNA-Seq reads was in 50 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the human RefSeq mRNA database.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to faciliate comparison among different samples.
Genome_build: hg19
Supplementary_files_format_and_content: text file of RPKM values for each Sample

growth_protocol: LNCaP and BicR cells were cultures in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Total RNA was extracted using ISOGEN reagent.
RNA sequencing (RNA-seq) library construction and sequencing was performed according to the manufacturer’s protocol for the Applied Biosystems SOLiD 3 Plus System (Applied Biosystems).

treatment_protocol: Cells were treated with vehicle, bicalutamide 1μM or DHT 10 nM for 24 h.

value: DHT 10 nM 24 h


title: LGG RNAseq

city: Atlanta

first: Rheinallt

middle: M

last: Jones

state: Georgia

address: 615 Michael

department: Pediatrics

institute: Emory Univeristy

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using TopHat2 with the default parameters and the UCSC mm9 knownGene.txt reference transcripome.
Transcripts were annotated using the HOMER package (Heinz S et al. Mol Cell. 2010) command: analyzeRepeats.pl rna mm9 -strand both -count exons -condenseGenes -noadj
Genome_build: mm9
Supplementary_files_format_and_content: HOMER output annotation file containing raw read counts for all mm9 RefSeq IDs including annotation of chromosomal coordinates and gene copy number

organism: Mus musculus

source_name: Colon, Dose LGG 2 x10E9

growth_protocol: 7-week-old age Germ free C57BL/6 mice were ordered from Taconic

extract_protocol:
Colonic tissues from respective treatment groups were homogenized in Trizol reagent, followed by chloroform/isopropyl alcohol extraction to generate crude RNA preparations. Crude RNA extracts were quantified using a nanodrop ND-1000 (Thermo Scientific, USA) and further cleaned up using on column RNase-free/DNase set (Qiagen, Cat #79254) treatment and RNAeasy spin column purification (Qiagen, Cat #74104).
Illumina TruSeq RNA Library Preparation Kit v2 according to the manufacturers instructions

treatment_protocol: Germ-free mice (7 weeks old) purchased from (Taconic farms Inc., NY, USA) were divided into three groups of treatment (n=4) that received an oral gavage of (2 X 10E9) cfu/mL of L. rhamnosus GG, E. coli and PBS respectively. Four hours after respective treatments mice were euthanized and colon tissues (4 cm) were excised and immediately frozen on dry ice in microcentrifuge tubes containing in 1 mL TRIzol® Reagent (Invitrogen, 15596-018).

value: colon

value: 7  weeks


title: PBS RNAseq

source_name: Colon, PBS


title: BicR Ethanol treated

value: ethanol 24h


title: Ecoli RNAseq

source_name: Colon, Dose Ecoli 2x10E9


title: LNCaP Bicaltamide treated

value: Bicalutamide 1μM 24h


title: NT RNAseq

source_name: Colon, Untreated


title: DS20134

description:
The following processed data files are pooled short read data from 2 biological replicates (GSM1289379 [DS21306] and GSM1824051 [DS20134]):
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.signal.bw
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.peaks.bed
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.signal.bw
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.peaks.bed

source_name: seed coat cell (7 days past anthesis)


title: LNCaP DHT treated

value: prostate cancer


title: E13Sertoli_input_2

city: Chicago

first: Danielle

last: Maatouk

address: 303 E. Superior St., Lurie 7-250

institute: Northwestern University

data_processing:
Base calls were performed using CASAVA version 1.8.2.
ChIP-seq reads were aligned with Bowtie (Langmead et al., 2009) with only uniquely aligning reads used for future processing. Peaks were called with SICER (Zang et al., 2009) with enrichment called for the histone modifications using the input track as the control. The species variable was set to mm9, redundancy threshold to 2, window size to 200, fragment size to 150, effective genome fraction to 0.7, gap size to 600 and FDR to 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: .txt file contains bed file of peaks across both replicates

source_name: E13.5 preSertoli cells

extract_protocol:
FACS purified preSertoli cells were pelleted, resuspended in 360 µl of PBS and cross-linked with 10 µl of 37% formaldehyde at room temperature for 10 minutes. Cross-linking was stopped by addition of 46.3 µl of 1M glycine for 5 minutes at room temperature. Cells were then pelleted, supernatant was removed and stored at -80oC. 1M cells were pooled from multiple sorts washed twice in 500 µl of PBS with protease inhibitors. Cells were resuspended in 500 µl of lysis buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS and protease inhibitors) and sonicated with a Branson 450 Sonicator (output power of 3, duty cycle of 30% for 16 cycles of 30 seconds with 1 minute rest time between sonications). Bead-antibody complexes were prepared by incubating 30 µl of dynabeads (Protein A; Life Technologies 10002D) with 2.5 µg antibody (Rabbit-anti-H3K27ac; Abcam ab4729). The sonicated lysate was spun down at 4oC for 10 minutes at 10 krpm with 40 µl of the supernatant set aside as input and 200 µl transferred to tubes containing pre-incubated bead-antibody complexes. We added 700 µl of ChIP Dilution Buffer (CDB) (1 % Triton X-100 (Sigma T8787), 2mM EDTA, 150mM NaCl, 20mM Tris (pH=8.0)) with protease inhibitors to IP tubes, and incubated overnight at 4oC. 160 µl of CDB and 8 µl of 5M NaCl were added to the input tube which was incubated at 65oC overnight. The following day, IP tubes were washed as follows: Once with Wash Buffer 1 (50mM Tris HCl, 1mM EDTA, 150 mM NaCl, 0.1% SDS, 0.1% Triton X-100, 0.1% Sodium deoxycholate), twice with Wash Buffer 2 (50mM Tris HCl, 1mM EDTA, 500 mM NaCl, 0.1% SDS, 0.1% Triton X-100, 0.1% Sodium deoxycholate), once with Wash Buffer 3 (10mM Tris HCl, 1mM EDTA, 1% NP-40, 1% Sodium deoxycholate, 250mM LiCl), twice with Wash Buffer 4 (50mM Tris HCl, 1mM EDTA, 500 mM LiCl, 1% NP-40, 0.7% Sodium deoxycholate), twice with TE buffer (pH=8.0). All washes were done in 1 ml, with added protease inhibitors, at 4oC for 5 minutes. Solutions for wash buffers were modified from the protocols posted on the Epigenomics Roadmap website.  DNA-protein complexes were eluted twice from the beads with 100 µl elution buffer (100mM sodium bicarbonate, 1% SDS, 8mM NaOH). 8 µl of NaCl was added to the eluates, as well as the input tube, and incubated at 65oC overnight. Samples were treated with 1 µl RNase-cocktail (Life Technologies AM2286) for 30 minutes at 37oC, then 4 µl of 0.5M EDTA, 8 µl of 1M Tris and 1 µl of Proteinase K was added for 60 minutes at 45oC. Finally, DNA was purified using PCR purification columns (Qiagen; 28104).
For library preparation for sequencing, DNA was concentrated using a vacuum centrifuge to ~10 µl. 10 µl of IP DNA and 1 µl of input DNA was used in the library preparation using the Rubicon ThruPLEX FD kit according to the manufacturer’s protocol. Size selection of smaller size amplified DNA was done with SPRI beads (Agencourt AMPure XP A63880) at 0.6x concentration. Sequencing was performed at Duke's Genome Sequencing and Analysis core facility on the Illumina HiSeq2000/2500.

