title: CTL09_PLntr_1

description:
Sample name: CTL09_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG


title: delta45_3

status: Public on Jul 02 2014

type: SRA

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Clip TruSeq adapters with cutadapt v1.1
Map to UCSC's mm9 assembly using TopHat v1.4.1 using default parameters with additional parameter –butterfly-search
Filter out reads mapping to repetitive elements annotated by UCSC's RepMask track
Count reads in exons of all genes annotated in Ensembl's release 67 GTF using HTSeq v 0.5.3p9
Perform differential expression analysis using DESeq v1.10.1, using sharingMode=fit-only, fitType=local, and variance=per-condition
Genome_build: mm9
Supplementary_files_format_and_content: Each counts file contains the number of reads in each library falling within exons of genes annotated in Ensembl's release 67, as counted by HTSeq v0.5.3p9.

molecule: polyA RNA

organism: Mus musculus

source_name: Induced MEL cells

extract_protocol:
RNA from induced WT MEL cells, LDB1 KD cells and KD cells expressing either LDB1 FL or LDB1Δ4/5 was isolated with the RNeasy Kit (QIAQEN)
RNA-seq libraries were constructed using TruSeq RNA Sample Prep Kit V2 (Illumina) according to the manufacturers protocol.

tag: cell line

value: MEL

tag: treatment

value: LDB1 KD, with Ldb1 delta 4/5 construct


title: FL_2

value: LDB1 KD, with full-length Ldb1 construct


title: IMEL_2

value: control


title: FL_3


title: IMEL_1


title: CTL10_PLntr_1

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Sample name: CTL10_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Base calling was done using CASAVA versions 1.6 - 1.8.2.
The data was processed as described in Brown et al. (2013, Front Genet, 4:145) using a curated miRNA (Farazi et al. 2011, 71:4443) and other non-coding and coding RNA transcriptomes.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files contain raw, i.e. not-normalized or transformed, miRNA counts based on unique miRNA sequences, or based on precursor clusters and sequence families.

molecule: total RNA

organism: Homo sapiens

source_name: healthy control-plasma-untreated

extract_protocol:
Total RNA was isolated using a modified TRIzol protocol including another acidic phenol chloroform extraction followed by ethanol precipitation; the myocardial samples were additionally treated by DNase I treatment and proteinase K digestion in the presence of 0.5 % SDS, and recovered by two ethanol precipitations. Total RNA from liquid specimen was isolated using TRIzol LS, followed by a 2-propanol precipitation in the presence of glycogen, a proteinase K digestion (f.c. 100 µg/ml in 0.5 % SDS for 20 min at 42 degrees C), another acidic phenol-chloroform extraction, and two ethanol precipitations.
The small RNA libraries for the solid tissue samples were prepared using the protocol described in Hafner et al. (2008, 44:3, 2012, 58:164). The libraries for for the serum and plasma samples had the following modifications: 1) the amount of the 10 spiked-in synthetic calibrator oligoribonucleotides was reduced from 0.5 fmol each per 2 µg total RNA input to 0.005 fmol each, 2) the synthetic P32-labeled 19-nt and 24-/35-nt ssRNAs used for size selection were not spiked-into the samples. Note: no calibrator oligoribonucleotides were spiked-in to library 8. The sequences of the 10 used calibrator oligoribonucleotides can be obtained from Hafner et al. 2012 (Methods, 58:164).

tag: age

tag: gender

value: Female

tag: race

value: Caucasian

tag: tissue

value: Plasma

tag: disease

tag: heart failure onset

tag: nyha

tag: ejection fraction

tag: lvad status

value: No LVAD

tag: lvad device

tag: days lvad

tag: pacemaker

value: Yes


title: CTL03_LVntr_1

description:
Sample name: CTL03_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TGTGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TGTGTTCGTATGCCGTCTTCTGCTTG

source_name: nonfailing left-ventricular myocardium, postnatal

value: Male

value: Asian

value: Cardiac Muscle


title: CTL02_LVntr_2

description:
Sample name: CTL02_LVntr_2
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 5
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TTGGT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTGGTTCGTATGCCGTCTTCTGCTTG


title: CTL10_SRntr_1

description:
Sample name: CTL10_SRntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 8
this sample does not contain spiked-in calibrator oligoribonucleotides.
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

source_name: healthy control-serum-untreated

value: Serum


title: CTL11_PLntr_1

description:
Sample name: CTL11_PLntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG

value: African American


title: CTL05_LVntr_1

description:
Sample name: CTL05_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 6
barcode: TTAAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TTAAGTCGTATGCCGTCTTCTGCTTG


title: CTL01_LVntr_2

description:
Sample name: CTL01_LVntr_2
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 2
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCTAG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCTAGTCGTATGCCGTCTTCTGCTTG


title: CTL09_SRntr_1

description:
Sample name: CTL09_SRntr_1
Processed data file: circulation_clusters.txt
Processed data file: circulation_seqfams.txt
Processed data file: circulation_unique.txt
Library: 7
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG


title: CTL07_LVntr_1

description:
Sample name: CTL07_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TCATC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCATCTCGTATGCCGTCTTCTGCTTG

value: No


title: CTL08_LVntr_1

description:
Sample name: CTL08_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TCCAC
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCCACTCGTATGCCGTCTTCTGCTTG


title: delta45_2


title: CTL01_LVntr_1

description:
Sample name: CTL01_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 2
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCGCG
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCGCGTCGTATGCCGTCTTCTGCTTG


title: CTL06_LVntr_1

description:
Sample name: CTL06_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 1
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG


title: delta45_1


title: FL_1


title: ILdb1_KD_2

value: LDB1 KD


title: ILdb1_KD_3


title: sperm (polyA replicate 2)

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequencing reads for each sample and stage were seperately mapped to the transcriptome using bwa with default parameters. For small RNAs reads were mapped to the genome
Reads were aggregated across all isoforms of a given gene.
Aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
Genome_build: WS190
Supplementary_files_format_and_content: Tab separated txt-file with gene identifiers and expression values in RPKM.

organism: Caenorhabditis elegans

source_name: sperm poly(A)-extracted mRNA library

growth_protocol: Strains were maintained using previously described methods(Brenner, 1974; Stiernagle, 2006) on OP50 seeded NGM plates at permissive temperatures.

extract_protocol:
Oocytes: Adult wild-type hermaphrodites (N2) were cut using a razorblade in PBS containing 0.5% BSA and 0.02%Tween. Oocytes were picked by mouth pipetting under a stereo microscope (Leica), washed thoroughly in PBS and lyzed in TriZol LS (Invitrogen, USA). Sperm: Sperm was isolated in principle as described previously(L’Hernault & Roberts, 1995) from males worms obtained from a fog-2(q71) mutant background strain. Males were cut in cold PBS containing protease inhibitors (Sigma-Aldrich, Germany). Sperm was subsequently purified by filtration (3x40µm, 2x10µm, 1x6µm nylon mesh) and washed twice in cold PBS. Sperm was then activated by incubation in PBS containing 200µg/mL Pronase (Sigma-Aldrich, Germany) for 30 minutes at 24°C. 1-cell embryos: 1-cell embryos were obtained by fluorescence activated cell sorting (eFACS) as described previously(Stoeckius et al, 2009) in an FACSAriaIII flow cytometer (BD Biosciences, USA).
mRNA-Seq: PolyA RNA was fragmented into approximately 250 nt fragments by chemical fragmentation (200 mM tris acetate pH 8.2, 500 mM potassium acetate, 150 mM magnesium acetate) at 94°C for exactly 3.5 min in a thermocycler. Fragmented RNAs were isolated with RNA Clean beads (Beckman Coulter, USA) according to manufacturer’s instructions. Fractionation was checked by capillary electophoresis in a RNA Pico 6000 chip using the Bioanalyzer (Agilent Technologies, USA). First strand cDNA synthesis was accomplished using Superscript III Reverse Transcriptase and random hexamers (Invitrogen, USA), followed by second strand synthesis using DNA Polymerase I and RNaseH (Invitrogen USA). Double-stranded DNA was purified with Agencourt AMPure beads XP (Beckman Coulter, USA) and quality was checked by capillary gelelectrophoresis on the Bioanalyzer with the Agilent DNA 1000 kit (Agilent Technologies, USA). dsDNA libraries subsequently processed for sequencing using the Genomic DNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s protocol. For small RNA-seq: 1 µg of total RNA per sample were used for small RNA library preparation. First total RNA was treated with RNA 5’ polyphosphatase (Epicentre Biotechnologies, USA) prior to small RNA library preparation to allow for subsequent cloning of multiphosphorylated endo-siRNAs. Small RNA cloning and library preparation was then performed with the TruSeq Small RNA Sample Preparation Kit (Illumina, USA) according to the manufacturer protocol.

tag: strain

tag: temperature

value: sperm


title: IMEL_3

value: MEL


title: sperm (polyA replicate 1)


title: CTL02_LVntr_1

description:
Sample name: CTL02_LVntr_1
Processed data file: tissue_clusters.txt
Processed data file: tissue_seqfams.txt
Processed data file: tissue_unique.txt
Library: 4
mRNA gene expression data from Illumina HumanHT-12 beadarrays accessible at GSE52601.
barcode: TCACT
common 3'-adapter: TCGTATGCCGTCTTCTGCTTG
complete 3'-adapter: TCACTTCGTATGCCGTCTTCTGCTTG


title: 2-cell embryos (polyA replicate 2)

source_name: 2-cell embryo poly(A)-extracted mRNA library

value: 2-cell embryo


title: 2-cell embryos (polyA replicate 1)


title: 1-cell embryos (polyA replicate 1)

source_name: 1-cell embryo poly(A)-extracted mRNA library

value: 1-cell embryo


title: ILdb1_KD_1


title: 1-cell embryos (polyA replicate 2)


title: dKO 6h LPS rep2

city: Montréal

first: Claude

last: Perreault

state: Québec

address: P.O. Box 6128, Downtown Station

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: dendritic cells

growth_protocol: Dendritic cells were produced from the bone marrow of mouse femur and tibiaes. 3 million bone marrow cells were plated in 10-cm uncoated petri dishes with 10 mL cRPMI supplemented with 10 n/mL GM-CSF. 10 mL and 5 mL of cRPMI supplemented with 10 and 20 ng/mL GM-CSF were added at days 3 and 6, respectively. Dendritic cells were harvested at day 9.

extract_protocol:
Dendritic cells were harvested, washed with PBS, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dendritic cells maturation was induced by adding lipopolysaccharide (LPS, 1 ug/mL) for indicated time at day 9 of culture, prior harvest.

