title: Sample 71, GluMspI,  Replicate 3

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
10 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
MAY_fc1.ch04
Helicos single molecule sequencing (SMS)

data_processing:
SMS reads were trimmed for leading “T” homopolymers, filtered for reads with a minimal length of 25 bases after trimming as well as for other standard Helicos quality metrics using a suite of Helicos tools available at: http://open.helicosbio.com/mwiki/index.php/Releases.
Alignments to the hg18 version of the human genome were conducted with indexDPgenomic
software freely available on the Helicos website (http://open.helicosbio.com/mwiki/index.php/Releases)
The sequence reads were aligned using a minimum normalized score of 4.3
Processed data file: Only uniquely-mapped reads were considered for the present analysis. Reads with a 5' coordinate < 3 bp from a target sequence (CCGG) were defined as target reads. Reads with a 5' coordinate > 200 bp away from a CCGG sequence (provided here as non-target reads) were used to normalize the read count in downstream analyses.
Genome_build: hg18
Supplementary_files_format_and_content: Processed data file: BED files of target reads (*coverage.txt) contain number of reads mapping to each CpG. BED files of non-target reads (NONTARGET.bed) contain number of reads mapping to the start coordinate of each non-target read.
Supplementary_files_format_and_content: Each sample has two results files: one for "target reads" (*coverage.bed)
Supplementary_files_format_and_content: and one for "nontarget reads" (*_NONTARGET.bed).
Supplementary_files_format_and_content: For target read files, the base position refers to the modifiable Cytosine
Supplementary_files_format_and_content: inside a restriction site (the second C of CCGG) which generated the read;
Supplementary_files_format_and_content: it is not the read start. For non-target read files, the base position
Supplementary_files_format_and_content: refers to the start of a read.

source_name: Frontal cortex (BA10) of the brain - post-mortem sample

extract_protocol: Micrococcus nuclease digestion was subjected to fragment genomic DNA to a median size of 500 bp and to reduce 3' hydroxyl end at the DNA fragments, where the latter is served as starting end for SMS. 5 µg of genomic DNA was treated with 1 U of micrococcal nuclease enzyme (NEB) and the reaction was stopped by adding access of EDTA (0.5M EDTA) in a time series. Samples with median fragment size of 500 bp were column purified with buffer PN (QIAquick Nucleotide Removal Kit columns, Qiagen). Glucosylation and control treatments were performed as described before (Online Methods) and 200ng of each glucosylated or non-glucosylated treated DNA was subjected to 10 U of restriction enzyme digestions respectively at 37 oC for 8h, and inactivated at 80oC for 20 minutes. 10 ng of each digested product, quantified by Quant-iTTM PicoGreen dsDNA Reagent Kit (Invitrogen), was then processed for Helicos sequencing. In brief 10ng of DNA was heat denatured at 95oC for 5 minutes prior to 3’ end labeling with 5 U of terminal transferase (NEB) in presence of 200 µmoles of dATP (Roche) and 5 mmoles of CoCl2 (NEB) in 20 µl reaction volume at 37oC for 1 h, inactivated at 70oC for 10 minutes. Fragments were biotinylated by repeating the terminal transferase enzymatic reaction step in presence of 100 µmoles of biotin labeled ddATP (Perkin Elmer) instead of dATP in a reaction volume of 30 µl. These processed samples were then sent to Helicos sequencing service facility (www.helicosbio.com; USA).

treatment_protocol: No treatment performed on tissue prior to DNA extraction

tag: enzyme digestion

tag: age

value: 49 years

tag: Sex

value: F

tag: post mortem interval


title: Sample 71, Undigested DNA,  Replicate 3

status: Public on Aug 24 2012

type: SRA

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
None
MAY_fc1.ch01
Helicos single molecule sequencing (SMS)

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: Frontal cortex (BA10) of the brain - post-mortem sample


title: Sample 71, MspI,  Replicate 3

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
10 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
MAY_fc1.ch02
Helicos single molecule sequencing (SMS)


title: U10_11_male

city: Zürich

first: Niklaus

last: Zemp

address: Universitätsstrasse 16

department: IBZ

country: Switzerland

institute: ETH Zurich

library_source: transcriptomic

molecule: total RNA

organism: Silene latifolia

source_name: male_small flower buds

extract_protocol: DNAse treatment; Transcripts purification;Transcripts breaking in presence of Zn; Double-stranded cDNA synthesis using random primers and RNase H; Ends repair;  3' A addition; Ligation of adapters; Gel purification to isolate fragments of specified inserts size; PCR amplification to generate the DNA Colonies Template Library, library purification;Quality control of the DNA Colony Template Library by cloning an aliquot into a TOPO plasmid and capillary sequencing of 4-8 clones;Library quantification and dilution at 10 nM; Flow-cell preparation on the cBot; High-throughput DNA sequencing on the illumina HiSeq 2000; Real-time base-calling on the HiSeq computer.

tag: population

value: 10 generation inbred line

value: small flower buds

tag: gender

value: male


title: N-Term-CIRBP CLIP RNA

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

institute: University of Geneva

description:
Clipped RNA, CLIP-seq
Several different lots/batches of streptavidin beads were used for CLIP
processed data file: clip.plus.bedgraph, clip.minus.bedgraph (available as Series supplementary files)

data_processing:
Reads were filtered for rRNA sequences by mapping on 45S rRNA sequence with Bowtie software (version 0.12.7)
Read mapping with Tophat software (version 1.2.0) using the UCSC genes as a guide for splice junction mapping.
A single hit at the same genomic position was allowed for CLIP reads.
Bedgraph counts expressed in log2(1+counts per 10^6 sequenced reads)
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files

organism: Mus musculus

source_name: NIH3T3_N-Term-CIRBP CLIP-seq

growth_protocol: NIH3T3 cells were grown according to standard protocols.

extract_protocol: For CLIP-seq, in vivo biotinylated and UV-crosslinked CIRP-RNA complexes were purified on streptavidin beads and CLIP-seq libraries were constructed according to (Yeo et al., 2009) except that linker ligations were directly carried out on streptavidin beads. Linker-equipped CIRP-RNA complexes were eluted by TEV protease cleavage, RNA was liberated by proteinase K digestion, reverse transcribed and PCR-amplified. Libraries were subjected to standard Illumina sequencing protocols. For RNA-seq, total RNA was extracted using TRI-reagent according to manufacturer’s instructions (Sigma). Ribosomal RNA was selectively removed from total RNA through hybridization using Ribominus reagents according to the supplier’s instructions (Invitrogen). Directional, strand-specific cDNA libraries were prepared  and subjected to standard Illumina sequencing protocols.

treatment_protocol: NIH3T3 cells were kept at at 33°C for 8 hours before harvesting.