value: fetal testis

tag: antibody

value: none, input


title: 293 PTBP1 and PTBP2 double knockdown_rep1


title: E13Sertoli_K27ac_2

tag: strain

value: Rabbit-anti-H3K27ac; Abcam ab4729


title: LNCaP Ethanol treated


title: E13Sertoli_input_1


title: DS20694

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to A. thaliana reference TAIR10 with bowtie version 0.12.7 with the following parameters: bowtie -p 8  --mm -n 2 -m 1 --best --phred33-quals
Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration except that peak thresholding was set to 95 percentile.
Tissue and cell type DNase I data were subsampled to a uniform lebel of 6.8 million reads (excluding ChrC/ChrM), subsequent processing steps were applied to this subsampled set
4DPA and 7DPA DNase I data were subsampled to a uniform lebel of 6.65 million reads (excluding ChrC/ChrM, and centromeric regions), subsequent processing steps were applied to this subsampled set
genome build: TAIR10
processed data files format and content: Dnase bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent per base Dnase cleavages in a 150bp window at 20bp steps across the genome.
processed data files format and content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites

source_name: root non hair cell 10 day


title: DS17499


title: DS21510

source_name: whole root 7 day


title: DS19056


title: DS17498

source_name: root non hair cell 7 day


title: E13Sertoli_K27ac_1


title: BicR Bialtamide treated

value: BicR


title: Rpl11 lox_TAM-treated_Rep4

city: Edinburgh

first: Lucía

last: Morgado

address: Edinburgh Bioquarter, 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16; allowing two mis- matches and five multihits. Transcripts assembly, estimation of their abundances and differential expres- sion were calculated with Cufflinks 1.3.0
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text matrix includes FPKMs values for each sample

source_name: Hematopoietic progenitor cells (Lin- Sca1+ cKIT+)

extract_protocol:
Bone marrows were harvested in cold PBS and cells were extracted by flushing. Hematopoeitic progenitors cells (Lin- Sca1+ cKIT+) were collected by fluorescence activated sorting in TRI-reagent and flash frozen in dry ice. RNA was extracted by using DirectZol (Zymo Research).
2-8 ng of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 7.5 to 9.3 (average 8.9) when assayed on an Agilent 2100 Bioanalyzer. Samples were first processed through the "SMARTer Ultra Low Input RNA Kit for Sequencing - v3 " (Clontech cat.# 634848). Double stranded cDNA was amplified in 11-14 cycles -depending on the yield of each sample- of PCR with SeqAmp DNA Polymerase (Clontech). ~10ng of resulting cDNA was fragmented in a Covaris S2 shearing instrument, and processed through successive enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Age-mached males were fed tamoxifen diet, starting at 6 weeks of age, for 20 weeks.

value: 26 weeks

tag: gender

value: male

value: Bone marrow

tag: genotype/variation

value: LOX (Rpl11+/lox::Tb.Ub-CreERT2)


title: Rpl11 lox_TAM-treated_Rep3

tag: tissue


title: Rpl11 lox_TAM-treated_Rep2


title: Rpl11 lox_TAM-treated_Rep1


title: DS20201 PE DNaseI-seq seed coat cell 4DPA

value: seed coat cell (4 days past anthesis)

tag: genetic background


title: DS21306 DNaseI-seq seed coat cell 7DPA

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to A. thaliana reference TAIR10 with bowtie version 0.12.7 with the following parameters: bowtie -p 8  --mm -n 2 -m 1 --best --phred33-quals
Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration except that peak thresholding was set to 95 percentile.
Genome_build: TAIR10
Supplementary_files_format_and_content: Dnase bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent per base Dnase cleavages in a 150bp window at 20bp steps across the genome.
Supplementary_files_format_and_content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites

growth_protocol: Root sample seedlings were planted on 1XMS, 0.8% agar, 1% sucrose, and stratified for 2-4 days before being placed vertically in an incubator with LD (16hr light, 22°C; 8hr dark, 20°C) conditions for 7 days. See coat samples were obtained by collecting whole siliques 4 or 7 days past anthesis.  For the flower samples, open or unopen flowers were collected and prepped.  Seed coat and flower samples were collected from soil grown plants grown in LD conditions.

extract_protocol:
DNaseI: Nuclei were extracted and isolated with biotin-capture methods. Nuclei were then treated with 45u of DNase I for 3 minutes at 25°C. Resulting genomic DNA was size fractionated and small (double cut) fragments were sequenced using Illumina technology.
Illumina  TruSeq v2

value: seed coat cell (7 days past anthesis)


title: Rpl11 wt_TAM-treated_Rep3

value: WT (Rpl11+/+::Tg.UbC-CreERT2)


title: DS21513 DNaseI-seq root hair cell 7 day

source_name: root hair cell 7 day

value: root hair cell 7 day

value: DNaseI-seq


title: DS16398 DNaseI-seq root non hair cell 10 day

value: root non hair cell 10 day


title: Rpl11 wt_TAM-treated_Rep1


title: DS20201 SE DNaseI-seq seed coat cell 4DPA


title: GFP+CTX2

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina CASAVA v1.8.2 software was used for basescaling.
RNA sequencing reads were analyzed using FastQC to detect potential problems. Then short reads were aligned to the mm9 reference genome using TopHat with default parameters.
FPKMs (Fragments per kilobase per million mapped reads) (Mortazavi et al. 2008) were determined for all RefSeq genes using CuffLinks. Read counts were obtained using HTseq (Anders et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values

source_name: GFP+ Tri-PyMT cells treated with CTX

growth_protocol: Cells were cultured in DMED with 10%FBS.

extract_protocol:
Cells were sorted usign BD Aria II sorter. The RNA was harvested from the sorted cells using Arcturus PicoPure RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used with 16-33ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols(Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001).

treatment_protocol: The CTX treated cells were cultured with 4-hydroperoxy-cyclophosphomide (4uM) for 7 days.

value: TriPyMT

tag: fluorescence

value: GFP+

value: breast tumor

tag: emt status

value: EMT

value: CTX treated


title: DS21511 DNaseI-seq whole root 7 day

value: whole root 7 day


title: GFP+CTX1


title: Rpl11 wt_TAM-treated_Rep2

tag: age


title: DS20427 DNaseI-seq open flowers

source_name: open flowers

value: open flowers


title: GFP1

source_name: GFP+ Tri-PyMT cells

value: untreated


title: mouse lv 1

source_name: Liver

value: Liver

tag: Sex

value: pooled male and female

value: 7-8 weeks

tag: protocol

value: dUTP stranded protocol


title: RFP2

source_name: RFP+ Tri-PyMT cells

value: RFP+

value: non-EMT


title: RFP1


title: mouse ht 1

source_name: Heart

value: Heart


title: mouse br 3

source_name: Brain

value: Brain


title: mouse br 2

description:
Ligation stranded protocol, paired-end reads
Strand-specific and paired-end RNA-seq

value: Ligation stranded protocol


title: IP_Male6

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Medicine Biomedical Sciences

institute: Florida State University

description: RNA from fru P1-expressing neurons

data_processing:
The unique reads were aligned to the D. melanogaster genome FB5.51 (FlyBase v5.51) using Bowtie (v0.12.9; --tryhard, --best, --strata, -m1, -v3).
Unaligned reads were aligned to FB5.51 using LAST (v247; -l 25, -Q 3).
Using FlyBase annotions, overlapping exons regardless of strand were combined into the maximum exonic region.
Expression was then quantified for each exonic region using Reads Per Kilobase Per Million Mapped Reads (RPKM).
Genome_build: FlyBase 5.51
Supplementary_files_format_and_content: Processed data files are in the CSV format. With the following columns: exonic region id, sample id, number of mapped reads, number of reads in the exonic region, coverage in exonic region (number of reads in exonic region / read length), exonic region length, average per nucleotide coverage, RPKM.