tag: cell type

value: bone marrow-derived dendritic cells

tag: genotype


title: dKO 6h LPS rep3


title: dKO 1h LPS rep4


title: dKO 6h LPS rep4


title: dKO 2h LPS rep2


title: dKO 2h LPS rep4


title: dKO 2h LPS rep1


title: WT 6h LPS rep4

value: Wild Type


title: dKO no LPS rep4


title: dKO no LPS rep3


title: WT 6h LPS rep3


title: dKO 1h LPS rep3


title: dKO 2h LPS rep3


title: WT 6h LPS rep1


title: WT 2h LPS rep4


title: dKO no LPS rep1


title: iPS-R1

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Sequencing reads were first trimmed for adapter sequence using Cutadapt.
All cytosines in the trimmed reads were then computationally converted to thymines and mapped twice, to a converted forward strand reference and to a converted reverse strand reference both based on the hg19 reference genome.
A converted reference is created by replacing all cytosines with thymines (forward strand) or all guanines with adenines (reverse strand) in the reference FASTA file.
For mapping we used Bowtie3 with the following options: "-S","-k 1","-m 1","--chunkmbs 3072","--best","--strata","-o 4","-e 80","-l 20", and "-n 0".
Any read that mapped to multiple locations was removed and one read from each starting location on each strand from each library was kept (i.e., clonal reads were removed).
To call methylated sites, we summed the number of reads that supported methylation at a site and the number of reads that did not. We used these counts to perform a binomial test with a probability of success equal to the non-conversion rate, which was determined by computing the fraction of methylated reads in the lambda genome (spiked in during library construction). The false discovery rate (FDR) for a given p-value cutoff was computed using Benjamini-Hochberg approach. Because the p-value distributions for each methylation context are different, this procedure was applied to each three nucleotide context independently (e.g., a p-value cutoff was calculated for CAT cytosines).
Genome_build: hg19
Supplementary_files_format_and_content: The processed data for the allc_<sample>_<chr>.tsv files contain a row of headers indicating the chromosome, position, strand, methylation class, methylation count, total coverage, and methylation call. This is a tab delimited file.

molecule: genomic DNA

source_name: Human induced Pluripotent Stem Cells Retro virus Sample 1

extract_protocol: One µg of genomic DNA was spiked with 5 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two One µg of genomic DNA was spiked with 5 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: pluripotent

value: fetal


title: iPS-R2

source_name: Human induced Pluripotent Stem Cells Retro virus Sample 2


title: iPS-S2

source_name: Human induced Pluripotent Stem Cells Sendai virus Sample 2


title: dKO 1h LPS rep2


title: dKO 6h LPS rep1


title: dKO 1h LPS rep1


title: dKO no LPS rep2


title: WT 2h LPS rep2


title: WT 6h LPS rep2


title: SCNT-4

source_name: Single Cell Nucleotide Transfer Sample 4


title: WT 1h LPS rep4


title: WT 1h LPS rep3


title: SCNT-2

source_name: Single Cell Nucleotide Transfer Sample 2


title: SCNT-3

source_name: Single Cell Nucleotide Transfer Sample 3


title: HESO-7

source_name: Human Embryonic Stem Cell


title: WT no LPS rep2


title: WT no LPS rep4


title: WT no LPS rep3


title: WT 2h LPS rep3


title: SCNT-1

source_name: Single Cell Nucleotide Transfer Sample 1


title: WT 1h LPS rep2


title: WT 2h LPS rep1


title: WT no LPS rep1


title: WT 1h LPS rep1


title: HESO-8


title: FP

city: Boca Raton

first: Marc

last: Kantorow

state: Florida

address: 777 Glades Rd

institute: Florida Atlantic University

description: Sample 5

data_processing:
Prepared libraries were sequenced uni-directionally with the illumina Genome Analyzer IIx.
Reads aligned to ENSEMBLE; Galgal4; GCA_000002315.2.
Data was then processed using the cufflinks pipeline with replicates under default parameters. (http://cufflinks.cbcb.umd.edu/)
Differential expression analysis performed by cuffdiff version 2.1.1
Genome_build: Gallus_gallus-4.0 (Synonym: galGal4)
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values and/or statistical analysis for the final assembled dataset

organism: Gallus gallus

source_name: Microdissected lens cortical fibers

extract_protocol:
The following protocol was performed in replicate.  100 Lenses were removed, microdissected (lens central epithelium, equatorial epithelium, cortical fibers, and central fiber core), pooled, and RNA was harvested using Trizol reagent. illumina directional mRNA-Seq  Sample Preparation was performed under manufacturer guidelines for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic day 13

value: Lens

tag: tissue (differentiation state-specific region)

value: cortical fibers

tag: #pooled microdissections


title: FP2

description: Sample 6

tag: age


title: FC

description: Sample 7

source_name: Microdissected lens central fibers

value: central fibers


title: EQ

description: Sample 3

source_name: Microdissected lens equatorial epithelium

value: equatorial epithelium


title: Sox4

city: Houston

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

institute: The University of Texas MD Anderson Cancer Center

description: Embryonic fetal liver derived progenitor B cells were sequentially transduced with BirA-, p190 Bcr-Abl-, SE-Cre- and BAP-Sox4-encoding retroviral constructs and  were sorted after each transduction.

data_processing:
Sequenced DNA tags were mapped to mouse genome mm9 using bowtie (version 0.12.8) with –m 1. To avoid PCR bias, for multiple tags that were mapped to the same genomic position, only one copy was retained for further analysis.
Peaks of Sox4 were detected by MACS (version 1.4.2) using the input DNA as control. The window size was set as 300 bp and the  P value cutoff was 1e-5.
The peak was classified by its location to the gene: upstream (-25kb to -5kb from TSS), promoter (-5kb to +0.5kb from TSS), exon, intron, TES (-0.5kb to +5kb from TES) and downstream (+5kb to +25kb from TES). For gene annotation, RefSeq genes downloaded from UCSC genome browser were used.
Genome_build: mm9
Supplementary_files_format_and_content: Sox4_peaks.txt: Sox4 peaks. Chr: chromosome of the peak; Start: start position of the peak; End: end position of the peak; Summit: summit of the peak; PVALUE: -10log10(pvalue) of the peak; NumTags: number tags in the peak; Fold: fold change to input; ClosestGeneID: RefSeq ID of the gene that has closest TSS to the peak; ClosestGeneSymbol: Gene Symbol of the closest gene; Dist2ClosestTSS: distance between the peak and the TSS of the closest gene; Dist2ClosestTES: distance between the peak and the TES of the closest gene; Location: location of peak related to the closest gene; AllGeneID: RefSeq ID of all the genes that are within +- 25kb of the peak; AllGeneSymbol: Gene Symbol of all the genes; Dist2AllTSS: distance between the peak and TSS of all the genes; Dist2AllTES: distance between the peak and TES of all the genes.

source_name: p190 Bcr-Abl immortalized progenitor B cells

extract_protocol:
Sonicated chromatin fragments were precipitated with streptavidin conjugated magnetic beads
Libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic fetal liver

tag: developmental stage

value: Progenitor B cells

tag: chip antibody


title: EQ2

description: Sample 4

tag: tissue


title: Input

value: input


title: FC2

description: Sample 8


title: EC2

description: Sample 2

source_name: Microdissected lens central epithelium

value: central epithelium


title: HDF

source_name: Human Dermal Fibroblast

value: fibroblast

value: somatic


title: oocytes (polyA replicate 1)

source_name: oocytes poly(A)-extracted mRNA library

value: oocyte


title: iPS-S1

source_name: Human induced Pluripotent Stem Cells Sendai virus Sample 1


title: EC

description: Sample 1


title: Day 21 CD45-tdTomato+ cells

status: Public on Jul 01 2014

first: Benjamin

last: tenOever

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Reads were aligned to a mouse transcriptome and influenza genome with bowtie2
Reads were normalized by total read count
Genome_build: GRCm38 genome and the influenza Influenza A virus (A/Puerto Rico/8/34/Mount Sinai(H1N1)
Supplementary_files_format_and_content: Read count for influenza and mouse genes

source_name: Whole lung

extract_protocol:
Indicated cells were sorted by a facs aria into a 96 well plate with 20ul RNA buffer. SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) was used as per manufacurers instruction
TruSeq DNA sample Preparation Kit (Illumina) as per the manufacturer’s instructions.  Samples were sequenced via 100nt single-end run on a HiSeq 2000

treatment_protocol: Mice were infected with 500 pfu of IAV_cre and lungs harvested at the indicated time points

value: lung

tag: cell number


title: Day 10 CD45-tdTomato- cells


title: Day 5 CD45-tdTomato+ cells


title: Day 10 CD45-tdTomato+ cells


title: Day 5 CD45-tdTomato- cells


title: Naïve CD45- cells


title: oocytes (polyA replicate 2)


title: Day 2 CD45-tdTomato- cells


title: Treated with 4-NQO [SAMPLE 20]

first: Xiaohan

last: Tang

address: 1300 York Avenue, Room E-405

institute: Weill Cornell Medical College

description: replicate 1

data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the GSNAP aligner version 2011.11.17 (with support Goby file format)   Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.  GobyWeb's Plugin GSNAP_GOBY version 1.1; Goby version 1.9.8.3 (20120216154520); GobyWeb version 1.7
differential expression analysis was performed using EdgeR plugin
Compression of structured high-throughput sequencing data, Campagne F, Dorff KC,  Chambwe N,  Robinson JT, Mesirov JP, Plos One, in press [see also our pre-print of this manuscript at http://arxiv.org/abs/1211.6664]
Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien Campagne. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One, 2013, 10.1371/journal.pone.0069666.
Genome_build: 1000 Genomes(GRCh37)

source_name: Tongue squamous cell carcinoma

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit and cleaned up wiith DNAse I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA sequencing was performed using Illumina TruSeqRNA technology, following the manufacturer’s protocol. Briefly, mRNA is purified using poly-T oligo-attached magnetic beads and subsequently fragmented. The cleaved RNA fragments are reverse transcribed into first strand cDNA using random primers. Next, second strand cDNA is synthesized using DNA Polymerase I and RNase H. The second strand cDNA fragments are subject to an end repair, the addition of a single ‘A’ base, and ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

tag: gender

value: Female


title: Not treated with 4-NQO [SAMPLE 9]

description: replicate 1

source_name: Tongue


title: Treated with 4-NQO [SAMPLE 17]

description: replicate 1


title: Not treated with 4-NQO [SAMPLE 1]

description: replicate 1


title: Treated with 4-NQO [SAMPLE 24]

description: replicate 1


title: Not treated with 4-NQO [SAMPLE 4]