tag: cell line

tag: clip beads

value: Dynabeads M-280 Streptavidin

tag: beads vendor

value: Invitrogen

tag: beads cat. #


title: Sample 71, Undigested DNA,  Replicate 1

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
None
MARCH_fc1.ch01
Helicos single molecule sequencing (SMS)


title: Sample 71, MspI,  Replicate 1

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
10 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
MARCH_fc1.ch02
Helicos single molecule sequencing (SMS)


title: Sample 71, GluMspI,  Replicate 1

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
10 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
MARCH_fc1.ch04
Helicos single molecule sequencing (SMS)


title: Sample 71, Undigested DNA,  Replicate 2

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
None
APRIL_fc1.ch01
Helicos single molecule sequencing (SMS)


title: Sample 71, MspI,  Replicate 2

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
10 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
APRIL_fc1.ch02
Helicos single molecule sequencing (SMS)


title: Sample 71, GluMspI,  Replicate 2

description:
Three technical replicates of the same human brain DNA sample digested by MspI enzyme with (GluMspI) or without (MspI) prior glucosylation. Undigested DNA was used as a second reference. Data from all three runs were pooled for analysis after each run had been separately normalized using the corresponding number of non-target reads.
10 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.
APRIL_fc1.ch04
Helicos single molecule sequencing (SMS)


title: siliques

status: Public on Aug 23 2012

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

data_processing:
FastaQ files of each sample were aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Expression level of each TU are presented by Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample produced by Cufflinks.

organism: Arabidopsis thaliana

source_name: siliques

growth_protocol: Arabidopsis plant (Col-0) materials were grown under long day conditions at 22℃. Aerial part and roots were collected from two-week old plants that grew on MS plate. Flowers and siliques were collected from five-week old plants that grew in soil.

extract_protocol: All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit according to the instructions (Illumina). Sequences were determined by HiSeq 2000 sequencing system in the genomic center in Rockefeller University.

value: siliques

tag: ecotype


title: leaves

source_name: leaves

value: leaves


title: roots

source_name: roots

value: roots


title: flowers

source_name: flowers

value: flowers


title: Whole cell extract

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description:
lane5
WCE

data_processing:
For quality control, fastqc results files were generated to show that adapter sequences were sequenced.
With fastx_clipper, adapter sequences were clipped.
The alignment to the reference genome (mm8) was done by Bowtie and the peak calling by MACS (1.4.0rc2).
Bed files for peaks and wig files were produced by MACS.
The wig files were normalized by the total number of reads in control.
To compare FGFOX and FITFOX directly, they were normalized again with their background noise level.
Genome_build: mm8
Supplementary_files_format_and_content: Bed files by MACS for the peaks. BigWig files for profiling.

source_name: CD4+ T cells, input

growth_protocol: Cells were activated with anti-CD3/CD28 beads (Invitrogen) at a ratio of one bead per cell, with addition of 20 U/ml of recombinant human IL-2 (Proleukin; Chiron) in complete culture medium (RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin/streptomycin and 50 microM 2-Mercaptoethanol).

extract_protocol:
Cells were lysed in lysis buffer (Hepes 50 mM; NaCl 140 mM;  EDTA 1 mM, Glycerol 10%; NP-40 0.5%; Triton X-100 0.25%). After chromatin immunoprecipitation, genomic DNA was isolated by phenol chloroform extraction and ethanol precipitation.
Library construction was performed using the ChIP-Seq DNA Sample Prep Kit for Illumina sequencing.

tag: strain/background

value: 6-8 weeks

value: lymph node

tag: cell type

value: primary CD4+ Tconv cells

tag: transduced factor

tag: chip antibody


title: FoxP3+GATA1_Pol II ChIP-seq

description:
lane4
ActCD4PolII

source_name: CD4+ T cells, FLAG-FoxP3+GATA1, Pol II ChIP

value: FLAG-FoxP3 + GATA1

value: anti-Pol II (N20)

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number


title: FoxP3 alone_FoxP3 ChIP-seq

description:
lane2
FITFOX

source_name: CD4+ T cells, FLAG-FoxP3, FLAG ChIP

tag: age

value: anti-FLAG, clone M2

value: Sigma


title: FoxP3+GATA1_FoxP3 ChIP-seq

description:
lane1
FGFOX

source_name: CD4+ T cells, FLAG-FoxP3+GATA1, FLAG ChIP


title: wild_type_DNase-seq

city: Urbana

first: Brian

last: Freeman

state: Illinois

address: B107 CLSL  601 S. Goodwin Avenue

department: Department of Molecular & Integrative Physiology

institute: UIUC

data_processing:
The libraries for Dnase-seq were sequenced on 1 lane for 100 cycles with an Illumina HiSeq2000 and TruSeq SBS sequencing kits version 3. Basecalls were performed with Casava1.8 (pipeline 1.9).
The generated sequence data were evaluated and aligned to the yeast reference  genome (sacCer3, UCSC) using bowtie (version 0.12.7) with following command: bowtie -p 4 -t --sam --best -v 1 -m 1  ~/indexes/SacCer3. Only uniquely mapped reads were retained for further analyses.
The DNase I  hypersensitive regions were identified using the F-seq Peak Caller v1.84 (command:fseq -v -f 0 -of bed -d ./WT -o ./WT
DNA  footprints within the DHSs were identified using a described algorithm (NATURE METHODS|Vol 6|No 4 pp283-298)
Genome_build: sacCer3 UCSC
Supplementary_files_format_and_content: Bed files contain the location of DHSs called by fseq (version 1.84). The fifth column is the kernel density at peak summits.

organism: Saccharomyces cerevisiae

growth_protocol: The strains used for the DNase-Seq experiments were the parent BY4741 (MATa) along with sba1Δ and gcn5Δ isolates (Open BioSystems). Yeast cells were grown in rich medium (YPD) supplemented with 2% glucose.