organism: Drosophila melanogaster

source_name: Adult head tissue

growth_protocol: Flies were raised on standard cornmeal food medium at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
Translated mRNA purification was performed as previously described (Thomas, A., P. J. Lee, J. E. Dalton, K. J. Nomie, L. Stoica et al., 2012 A versatile method for cell-specific profiling of translated mRNAs in Drosophila. PLoS One 7: e40276)  with the following modifications: approximately 1,000 heads per genotype were collected and homogenized in extraction buffer (20mM HEPES, pH 7.4, 150mM KCl, 5mM MgCl2, 0.5mM DTT, 100 g/mL Cyclohexamide, 100U/mL RNase OUT, 1X Complete Protease Inhibitor (Roche)). The sample was centrifuged at 4°C for 10 minutes at 2,000 x g and the supernatant was collected. 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC; Avanti®Polar Lipids, Inc.) and NP-40 were added to a final concentration of 30mM and 1%, respectively, to the supernatant and incubated on ice for 5 minutes. The lysate was then centrifuged at 4°C for 10 minutes at 20,000 x g. 40 μL of the supernatant was retained and placed directly into 200 μL of Lysis Solution  [Ambion® MicroPoly(A) Purist Kit] to be used to analyze the input RNA fraction. The remaining supernatant was added to Dynal Protein G magnetic beads conjugated to mouse anti-GFP (Memorial Sloan-Kettering Monoclonal Antibody Facility19C8/19F7). The lysate-bead slurry was incubated for 30 minutes at 4°C followed by washing in Wash Buffer (20mM HEPES, pH 7.4, 5mM MgCl2, 350mM KCl, 1% NP-40, 0.5mM DTT, and 100μg/mL Cyclohexamide) at 4°C. The IP was resuspended in Lysis Solution [Ambion®  MicroPoly(A) Purist Kit] and mRNA was directly isolated following the manufacturer’s protocol.
Poly(A)+ transcripts were isolated using Ambion® MicroPoly(A)Purist™ Kit. 100 ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. Following first strand synthesis, the second strand of the cDNA was synthesized by addition of DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™).  The DNA from this and all subsequent reactions was purified using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using  End-It™ Repair Kit (Epicentre®). Next, A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.). Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were amplified by performing polymerase chain reaction (PCR; 18 cycles). The product was isolated by gel purification of 250-550 base pair fragments.

treatment_protocol: For each experimental condition, approximately 1,000 flies that were 8 to 24 hours post-eclosion were used. All flies were collected 0 to 8 hours post-eclosion under anesthetization and allowed to recover for 16 hours before being snap frozen in liquid nitrogen. Snap frozen whole animals were stored at -80˚C until heads were collected. Adult heads were separated from bodies by vigorous vortexing and collected using mesh sieves.

value: male

tag: developmental stage

value: adult


title: ILK-KO (ILK-K5)-rep1

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

description:
TopHat alignment
KO111

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences, ribosomal sequences were removed, then mapped to GRCm38_79 whole genome using bowtie TopHat 2.0.14 and Bowtie 2.2.4 with parameters --library-type fr-firststrand -p 20
DESeq2 (1.6.3) was used to compute the differential gene expressioon according to the manual. Adjusted p-values for 5,10,15, and 20% have been computed
Genome_build: m38
Supplementary_files_format_and_content: tab-delimited text files include gene expression values for differentially expressed genes

source_name: epidermis

growth_protocol: Bulge hair follicle stem cells were FACS purified as a alpha6 integrin high / CD34 + population from 21d old mouse epidermis. Cells were directly sorted into TrizolLS for RNA isolation

extract_protocol:
RNA was isolated according to manufacturers instructions for TrizolLS (Invitrogen), amplified cDNA was prepared using Ovation RNA-Seq System V2 (NuGen)
Libraries were prepared from amplified cDNA using Nextera XT library preparation kit (Illumina)

tag: cell type

value: hair follicle bulge stem cell

value: post natal day 21

tag: genotype

value: ILK -/-


title: mouse br 1


title: ILK-KO (ILK-K5)-rep2

description:
TopHat alignment
KO1252


title: IP_Male4

description: RNA from fru P1-expressing neurons


title: IP_Male5

description: RNA from fru P1-expressing neurons


title: ctrl-rep2

description:
TopHat alignment
Ctrl1252

value: ILK +/-


title: DS20434 DNaseI-seq up-open flowers

source_name: up-open flowers

value: up-open flowers

value: DNaseI-seq


title: IP_Male3

description: RNA from fru P1-expressing neurons


title: GFP2

tag: cell line

value: TriPyMT

value: GFP+

value: breast tumor

value: EMT

tag: treatment

value: untreated


title: Rpl11 wt_TAM-treated_Rep4

value: 26 weeks

value: Bone marrow

value: WT (Rpl11+/+::Tg.UbC-CreERT2)


title: mouse ts 1

description:
dUTP stranded protocol, paired-end reads
Strand-specific and paired-end RNA-seq

source_name: Testis

value: Testis

value: pooled male and female

value: 7-8 weeks

value: dUTP stranded protocol


title: YoungBeta_BIS-Seq

city: Jerusalem

first: Dana

last: Avrahami Tzfati

address: Ein-Kerem

department: Developmental Biology and cancer research

country: Israel

institute: Hadassah Hebrew University School of medicine

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
Peak calling was done using HOMER for H3K4me1 and H3K27Ac marks at FDR=0.01 with respect to corresponding Input. Peak calling using STAR was done for H3K27me3 marks at FDR=0.01.
BIS-Seq: DNA sequencing data was aligned to mouse genome (mm9) with the BS Seeker program. Data was reported as the fraction of reads that were methylated, calculated as the ratio of cytosine bases (indicating methylated CpGs) to total reads for each CpG coordinate.  Unmethylated cytosines are ultimately converted to thymine bases during the bisulfite conversion process.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file of transcript raw read counts.
Supplementary_files_format_and_content: Tab delimited file of transcript FPKM counts.
Supplementary_files_format_and_content: Peak files are tab-delimited listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.
Supplementary_files_format_and_content: Tab-delimited files of loci, fraction of methylated cytosines and total read count.
Supplementary_files_format_and_content: RawReadCounts.txt: Raw transcript counts
Supplementary_files_format_and_content: TrancriptFPKMCounts.txt: Transcript FPKM counts
Supplementary_files_format_and_content: Old_H3K4me1.peaks.txt: peak
Supplementary_files_format_and_content: Old_H3K27me3.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K4me1.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K27me3.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K27Ac.peaks.txt: peak
Supplementary_files_format_and_content: OldBeta_bs_seeker-CG.tab: Percent methylated cytosines
Supplementary_files_format_and_content: YoungBeta_bs_seeker-CG.tab: Percent methylated cytosines