description: replicate 1


title: H02

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

description: Pooled sequences from 10 bisulfite PCR amplicon amplicons

data_processing:
fastq conversion, sff_extract 0.2.13, sff_to_fastq -Q -C
filter reads,FASTX Toolkit 0.0.13.2, fastx_clipper -l 100 -Q33
align to amplicon sequences, Bismark v0.7.7, bismark —fastq —bowtie2 —non_directional  -N 1 -L 15 -D 20 -R 4
call SNPs, samtools 0.1.19-44428cd, samtools mpileup -D -E -Q 10 -u | bcftools view -Ig
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited, content describes genotype (0=homozygous alternate allele, 1=heterozygous, 2=homozygous reference allele) and information about SNP and CpG features including amplicon examined, feature ID (CpGID used in publication or SNP rsID), chromosomal location and SNP allele (0=alternate, 1=reference) or CpG methylation status (0=unmethylated, 1=methylated) for individual reads)CpG methylation calls for all reads

source_name: whole blood

extract_protocol:
DNA extracted from whole blood and bisulfite treated with Qiagen EpiTect bisulfite conversion kits
Qiagen EpiTect bisulfite conversion kits

tag: ethnicity

value: Not Hispanic

value: whole blood

tag: race

value: White


title: G08

value: Male


title: G12


title: H01


title: G11


title: Not treated with 4-NQO [SAMPLE 6]

description: replicate 1


title: G06


title: G10


title: Not treated with 4-NQO [SAMPLE 2]

description: replicate 1


title: G09


title: G05


title: Day 21 CD45-tdTomato- cells


title: Day 2 CD45-tdTomato+ cells


title: G03


title: G02


title: G01


title: F11


title: F10


title: F09

description:
Pooled sequences from 10 bisulfite PCR amplicon amplicons
failed QC


title: G07


title: F08


title: F02


title: F04


title: F01


title: E07


title: F05


title: E10


title: F03


title: F06


title: E11


title: E08


title: E09


title: E12


title: E03


title: E04


title: E06


title: E02


title: E01


title: E05


title: G04


title: D12


title: F12


title: D08


title: D09


title: D10


title: D07


title: D03


title: D05


title: D06


title: D04


title: C12


title: C11


title: D02


title: D01


title: C06


title: C09


title: C03


title: C04


title: C07


title: B12


title: B09


title: B11


title: D11


title: C01


title: B08


title: B07


title: B06


title: B10


title: C02


title: B02


title: B05


title: B04


title: B03


title: C10


title: A11


title: A10


title: A09


title: A06


title: A03


title: A01


title: A08


title: A07


title: 1308388 NTL [expression]

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

description:
s11_P
Processed data file: s12_C-VS-s11_P.GeneExp.txt.gz

data_processing:
Firstly, data cleaning (or data filtering) is performed to obtain clean reads (or "clean data") for further analysis. The procedure includes the following steps: 1, Remove reads with adaptor sequences; 2, Remove reads in which the percentage of unknown bases (N) is greater than 10%; and 3, Remove low-quality reads. If the percentage of the low-quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality. Then, clean reads were mapped to genomic sequences or reference gene set using SOAPaligner/SOAP2 with no more than 2 mismatches.
The gene expression level is calculated by using the RPKM (Reads Per kb per Million reads) method (Mortazavi, A., B. A. Williams, et al.), and the formula is shown as follows: RPKM= (10^6*C)/(NL⁄10^3 ). Here C is number of reads that uniquely aligned to gene A, N is total number of reads that uniquely aligned to all genes, and L is number of bases of gene A. The RPKM method is able to eliminate the influence of different gene length and sequencing discrepancy on the calculation of gene expression level. Therefore, the RPKM values can be directly used for comparing the difference of gene expression among samples. If there is more than one transcript for a gene, the longest one is used to calculate its expression level and coverage. To identify differentially expressed genes between two samples, a more strict algorithm to be used to calculated the P-value corresponds to differential gene expression test (Audic, S and J. M. Claverie). The multiple tests P-values were then adjusted by FDR (False Discovery Rate). Lastly, we use "FDR ≤ 0.001 and the absolute value of fold-change value ≥ 1" as the threshold to judge the significance of gene expression difference.
Integration of promoter methylomic and transcriptomic profiling. To further clarify the genes that are potentially regulated by promoter methylation, we further performed pair-wise comparisons on promoter methylomes to identify specific DMRs between HCCs and peripheral normal tissues. Furthermore, we evaluated differential gene expression between 8 pairs of HCC and PN samples using Illumina high-throughput RNA-seq technology.
Genome_build: GRCh37 (UCSC hg19)
Supplementary_files_format_and_content: *.GeneExp.txt.gz files include all genes expressing in tumor and NTL sample pair. These files contain 10 columns. The format is: (1) geneID; (2) geneLength; (3) ctrl-Expression; (4) case-Expression; (5) ctrl-RPKM; (6) case-RPKM; (7) log2 Ratio (case/ctrl); (8) Up-Down-Regulation (case/ctrl); (9) P-value; and (10) FDR.

source_name: liver, NTL

extract_protocol:
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.
cDNA libraries were prepared according to the manufacturer's instructions (Illumina). The poly(A)-containing mRNA molecules were purified using Oligo(dT) Beads (Illumina) from 20 ug of total RNA from each sample. Tris–HCl (10 mM) was used to elute the mRNA from the magnetic beads. To avoid priming bias when synthesizing cDNA, mRNA was fragmented before the cDNA synthesis. Fragmentation was performed using divalent cations at an elevated temperature. The cleaved mRNA fragments were converted into double-stranded cDNA using SuperScript II, RNaseH and DNA Pol I, primed by random primers. The resulting cDNA was purified using the QIAquick PCR Purification Kit (Qiagen). Then, cDNA was subjected to end-repair and phosphorylation using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. Subsequent purifications were performed using the QIAquick PCR Purification Kit (Qiagen). These repaired cDNA fragments were 3'-adenylated using Klenow Exo- (Illumina) and purified using the MinElute PCR Purification Kit (Qiagen), producing cDNA fragments with a single 'A' base overhang at the 3'-end for subsequent ligation to the adapters. Illumina PE adapters were ligated to the ends of these 30-adenylated cDNA fragments and then purified using the MinElute PCR Purification Kit (Qiagen). To select a size range of templates for downstream enrichment, the products of the ligation reaction were purified on a 2% TAE-agarose gel (Certified Low-Range Ultra Agarose, Biorad). cDNA fragments (200±20bp) were excised from the gel and extracted using the QIAquick Gel Extraction Kit (Qiagen). Fifteen rounds of PCR amplification were performed to enrich the adapter-modified cDNA library using primers complementary to the ends of the adapters [PCR Primer PE 1.0 and PCR Primer PE 2.0 (Illumina)]. The 200±20 bp PCR products were purified using QIAquick Gel Extraction Kit (Qiagen), using the MinElute spin columns (Qiagen). Finally, after detection on an Agilent Technologies 2100 Bioanalyser using the Agilent DNA 1000 chip kit and quantification on a StepOne plus qPCR (ABI), the cDNA library products were sequenced by a pair-end 90bp strategy using the Illumina Genome Analyser.

tag: disease status

value: hepatocellular carcinoma (HCC)

value: non-tumor liver

value: M

tag: age (y)

tag: patient


title: 1303277 Tumor [expression]

description:
s16_C
Processed data file: s16_C-VS-s15_P.GeneExp.txt.gz

source_name: liver, HCC tumor

value: liver tumor

value: F


title: 1304203 NTL [expression]

description:
s14_P
Processed data file: s13_C-VS-s14_P.GeneExp.txt.gz


title: 1308849 NTL [expression]

description:
s10_P
Processed data file: s09_C-VS-s10_P.GeneExp.txt.gz


title: 1303277 NTL [expression]

description:
s15_P
Processed data file: s16_C-VS-s15_P.GeneExp.txt.gz


title: 1306706 NTL [expression]

description:
s96_P
Processed data file: s95_C-VS-s96_P.GeneExp.txt.gz


title: 1304203 Tumor [expression]

description:
s13_C
Processed data file: s13_C-VS-s14_P.GeneExp.txt.gz


title: 1308849 Tumor [expression]

description:
s09_C
Processed data file: s09_C-VS-s10_P.GeneExp.txt.gz


title: 1306734 Tumor [expression]

description:
s02_C
Processed data file: s02_C-VS-s01_P.GeneExp.txt.gz


title: 1159804 Tumor [expression]

description:
s05_C
Processed data file: s05_C-VS-s06_P.GeneExp.txt.gz


title: F13

status: Public on Jul 03 2014

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Base calls and quality scores were generated using Illumina's Real-Time Analysis software v1.8.7.  Binary base call files were converted to text formatted qseq files via OLB 1.9.0, which were then filtered and converted to fastq format by CASAVA 1.7, using the default Chastity threshold of 0.6.
Read counts for the genes are collected by Bioconductor Biostrings and IRanges packages.  Reads that are mapped ambiguously to M locations are counted as 1/M at each occurrence.
Genome_build: hg19
Supplementary_files_format_and_content: biopsy.gene.counts.csv.gz contains the read counts for each gene for FSHD/control biopsy samples
Supplementary_files_format_and_content: cultured.gene.counts.csv.gz contains the read counts for each gene for myotubes and myoblasts from FSHD/control samples

source_name: Male FSHD2 biopsy F13

growth_protocol: Muscle cell cultures: Muscle cells derived from two FSHD1 and three FSHD2 were cultured and RNA was harvested from both myoblasts and myotubes. These cultures were described previously (24). As previously described, Primary myoblast cell lines were received from the University of Rochester biorepository (http://www.urmc.rochester.edu/fields-center) and were cultured in DMEM/F-10 media (Gibco) in the presence of 20% heat-inactivated fetal bovine serum (Gibco), 1% penicillin/streptomycin (Gibco). Media was supplemented with 10ng/ml rhFGF (Promega) and 1μM dexamethasone (SIGMA). Myoblasts were fused at 80% confluence in DMEM/F-12 Glutamax media containing 2% KnockOut serum replacement formulation (Gibco) for 36 hours.