extract_protocol: The DNase-Seq protocol was adapted from a previous method with minor modifications(NATURE METHODS|Vol 6|No 4 pp283-298). In brief, the parent (WT), sba1Δ and gcn5Δ yeast were cultured overnight in rich medium (YPD) at 30°C, diluted into 500 mL of fresh YPD to an OD595 = 0.25 and allowed to propagate to OD595 = 1.0. Nuclei were prepared by collecting the cells by centrifugation (5 min at 3000xg), washing the cells 1x with cold dH2O, washing the cells 2x with spheroplasting buffer (50 mM potassium phosphate pH 6.5, 1 M sorbitol, 0.018% ß-mercaptoethanol), resuspending the cell pellets in spheroplasting buffer (4.5 mL) supplemented with Zymolase 20T (40 U mL-1), incubating the cells at 30°C for 45 min with gentle agitation, adding 25 mL lysis buffer (20 mM potassium phosphate pH 6.8, 18% Ficoll 400, 1 mM CaCl2, 0.5 mM EDTA, 3 mM DTT, 1 mM PMSF, 2 mM Benzamidine, 0.5 µg mL-1 Leupeptin and 1.5 µg mL-1 Pepstatin) and lysing the cells with 20 strokes of a Dounce homogenizer using a pestle A.The samples were clarified by centrifugation at 3000xg for 10 min at 4°C, the supernatant was transferred to fresh tubes, samples were clarified by centrifugation at 6700xg for 10 min at 4°C, the supernatant was again transferred to fresh tubes and clarified by centrifugation at 50,000xg for 35 min at 4°C. The supernatants were carefully removed and the nuclei pellets were used for DNase I treatment. To digest the DNA, the yeast nuclei were resuspended in 2.5 mL cold Buffer A (15 mM Tris-HCl pH 8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine and 11% sucrose) by gentle swirling and agitation. Nuclei were counted by light microscopy with a typical yield being 2x109 nuclei per preparation. The mixtures were separated into 10 aliquots of 250 µL, each sample was combined with 250 µL 2x reaction buffer (Buffer A supplemented with 12 mM CaCl2,150 mM NaCl and varying levels of DNase I (Roche Applied Science) to give 0, 0.5, 1, 2 or 4 U ml-1). The reactions were incubated at 22°C for 5 min and terminated by the addition of 500 µl stop solution (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.1% SDS, 100 mM EDTA, 10 mg ml-1 Ribonuclease A, 1 mM spermidine and 0.3 mM spermine). Pronase was added to 20 mg ml-1 and the reaction was incubated at 55°C overnight. Aliquots (10 µl) of the digested samples were resolved on a 1% agarose gel to validate digestion quality and to select the DNase I concentration at which a very small portion of genomic DNA was digested and a smear under the major high molecular weight band appeared. The 2 U ml-1 DNase I condition was used to proceed to DNA size fractionation and construction of the libraries for deep-sequencing. DNA fragments of 100-500 bp in length were recovered following size fractionation on a 1% agarose gel and purified using microspin columns (Qiagen). DNase I libraries were constructed using the TruSeq DNA Sample Prep kit (Illumina) with the following modifications: 10 ng per sample were used as DNA input, adaptors were diluted 1:20 and final amplification of the adaptored DNA was done for 12 cycles. The libraries were were quantitated by qPCR (Library Quantification Kit, Kapa Biosystems). and equimolar amounts were combined.

tag: strain

value: BY4741 (MATa)

tag: genotype

value: wild type


title: EC-IgG

status: Public on Aug 22 2012

city: Paris

first: Eric

last: Batsche

address: 7-9, Quai Saint Bernard

department: B2A Biological Adaptation and Ageing - UMR8256 CNRS

country: France

institute: IBPS - Institut Biologie Paris Seine

description: immunoprecipitation of the cytoplasmic extract by rabbit non immun IgG (Sigma Aldrich)) linked to protein-A-dynabeads (Invitrogen) and rat non immun IgG (Sigma Aldrich) linked to protein-G-dynabeads (Invitrogen)

data_processing:
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion).  Alignments were filtered to include only the best matches for each sequence.  Sequences with >5 alignments were filtered out.
BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to

source_name: HeLa cells (ATCC)

extract_protocol: Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated  with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.

treatment_protocol: Hela cells were UV cross-linked (400 mJ/cm2) and subfractionated as described in Ameyar et al., (2012) Nat Struc Mol Biol in press. Inputs and immunoprecipitated extracts (incubated with either IgG as negative control or with anti-AGO2 antibodies) from cytoplasmic (EC) and chromatin (Chr) fractions were treated with Proteinase K, and RNA was extracted with phenol-chlorophorm.

tag: sample type

value: Cytoplasm

tag: antibody

value: IgG

value: HeLa

tag: sample fraction

value: immunoprecipitation


title: sba1_deletion_DNase-seq


title: EC-AGO2

description: immunoprecipitation of the cytoplasmic extract by rabbit anti-AGO2 (Millipore 07-590) linked to protein-A-dynabeads (Invitrogen) and rat anti-AGO2 (Sigma Aldrich SAB4200085) linked to protein-G-dynabeads (Invitrogen)

tag: cell line


title: EC-input

description: Cells were lysed in hypotonic buffer (10 mM Tris-HCl (pH 7.65), 1.5 mM MgCl2, and 10 mM KCl) and disrupted by 18 strokes of a tight-fitting Dounce homogenizer. The cytosolic fraction was separated from the pellet by centrifugation at 4 °C

value: Input

value: extract


title: Chr-IgG

description: immunoprecipitation of the chromatin extract by rabbit non immun IgG (Sigma Aldrich)) linked to protein-A-dynabeads (Invitrogen) and rat non immun IgG (Sigma Aldrich) linked to protein-G-dynabeads (Invitrogen)

value: Chromatin


title: Chr-AGO2

description: immunoprecipitation of the chromatin extract by rabbit anti-AGO2 (Millipore 07-590) linked to protein-A-dynabeads (Invitrogen) and rat anti-AGO2 (Sigma Aldrich SAB4200085) linked to protein-G-dynabeads (Invitrogen)


title: Resilient R1

status: Public on Aug 21 2012

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
R1.fpkm_tracking: mm9

source_name: Ventral Tegmental Area

extract_protocol: Total RNA is isolated by using Trizol reagent (Invitrogen, California) following the product instructions. Four micrograms of total RNA is then used for mRNA library construction with the Illumina mRNA sample prep kit (cat#RS-100-0801). In brief, the poly-A containing mRNA is purified using poly-T oligo-attached magnetic beads. The mRNA is then fragmented into small pieces and converted into cDNA. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products are then gel purified and enriched with PCR to create the final cDNA libraries.

treatment_protocol: C57BL/6J male mice were exposed to either emotional stress, physical stress, or control for 10 days.  24 hr later, VTA punches were taken.

tag: tissue

value: Ventral Tegmental Area

tag: stress

value: Resilient physical stress

tag: exposure time

value: 10 days

tag: gender

value: male


title: Susceptible R3

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
S3.fpkm_tracking: mm9

value: Susceptible physical stress


title: Resilient R3

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
R3.fpkm_tracking: mm9


title: Bb2860 NaCl 30m

city: Hangzhou

first: zheng-liang

last: wang

address: Yu-hang-tang Road 388

department: Institute of Microbiology

institute: Zhejiang University

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 21 bp tag fragments were mapped to the sequenced genome of Bb2860 with the precision of no more than one nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Bb2860
Supplementary_files_format_and_content: Excel files include GeneID, gene_length, RPKM values and false discovery rate (FDR)  for each Sample

organism: Beauveria bassiana ARSEF 2860

source_name: WT

growth_protocol: The hyphal cells of wild-type and ΔBbssk1 harvested from 2-day SDB cultures at 25ºC were transferred to fresh SDB containing 0.5 M NaCl, followed by 3 h incubation at 25ºC.