source_name: Pancreatic Beta Cells

extract_protocol:
RNA-Seq: Flow cytometry sorting was performed on live β cells from isolated pancreatic islets of young and old MIP-GFP mice. Total RNA were isolated using the RNeasy kit (Qiagen). ChIP-Seq: ChIP was performed on sonicated chromatin obtained from sorted old and young mouse β cells using antibody against H3K27ac (39685, Active Motif), H3K4me1 (ab8895, Abcam) and H3K27me3 (07-449, upstate). Input and bound DNA fractions were purified using PCR purification kit (Qiagen) for library preparation. BIS-Seq: Genomic DNA was extracted from FACS sorted old and young beta cells using FFPE AllPrep kit (Ambion), sonicated and bisulfite converted by Qiagen Epitect Bisulfite Kit and used for preparation of libraries.
RNA-Seq:Libraries were constructed from 200ng of total RNA using the standard TruSeq RNA sample prep kit (Illumina) using manufacturer's protocols. ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions. BIS-Seq: Libraries were prepared following manufacturer's instructions using NEBNext ChIP-seq library prep reagent kit with methylated adapters (NEB).

value: 4-6 weeks


title: IP_Male2

description: RNA from fru P1-expressing neurons

value: male

value: adult


title: OldBeta_BIS-Seq

value: 16-18 months


title: IP_Male1

description: RNA from fru P1-expressing neurons


title: IP_Female5

description: RNA from fru P1-expressing neurons

value: female


title: YoungBeta_H3K27Ac_Input


title: IP_Female4

description: RNA from fru P1-expressing neurons


title: IP_Female3

description: RNA from fru P1-expressing neurons


title: YoungBeta_H3K4me1_ChIP

value: H3K4me1, ab8895, Abcam


title: IP_Female2

description: RNA from fru P1-expressing neurons


title: Young_H3K4me1_or_H3K27me3_Input


title: ctrl-rep3

description:
TopHat alignment
Ctrl2252

value: hair follicle bulge stem cell

value: post natal day 21

value: ILK +/-


title: Input_Male6

description: total RNA input


title: OldBeta_H3K4me1_Input


title: IP_Female1

description: RNA from fru P1-expressing neurons


title: OldBeta_H3K27me3_ChIP


title: Input_Male5

description: total RNA input


title: ctrl-rep1

description:
TopHat alignment
Ctrl111


title: OldBeta_H3K4me1_ChIP


title: Input_Male3

description: total RNA input


title: Input_Male4

description: total RNA input


title: YoungBeta_Rep1_RNASeq

description: RawReadCounts.txt, TrancriptFPKMCounts.txt


title: Input_Male1

description: total RNA input


title: Input_Male2

description: total RNA input


title: OldBeta_Rep3_RNASeq

value: 17 months


title: OldBeta_Rep2_RNASeq

value: 16 months


title: Input_Female5

description: total RNA input


title: Input_Female4

description: total RNA input


title: YoungBeta_H3K27Ac_ChIP

value: H3K27Ac, 39685, Active Motif


title: Input_Female2

description: total RNA input


title: 13903-WT-422_Bcell_nostim

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

description:
PolyA+ RNA
WT-Bcell_nostim

data_processing:
base calling: Casava1.8
read alignment, RNA-seq data: TopHat 1.4.1
bedgraph track generation: custom-written python script
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

extract_protocol:
B cells were purified from miR-212/132-/- and WT mice and subsequently either left unstimulated, or stimulated for 8 hours or 20 hours with anti-IgM (5µg/mL). RNA was then harvested from these cells using the miRNAeasy RNA prep kit (Qiagen). To isolate B cells, RBC depleted bone marrow or spleen samples were sorted on MACS columns (Miltenyi). Briefly, bone marrow or spleen cells were incubated first with biotin-conjugated CD19 (positive-selection) or CD43 (negative selection) antibodies (BioLegend) in MACS sorting buffer (Miltenyi), followed by incubation with streptavidin-conjugated magnetic beads (Miltenyi) as per manufacturers protocol, before being separated on the columns.
TruSeq RNA Sample Preparation Kit

value: B cell

value: wild type


title: 13900-KO-413_Bcell_aIgM_20h

description:
PolyA+ RNA
KO-Bcell_aIgM_20h

value: IgM 20 h


title: 13901-WT-422_Bcell_aIgM_20h

description:
PolyA+ RNA
WT-Bcell_aIgM_20h


title: 13899-WT-422_Bcell_aIgM_8h

description:
PolyA+ RNA
WT-Bcell_aIgM_8h

value: IgM 8 h


title: 13902-KO-413_Bcell_nostim

description:
PolyA+ RNA
KO-Bcell_nostim


title: 13898-KO-413_Bcell_aIgM_8h

description:
PolyA+ RNA
KO-Bcell_aIgM_8h


title: Input_Female1

description: total RNA input


title: RNase-Y-active-site-mutation, EMOTE assay, replicate 2

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description:
EMOTE_Yaa_v2
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt

data_processing: EMOTE reads are processed with emoteConv software package (http://sourceforge.net/projects/emoteconv/), limiting the analysed reads length to 50bp.

organism: Staphylococcus aureus

source_name: Liquid culture

growth_protocol: Mueller-Hinton medium, 37°C

extract_protocol:
EMOTE
Silica-column based RNA isolation, DNase treatment, followed by ribo depletion

value: PR01 + RNase Y active site mutation


title: RNase-Y-active-site-mutation, EMOTE assay, replicate 1

description:
EMOTE_Yaa_v1
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt


title: macaque ts 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences using Condetri with the following settings (-hq=30 –lq=10). Adapters were trimmed from filtered reads if at least 5 nucleotides of the adaptor sequence matched the end of each read. In all experiments, reads below 50 nucleotides or with only one member of the pair were not considered.
We aligned the reads to the correspondent reference species genome with Tophat (v. 2.0.8) with parameters –N 3, -a 5 and –m 1, and including the correspondent parameters for paired-end and strand-specific reads whenever necessary. Multiple mapping to several locations in the genome was allowed unless otherwise stated.
Genome_build: hg19, panTro4, rheMac2 (Mmul_051212), mm10
Supplementary_files_format_and_content: Cufflinks output (isoforms.fpkm_tracking) containing abundance measurements and transcript assembly coordinates

organism: Macaca mulatta

extract_protocol:
Total RNA was extracted using a miRNeasy Mini kit.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer’s protocol.  Poly (A)-positive RNA was purified from 250-500 mg of total RNA using streptavidin-coated magnetic beads (AMPure XP) and subsequently fragmented to ~300 bp. cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen) and random primers. The strand-specific RNA-Seq library preparation was based on the incorporation of dUTP in place of dTTP in the second strand of the cDNA. Double-stranded DNA was further used for library preparation. Such dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and they were quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems). Sequencing was done with a Illumina HiSeq 2000 sequencer in a paired-end design according to the manufacturer’s instructions.