extract_protocol:
Muscle biopsy samples were obtained under local anesthesia by the minimally needle biopsy technique utilizing the modified Bergstrom needle. RNA was extracted, poly(A) selected, and subjected to Illumina sequencing using standard protocols to generate 100bp  single-end reads.
Sequencing libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

value: FSHD2 Muscle biopsy


title: 1306734 NTL [expression]

description:
s01_P
Processed data file: s02_C-VS-s01_P.GeneExp.txt.gz


title: A12


title: B01


title: 1305780 Tumor [expression]

description:
s00_C
Processed data file: s00_C-VS-s99_P.GeneExp.txt.gz


title: A04


title: A05


title: CBP215 [healthy_LGA]

city: BRONX

first: Fabien

last: Delahaye

address: 1300 Morris Park Avenue

department: Genetics

institute: AECOM

data_processing:
library strategy: HELP tagging
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: The wig files were generated using in house pipeline; Scores represent degree of unmethylation

source_name: healthy_large for gestational age (LGA)_male

extract_protocol:
Human Cord Blood CD34+ Hematopoietic Stem Cells were separated using Ficoll-Paque or PrepaCyte-WBC and immunomagnetic selection (AutoMACS Separator) from umbilical cord blood blood. Genomic DNA samples were extracted uisng standard protocol.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA , 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  The product then underwent gel extraction (Qiagen).

value: male

tag: clinical phenotype

value: healthy_large for gestational age (LGA)

value: Human Umbilical Cord Blood CD34+ Hematopoietic Stem Cells


title: 1306706 Tumor [expression]

description:
s95_C
Processed data file: s95_C-VS-s96_P.GeneExp.txt.gz


title: CBP242 [healthy_LGA]


title: CBP265 [healthy_LGA]


title: 1159804 NTL [expression]

description:
s06_P
Processed data file: s05_C-VS-s06_P.GeneExp.txt.gz


title: 1308388 Tumor [expression]

description:
s12_C
Processed data file: s12_C-VS-s11_P.GeneExp.txt.gz


title: CBP197 [healthy_LGA]


title: CBP214 [healthy_LGA]


title: CBP223 [healthy_LGA]


title: CBP048 [healthy_LGA]


title: CBP128 [healthy_LGA]


title: CBP100 [healthy_LGA]


title: 1305780 NTL [expression]

description:
s99_P
Processed data file: s00_C-VS-s99_P.GeneExp.txt.gz


title: CBP147 [healthy_LGA]

source_name: healthy_large for gestational age (LGA)_female

value: female


title: CBP047 [healthy_LGA]


title: CBP154 [healthy_LGA]


title: CBP198 [healthy_LGA]


title: CBP263 [healthy_LGA]


title: CBP146 [healthy_LGA]


title: CBP141 [healthy_LGA]


title: CBP094 [healthy_IUGR]

source_name: healthy_intrauterine growth restriction (IUGR)_male


title: CBP151 [healthy_IUGR]

value: healthy_intrauterine growth restriction (IUGR)


title: CBP165 [healthy_LGA]


title: CBP120 [healthy_LGA]


title: CBP092 [healthy_IUGR]


title: CBP164 [healthy_LGA]


title: CBP156 [healthy_IUGR]


title: CBP136 [healthy_IUGR]


title: CBP153 [healthy_IUGR]


title: CBP184 [healthy_IUGR]

source_name: healthy_intrauterine growth restriction (IUGR)_female


title: CBP127 [healthy_IUGR]


title: CBP152 [healthy_IUGR]


title: CBP090 [healthy_IUGR]


title: CBP218 [healthy_IUGR]


title: CBP091 [healthy_IUGR]


title: CBP050 [healthy_IUGR]


title: CBP083 [healthy_IUGR]


title: CBP220 [healthy_IUGR]


title: CBP045 [healthy_IUGR]


title: CBP159 [healthy_IUGR]


title: CBP256 [healthy_control]


title: CBP212 [healthy_LGA]


title: CBP148 [healthy_IUGR]


title: CBP250 [healthy_control]


title: CBP229 [healthy_control]


title: CBP233 [healthy_IUGR]


title: CBP113 [healthy_control]


title: CBP193 [healthy_control]


title: CBP110 [healthy_control]


title: CBP234 [healthy_control]


title: CBP188 [healthy_control]


title: CBP103 [healthy_control]


title: CBP102 [healthy_control]


title: CBP084 [healthy_IUGR]


title: CBP111 [healthy_control]


title: CBP087 [healthy_control]


title: CBP086 [healthy_control]


title: CBP085 [healthy_control]


title: CBP008 [healthy_control]


title: CBP026 [healthy_control]


title: CBP079 [healthy_control]


title: CBP042 [healthy_control]


title: CBP231 [healthy_control]


title: CBP041 [healthy_control]


title: CBP256

description: library strategy: HELP tagging

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: The wig files were generated using in house pipeline; Scores represent degree of unmethylation

source_name: Umbilical Cord Blood CD34+ Hematopoietic Stem Cells

value: Healthy Control

value: newborn


title: CBP250

description: library strategy: HELP tagging

value: Umbilical Cord Blood CD34+ Hematopoietic Stem Cells


title: CBP253

description: library strategy: HELP tagging


title: CBP252

description: library strategy: HELP tagging


title: Δczt-1 Staurosporine

city: Berkeley

first: António Pedro

last: Gonçalves

address: 341A Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
Illumina Casava1.8.0 software used for basecalling.
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G --compatible-hits-norm --max-bundle-frags=100000000)
Differential Expression was estimated with Cuffdiff (options: -u -N -b --compatible-hits-norm --max-bundle-frags=100000000)
Genome_build: OR74A version 10 (call 5) from the Broad Institute (n_crassa_or74a__transcripts_plus_mito_jan_2012)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Neurospora crassa

source_name: 6h+1h 20 μM STS

growth_protocol: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ºC, 140 rpm, constant light).

extract_protocol:
Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies).
The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturer’s protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer.

treatment_protocol: Addition of staurosporine (or DMSO) and growth for 1 more hour.

tag: strain

tag: growth stage

value: 6 hr conidia culture

tag: treatment

value: 20 μM STS


title: Δczt-1 DMSO

source_name: 6h+1h DMSO

value: 1h DMSO


title: Wild type DMSO

value: Wild type


title: CBP248

description: library strategy: HELP tagging

tag: cell type


title: CBP234

description: library strategy: HELP tagging


title: CBP229

description: library strategy: HELP tagging


title: CBP188

description: library strategy: HELP tagging


title: CBP193

description: library strategy: HELP tagging


title: CBP231

description: library strategy: HELP tagging


title: Wild type Staurosporine


title: CBP144

description: library strategy: HELP tagging


title: CBP186

description: library strategy: HELP tagging


title: CBP113

description: library strategy: HELP tagging


title: CBP140

description: library strategy: HELP tagging


title: CBP240

description: library strategy: HELP tagging


title: CBP189

description: library strategy: HELP tagging


title: CBP110

description: library strategy: HELP tagging


title: CBP111

description: library strategy: HELP tagging


title: CBP103

description: library strategy: HELP tagging


title: CBP085

description: library strategy: HELP tagging


title: CBP087

description: library strategy: HELP tagging


title: CBP086

description: library strategy: HELP tagging


title: CBP096

description: library strategy: HELP tagging


title: CBP041

description: library strategy: HELP tagging


title: CBP042

description: library strategy: HELP tagging


title: CBP102

description: library strategy: HELP tagging


title: hid1 rep3

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

description: polyA RNA isolated

data_processing:
RNA-seq reads were mapped to TAIR10 using Tophat (version 2.0.9) (1). Differentially expressed genes were defined as those that differed by >2-fold with an adjusted P value ≤0.05 that was identified using Cuffdiff software (version 2.0.0)
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Total RNA was isolated from 5-day-old cR-grown WT and hid1(hidden treasure 1)seedlings using RNeasy Plant Mini Kits (Qiagen). Three biological replicates for each sample were subjected to RNA-seq. Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: hid1(hidden treasure 1)

value: 5 day old


title: CBP026

description: library strategy: HELP tagging

tag: age


title: hid1 rep2

description: polyA RNA isolated


title: WT rep3

description: polyA RNA isolated

value: cR-grown WT


title: WT rep1

description: polyA RNA isolated


title: hid1 rep1

description: polyA RNA isolated


title: WT rep2

description: polyA RNA isolated


title: CBP008

description: library strategy: HELP tagging


title: H2AZ-ChIP-Seq_Control_1

city: Copenhagen

first: Sheroy

last: Minocherhomji

state: Copenhagen N

address: Blegdamsvej 3B, Building 18.1

department: Nordea Centre for Healthy Aging, Faculty Of Health Sciences Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Chromatin IP against H2A.Z

data_processing:
Alignment: Sequence reads were obtained and mapped to the human hg81/NCBI build 36 (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm
Genome_build: hg18
Supplementary_files_format_and_content: wig files

source_name: EBV-Transformed peripheral blood B lymphocytes

growth_protocol: For ChIP-Seq experiments B-lymphocytes from normal controls peripheral whole blood were EBV transformed and maintained using standard protocols

extract_protocol:
Library generation of immunoprecipitated chromatin for Solexa sequencing (ChIP-Seq) was performed using an Illumina recommended method.
Library sequenced on a Genome Analyzer II (Illumina).

value: normal control

value: EBV-Transformed B lymphocytes

value: whole blood

value: H2A.Z (Abcam Plc., ab4174)


title: H2AZ-ChIP-Seq_Control_2

description: Chromatin IP against H2A.Z


title: CBP079

description: library strategy: HELP tagging


title: ChIP-Seq_Sample_1_H2A.Z

description: Chromatin IP against H2A.Z

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

growth_protocol: For Methylation experiments genomic DNA from B lymphocytes obtained from peripheral whole blood was used. For ChIP-Seq experiments B-lymphocytes from patient  peripheral whole blood were EBV transformed and maintained using standard protocols

extract_protocol: Library generation of immunoprecipitated chromatin, methylated/unmethylated gDNA or total RNA (from various human tissues) for Solexa sequencing (ChIP-Seq, MBD-Seq and MRE-Seq) was performed using an Illumina recommended method and sequenced on a Genome Analyzer II (Illumina). Following high throughput sequencing, reads were aligned back to the hg18 (NCBI build 36) assembly using Bowtie. Two mismatches within the seed sequence (28-32 bases) of each unique read aligned were used as cut-offs to match back to the hg18 human genome assembly. Regions enriched for each modification were analyzed using Cisgenome software and a false discovery rate (FDR) of <0.01. Converted WIG files were visualized using the UCSC genome browser. ChiP-Seq experiments were analyzed using Cisgenome parameters for one/two sample analyses and IgG or histone 3+ (H3) as negative controls. Genome-wide comparisons of MBD-Seq data were performed using the R statistical software.