extract_protocol: Total RNA was isolated from frozen mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA), double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays

tag: genetic background

tag: treatment

value: 0.5M NaCl

value: wt

tag: culture time

value: 3 days

value: mycelia


title: Susceptible R1

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
S1.fpkm_tracking: mm9


title: Resilient R2

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
R2.fpkm_tracking: mm9


title: Emotional Stress R3

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
E3.fpkm_tracking: mm9

value: Emotional stress


title: ΔBbssk1 NaCl 30m

value: Bbssk1  null


title: Emotional Stress R1

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
E1.fpkm_tracking: mm9


title: Control R1

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
C1.fpkm_tracking: mm9

value: Unstressed control


title: Control R2

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
C2.fpkm_tracking: mm9


title: Emotional Stress R2

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
E2.fpkm_tracking: mm9


title: Colon tissue from human s3,cancerous

city: guangzhou

first: qianru

last: ai

address: xingang xi road No135

institute: igenomic

data_processing:
We used TopHat 1.31 software to align the sequence reads to reference genome (hg19) and used the cufflink program of Cufflinks 1.0.3 to call the expression values (FPKM, Fragments Per Kilobase of exon model per Million mapped fragments) of mapped human genes and the cuffdiff program of Cufflinks 1.0.3 to detect differentially expressed genes and the differentially expressed isoforms.
Series supplementary files: cuffdiff_gene.gz: Gene Expression Difference; cuffdiff_isoform.gz:Isoform Expression Difference

source_name: Colon tissue,cancerous

extract_protocol:
RNA was extracted with Trizol.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. Briefly, 10 ug of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by thermal mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (Super- Script II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase) and 3-'A' add process (Klenow exo- fragment), was finally ligated to Illumina Truseq adaptors. Size selection was performed using a 2% agarose gel, generating cDNA libraries ranging in size 380 bp. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 11 pM on one Genome Analyzer (GAII) lane using 115 bp sequencing. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Colon tissue

tag: disease status

value: cancerous


title: Colon tissue from human s2,paracancerous

source_name: Colon tissue,paracancerous

value: paracancerous


title: Control R3

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
C3.fpkm_tracking: mm9


title: Colon tissue from human s1,normal

source_name: Colon tissue,normal

value: normal


title: Chr-input

description: Chromatin was prepared as described in Ameyar-Zazoua et al. (2012) from Intact nuclei purified on sucrose gradients (and are devoid of P-bodies components)

value: Chromatin

value: Input

value: HeLa

value: extract


title: gcn5_deletion_DNase-seq

value: BY4741 (MATa)


title: wild type neuron 2

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description: Sample 8

data_processing:
Basecalls performed using Bustard v1.8.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
Aligned reads in valid pairs are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with FlyBase annotation (r5.44) were allowed and counted towards the number of mapped hits used in the FPKM denominator.  snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The aligned reads were counted with HTSeq. Counts for technical replicates are summed up. The polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.8.3). DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010). 'DESeq.nbVsneuron-orig-FDR0.01.txt' data file for  differential expression (FDR<0.01) is available on a Serie records.
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: wild type neuron

growth_protocol: Flies expressing UAS-stingerGFP under asense-Gal4 were flipped on fresh food, left to lay for 24 h, and then kept at 25 degree for another five days, before dissection of larval brains.

extract_protocol: Neuroblasts and neurons were FACS sorted, and RNA was isolated using Trizol reagent. Total RNA(~1µg) was enriched for polyA mRNA, fragmented and first strand and second strand (dUTP, instead dTTP was used) was generated. Library preparation was done using a modified protocol from Illumina with NEBNext DNA sample Prep Reagent kits (NEB), and UGDase treatment was done to confer strand specificity.

tag: tissue source

value: larval brain

tag: cell type

value: neuron (differentiated daughter cells)

tag: Stage

value: late third instar

tag: marker

value: cells expresses nuclear GFP marker (UAS-stingerGFP)


title: Susceptible R2

data_processing:
Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
emo=Emotional
res=Resilient
sus=Susceptible
Genome Build:
S2.fpkm_tracking: mm9

value: Ventral Tegmental Area

value: Susceptible physical stress

value: 10 days

tag: strain

value: male


title: wild type neuron 1 (tech. Repl. 1)

description: Sample 6


title: wild type neuroblast 3 (tech. Repl. 1)

description: Sample 4

source_name: wild type neuroblast

value: neuroblasts


title: wild type neuroblast 3 (tech. Repl. 2)

description: Sample 5


title: wild type neuron 1 (tech. Repl. 2)

description: Sample 7


title: wild type neuroblast 2 (tech. Repl. 1)

description: Sample 2


title: wild type neuroblast 2 (tech. Repl. 2)

description: Sample 3


title: wild type neuroblast 1

description: Sample 1


title: EmptyVector_WCE_ChIPSeq

first: Richard

last: Koche

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-Seq reads were aligned to the human genome reference assembly hg19.
MAQ version 0.7.1 was used with the default parameters, with reads discarded if they align to more than 10 places.
To create density files, the 36 bp reads were extended to 200 bp and converted to BigWig using UCSC BedTools.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing the read densities for all regions.

growth_protocol: Human leukemia cell lines were cultured in RPMI-1640 medium supplemented with 10% FBS+1mM hydrocortisone+10% horse serum.

extract_protocol: Cells were crosslinked in 1% formaldehyde, lysed and sonicated with a Branson 250 Sonifier to obtain chromatin fragments in a size range between 200 and 700 bp. Solubilized chromatin was diluted in ChIP dilution buffer (1:10) and incubated overnight with antibody at 4oC. Protein A sepharose beads (Sigma) were used to capture the antibody-chromatin complex and washed twice with each of the wash buffers (low salt wash buffer, LiCl wash buffer and TE (pH 8.0)). Bound chromatin fragments were eluted at 65oC for 10 min, subjected to crosslink reversal at 65oC for 5 hrs. After Proteinase K treatment for two hours at 37 4oC (1 mg/ml), DNA was extracted by phenol-chloroform-isoamyl alcohol followed by overnight ethanol precipitatation at -20oC  ChIP DNA was then quantified by QuantiT Picogreen dsDNA Assay kit (Invitrogen). ChIP experiments for ASXL1 were carried out on nuclear preps. Crosslinked cells were incubated in swelling buffer (0.1 M Tris pH 7.6, 10 mM KOAc, 15 mM MgOAc, 1% NP40), on ice for twenty minutes, passed through a 16G needle 20 times and centrifuged to collect nuclei. Isolated nuclei were then lysed, sonicated and immunoprecipitated as described above.

value: Leukemia cell line

tag: variation

value: EmptyVector

value: none (WCE)


title: EmptyVector_H3K27me3_ChIPSeq

tag: antibody

value: H3K27me3 Milipore Cat# 7449 Lot # DAM151401


title: ASXL1sh1_H3K4me3_ChIPSeq

value: H3K4me3 Milipore Cat# 07-473 Lot# R0903B0054


title: ASXL1sh1_WCE_ChIPSeq


title: ASXL1sh2_H3K4me3_ChIPSeq


title: ASXL1sh2_WCE_ChIPSeq


title: ASXL1sh1_H3K27me3_ChIPSeq


title: S2-dsMbl-ins

status: Public on Aug 17 2012

city: Gainesville

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

description:
Mbl_ins
RNA-Seq, paired end
Insoluble RNA
Processed data file: fly_fractionation_RPKM.txt

data_processing:
Reads were aligned to the dm3 Drosophila genome and splice junctions using Bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
Genome_build: dm3
Supplementary_files_format_and_content: tissue_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: fly_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_ribo_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: B6Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: 129Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Heart_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Muscle_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: C2C12_clusters.bed: Bed file of CLIPseq clusters.