value: Testis

value: Male

value: 7 weeks

value: dUTP stranded protocol


title: Mutant RNase-Y-N-terminal-deletion, EMOTE assay, replicate 2

description:
EMOTE_YdNT_v2
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt

value: PR01 + N-terminal deletion of RNase Y


title: YoungBeta_Rep2_RNASeq

value: 4-6 weeks


title: macaque ht 1

value: Heart


title: macaque lv 1

value: Liver


title: KO-highfat_2

first: Daniel

last: Toft

state: IL

address: 675 N. St. Clair Street, 14-100

department: Endocrinology

data_processing:
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
Reads that aligned to mouse rRNA sequences were discarded
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  FPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: muscle, hind limb_ko_highfat

extract_protocol:
RNA was extracted from proximal hind limb skeletal muscle using Rneasy Mini Kit (Qiagen catalogue #74104). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: FVB

value: skeletal muscle

tag: anatomy

value: hind limb

value: 22 weeks


title: KO-highfat_1


title: KO-highfat_3

value: alphaB-crystallin/HspB2 knock out


title: Mutant RNase-Y-full-deletion, EMOTE assay, replicate 2

description:
EMOTE_dY_v2
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt

value: PR01 + full deletion of RNase Y


title: KO-control_3

source_name: muscle, hind limb_ko_control

value: wild type


title: OldBeta_Rep1_RNASeq

value: 15 months

tag: strain

tag: antibody


title: macaque br 1

value: Brain


title: Mutant RNase-Y-full-deletion, EMOTE assay, replicate 1

description:
EMOTE_dY_v1
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt

tag: genotype/variation


title: KO-control_2

tag: tissue


title: Input_Female3

description: total RNA input

value: female

value: adult


title: WT, EMOTE assay, replicate 1

description:
EMOTE_WT_v1
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt


title: KO-control_1


title: Flox-highfat_3

source_name: muscle, hind limb_flox_highfat


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 600s, replicate 2

description:
dY_t600_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

extract_protocol:
stranded RNA
Silica-column based RNA isolation, DNase treatment, followed by ribo depletion

tag: decay delay

tag: treatment protocol

value: rifampicin at t=0


title: Flox-highfat_2


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 600s, replicate 1

description:
dY_t600_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt


title: Flox-highfat_1


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 300s, replicate 2

description:
dY_t300_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt


title: Mutant RNase-Y-N-terminal-deletion, EMOTE assay, replicate 1

description:
EMOTE_YdNT_v1
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt


title: Flox-control_3

source_name: muscle, hind limb_flox_control


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 300s, replicate 1

description:
dY_t300_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt


title: Flox-control_2


title: Flox-control_1


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 150s, replicate 1

description:
dY_t150_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt


title: WT, RNA decay assay at 600s, rifampicin t=2, replicate 1

description:
PR01_t600_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=2


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 0s (steady state), replicate 1

description:
dY_t000_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt


title: WT, EMOTE assay, replicate 2

description:
EMOTE_WT_v2
N315_EMOTE_unambiguous.txt
N315_EMOTE_ambiguous.txt


title: KO RNA-seq_1

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling was done using the Illumina Pipeline (v.1.8.2)
Alignment to the mm9 genome was performed using Bowtie
BAM files were created from bowtiefiles using samtools
*_norm_rmdup.bedgraph.gz files were generated as follows:  ChIP-seq reads were aligned to UCSC mm9 with bowtie, then duplicates and unmapped reads were filtered by samtools, then normalized bedgraphs were generated with bedtools.
*_tss_filt_reads_per_gene.txt files were generated as follows:  ChIP-seq reads were counted for UCSC mm9 transcriptional start sites using a custom python script based on the HTSeq package.
*.bedgraph.gz files were generated as follows:  RNA-seq reads were aligned to UCSC mm9 with tophat, then replicate samples were merged and sorted using samtools, then bedgraphs were generated with bedtools.
*_counts.txt files were generated as follows:  RNA-seq reads were counted for UCSC mm9 genes using htseq-count.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files and tab delimited text files

source_name: CD4+CXCR5+CD62Llo T cells

extract_protocol:
Cells were collected for RNA.
RNA purified on oligo(dT) dynabeads for cDNA amplification, then Illumina barcode adaptors were ligated and amplified.

treatment_protocol: Mice were infected with chronic LCMV and sorted for Tfh on day 21 pi (sorted for: CD4+CXCR5+CD62Llo T cell)

value: Utx fl/fl Lck-Cre

tag: Stage

value: Day 21 post infection

value: Spleen

value: CD4+CXCR5+CD62Llo T cells


title: KO RNA-seq_2


title: WT RNA-seq_2

value: Utx fl/fl


title: KO RNA-seq_3


title: WT RNA-seq_1


title: WT, RNA decay assay at 300s, rifampicin t=4, replicate 1

description:
PR01_t300_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=4


title: KO H3K27me3_3

extract_protocol:
Cells were fixed for Chromatin Imunoprecipitation.
DNA was end repaired, A-tailed, then Illumina barcode adaptors were ligated and amplified.

tag: chip antibody

value: Abcam ab6002 anti-H3K27me3


title: KO H3K27me3_2


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 0s (steady state), replicate 2

description:
dY_t000_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt


title: WT, RNA decay assay at 150s, rifampicin t=6, replicate 1

description:
PR01_t150_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=6


title: WT, RNA decay assay at 150s, rifampicin t=5, replicate 2

description:
PR01_t150_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=5


title: Mutant Rnase-Y-full-deletion, RNA decay time course at 150s, replicate 2

description:
dY_t150_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: PR01 + full deletion of RNase Y


title: WT, RNA decay assay at 600s, rifampicin t=1, replicate 2

description:
PR01_t600_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=1


title: WT H3K27me3_3


title: WT RNA-seq_3


title: WT H3K27me3_1


title: WT, RNA decay assay at 0s (steady state), rifampicin t=8, replicate 1

description:
PR01_t000_v1
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=8


title: Input

value: Pooled Utx fl/fl and Utx fl/fl Lck-Cre


title: WT, RNA decay assay at 300s, rifampicin t=3, replicate 2

description:
PR01_t300_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=3


title: Sample_WT_stat_w-o_no-1

city: Konstanz

first: Jörg

last: Hartig

address: Universitätsstraße 10

department: Chemistry

institute: Universität Konstanz

description: without crosslink

data_processing:
Library strategy: Hi-C
Paired end reads were seperately aligned to the MG1655 reference genome NC_000913.3 using RazerS3.
Uniquely aligning reads were assigned to their corresponding MluI restriction fragment by means of their position on the genome.
Paired reads which have been assigned to their restriction fragments are then rejoined by means of their identical read-id.
Only pairs where both reads were assigned to different restriction fragments were used for further analysis.
Interactions between restriction fragments (paired reads that were assigned to different restriction fragments count as one interaction of those restriction fragments) were then converted into interactions between equally sized bins with a size of 20 kb, each, resulting in an interaction matrix of interactions between bins.
The interaction matrix was normalized using a method similar to Imakaev et al., 2012.
Normalized Hi-C contact maps from samples obtained under the same conditions (crosslink or non-crosslink; exponential or stationary phase) were compared by Pearson correlation and yielded values above 0.92.
Binning and normalization was thus performed on pooled data sets (all crosslink exponential phase samples, all non-crosslink exponential phase samples, all crosslink stationary phase samples and all non-crosslink stationary phase samples).
In order to detect crosslink-independent interactions, we divided the Hi-C contact matrices of the crosslinked samples by the Hi-C contact matrices of the corresponding non-crosslinked samples and logarithmized the resulting values. The resulting Hi-C contact matrices show the genomic crosslink-independent interactions.
Genome_build: NC_000913.3