tag: antibody vendor & cat. number

value: Abcam Plc., ab4174


title: MRE-Seq_Sample_1 using HpaII

description: Restriction Enzyme digestion of gDNA using HpaII

value: Peripheral blood B-lymphocytes

tag: restriction enzyme

value: HpaII  (New England Biolabs, R0171L)


title: ChIP-Seq_Sample_2_H3K4me3

description: Chromatin IP against H3K4me3

tag: tissue

tag: chip antibody

value: Cell Signalling Technology, Inc.,  9727S


title: ChIP-Seq_Sample_1_H3K27me3

description: Chromatin IP against H3K27me3

value: Active Motif, 39155


title: MRE-Seq_Sample_2 using HpaII


title: MBD-Seq_Control_1 using his-MBD2B

description: IP against Methylated gDNA using his-MBD2B

tag: mbd

value: Active Motif, 5502 (Methyl Collector Kit)


title: MBD-Seq_Control_2 using his-MBD2B


title: ChIP-Seq_Sample_1_IgG

description: Chromatin IP against IgG

value: IgG

value: Cell Signalling Technology, Inc.,  2729S


title: MRE-Seq_Control_2 using  HpaII


title: ChIP-Seq_Sample_2_H3+

description: Chromatin IP against H3+

value: Abcam Plc., ab1791


title: MRE-Seq_Control_1 using  HpaII


title: MBD-Seq_Sample_2 using his-MBD2B


title: Fliver

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

description: FL

data_processing:
Basecalls performed using RTA 1.9 and CASAVA 1.7.0.
The sequence reads were trimmed and removed for adaptor sequences and the expression values.
The filtered sequence reads were mapped with miRBase v17 using NCBI BLAST v2.2.19.
The abundance for miRNAs were calculated by reads per miRNA per million sequenced reads.
Genome_build: miRBase v17
Supplementary_files_format_and_content: tab-delimited text files include miRNA sequences, lengths and abundances.

organism: Oryzias melastigma

source_name: breeding marine medaka

extract_protocol:
Total RNA from pooled tissue samples was extracted using the mirVanaTM miRNA isolation kit (Applied Biosystems) and treated with DNase (Ambion) to remove contaminating genomic DNA.
The total RNA libraries were constructed from brain, liver, ovaries from female and brain, liver, testis from male, with each prepared from 1 µg of total RNA.  Small RNAs were gel purified for enrichment to under 30 nt in length, and Illumina adaptors (Integrated DNA technology) were ligated to their 5’ and 3’ ends to construct strand-specific cDNA libraries. The ligation products were used as a template for cDNA synthesis using SuperScript II Reverse Transcriptase (Invitrogen) and an oligonucleotide primer with sequence complementary to 3’ adapter was used to initiate cDNA synthesis. The cDNA was amplified by 12 cycles using AccuPrime™ Pfx DNA Polymerase (Life Technologies) and purified on Novex 8% TBE polyacrylamide gel (Invitrogen).  Amplified DNA of 140-190 nt was extracted from the gel and purified using the QiaQuick Gel Extraction Kit (Qiagen).

tag: gender

value: female

value: liver

tag: molecule subtype

value: size-selected RNA


title: Fbrain

description: FB

value: brain


title: MBD-Seq_Sample_1 using his-MBD2B


title: Fovary

description: FO

value: ovaries


title: Mtestis

description: MT

value: male

value: testes


title: Mbrain

description: MB


title: HA-Siwi IP  #rep2

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description: small RNA

data_processing:
A custom pipeline that generates genome annotations based on that found in http://kaikogaas.dna.affrc.go.jp/
Genome_build: Bombyx mori genome at http://kaikogaas.dna.affrc.go.jp/

organism: Bombyx mori

source_name: HA-Siwi IP  #rep2

growth_protocol: Transfected BmN4 cells were used.

extract_protocol: Nucleic acids were isolated from immunoprecipitated HA-tagged protein complexes and resolved by 15% urea-PAGE. Bands corresponding to piRNAs were excised from the gel and extracted with 400 µl of 0.3M NaCl solution at 25°C overnight. After purification by phenol-chloroform extraction, deep sequencing libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions. Libraries were sequenced on Illumina HiSeq 2000 platform (EMBL Heidelberg Gene core facility).

tag: cell line

value: BmN4 cells

tag: antibody

value: Immunoprecipitation with anti-HA


title: HA-Ago3 IP  #rep2

description: small RNA

source_name: HA-Ago3 IP  #rep2


title: HA-Siwi-Ago3 chimera  #rep1

description: small RNA

source_name: HA-Siwi-Ago3 chimera  #rep1


title: HA-Ago3 IP  #rep1

description: small RNA

source_name: HA-Ago3 IP  #rep1


title: HA-Siwi-Ago3 chimera  #rep2

description: small RNA

source_name: HA-Siwi-Ago3 chimera  #rep2


title: HA-Siwi-Ago3 chimera  #rep3

description: small RNA

source_name: HA-Siwi-Ago3 chimera  #rep3


title: HA-Siwi IP  #rep1

description: small RNA

source_name: HA-Siwi IP  #rep1


title: Mliver

description: ML


title: tbh_rep2

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

description: Sample 4

data_processing:
library strategy: Digital Gene Expression
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence. Only 21nt tags without any 'N' nucleotide and with count > 1 in a library were kept as clean tags.
Counts of tags were normalized to transcript per million (TPM) according to total number of clean tags in each library
Genome_build: v2i available at http://cucumber.genomics.org.cn/
Supplementary_files_format_and_content: Each file contains three columns: tag sequence, raw count, normalized count (transcript per million, TPM)

organism: Cucumis sativus

source_name: tbh mutant_fruit spine

extract_protocol:
Total RNA were extracted using Huayueyang RNA extraction kit (China)
6ug total RNA was used in library construction.Double-stranded cDNAs were synthesized using oligo(dT) beads (Invitrogen).The cDNAs were then digested with an anchoring restriction enzyme (NlaIII) and ligated to a 5' adapter, which contains a recognition site for the type IIS restriction enzyme MmeI (New England Biolabs). Following MmeI digestion, 3' adapter was ligated. Tags flanked by both adapters were enriched by PCR for 15 cycles. The PCR products were run on a 6% PAGE gel, and the 105-bp DNA band was excised and purified. The DNA samples were sequenced on an Illumina HiSeq 2000 sequencer.

value: tbh mutant

tag: developmental stage

value: 4 days before anthesis

value: fruit spine


title: Y05_rep2

description: Sample 6

source_name: WT_fruit spine_0.5cm fruit

value: wild type

value: 7 days before anthesis

value: fruit spine on fruits of 0.5cm long


title: Y05_rep1

description: Sample 5


title: Y16_rep1

description: Sample 7

source_name: WT_fruit spine_1.6cm fruit

value: fruit spine on fruits of 1.6cm long


title: Y16_rep2

description: Sample 8


title: PpsR_3xMyc_ChIP_Seq

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

data_processing:
100 bp reads were trimmed to 70bp to remove unreliable base calls. 50bp reads were not trimmed
Mapping was done to the R. sphaeroides reference genome using SOAP version 2.21 allowing for 3 mismatches for 70bp reads and 2 mismatches for 50bp reads
Peaks were identified using MOSAiCS at a false discovery rate of 0.05 using a two-sample analysis with Input DNA or mock chip used as control.
Genome_build: ASM1290v2, ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Rhodobacter_sphaeroides_2_4_1_uid57653/
Supplementary_files_format_and_content: Processed data files are provided as wig files with scores representing the normalized ratio of reads between a sample ChIP and INPUT DNA

organism: Cereibacter sphaeroides 2.4.1

source_name: Bacteria culture (SIS - Aero)

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) or aerobically (bubbling with 69% N2, 30% O2, 1% CO2) on Sistrom's minimal media and harvested at exponential phase. Where necessary 1 to 5μL of IPTG was added at the start of the culture to induce protein expression.

extract_protocol:
At midexponential phase (~2×108 colony-forming units/ml), formaldehyde and sodium phosphate were added to a final concentration of 1% and 10 mM, respectively. This mixture was incubated at 30 °C for 4 min before glycine was added to 100 mM, and the solution was placed on ice for 30 min with gentle agitation to quench excess formaldehyde. Cells were centrifuged at 3000g, washed twice with chilled phosphate buffered saline, centrifuged, and flash-frozen at −80 °C. About 2×1010 cells were suspended in 0.5 ml of 100 mM Tris (pH 8.0), 300 mM NaCl, 2% Triton X-100, RNase A (0.5 μg) and 1 mM phenylmethylsulfonyl fluoride, and sonicated in a Misonix water bath for 8 mins with 10s pulses and intervals. Cell debris was removed by centrifugation for 10 min at 12,000g, and an aliquot was removed to analyze DNA fragmentation by agarose gel eletrophoresis (desired size of ~200–1000 bp with enrichment for ~500-bp molecules). The resulting supernatant was incubated with gentle mixing with 20 μl of Staphylococcus aureus protein A Sepharose beads (Sigma-Aldrich, St. Louis, MO) for 3 h at 4 °C as pretreatment to remove potential nonspecific binding to the beads. After the beads had been removed by centrifugation (5 min at 3000g), one-tenth of the sample was removed and used as non-antibody-treated control. Five microlitre of Myc epitope antibody (ab9132, Abcam plc) was added and the mixture was incubated overnight at 4 °C with gentle mixing before being incubated with protein A Sepharose beads (30 μl) for 3 h at 4 °C. The beads were recovered by centrifugation; washed once (4 °C) with 250 mM LiCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 600 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 300 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; and washed twice with TE buffer (10 mM Tris pH 8.0 and 1 mM EDTA). Protein–DNA complexes were eluted from the beads by incubating at 65 °C for 30 min in 50 mM Tris (pH 8.0), 10 nM EDTA, and 1% sodium dodecyl sulfate. The beads were removed by centrifugation, and protein–DNA cross-linking was reversed by incubating the samples for 12 h at 65 °C. DNA was purified using the QIAquick PCR Purification Kit. Samples were sent to UW-Madison Biotech center for further processing and sequencing.
Libraries were prepared according to Illumina's instructions by UW-Madison biotech center

value: Pps1 complemented with 3xMyc tagged PpsR from an IPTG inducible plasmid

tag: chip-antibody


title: UNM

city: Leicester

first: David

last: Twell

state: Leicestershire

address: Department of Biology

country: United Kingdom

institute: University of Leicester

description: small RNA sequencing

data_processing:
UNM.txt; genome build: TAIR9
The 5' small RNA adapters and  3’-polyA adaptors were removed using an exact match to the sequence. Unique sequences were then matched to the TAIR9 version of Arabidopsis thaliana genome. Only sequences perfectly matching the genome were conserved. The data provided correspond to unique sequences (with the attached number of reads) perfectly matching the Arabidopsis genome.