source_name: Drosophila S-2R+ cell, Mbnl depleted, insoluble fraction

extract_protocol:
S-2R+ cells were fractionated using hypotonic lysis and ultracentrifugation to obtain cytosolic, membrane, and insoluble fractions. RNA was isolated by Trizol.
RNA-seq libraries were prepared using paired end Illumina adapters.

tag: subcellular fraction

value: insoluble


title: S2-control-cyto

description:
GFP_cyto
RNA-Seq, paired end
Cytosolic RNA
Processed data file: fly_fractionation_RPKM.txt

source_name: Drosophila S-2R+ cell, control, cytosolic fraction

tag: cell line

value: cytosolic


title: HEK293T_EGF_GF109203X

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description:
Barcode name: G4
Barcode sequence: TAAGATCA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.G4.bed: hg18

growth_protocol: HEK293T and Hela cells were cultured in Dulbecco's modified Eagle's medium plus 10% fetal bovine serum supplemented with penicillin and streptomycin at 37°C in 5% CO2.

extract_protocol:
1 µg of HEK293T total RNA was mixed with 100 fmol of human RASL oligos (for detecting 3726 splicing events), 2 pmol of biotinylated-oligo-dT and 5 µl of streptavidin magenetic beads. Followed by one hour of annealing at 45ºC, magnetic beads were washed 3 times by washing buffer. Then ligation was achieved by adding 5U of T4 DNA ligase for 1 hour at 37ºC. After 3 times of wash, ligated oligos were eluted to water by heating at 65ºC for 5 minutes, and then PCR amplified using primers containing sequencing adaptor and barcode sequences. PCR products were purified and sequenced.
library strategy: RASL-Seq

treatment_protocol: 10 mM GF109203X followed by EGF treatment (100 ng/ml)


title: S2-control-mem

description:
GFP_mem
RNA-Seq, paired end
Membrane RNA
Processed data file: fly_fractionation_RPKM.txt

source_name: Drosophila S-2R+ cell, control, membrane fraction

value: membrane


title: HEK293T_EGF_U0126

description:
Barcode name: E4
Barcode sequence: TAAGTGGA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.E4.bed: hg18

treatment_protocol: 10 µM U0126  followed by EGF treatment (100 ng/ml)


title: S2-dsMbl-mem

description:
Mbl_mem
RNA-Seq, paired end
Membrane RNA
Processed data file: fly_fractionation_RPKM.txt

source_name: Drosophila S-2R+ cell, Mbnl depleted, membrane fraction


title: S2-dsMbl-cyto

description:
Mbl_cyto
RNA-Seq, paired end
Cytosolic RNA
Processed data file: fly_fractionation_RPKM.txt

source_name: Drosophila S-2R+ cell, Mbnl depleted, cytosolic fraction


title: HEK293T_EGF_Rapamycin

description:
Barcode name: F4
Barcode sequence: TAAAACGA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.F4.bed: hg18

treatment_protocol: 100 nM Rapamycin followed by EGF treatment (100 ng/ml)


title: S2-control-ins

description:
GFP_ins
RNA-Seq, paired end
Insoluble RNA
Processed data file: fly_fractionation_RPKM.txt

source_name: Drosophila S-2R+ cell, control, insoluble fraction


title: HEK293T_EGF_WP1066

description:
Barcode name: C4
Barcode sequence: TAAGGGTA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.C4.bed: hg18

treatment_protocol: 3 mM WP1066  followed by EGF treatment (100 ng/ml)


title: HEK293T_EGF_Wortmannin

description:
Barcode name: D4
Barcode sequence: TAAGGGTA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.D4.bed: hg18

treatment_protocol: 20 nM Wortmannin followed by EGF treatment (100 ng/ml)


title: HEK293T_EGF

description:
Barcode name: B4
Barcode sequence: TAAAGAAC

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.B4.bed: hg18

treatment_protocol: EGF treatment (100 ng/ml)


title: EmptyVector_H3K4me3_ChIPSeq


title: ASXL1sh2_H3K27me3_ChIPSeq


title: HEK293T_siRNA_SRPK1/K2

description:
Barcode name: D3
Barcode sequence: TAGGTATA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane1.D3.bed: hg18

treatment_protocol: Transfection of siRNA against SRPK1/K2


title: Water_control

description:
Barcode name: H4
Barcode sequence: TAAACCCA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane1.H4.bed: hg18

treatment_protocol: Water


title: HEK293T_siRNA_SRPK1/K_EGF

description:
Barcode name: E3
Barcode sequence: TAGAATGA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane1.E3.bed: hg18

treatment_protocol: Transfection of siRNA against SRPK1/K3 followed by EGF treatment (100 ng/ml)


title: HEK293T_control

description:
Barcode name: A4
Barcode sequence: TAAGCGAC

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane2.A4.bed: hg18

treatment_protocol: DMSO


title: HEK293T_siRNA_control_EGF

description:
Barcode name: C3
Barcode sequence: TAGATGTA

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane1.C3.bed: hg18

treatment_protocol: Transfection of control siRNA followed by EGF treatment (100 ng/ml)


title: muscleWT5

description:
RNA-Seq, single end
PolyA RNA
Processed data file: tissue_RPKM.txt

data_processing:
Reads were aligned to the mm9 mouse genome and splice junctions using Bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
For CLIP-seq data, adapters were trimmed prior to mapping.
CLIP clusters were defined as previously described (Yeo et al., NSMB 2009 (PMID 19136955)).
For ribosome footprinting data, polyA tails were trimmed prior to mapping.
Genome_build: mm9
Supplementary_files_format_and_content: tissue_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: fly_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_ribo_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: B6Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: 129Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Heart_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Muscle_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: C2C12_clusters.bed: Bed file of CLIPseq clusters.

source_name: vastus lateralis, WT

extract_protocol:
Five 16-week-old 129/SvJ Mbnl1∆E3/∆E3 mice and littermate WT mice were sacrificed for isolation of whole brain, heart, and skeletal muscle (vastus lateralis). Total RNA was prepared by lysis in guanidium isothiocyanate, followed by phenol/chloroform extraction.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for single-end RNA sequencing using Illumina single end sequencing primers.