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655 stationary phase, non-crosslink

growth_protocol: Cells were grown in M9 minimal medium with glycerol as carbon source and harvested during exponential or stationary growth phase.

extract_protocol:
Hi-C was performed similar to a previous study by van Berkum et al. (2010) with the following changes. 5x10^9 cells grown in M9 minimal medium with glycerol as carbon source were fixed in 1% formaldehyde in PBS buffer for 20 min at room temperature. In the case of non-crosslink controls, cells were incubated in pure PBS buffer. After quenching of fixation in 0,125 M glycine, cells were lysed with Ready-Lyse lysozyme (Epicentre Biotechnologies) in TE buffer for 20 min at room temperature. Lysis was stopped by incubation in 1% SDS for 30 min at room temperature. DNA was digested with 500 U MluI (NEB). DNA was extracted with PCIAA pH7.9 (roth) twice and chloroform once. DNA was precipitated in TE with 50 µg/ml glycogen and 0.3 M sodium acetate and 1 volume isopropanol. DNA was sheared to a size of 300-500 bp in a Nebulizer according to the Illumina Kit protocol and purified using the QIAquick PCR Purification Kit. Raw data files with denomination „no-3“ are from samples in which biotin-labeling and subsequent enrichment of ligation products was omitted.
Libraries were prepared for sequencing according to the Illumina TruSeq DNA Sample Prep v2 Low Throughput protocol.

tag: growth phase

value: stationary phase


title: KO H3K27me3_1


title: Sample_WT_stat_w-o_no-2

description: without crosslink


title: Sample_WT_stat_w-o_no-3

description: without crosslink


title: WT H3K27me3_2


title: Sample_WT_stat_plusF_no-3

description: crosslinked

source_name: E. coli MG1655 stationary phase, crosslink


title: Sample_WT_exp_w-o_no-3

description: without crosslink

source_name: E. coli MG1655 exponential phase, non-crosslink

value: exponential phase


title: FL10 (MEF2)

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component.
The quality of the data was assessed using fastqc from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2)
Reads are mapped to a mm10 reference genome with a splice-aware aligner (TopHat v2.0.8b) using GTF file (genes.gtf downloaded from UCSC on : March 6, 2013) to facilitate mapping reads across exon-exon junctions
HTSeq-count (0.5.3p9) was used to count reads overlapping genes.
Gene counts were normalized using the trimmed mean of M values from edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample

source_name: Oct4-GFP MEF

growth_protocol: MEF were grown in DMEM 10% FCS, iPS cells in KSR+LIF media

extract_protocol:
RNA were extracted using Nucleospin RNA extraction kit (Macherey Nagel)
Libraries were generated using the « Truseq RNA sample prep kit V2 » from Illumina (RS-122-2001).
Briefly, the polyadenylated RNA were isolated from 1µg of total RNA using oligo(dT) magnetic beads. Isolated mRNA were fragmented and primed using random hexamer before reverse transcription. A second strand synthesis was performed. Double stranded cDNA was repaired resulting in blunt ends double stranded cDNA. Both 3' ends were adenylated and Illumina's indexed adapters were ligated to the cDNA. A 15 cycles PCR was performed for each library using Illumina's PCR primers.
Libraries were validated using a DNA1000 chip on a Bioanalyzer (Agilent) and quantified by qPCR using the « Library Quantification Kit - Illumina/Universal » from KAPA (KK4824).
Prior to clustering, 10 libraries were equimolarily pooled, denatured using NaOH and diluted to 7 pM.
Clustering and 50nt single read sequencing were performed on a single lane following the manufacturer's instructions.

treatment_protocol: Netrin-1 derived iPS cells were derived from Oct4-GFP Mef that have been reprogrammed using Oct4, Sox2, Klf4 and c-Myc retroviruses

value: cross of mf1 and 129

tag: passage


title: Sample_WT_stat_plusF_no-1

description: crosslinked


title: Sample_WT_exp_w-o_no-1

description: without crosslink


title: FL8

source_name: mouse pre-iPS cells


title: FL9 (MEF1)


title: WT, RNA decay assay at 0s (steady state), rifampicin t=7, replicate 2

description:
PR01_t000_v2
N315_RNA-decay_raw.txt
N315_RNA-decay_normalized.txt

value: rifampicin at t=7


title: RNAPol2Ser5_ChIPbisSeq

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

data_processing:
Bisulfite treated DNA reads were aligned using Bismark v0.7.7 (non-directional, <= 2 mismatches in the first 30bp). Duplicate reads were removed using the deduplicate_bismark_alignment_output.pl script from Bismark v0.7.7.
Chip-seq reads were aligned using Bowtie v0.12.7 (only unique alignments permitted).  Duplicate alignments were removed using MarkDuplicates from PicardTools v1.37.
Methylation levels at individual bases were extracted using the bismark_methylation_extractor script from Bismark v0.7.7.
Chip-seq read count profiles were generated using makeTagDirectory from HOMER v20121121 (with -unique and -single options).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file showing methylation levels for each CpG site; columns: chromosome, start, end, methylation level, number methylated reads, number unmethylated reads (Bismark output)
Supplementary_files_format_and_content: Tab-delimited file showing chip-seq read counts; columns: blank, chromosome, position, strand, number of reads, read length (HOMER output)

growth_protocol: Naïve male C57BL/6 mice of 2 months old

extract_protocol:
Cortices of 3 mice were homogenized in 1 X PBS including 1% formaldehyde, and the homogenates were kept for 10 min at 25°C. Cross-linking reactions were stopped by the addition of glycine (125 mM) for 10 min at 25°C. Fixed chromatin samples were then homogenized in cell lysis solution (PIPES 5 mM (pH 8), KCl 85 mM, NP40 0.5%) and centrifuged for 5 min at 3000 rpm, 4°C. Pellets were resuspended in RIPA-light solution (NaCl 150 mM, SDS 0.3%, Tris-HCl 50 mM (pH 8)) and sonicated using a covaris E220. Sonicated chromatin samples were then centrifuged for 15 min at 14000 rpm, 4°C. Pellets were resuspended in 1 ml of RIPA-light solution. Chromatin samples were pre-cleared with 50 ul of dynabeads protein G (Life Technologies) pre-blocked with BSA and incubated overnight at 4°C with antibodies anti- RNAPolII phosphorylated in serine 5 (clone 4H8) (Abcam, ab5408). Antibodies and chromatin were then mixed with 100 ul of dynabeads protein G for 3 hours at 4°C. The beads were then washed with RIPA-light solution, washing-solution (Tris-HCl 100 mM (pH 8), LiCl 500 mM). Protein-DNA complexes were eluted from the beads, de-cross-linked, treated with proteinase K and purified. The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen)
A total of 100 ng RNAPolII-immunoprecipated DNA was used for the preparation of the library. The immunoprecipitated DNA and input DNA were sheared a second time with the Covaris E220 instrument in 53µl reaction volume (duty factor 10%, Pic Incident Power 175, Cycles per burst 200, time 360 sec) to obtain fragments in the size range of 150 bp followed by purification with AMPure XP beads (x1.8v/v) (Beckman Coulter A63881). Purified DNA was resuspended in 45 µl elution buffer. A library of the chromatin immunoprecipitated DNA fragments was prepared using the TruSeq DNA Low Throughput Protocol (Illumina). Bisulfite conversion was performed using the EZ DNA Methylation-Gold Kit (Zymo Research). PCR enrichment of ligation products was performed using the Illumina Primer Cocktail; 15 cycles of PCR were performed for ChIP libraries and 10 cycles for the input. The libraries were purified using AMPure XP beads x1.0 v/v. Quality of libraries was validated by 260 nm absorbance measurement, quality control on HSdna chip (Agilent Bioanalyzer : size of libraries around 275bp bp) and quantification  by Q-PCR with Kappa Library Quantification kit for Illumina Sequencing Platforms (KAPPA Biosystems). The DNA concentration of the different sequencing libraries was from 40 to 500 nM. Clusters (13.5 pM) were generated using TruSeq PE Cluster Kit v3, for cBot protocol, which was followed by Pair End Sequencing, 50 cycles, on an Illumina HiSeq 2000, according to the manufacturer recommendations.