source_name: Uninucleate microspore stage of Arabidopsis pollen development

growth_protocol: Arabidopsis thaliana ecotype Landsberg erecta (Ler-0) plants were grown in controlled-environment growth rooms at 21°C with a 16-h photoperiod. Isolated spores from different stages of pollen development (uni-nucleate microspore (UNM), bi-cellular pollen (BCP) and tri-cellular pollen (TCP)) were obtained following a protocol modified from Honys, D. and Twell, D. (2004) Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol. 5/11/R85. Mature pollen (MP) from flowering plants was isolated as described previously (Honys, D. and Twell, D. (2003). Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol 132, 640-652).

extract_protocol: The four samples (UNM, BCP, TCP and MP) were ground in liquid nitrogen. From the tissue powders total RNA and small RNA fractions (smaller than 200 nt) were isolated using the mirVana miRNA isolation kit (Invitrogen, Life Technologies Corp.). Small RNAs were first poly(A)-tailed using poly(A) polymerase followed by a ligation of an RNA adapter to the 5´-phosphate end of the small RNA. First-strand cDNA synthesis was then performed using an oligo(dT)- adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase. The primers used for PCR amplification were designed for amplicon sequencing according to the instructions of Illumina/Solexa. The following adapter sequences flank the cDNA inserts: 5’- end (53 bases): 5´- AATGATACGGCGACCACCGACAGGTTAGAGTTCTACAGTCCGACGATCNNNN-3’; 3’-end (45 bases):  5’- CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTTTTT-3’. The combined length of the flanking sequences is 98 bases. Contaminating smaller PCR products visible in some samples were removed by isolating the 120 bp fraction of the cDNAs from preparative 6% PAA-gels.  cDNA sequencing was performed using the Illumina GA II Genome Analyzer. Two samples were sequenced  per Illumina channel, each cDNA from a given sample having a specific barcode at the 3’ end of the 5’ adaptor (UNM: ACTA – BCP: GTAA - TCP: TACA - MP: ATGA). Around 10 million cDNAs were sequenced per channel.

treatment_protocol: No treatment

tag: ecotype

value: pollen

value: Uninucleate microspore


title: TCP

description: small RNA sequencing

data_processing:
TCP.txt; genome build: TAIR9
The 5' small RNA adapters and  3’-polyA adaptors were removed using an exact match to the sequence. Unique sequences were then matched to the TAIR9 version of Arabidopsis thaliana genome. Only sequences perfectly matching the genome were conserved. The data provided correspond to unique sequences (with the attached number of reads) perfectly matching the Arabidopsis genome.

source_name: Tricellular stage of Arabidopsis pollen development

value: Tricellular


title: BCP

description: small RNA sequencing

data_processing:
BCP.txt; genome build: TAIR9
The 5' small RNA adapters and  3’-polyA adaptors were removed using an exact match to the sequence. Unique sequences were then matched to the TAIR9 version of Arabidopsis thaliana genome. Only sequences perfectly matching the genome were conserved. The data provided correspond to unique sequences (with the attached number of reads) perfectly matching the Arabidopsis genome.

source_name: Bicellular stage of Arabidopsis pollen development

value: Bicellular


title: Campylobacter jejuni fur perR mutant dRNA-seq +TEX

city: Norfolk

first: Arnoud

last: van Vliet

address: Colney Lane

department: Gut Health and Food Safety Programme

institute: Institute of Food Research

data_processing:
Sequences were obtained from SFF files, processed by the software provided by the 454 Titanium sequencing service at The Genome Analysis Centre, Norwich, UK
Sequencing reads were grouped based on the barcode tag, the 5' adapter was clipped, and reads of >70% A were removed.
The remaining reads were aligned against the C. jejuni genome NCTC 11168 genome sequence using Segemehl version 0.0.9.3 (Hoffmann et al., 2009), and converted into number of reads per nucleotide position, for the plus and minus strand of the genome
Graphs representing the number of mapped reads per nucleotide were loaded in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009).
Genome_build: Campylobacter jejuni  NCTC11168: NC_002163.1
Supplementary_files_format_and_content: Histogram files for use in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009). Scores represent the number of reads per nucleotide position

organism: Campylobacter jejuni

source_name: Bacteria

growth_protocol: The fur perR mutant of Campylobacter jejuni strain NCTC 11168  was grown to late log phase

extract_protocol:
Total RNA was purified omitting size selection, to avoid the loss of small RNA molecules. The exclusion of rRNA and tRNA was also omitted, to avoid the potential loss of other RNA species. RNA was isolated using hot phenol (Mattatall & Sanderson, 1996), to ensure that small RNAs would not be removed by the extraction procedure. The RNA was treated with DNase I to remove residual genomic DNA.
The RNA sample was split in two equal fractions, and one of the two fractions was treated with Terminator Exonuclease (TEX, Peicentre Biotechnology) for enrichment of primary RNAs (Sharma et al., 2010). Both samples were treated with Tobacco Acid Phosphatase (TAP, Cambio, UK) to generate 5'-P ends for downstream ligation of 454 adapters. After ligation of an RNA oligonucleotide to the phosphorylated 5’-ends of RNA, and polyadenylation of RNA, first strand cDNA was generated using an oligo-dT containing 454-B primer. The cDNA fragments were barcoded and amplified, and used for generation of cDNA libraries for the 454 FLX system at Vertis Biotech, Germany. These libraries were subsequently analysed using a Roche FLX/Titanium sequencer using standard protocols from the manufacturer.

tag: strain

value: fur::kan perR:cm

tag: phase

value: late log growth

value: terminator exonuclease


title: MP

description: small RNA sequencing

data_processing:
MP.txt; genome build: TAIR9
The 5' small RNA adapters and  3’-polyA adaptors were removed using an exact match to the sequence. Unique sequences were then matched to the TAIR9 version of Arabidopsis thaliana genome. Only sequences perfectly matching the genome were conserved. The data provided correspond to unique sequences (with the attached number of reads) perfectly matching the Arabidopsis genome.

source_name: Mature pollen grain stage of Arabidopsis pollen development

value: Mature


title: WT_rep2

description: Sample 2

source_name: WT_fruit spine


title: Input_DNA

source_name: Bacteria culture (SIS)

value: wildtype

value: none, input


title: WT_rep1

description: Sample 1

value: 4 days before anthesis


title: MPK1 deletion in KN99a background Mpk1_n

city: St. Louis

first: Maureen

last: Donlin

state: MO

address: 1100 South Grand

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed of adaptor sequences, low-quality reads and then aligned to C. neoformans genome (Broad H99, assembly 2) using TopHat version 2.0.0 using Bowtie, version 1.6
Transcript files were generated using Cufflinks version 2.02
Comparisons between the deletion strains and wild-type merged transcript files were done using CuffCompare at the gene level with the C. neoformans transcript file from the 2nd assembly of the H99 genome as a reference
Differentially expressed genes were identified using CuffDiff version 2.0.2
Genome_build: Broad C. neoformans H99 assembly 2 (2008)
Supplementary_files_format_and_content: transcript files generated by cufflinks (gtf format); fpkm values from merged transcript files generated by CuffCompare (tab-delimited) and gene experession differences generated by CuffDiff (tab-delimited).

organism: Cryptococcus neoformans

source_name: RNA isolated from cells growing in YPD+sorbitol at 30 degress

growth_protocol: KN99a or deletion strains were grown in YPD + 1M sorbitiol at 30 degrees with shaking until OD600 = 1.0

extract_protocol:
RNA was isolated from the cells using the Qiagen RNeasy Plant Mini Kit
Single-end libraries were generated using Illumina TruSeq RNA Sample Preparation Kit v2

tag: biological replicate

value: second of three replicates

tag: genotype

value: MPK1 deletion in KN99a background


title: MPK1 deletion in KN99a background Mpk1_o

value: third of three replicates


title: WT2

city: Davis

first: Shajahan

last: Anver

address: 1002 LSA, One Shields Av

department: Plant Biology

institute: University of California Davis

description: Sample 2

data_processing:
All quality control steps were performed using the fastx_tool kit (http://hannonlab.cshl.edu/ fastx toolkit/index.html).
Reads were mapped to the complete S. pombe cDNA (EF2.12) and genomic DNA (from ftp.ensemblgenomes.org) using BWA (ver. 0.5.8c, Li and Durbin 2009, Bioinformatics 25(14): 1754-1760).
Differential expression analysis was performed using edgeR (Robinson et al. 2010)
Genome_build: Ensembl EF2.12 (ftp://ftp.ensemblgenomes.org/pub/fungi/release-12/fasta/schizosaccharomyces_pombe/cdna/Schizosaccharomyces_pombe.EF2.12.cdna.all.fa.gz)
Supplementary_files_format_and_content: Differential expression analyses  for sense transcripts, antisense transcripts, all annotated long terminal repeat (LTR) sequences and all intergenic region sequences in Δxap5, Δpht1 and Δxap5Δpht1

organism: Schizosaccharomyces pombe

source_name: wild type strain haploid cells

growth_protocol: cells initially grown in YES medium at 30C overnight and these cultures were used to inoculate cultures in EMM50 at 37C. Exponentially growing cells at 37C in EMM50 were used for RNA extraction with three replicates per each genotype.

extract_protocol:
Cell lysis was performed as recommended by Sabatinos and Forsburg (2010, Yeast 23(3): 173-183) in 1 ml Trizol reagent (Invitrogen). RNA was extracted as per the Invitrogen Trizol reagent protocol. Extracted RNA was digested with DNase I (Qiagen) for 30 minutes at room temperature and cleaned up with 3M sodium acetate. rRNA was removed using the Ribo-Zero rRNA removal kit (human/mouse/rat, Epicentre) following the manufacturer’s protocol.
Strand specific cDNA libraries were made with random primers using a protocol by Wang et al. (2011, PloS one 6(10): e26426) after optimizations. Barcodes: WT1 - AACCG, WT2 - ACCAT, WT3 - GCTAT, WT4 - CATAT, xap5m1 - AGCTT, xap5m2 - CATTA, xap5m3 - CCTAG, pht1_1 - AATAG, pht1_2 - TAATG, pht1_3 - GGCTC, dm1 - ACCTA, dm2 - TTAGA, dm3 - GTATT
Samples were multiplexed and 100 bp single reads were sequenced in an Illumina Hi-seq sequencer (Hi-Seq 2000) in two lanes with an average sequence coverage of 11.8 million /library.