tag: strain/background

tag: genotype

value: wildtype

tag: age

value: 16 weeks

tag: tissue

value: skeletal muscle (vastus lateralis)


title: muscleKOd

source_name: vastus lateralis, Mbnl1 KO

value: Mbnl1 knockout


title: muscleWT3


title: muscleWT2


title: muscleKOe


title: muscleWT4


title: muscleKOc


title: muscleKOb


title: muscleKOa


title: heartWT3

source_name: whole heart, WT

value: whole heart


title: heartWT5


title: heartWT1


title: heartWT2


title: heartKOe

source_name: whole heart, Mbnl1 KO


title: heartKOd


title: heartKOc


title: heartKOb


title: heartKOa


title: brainWT4

source_name: whole brain, WT

value: whole brain


title: HEK293T_siRNA_control

description:
Barcode name: B3
Barcode sequence: TAGGGAAC

data_processing:
After decoding using barcode sequence starting at position 37, the first 36 bases sequenced were mapped to the oligo pool sequences by Bowtie. The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.
Genome Build:
lane1.B3.bed: hg18

treatment_protocol: Transfection of control siRNA


title: blood from human pancreatic cancer patient 19 processed by IgG CTC-Chip

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description:
PDAC_19.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

data_processing:
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.
Genome_build: hg18
Supplementary_files_format_and_content: GSE40174_human_processed_data.txt: Tab-delimited text file of aligned read counts. Row names are UCSC known Gene transcript IDs or gene symbols, and column names are sample IDs. The 'GSE40174_human_processed_data.txt' file is linked to the Series record as a supplementary file.

source_name: pancreatic cancer patient, blood, IgG CTC-Chip

extract_protocol: Qiagen RNeasy MinElute kit followed by Helicos single-molecule sequencing. See Pubmed IDs 18388294, 20133332.

tag: donor

value: pancreatic cancer patient 19

tag: disease state

value: pancreatic cancer

value: blood

tag: ChIP

value: IgG CTC-Chip

value: circulating tumor cell (CTC)


title: blood from human pancreatic cancer patient 20 processed by IgG CTC-Chip

description:
PDAC_20.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 20


title: blood from human pancreatic cancer patient 19 processed by EpCAM CTC-Chip

description:
PDAC_19.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: pancreatic cancer patient, blood, EpCAM CTC-Chip

value: EpCAM CTC-Chip


title: brainWT3


title: brainWT5


title: blood from human pancreatic cancer patient 16 processed by EpCAM CTC-Chip

description:
PDAC_16.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 16


title: blood from human pancreatic cancer patient 16 processed by IgG CTC-Chip

description:
PDAC_16.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: brainWT1


title: blood from human pancreatic cancer patient 12 processed by IgG CTC-Chip

description:
PDAC_12.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 12


title: Dicer_Het

status: Public on Aug 20 2012

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

data_processing:
Raw reads were processed to remove traces of 3' linker and summarized by sequence identity (observations). Additional data processing details are available in the accompanying manuscript.

Genome build: mm9

source_name: Dicer f/- murine sarcoma cell line (KRasG12D,p53 -/-)

growth_protocol: Dicer-heterozygous tumors were generated by injection of Adeno-Cre virus into the hindlimbs of Kras-LSL-G12D, p53f/f, Dicerf/f mice. From Kras-LSL-G12D, p53-/-, Dicerf/- tumors, sarcoma cell lines were established. The remaining allele of Dicer was deleted by transducing the cells with a retroviral construct encoding Puro.CreERT2 and then activating recombination in vitro with tamoxifen treatment.

extract_protocol: Total RNA was extracted from Dicer f/- and Dicer -/- murine sarcoma cells using Trizol. Small RNAs in the 15-50 nt range were cut from a 15% polyacrylamide TBE-urea gel. Small RNA libraries were cloned and sequenced using the standard Illumina protocol.

tag: background strain

value: KRasG12D,p53 -/- murine sarcoma cells

value: Dicer f/-


title: blood from human pancreatic cancer patient 18 processed by IgG CTC-Chip

description:
PDAC_18.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 18


title: brainWT2

value: wildtype

value: 16 weeks


title: blood from human pancreatic cancer patient 12 processed by EpCAM CTC-Chip

description:
PDAC_12.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: heartWT4


title: muscleWT1

value: skeletal muscle (vastus lateralis)


title: brainKOe

source_name: whole brain, Mbnl1 KO

value: Mbnl1 knockout


title: blood from human pancreatic cancer patient 20 processed by EpCAM CTC-Chip

description:
PDAC_20.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: blood from human pancreatic cancer patient 11 processed by IgG CTC-Chip

description:
PDAC_11.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 11


title: blood from human pancreatic cancer patient 9 processed by IgG CTC-Chip

description:
PDAC_9.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 9


title: brainKOd

value: whole brain


title: blood from human pancreatic cancer patient 11 processed by EpCAM CTC-Chip

description:
PDAC_11.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer

value: blood


title: blood from human pancreatic cancer patient 9 processed by EpCAM CTC-Chip

description:
PDAC_9.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: circulating tumor cell (CTC)


title: blood from human pancreatic cancer patient 18 processed by EpCAM CTC-Chip

description:
PDAC_18.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: blood from human pancreatic cancer patient 7 processed by IgG CTC-Chip

description:
PDAC_7.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 7

value: IgG CTC-Chip


title: brainKOc

description:
RNA-Seq, single end
PolyA RNA
Processed data file: tissue_RPKM.txt


title: blood from human pancreatic cancer patient 4 processed by IgG CTC-Chip

description:
PDAC_4.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 4


title: brainKOa


title: blood from human pancreatic cancer patient 6 processed by EpCAM CTC-Chip

description:
PDAC_6.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 6

value: EpCAM CTC-Chip


title: blood from human pancreatic cancer patient 6 processed by IgG CTC-Chip

description:
PDAC_6.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: blood from human pancreatic cancer patient 4 processed by EpCAM CTC-Chip

description:
PDAC_4.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: brainKOb


title: blood from human pancreatic cancer patient 7 processed by EpCAM CTC-Chip

description:
PDAC_7.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: blood from healthy human donor 4 processed by IgG CTC-Chip

description:
HD_4.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: healthy donor, blood, IgG CTC-Chip

value: healthy donor 4

value: healthy


title: GATA1_async_ChIPseq

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
Rescued subline of G1E expressing a Gata1-estrogen receptor (ER) transgene; recapitulates erythroid differentiation after induction by estradiol treatment for 24hr.
Chromatin IP against GATA1, re-analysis of GSM453997

data_processing:
Reads generated from a sample ran on more than one lane were concatenated
Concatenated ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with default settings on the Galaxy platform
Artifactual reads mapping to the coding exons of GATA1, BRD3,GATA2,ZFPM1 were filtered using Samtools.
Peaks were called on filtered  mapped  reads with repsective inputs as ChIP-seq control file using MACS 1.3  with the option mfold 10  on the Galaxy platform
Genome_build: mm9
Supplementary_files_format_and_content: Alignment files contain reads mapped to mm9 build for each sample. Peak files are bed  format files containing MACS identified GATA1 occupied regions for the indicated samples.

source_name: asynchrnous G1E-ER4+E2 cells

growth_protocol: G1E-ER4 cells were grown in IMDM media with 15% fetal calf serum 2U/ml erythropoietin (Amgen’s EpoGen) and 50ng/ml stem cell factor.