tag: age

value: 2 months

tag: Sex

value: male

value: Cerebral cortex

value: RNAPol2Ser5 clone4H8

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: molecule subtype

value: genomic DNA bisulfite converted


title: Sample_WT_exp_w-o_no-2

description: without crosslink


title: FL5

source_name: mouse control iPS cells


title: RNAPol2Ser5_ChIPSeq

value: genomic DNA


title: FL6

source_name: mouse "Netrin-1 derived" iPS clone1


title: Sample_WT_exp_plusF_no-3

description: crosslinked

source_name: E. coli MG1655 exponential phase, crosslink


title: FL4


title: Sample_WT_exp_plusF_no-2

description: crosslinked


title: Sample_WT_exp_plusF_no-1

description: crosslinked


title: FL3

source_name: mouse "Netrin-1 derived" iPS clone2


title: Seedling_degradome2_raw

city: Cuernavaca

first: Damien

last: Formey

state: Morelos

address: Avenida de la Universidad

department: Center for Genomic Science

country: Mexico

institute: UNAM

description: Degradome

data_processing:
Library strategy: degradome-Seq
raw reads from the Illumina Pipeline 1.4 for the small RNA libraries were cleaned of sequence adapters, low quality tags and small sequences (< 16 nt long)
Genome_build: Phaseolus vulgaris v1.0 (Common bean)
Supplementary_files_format_and_content: sequences and counts

organism: Phaseolus vulgaris

source_name: Degradome

growth_protocol: moist vermiculite watered to substrate capacity and maintained at 24°C for 48 hours with 16h/8h light/dark day cycles

extract_protocol:
Total RNA was isolated from frozen samples using the Trizol reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA) and 40 µg of each sample were prepared
The protocol used to obtain cDNA libraries for degradome analysis was carried out essentially as previously described (Addo-Quaye et al, 2008; German et al, 2009)

tag: ecotype

value: Negro Jamapa

value: seedling


title: FL1


title: Seedling_degradome1_raw

description: Degradome


title: Sample_WT_stat_plusF_no-2

description: crosslinked


title: Nodule_raw

description: Small RNA

data_processing:
raw reads from the Illumina Pipeline 1.4 for the small RNA libraries were cleaned of sequence adapters, low quality tags and small sequences (< 16 nt long)
redundancy were removed and the count for each read added
Genome_build: Phaseolus vulgaris v1.0 (Common bean)
Supplementary_files_format_and_content: small RNAs and counts

source_name: Nodule

extract_protocol:
Total RNA was isolated from frozen samples using the Trizol reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA) and 10 µg of each sample were prepared
Illumina's Small RNA alternative sample preparation protocol v1.5

treatment_protocol: 1 ml of the R. tropici CIAT899 culture (grown on PY liquid medium supplemented with CaCl2 (7 µM), rifampicin (50 µg/ml), and nalidixic acid (20 µg/ml) at 30 ºC to a cell density of 5 × 108  ml-1)

value: Nodule


title: Leaf_raw

description: Small RNA

source_name: Leaf

value: Leaf


title: 9071X4_TA_RNA

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

description: rRNA subtracted, total RNA mapped to RefSeq transcripts

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Fastq files were trimmed for adapter sequence and low-quality reads were filtered using the FASTX- Toolkit
Fastq files were mapped against these RefSeq protein-coding transcripts using bowtie alignment parameters: –v 2 –a –best – strata.
Alignments were screened for transcripts with high (> 50%) multiple mapping reads, and these transcripts and reads were rejected except for the myosin heavy chain gene family and obscurin.  These reads were re-mapped against these transcripts to estimate the concentration of each transcript by their uniquely mapping reads. The multiple mapping reads were re-mapped using exact matching to remove mismatched reads and the remaining exact multiple mappers were apportioned to transcripts by the estimated transcript concentration.
Mouse RefSeq fasta sequences were retrieved from the UCSC genome browser (mm9 assembly, RefSeq Genes table downloaded Apr. 2012) using the sequence retrieval and formatting options for 5’ UTR, CDS, 3’ UTR exons as one record per transcript.   These fasta files were reduced to protein-coding genes corresponding to 18,499 Genbank RefSeq accessions. The 5’ end of mapped reads were assigned to their transcript position rejecting mapped reads with more than 1 mismatch in their bowtie alignment.  Nomalized abundance (reads per million mapped reads) was determined by the total number of reads mapping to transcripts with a minimum cutoff of 20 mapped reads per transcript.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include reads per million mapped reads (RPM) values for each Sample.

source_name: tibialis anterior muscle

growth_protocol: Ten-week-old male C57BL/6J mice were obtained from The Jackson Laboratory

extract_protocol:
For each experiment, 100 mg of frozen tissue was placed in a 2 ml tube containing a ¼” diameter stainless steel ball with 1.5 ml of lysis buffer (10mM Tris-Cl (pH 7.5), 300mM KCl, 10mM MgCl2, 200ug/ml cycloheximide, 1mM DTT and 1% Triton X-100). The samples were homogenized by agitation at full speed for 45 seconds in the Mini-Beadbeater-8 (Biospec Products Inc).  RNA-Seq: 300 μls of crude lysate was transferred to 2 mls of TRIzol reagent (Life Technologies) and total RNA extracted according to manufacturer’s specification. RPF-Seq: The remaining lysate was incubated with 500 units of RNase I (Life Technologies) for 30 minutes at 25oC. Ribonuclease digested extracts were centrifuged at 48000 RPM for 2 hours in a TL100 ultracentrifugation (Beckman Coulter). Low speed centrifugation for clarification prior to ultracentrifugation was omitted to avoid loss of the large muscle transcripts.  Ribonuclease-resistant RNA fragments were isolated from the pellet by TRIzol extraction, and electrophoresed on a 15% polyacrylamide/8M UREA gel. The region of the gel containing 26-36 nucleotide size RNA fragments was excised and the RNA isolated by passive elution prior to library construction.
RNA-Seq: 4 μg of TRIzol-extracted total RNA from each sample was depleted for rRNA using Ribo-Zero rRNA Removal Kit Human/Mouse/Rat (Epicentre).  The rRNA-depleted total RNA was then processed using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s specifications using Superscript II (Invitrogen). RPF-SEQ: 1 μg of heart or skeletal muscle gel-purified RNA fragments were treated with 5 units of Antarctic Phosphatase (NEB,) in the presence of 40 units of RNase Inhibitor (Ambion) for 30 min. at 37oC, followed by 5 min. at 65oC to deactivate the enzyme.  Fragments were then treated with 20 units of Polynucleotide kinase (NEB) for 60 min. at 37oC and purified using RNeasy MinElute columns (Qiagen) according to the manufacturer’s recommendations for small RNA.  RPF libraries were built using the TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s specifications, using Superscript II (Invitrogen).  After PCR to enrich for ligated fragments, the final gel purification was eliminated and instead the amplified library samples were cleaned using 50 μl of AMPure XP magnetic beads (Agencourt) according to the manufacturer’s specifications.