tag: strain background

tag: genotype/variation

value: wild type; h+, ade6-M216, ura4-D18, leu1-32

value: exponentially growing haploid cells


title: WT4

description: Sample 4


title: MPK1 deletion in KN99a background Mpk1_m

value: one of three replicates


title: MKK2 deletion in KN99a background Mkk2_k

value: MKK2 deletion in KN99a background


title: MKK2 deletion in KN99a background Mkk2_l


title: MKK2 deletion in KN99a background Mkk2_j


title: tbh_rep1

description: Sample 3

value: tbh mutant

value: fruit spine


title: Tumor RNA BT122

city: Bar Harbor

first: Edison

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Sequenced reads were aligned to the human genome hg18 assembly using BioScope v1.3.1
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cufflinks, version 1.0.3 (Trapnell et al., Nature Biotechnology, 2010) and the hg18 RefSeq Genes track downloaded from the UCSC genome browser as the gene annotation file. Gene-based values were generated as the sum of the FPKM of all of the transcripts correspoding to the same gene.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include trasncript- and gene-based FPKM values for each sample

source_name: Primary breast cancer

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini kit (Qiagen) and enriched for poly(A) mRNA using a μMACS™ poly(T) kit (Life Technologies). 500 ng of purified poly(A) RNA was used for library preparation.
RNA libraries were prepared for sequencing using a SOLiD™ Total RNA-Seq Kit (Applied Biosystems), according to the manufacturer's instructions.

value: breast cancer tumor

tag: breast cancer subtype

value: TNB

tag: library id


title: BCK1 deletion in KN99a background Bck1_i

value: BCK1 deletion in KN99a background


title: BCK1 deletion in KN99a background Bck1_g


title: wild-tye Kn99a Kn99_a

value: wild-tye Kn99a


title: WT3

description: Sample 3

tag: tissue


title: Tumor RNA BT55

value: Luminal B


title: W_14_2PM_7

city: Austin

first: Thomas

middle: E

last: Juenger

state: TX

address: 2401 Speedway

institute: University of Texas, Austin

data_processing:
Trim four non-template bases from 5' end of each read
discard reads with more than 10 low quality (score<20) bases
discard reads containing homopolymers greater than 10 bp in length
discard reads matching adaptors used during library construction (cross_match, score>10)
align in color-space using SHRiMP 2.1.1b against reference transcriptome assembly
exclude short and low-quality matches
count number of reads mapping uniquely to each isogroup in the reference assembly
Genome_build: Custom transcriptome assembly (Alamo AP13) (http://datadryad.org/resource/doi:10.5061/dryad.6630k)
Supplementary_files_format_and_content: Text file listing the number of reads in each sample uiniquely mapped to each isogroup.

organism: Panicum virgatum

source_name: control_14 d_2PM

extract_protocol:
Spectrum Plant Total RNA kit, Sigma-Aldrich
3' cDNA tag libraries constructed as described in: Meyer et al (2011), Molecular Ecology, 20(17), 3599-3616.

treatment_protocol:
control: watered 1L per day
drought: no water provided during the 14-d experiment
recovery: plants from the drought treatment that were re-watered on d 14

tag: treatment

value: control

tag: sampling day

tag: sampling time

value: Leaf


title: W_14_5AM_9

source_name: control_14 d_5AM


title: W_14_2PM_5


title: W_13_5AM_5

source_name: control_13 d_5AM


title: RW_14_10AM_3

source_name: recovery_14 d_10AM

value: recovery


title: D_14_10AM_11

source_name: drought_14 d_10AM

value: drought


title: D_14_10AM_21


title: WT1

description: Sample 1


title: D_14_2PM_10

source_name: drought_14 d_2PM


title: W_14_12PM_19

source_name: control_14 d_12PM


title: D_13_5AM_1

source_name: drought_13 d_5AM


title: RW_14_2PM_20

source_name: recovery_14 d_2PM


title: Tumor RNA BT146


title: W_14_10AM_16

source_name: control_14 d_10AM


title: D_14_5AM_12

source_name: drought_14 d_5AM


title: W_14_2PM_2


title: PC3_AR-K2R_R1881_rep2

city: Kuopio

first: Päivi

last: Sutinen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
The quality of raw reads was analyzed by FastQC
FASTX-toolkit was used for preprocessing (removal of artifacts, trimming (50bp), quality filtering and collapsing identical reads)
Reads were alignment Bowtie (0.12.7)(one mismatch and best alignment)
Analysis were done with HOMER software (4.2). Binding sites were determined with findpeaks (using -factor mode and input as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (find in both replicates)

source_name: PC-3 cells

growth_protocol: PC-3 cells were grown in F-12 (10% FBS, 1% penicillin/streptomycin) under G418 selection (400 µg/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols, as utilized at the Gene Core in EMBL, Heidelberg, Germany

treatment_protocol: PC-3 cells were growth 72h in transfection medium (5% stripped FBS in F-12) before treating 1 h with 10 nM R1881 or ethanol (vehicle).

tag: cell line

value: PC-3 prostate cancer cells

value: rabbit antiserum against AR

value: SUMOylation-deficient AR


title: D_14_12PM_21

source_name: drought_14 d_12PM


title: RW_14_2PM_3


title: wild-tye Kn99a Kn99_b

value: second of three replicates


title: wild-tye Kn99a Kn99_c

value: third of three replicates


title: BCK1 deletion in KN99a background Bck1_h


title: W_14_10AM_4


title: RW_14_12PM_12

source_name: recovery_14 d_12PM


title: D_14_12PM_11


title: D_14_10AM_1


title: RW_14_10AM_26


title: D_13_5AM_23


title: D_13_5AM_14


title: RW_14_12PM_6


title: RW_14_10AM_12


title: W_14_12PM_5


title: W_14_10AM_9


title: D_13_2PM_26

source_name: drought_13 d_2PM


title: D_13_2PM_13


title: W_13_2PM_28

source_name: control_13 d_2PM


title: D_13_2PM_11


title: W_13_5AM_7


title: D_14_2PM_17


title: D_13_5AM_11


title: RW_14_12PM_27


title: D_14_10AM_18


title: W_13_5AM_2


title: W_14_2PM_4


title: D_14_5AM_8


title: W_13_5AM_28


title: D_13_2PM_8b


title: W_13_2PM_19


title: D_13_5AM_18


title: RW_14_10AM_6


title: D_14_2PM_18


title: D_13_5AM_3


title: D_14_5AM_20


title: D_14_12PM_18


title: W_14_12PM_28


title: D_14_2PM_21


title: D_13_2PM_27


title: W_14_12PM_9


title: W_14_2PM_19


title: D_14_5AM_26


title: 600_d63

city: Rensselaer

last: Kiehl

address: One Discovery Drive

institute: Neural Stem Cell Institute

description:
processed data file: Test_normalized.csv
st600_d63

data_processing:
Data was mapped to human genome 19 using BFAST
Mapped files were analyzed utililzing R in conjunction with multiple packages: GenomicFeatures, rtracklayer, Rsamtools, GenomicRanges, edgeR, Mfuzz, DESeq, DESeq2, goseq, SPIA, ggplot2, igraph, RcolorBrewer, GO.db, org.Hs.eg.db, foreach, parallel, multicore, doMC
Genome_build: hg19
Supplementary_files_format_and_content: text, counts normalized for library size with DESeq

source_name: in vitro_hESC_test_d63

growth_protocol: H9 cells were cultured in HES-medium (all reagents were obtained from Life Technologies): DMEM/F12 (1:1) with 20% (v/v) KSR, 1 mM L-glutamine, 100 µM non-essential amino acids, 55 µM 2-mercaptoethanol, and 10 ng ml-1 FGF-2.

extract_protocol:
Samples were collected using RNAprotect cell reagent (Qiagen), homogenized with QIAshredder (Qiagen), and total RNA extracted using RNeasy plus mini kit (Qiagen), according to manufacturer’s protocol.
Samples were prepared for RNA-seq (including library preparation, bar-coding, etcetera) by Expression Analysis (Durham, NC, USA), or Covance (Seattle, WA, USA)

treatment_protocol: When cultures were at ~90% confluency the culture medium was changed to KSR-medium (all reagents were obtained from Life Technologies unless indicated otherwise): knockout-DMEM with 15% (v/v) KSR, 2mM L-glutamine, 100 µM non-essential amino acids, 55 µM 2-mercaptoethanol, supplemented with 100 nM LDN193189 (Stemgent) and  10 µM SB431542 (Tocris). Medium was changed daily, on the third day 1µM cyclopamine (Stemgent) was added. Medium was changed every other day, as of day five increasing amounts of N2-medium (25%, 50%, 75%, 100%) was added, cyclopamine concentration was maintained at 1 µM. N2-medium (all reagents were obtained from Life Technologies unless indicated otherwise): DMEM/F12 (1:1) with N-2 supplement and 0.775 g glucose (Sigma). In the Test case, the protocol was started when cells were ~65% confluent.

tag: cell type

value: hESC (WA-09)