extract_protocol: For ChIP-seq, ChIP DNA or input DNA was amplified by Illumina ChIP-Seq library preparation kit. To prepare the sequencing libraries, the ChIP DNA fragments were repaired to generate blunt ends, with a single A nucleotide adding to each end. Double-stranded Illumina adaptors were ligated to both ends of the fragments. Ligation products were amplified by 18 cycles of PCR, and the PCR products between 250 and 300 bp were gel purified. Libraries were quantified with a Quant-iT dsDNA HS Assay Kit.

treatment_protocol:
For asynchronous ChIP, G1E-ER4 cells were induced with 100 nM estradiol for 24 hours. Cells were crosslinked with 1% (0.33 M) formaldehyde in PBS at room temperature for 10 min and quenched with 0.125 M glycine for 5 min
For mitotic ChIP, G1E-ER4 cells were induced with 100 nM estradiol for 18 hours. Nocodazole  was added (200 ng/mL) for 6-7 hours before harvest. Cells were crosslinked with 1% (0.33 M) formaldehyde in PBS at room temperature for 10 min and quenched with 1 M glycine for 5 min .Cells were stained with anti-H3S10ph antibodies and Dy649-conjugated anti-rabbit IgG F(ab’)2 antibody fragments in PBS/2% FBS/2 mM EDTA, 1 mM PMSF, and protease inhibitor cocktail (Sigma). 107 H3S10ph-positive cells per IP were sorted on a FACSAria II (Beckton Dickinson).

tag: developmental stage

value: Rescued subline of G1E  expressesing a Gata1-estrogen receptor (ER) transgene; recapitulates erythroid differentiation after induction by estradiol treatment for 24hr.

tag: chip antibody

value: GATA1 (Santacruz,clone N6, sc-265)


title: blood from human pancreatic cancer patient 3 processed by EpCAM CTC-Chip

description:
PDAC_3.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 3

tag: cell type


title: blood from human pancreatic cancer patient 2 processed by EpCAM CTC-Chip

description:
PDAC_2.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: pancreatic cancer patient 2


title: blood from human pancreatic cancer patient 3 processed by IgG CTC-Chip

description:
PDAC_3.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: blood from human pancreatic cancer patient 2 processed by IgG CTC-Chip

description:
PDAC_2.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: blood from healthy human donor 4 processed by EpCAM CTC-Chip

description:
HD_4.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: healthy donor, blood, EpCAM CTC-Chip


title: HEK293 cells transfected with pGL4-SV40 plasmid

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

description:
pGL4-SV40
Plasmid pGL4-SV40 was constructed in our laboratory during the study and is described in more details in the accompanying paper
When we looked for the plasmid sequence, we relied on the manufacturer's websites and datasheets (links will be included in the paper), rather than on the GenBank.

data_processing:
Sequence reads of 18-50 nt length (after subtracking the adaptor sequence) were obtained and mapped onto specified plasmid allowing only perfectly matched reads. In the second round of mapping (Edited reads), A-to-G mischatches were allowed during mapping.
Columns in processed files are as follows: Sequence = sequence of the particular read mapped; Count = number indicating, how many times is the particular read present in the dataset; Strand = indicates if the read was mapped on a sense or an antisense strand of the plasmid; Length = length of the read; Edited nucleotides = number of A-to-G mismatches present within the mapped read.

source_name: cell line

growth_protocol: HEK293 cells were grown under standard tissue culture conditions (DMEM + 10% FCS).

extract_protocol: Total RNA was isolated using RNAzol RT (Molecular Research Center). Further sample processing and SOLiD sequencing was performed by Seqomics Ltd. (Hungary). Briefly, samples were depleted of ribosomal RNA using RiboMinus rRNA Removal Kit, eluted twice into 15 ul and treated with DNase I (5 ul 10x DNase I buffer, 2.5 U DNase I and water up to 50 ul reaction) 20 min at 37°C. Samples were ethanol-precipitated, eluted into 10 ul TE buffer and fragmented by RNase III treatment (1 ul 10x RNaseIII buffer, 8 ul sample, 1 ul RNaseIII) 10 min at 37°C. Fragmented samples were precipitated by ethanol and eluted into 4 ul. Adaptor was hybridized and ligated to each sample (10 ul 2x ligase buffer, 2 ul Adaptor mix, 3 ul hybridization solution, 2 ul ligation enzyme) by incubating O.N. at 16°C. Adaptor-ligated RNA was subjected to reverse transcription (4 ul 10x RT buffer, 2 ul dNTP mix, 2 ul RT primer, 1 ul ArrayScript RT, 13 ul water) for 40 min at 42°C. Resulting cDNA was purified using PCR Purification kit (Qiagen) and eluted into 10 ul. cDNA was run on 6% TBE-Urea gel and fragments 150-250 nt in length were excised. Isolated cDNA was amplified for 15 cycles using AmpliTaq DNA polymerase and purified by PCR Purification kit (elution twice in 10 ul). Second round of size selection on PAGE gel was performed and PCR products 110-130 nt in length were excised from gel and isolated.  Purified amplicons were sequenced using Abi SOLiD 4 platform.

treatment_protocol: HEK293 cells were transiently transfected with 3 micrograms of phRL-SV40, pGL4-SV40 or a 1:1 mixure of pBLuescript and pEGFP-C1 plasmids (per well in a 6-well plate) using TurboFect (Fermentas) transfection reagent.

tag: passages

tag: transfected plasmid


title: HEK293 cells transfected with a 1:1 mixture of pBluescript and pEGFP-C1 plasmids

description:
pBS-EGFP
pBluescript GenBank accession number: U26267.1
pEGFP-C1 GenBank accession number: U55763.1
When we looked for the plasmid sequence, we relied on the manufacturer's websites and datasheets (links will be included in the paper), rather than on the GenBank.

value: pBluescript + pEGFP-C1


title: blood from healthy human donor 3 processed by EpCAM CTC-Chip

description:
HD_3.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: healthy donor 3


title: blood from healthy human donor 2 processed by EpCAM CTC-Chip

description:
HD_2.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: healthy donor 2


title: blood from healthy human donor 2 processed by IgG CTC-Chip

description:
HD_2.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: HEK293 cells transfected with phRL-SV40 plasmid

description:
phRL-SV40
phRL-SV40 GenBank accession number: AF362548
When we looked for the plasmid sequence, we relied on the manufacturer's websites and datasheets (links will be included in the paper), rather than on the GenBank.


title: EAR003_siRNA-tdg

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

data_processing:
Basecalls were performed using CASAVA pipeline version 1.5-1.7.
Reads were aligned to the mouse reference genome (UCSC version mm9) using bwa 0.6.1 with default settings.
Reads mapped with MAPQ < 15 were filtered out.
Genomic regions enriched in 5fC were identified with the program rseg (Song and Smith, Bioinformatics 2011) in mode 2 using the input library as control and setting the bin size to 100 bp.
Genome_build: mm9
Supplementary_files_format_and_content: Domain files in bed format produced by rseg (Song and Smith, Bioinformatics 2011). Each file contains the coordinates of the 5fC-enriched regions (where 4th column= 'ENRICHED') and background regions (where 4th column= 'BACKGROUND'). Please refer to the rseg manual for further details (http://smithlab.usc.edu/histone/rseg/).

source_name: Embryonic stem cells, TDG siRNA, 5fC

growth_protocol: Cell culturing was done on the J1 ES cell line (129S4/SvJae), purchased from ATCC (catalogue no. SCRC-1010) and grown on a γ-irradiated pMEF feeder layer at 37°C and 5% CO2 in complete ES medium (DMEM 4,500 mgl-1 glucose, 4 mM L-glutamine and 110 mg l-1 sodium pyruvate, 15% fetal bovine serum, 100 U of penicillin/100 mg of streptomycin in 100 ml medium, 0.1mM non-essential amino acids, 50mM β-mercaptoethanol, 103U LIF ESGRO).

extract_protocol:
DNA was extracted from cells using the AllPrep DNA/RNA Kit from Qiagen (UK) following the manufacturer's instructions.