treatment_protocol: Following euthanasia, the heart and tibialis anterior muscle groups were harvested, cut into 0.1 – 0.2 cm3 portions and immediately frozen in liquid nitrogen.

value: tibialis anterior muscle

value: post natal week 10


title: FL7


title: 9071X4_TA_RPF

description: ribosome-protected fragments mapped to RefSeq transcripts

data_processing:
Library strategy: RPF-Seq
Illumina Casava1.8.2 software used for basecalling.
Fastq files were trimmed for adapter sequence and low-quality reads were filtered using the FASTX- Toolkit
Fastq files were mapped against these RefSeq protein-coding transcripts using bowtie alignment parameters: –v 2 –a –best – strata.
Alignments were screened for transcripts with high (> 50%) multiple mapping reads, and these transcripts and reads were rejected except for the myosin heavy chain gene family and obscurin.  These reads were re-mapped against these transcripts to estimate the concentration of each transcript by their uniquely mapping reads. The multiple mapping reads were re-mapped using exact matching to remove mismatched reads and the remaining exact multiple mappers were apportioned to transcripts by the estimated transcript concentration.
Mouse RefSeq fasta sequences were retrieved from the UCSC genome browser (mm9 assembly, RefSeq Genes table downloaded Apr. 2012) using the sequence retrieval and formatting options for 5’ UTR, CDS, 3’ UTR exons as one record per transcript.   These fasta files were reduced to protein-coding genes corresponding to 18,499 Genbank RefSeq accessions. The 5’ end of mapped reads were assigned to their transcript position rejecting mapped reads with more than 1 mismatch in their bowtie alignment.  Nomalized abundance (reads per million mapped reads) was determined by the total number of reads mapping to transcripts with a minimum cutoff of 20 mapped reads per transcript.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include reads per million mapped reads (RPM) values for each Sample.


title: 9071X2_Heart_RPF

source_name: heart

value: heart


title: 9071X2_Heart_RNA


title: Seedling_raw

description: Small RNA

source_name: Seedling

value: Seedling


title: Flower_raw

description: Small RNA

source_name: Flower

value: Flower


title: Skin_Langerhans_cells_Rep2

status: Public on Aug 31 2015

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

description: 3' RNA-seq for digital gene expression quantitation

data_processing:
bcl2fastq v2.15.0.4
alignment: tophat --max-intron-length 10000 --max-multihits 1
Expression table done using ESAT http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes mRNA molecule count values for each Sample

source_name: Skin LCs

extract_protocol:
10^4 cells from each cell type were sorted in 100 ul of Lysis/Binding Buffer (Life technologies), lysed for 5 min and frozen at -80°C. Cell lysates were thawed and mRNA was captured with 12 ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines. Purified messenger RNA was eluted at 70°C with 10 ul of 10 mM Tris-Cl pH 7.5 and stored at -80°C
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina HiSeq 1500.

tag: cell type

value: Skin LC


title: S. enterica transcriptome analysis in mouse B cells FACS sorted from the spleen

city: San Diego

first: Marcus

last: Jones

address: 4120 Torrey Pines Road

institute: JCVI

data_processing:
CLC workbench
RNASeq analysis protocol
Mapping was limited to a minimum length franction of 0.8, and minimum similarity fraction of 0.8 and a maximum hit of 10.
Genome_build: reference mapping genome S. enterica 14028
Supplementary_files_format_and_content: tab text-delimited with total and unique reads. Also contains RPKM values, chromosomal coordinates and feature ID.

source_name: RNA extracted from FACS sorted B cells infected with S. enterica 14028

extract_protocol: Mice were infected with S. enterica strain 14028. Spleens were collected, homogenized and cells FACS sorted. Total RNA was extracted using the Ambion mirVana RNA isolation kit. Purified RNA was depleted of rRNA utilizing the epicentre ribozero metabacteria and eukaryotic kits. Illumina standard HISeq library construction.

tag: infection

value: Samonella enterica strain 14028

value: spleen


title: b02_lung_Expr2

description:
GSM1546047
3' RNA-seq for digital gene expression quantitation

source_name: Lung macrophages

tag: strain

value: Lung macrophage


title: Mucosal_CD11b_P_LC_Rep2

source_name: Mucosal LCs CD11b+

value: mucosal CD11b+ LC


title: Mucosal_CD11b_P_LC_Rep3


title: Skin_Langerhans_cells_Rep1


title: b17_lung_mac2_Expr2

description:
GSM1546048
3' RNA-seq for digital gene expression quantitation


title: Mucosal_CD11b_P_LC_Rep4


title: Mucosal_CD103_P_LC_Rep4

source_name: Mucosal LCs CD103+

value: mucosal CD103+ LC


title: Mucosal_CD11b_P_LC_Rep1


title: FL2

value: cross of mf1 and 129


title: Mucosal_CD103_P_LC_Rep2


title: Mucosal_CD103_P_LC_Rep1


title: Lungs_Langerin_P_CD103_P_Rep2

source_name: Lung DCs Langerin+ CD103+

value: Lung DC


title: Lungs_Langerin_P_CD103_P_Rep1


title: Root_raw

description: Small RNA

source_name: Root

value: Negro Jamapa

value: Root


title: IUGR fetus  in twins 7

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
After removing the adapter sequences and filtering out the low quality reads, the bisulfite sequencing reads were directly aligned to the human reference genome (UCSC hg19) using BSMAP 2.73 with default parameters, which combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping.
We filtered out the CpG sites with less than 4X sequencing depth in order to guarantee accurate calculation of methylation levels. Then analysed differential promoter DNA methylation between IUGR and normal fetus.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: *.cout.gz files contain 8 columns. The format is that: (1)Chromosome ID, (2)Cytosine position, (3)+/- Watson/Crick chain, (4)Type (CG/CHH/CHG), (5)Base pattern, (6)Methylation Ratio, (7)Methylated reads num, (8)Un-methylated reads num.

source_name: IUGR placentas

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen). 1µg of genomic DNA was fragmented into approximately 200-300bp using a Covarias sonication system (Covarias). After purification, the fragmented fractions were treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair blunt and phosphorylate ends. Total RNA was extracted using the Invitrogen TRIzol® Reagent and then treated with RNase-free DNase I (Ambion) for 30 min. The integrity of total RNA was checked using an Agilent 2100 Bioanalyser.
After purification, the fragmented fractions were treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair blunt and phosphorylate ends. The blunt DNA fragments were subsequently 3'-adenylated using Klenow Fragment (3-5' exo-) and then ligated by T4 DNA Ligase to adapters that were synthesized with 5'-methylcytosine instead of 5'-cytosine and contain index sequences inside. After each step, the reaction products were purified using QIAquick PCR purification kit (Qiagen).  The constructed libraries were quantified using a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen).

value: placentas

tag: gender

value: F

tag: gestational weeks

tag: condition

value: IUGR