tag: run id

value: Test Case


title: 606_d77

description:
processed data file: Test_normalized.csv
st606_d77

source_name: in vitro_hESC_test_d77


title: 605_d77

description:
processed data file: Test_normalized.csv
st605_d77


title: RW_14_2PM_26


title: RW_14_10AM_23


title: 593_d49

description:
processed data file: Test_normalized.csv
st593_d49

source_name: in vitro_hESC_test_d49


title: D_14_12PM_10


title: 599_d63

description:
processed data file: Test_normalized.csv
st599_d63


title: D_14_5AM_18


title: 581_d33

description:
processed data file: Test_normalized.csv
st581_d33

source_name: in vitro_hESC_test_d33


title: RW_14_2PM_27


title: 564_d25

description:
processed data file: Test_normalized.csv
st564_d25

source_name: in vitro_hESC_test_d25


title: D_14_2PM_11


title: D_13_2PM_18


title: D_13_2PM_10


title: 552_d19

description:
processed data file: Test_normalized.csv
st552_d19

source_name: in vitro_hESC_test_d19


title: 546_d16

description:
processed data file: Test_normalized.csv
st546_d16

source_name: in vitro_hESC_test_d16


title: 551_d19

description:
processed data file: Test_normalized.csv
st551_d19


title: 545_d16

description:
processed data file: Test_normalized.csv
st545_d16


title: 563_d25

description:
processed data file: Test_normalized.csv
st563_d25


title: D_14_5AM_17


title: W_14_5AM_5

source_name: control_14 d_5AM


title: 534_d12

description:
processed data file: Test_normalized.csv
st534_d12

source_name: in vitro_hESC_test_d12


title: 594_d49

description:
processed data file: Test_normalized.csv
st594_d49


title: 582_d33

description:
processed data file: Test_normalized.csv
st582_d33


title: 527_d7

description:
processed data file: Test_normalized.csv
st527_d7

source_name: in vitro_hESC_test_d7


title: W_14_2PM_9

source_name: control_14 d_2PM


title: W_14_10AM_2

source_name: control_14 d_10AM


title: 522_d0

description:
processed data file: Test_normalized.csv
st522_d0

source_name: in vitro_hESC_test_d0


title: 528_d7

description:
processed data file: Test_normalized.csv
st528_d7


title: W_14_12PM_2

source_name: control_14 d_12PM


title: D_14_10AM_8

source_name: drought_14 d_10AM


title: W_13_2PM_5


title: W_13_5AM_9

source_name: control_13 d_5AM


title: D_13_2PM_8a

source_name: drought_13 d_2PM


title: D_13_5AM_17

source_name: drought_13 d_5AM


title: W_14_5AM_16


title: Day 63 B

description:
processed data file: Cortecon_normalized.csv
fin2_d63

source_name: in vitro_hESC_cortecon_day 63

tag: Stage

value: Upper Layer Formation

value: Cortecon


title: Day 77 A

description:
processed data file: Cortecon_normalized.csv
297_d77

source_name: in vitro_hESC_cortecon_day 77


title: Day 63 A

description:
processed data file: Cortecon_normalized.csv
fin1_d63


title: RW_14_12PM_20

source_name: recovery_14 d_12PM


title: W_13_2PM_2

source_name: control_13 d_2PM


title: Day 33 B

description:
processed data file: Cortecon_normalized.csv
273_d33

source_name: in vitro_hESC_cortecon_day 33

value: Deep Layer Formation


title: D_14_5AM_1

source_name: drought_14 d_5AM


title: Day 49 B

description:
processed data file: Cortecon_normalized.csv
285_d49

source_name: in vitro_hESC_cortecon_day 49


title: Day 49 A

description:
processed data file: Cortecon_normalized.csv
284_d49


title: D_13_5AM_26


title: Day 33 A

description:
processed data file: Cortecon_normalized.csv
272_d33


title: 533_d12

description:
processed data file: Test_normalized.csv
st533_d12

source_name: in vitro_hESC_test_d12


title: D_13_2PM_23


title: Day 26 B

description:
processed data file: Cortecon_normalized.csv
168_d26

source_name: in vitro_hESC_cortecon_day 26


title: 521_d0

description:
processed data file: Test_normalized.csv
st521_d0


title: W_14_10AM_19


title: RW_14_10AM_20

source_name: recovery_14 d_10AM


title: D_14_2PM_14

source_name: drought_14 d_2PM


title: D_13_5AM_27


title: D_14_10AM_17


title: RW_14_10AM_27


title: Day 19 D

description:
processed data file: Cortecon_normalized.csv
104_d19

source_name: in vitro_hESC_cortecon_day 19

value: Cortical Specification


title: Day 19 B

description:
processed data file: Cortecon_normalized.csv
244_d19


title: Day 26 A

description:
processed data file: Cortecon_normalized.csv
167_d26


title: Day 19 A

description:
processed data file: Cortecon_normalized.csv
243_d19


title: Day 19 C

description:
processed data file: Cortecon_normalized.csv
103_d19


title: Day 77 B

description:
processed data file: Cortecon_normalized.csv
298_d77


title: D_13_2PM_20


title: D_13_2PM_1


title: Day 7 D

description:
processed data file: Cortecon_normalized.csv
90_d7

source_name: in vitro_hESC_cortecon_day 7

value: Neural Differentation


title: Day 12 B

description:
processed data file: Cortecon_normalized.csv
95_d12

source_name: in vitro_hESC_cortecon_day 12


title: Day 7 C

description:
processed data file: Cortecon_normalized.csv
89_d7


title: D_14_5AM_27


title: Day 7 B

description:
processed data file: Cortecon_normalized.csv
220_d7


title: Day 0 D

description:
processed data file: Cortecon_normalized.csv
87_d0

source_name: in vitro_hESC_cortecon_day 0

value: Pluripotency


title: W_13_2PM_16

value: control


title: W_14_10AM_28

source_name: control_14 d_10AM

value: Leaf


title: Day 7 A

description:
processed data file: Cortecon_normalized.csv
219_d7


title: Day 12 A

description:
processed data file: Cortecon_normalized.csv
94_d12


title: Day 0 C

description:
processed data file: Cortecon_normalized.csv
86_d0


title: D_13_2PM_6

source_name: drought_13 d_2PM


title: D_14_5AM_3


title: W_14_12PM_16

source_name: control_14 d_12PM


title: W_13_5AM_4

source_name: control_13 d_5AM


title: D_14_5AM_10


title: W_14_5AM_7

source_name: control_14 d_5AM


title: W_13_2PM_9

source_name: control_13 d_2PM


title: D_13_2PM_21


title: W_14_5AM_19


title: SKOV3ip1_NOP58KD_2

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

description: small RNA (<200nt)

data_processing:
Because many small RNAs isolated using our procedure are shorter than the sequencing read length (100 nt), the 3’ adapters were still present in the fastq files for many read pairs. Cutadapt was used to remove the adapters and control the quality of the sequences. Parameters were set to -minimum-length 2, -match-read-wildcards, -q 3 and the adapter sequences were TGGAATTCTCGGGTGCCAAGG (R1 file) and GATCGTCGGACTGTAGAACTCTGAAC (R2 file).
The resulting reads were aligned to the build hg19 of the human genome using Bowtie2 with parameters –local, -I 13.
SAMtools and BEDTools were used to obtain the positions of all reads mapping to box C/D snoRNAs and calculate alignment statistics.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file which includes the sequence of each snoRNA form identified and its abundance in counts per million for each Sample.

source_name: SKOV3ip1 cell line

extract_protocol:
Total RNA extractions were performed using miRNeasy kit (Qiagen) as recommended by the manufacturer. RNA integrity of each sample was assessed with an Agilent 2100 Bioanalyzer. Small RNA (<200 nucleotides in length) were isolated using a low molecular weight RNA extraction kit (mirVana, Invitrogen).
cDNA libraries were prepared using the NEBNext Multiplex Small RNA Library Preparation Set for Illumina. The resulting cDNA libraries were paired-end sequenced on Illumina HiSeq sequencers at the McGill University and Genome Quebec Innovation Centre. For these sequencing runs, 8 samples were multiplexed per lane, resulting in between 15M and 24M paired reads per dataset. Paired-end sequencing was chosen because the length of some of the molecules of interest surpassed the read length (which was 100 nt). Additionally, the paired-end sequencing ensured high-quality sequences at both ends of the RNAs of interest.

value: ovarian adenocarcinoma

tag: growth protocol

value: grown in DMEM/F12 (50/50) medium (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine, cells passaged as recommended by ATCC

value: Treated with siRNA targeting NOP58 (GACAAGUCCCAAACACAAA). Transfection was performed in suspension using Lipofectamine 2000 (Life technologies) according to the manufacturer’s protocol and 20 nM of siRNA (Sigma) for 48 hours.


title: SKOV3ip1_LF_2

description: small RNA (<200nt)

value: Lipofectamine 2000 treated


title: D_13_5AM_6

source_name: drought_13 d_5AM

tag: strain

value: drought


title: SKOV3ip1_LF_3

description: small RNA (<200nt)


title: D_13_5AM_8


title: RW_14_2PM_13

source_name: recovery_14 d_2PM

value: recovery


title: SKOV3ip1_LF_1

description: small RNA (<200nt)


title: RW_14_12PM_13

source_name: recovery_14 d_12PM


title: RW_14_12PM_26


title: D_13_2PM_12


title: D_14_5AM_6

source_name: drought_14 d_5AM


title: MCF7_WT_2

description: small RNA (<200nt)

source_name: MCF7 cell line

value: breast adenocarcinoma

value: grown in EMEM (Wisent) supplemented with 1 mM sodium pyruvate and MEM nonessential amino acid (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine, cells passaged as recommended by ATCC


title: BJ-Tielf_WT_2

description: small RNA (<200nt)

source_name: BJ-Tielf cell line

value: BJ-Tielf

value: immortalized normal skin fibroblast

value: grown in alpha-MEM (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine, cells passaged as recommended by ATCC


title: BJ-Tielf_WT_1

description: small RNA (<200nt)


title: Day 0 A

description:
processed data file: Cortecon_normalized.csv
212_d0

value: hESC (WA-09)

value: Cortecon


title: INOF_WT_1

description: small RNA (<200nt)

source_name: INOF cell line

value: INOF

value: immortalized normal ovarian fibroblast

value: grown in OSE medium (Wisent) , supplemented with 10 % fetal bovine serum and 2 mM L-glutamine, cells passaged as recommended by ATCC


title: W_14_5AM_28

value: control

value: Leaf


title: Day 0 B

description:
processed data file: Cortecon_normalized.csv
214_d0

value: Pluripotency


title: D_13_2PM_17


title: D_14_12PM_8

source_name: drought_14 d_12PM


title: MCF7_WT_1

description: small RNA (<200nt)


title: SKOV3ip1_WT_2

description: small RNA (<200nt)

value: ovarian adenocarcinoma

value: grown in DMEM/F12 (50/50) medium (Wisent), supplemented with 10 % fetal bovine serum and 2 mM L-glutamine, cells passaged as recommended by ATCC


title: SKOV3ip1_NOP58KD_1

description: small RNA (<200nt)

value: Treated with siRNA targeting NOP58 (CUUCUACCGUUCAGAUUCU). Transfection was performed in suspension using Lipofectamine 2000 (Life technologies) according to the manufacturer’s protocol and 20 nM of siRNA (Sigma) for 48 hours.


title: W_13_2PM_4


title: SKOV3ip1_RBFOX2KD_2

description: small RNA (<200nt)

value: Treated with siRNA targeting RBFOX2 (CACCUCCGCAGAAUGGAAU). Transfection was performed in suspension using Lipofectamine 2000 (Life technologies) according to the manufacturer’s protocol and 20 nM of siRNA (Sigma) for 48 hours.


title: SKOV3ip1_RBFOX2KD_1

description: small RNA (<200nt)

value: Treated with siRNA targeting RBFOX2 (GAUGGUCACACCAUAUGCA). Transfection was performed in suspension using Lipofectamine 2000 (Life technologies) according to the manufacturer’s protocol and 20 nM of siRNA (Sigma) for 48 hours.


title: D_14_10AM_10

source_name: drought_14 d_10AM

value: drought


title: SKOV3ip1_WT_1

description: small RNA (<200nt)


title: D_14_5AM_23


title: INOF_WT_2

description: small RNA (<200nt)


title: D_13_5AM_20