We devised a method to map 5-formylcytosine (5fC) by linking a biotin tag to 5fC for pulldown and high-throughput sequencing.
After chemical pulldown, the ends of the DNA fragments were repaired and paired-end sequencing-specific adaptors (Illumina) were ligated using the NEBNext DNA Sample Prep Reagent Set 1 (NEB). Following adaptor ligation, DNA and 2 μg poly-dI:dC were incubated with 50 μg streptavidin-coated magnetic beads (MagneSphere Promega) in 50 μL 2x binding buffer (10 mM Tris pH 7.5, 1 mM EDTA, 2M NaCl, 0.1% TWEEN) for 15 min at room temperature. Beads were washed with 5x 500 μL binding buffer and transferred into a new eppendorf. For elution, beads were incubated with 100 uL elution solution (95% formamide, 10 mM EDTA and 400 nM biotin) at 90°C for 5 min and the eluant was collected and immediately placed on ice. This step was repeated to elute any residual DNA. Eluted DNA was then precipitated in ethanol and the DNA pellet was resuspended in 15 uL ddH2O. Fragments were amplified with 16 cycles using adaptor-specific primers (Illumina); fragments ranging between 200 and 500 bp in size were gel-purified before cluster generation and sequencing. Sequencing was done on an Illumina Genome Analyzer GAIIX using Cluster Generation v4 and 5 chemistries as well as Sequencing by Synthesis Kit v5. Data collection was performed using Sequencing Control Software v2.6 and 2.9. Real-time Analysis (RTA) 1.6 and 1.9 were used for base calling.

treatment_protocol: RNA interference experiments were performed in J1 ES cells without feeders with three rounds of transfections with siRNA every second day. In the first day, 1 x 10^5 cells were seeded per well (3.8cm2) of a 12-well plate and adherent cells were transfected the next day with 20 pmol siRNA: 3 mL Lipofectamine™2000 complexes in media without antibiotics according to the manufacturer's instructions. After 8 hours, fresh media with antibiotics was added to the cells. This procedure was repeated 48 and 96 hours after the first transfection, both these times on cells in suspension. Cells were passaged and transfections were scaled up when necessary. Transfections were done with Dharmacon (Thermo Fisher Scientific) siGENOME SMARTpool against mouse Tdg (catalogue no. M-040666-01; gaagugcaguauacauuug, gaguaaagguuaagaacuu, caaagaagauggcuguuaa, gcaaggaucugucuaguaa) and siGENOME non-targeting siRNA#2 (catalogue no. D-001210-02; sequence not available). Cells were harvested after three rounds of transfection for DNA/RNA isolation.

value: embryonic stem cells

tag: sirna

value: TDG-KD

tag: pulldown target

value: 5-formylcytosine (5fC)


title: blood from healthy human donor 1 processed by EpCAM CTC-Chip

description:
HD_1.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: healthy donor 1

value: blood

value: circulating tumor cell (CTC)


title: EAR001_siRNA-control

source_name: Embryonic stem cells, siRNA control, 5fC

value: non-targeting (control)


title: blood from healthy human donor 1 processed by IgG CTC-Chip

description:
HD_1.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: IgG CTC-Chip


title: BHAM480_siRNA-tdg


title: Mouse pancreatic NB508 cells with vector control grown under non-adherent 3-D sphere-forming conditions

description:
NB508-Vec_Sphere
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

data_processing:
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.
Genome_build: mm9
Supplementary_files_format_and_content: GSE40171_mouse_processed_data.txt: Tab-delimited text file of aligned read counts. Row names are UCSC known Gene transcript IDs or gene symbols, and column names are sample IDs. The 'GSE40171_mouse_processed_data.txt' file is linked to the Series record as a supplementary file.

source_name: pancreatic cell line, non-adherent, vector

value: pancreatic cells

tag: wnt2 expression

value: no

tag: growth conditions

value: non-adherent 3-D sphere-forming


title: Dicer_Null

source_name: Dicer -/- murine sarcoma cell line (KRasG12D,p53 -/-) derived from Dicer f/- parental line

value: KRasG12D,p53 -/- murine sarcoma cells

value: Dicer -/-


title: Mouse pancreatic NB508 cells induced to express Wnt2 grown under non-adherent 3-D sphere-forming conditions

description:
NB508-Wnt2_Sphere
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: pancreatic cell line, non-adherent, Wnt2

tag: cell line

value: yes


title: Mouse pancreatic NB508 cells with vector control

description:
NB508-Vec
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: pancreatic cell line, adherent, vector

value: adherent


title: BHAM479_siRNA-control

tag: strain/background


title: Mouse pancreatic NB508 cells induced to express Wnt2

description:
NB508-Wnt2
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: pancreatic cell line, adherent, Wnt2


title: Ascites from mouse model 10 of pancreatic cancer

description:
MPANC_10.Ascites
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: mouse pancreatic cancer model, ascites

tag: background/strain

value: FVB

tag: mouse model

value: MPANC 10

value: pancreatic cancer

value: ascites from pancreatic tumor


title: BHAM470_WT

source_name: Embryonic stem cells, WT, 5fC

value: embryonic stem cells

tag: genotype

value: wild-type

value: 5-formylcytosine (5fC)


title: Tumor from mouse model 10 of pancreatic cancer

description:
MPANC_10.Tumor
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: mouse pancreatic cancer model, tumor

tag: disease state

tag: tissue

value: primary pancreatic tumor


title: Blood from mouse model 10 of pancreatic cancer processed by IgG CTC-Chip

description:
MPANC_10.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: mouse pancreatic cancer model, blood, IgG CTC-Chip

value: blood

tag: ChIP

value: circulating tumor cell (CTC)


title: BHAM385_WT

source_name: Embryonic stem cells, WT, input

value: input


title: BHAM359_WT


title: Blood from mouse model 9 of pancreatic cancer processed by IgG CTC-Chip

description:
MPANC_9.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

value: MPANC 9

value: IgG CTC-Chip


title: Blood from mouse model 9 of pancreatic cancer processed by EpCAM CTC-Chip

description:
MPANC_9.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: mouse pancreatic cancer model, blood, EpCAM CTC-Chip

value: EpCAM CTC-Chip


title: C2C12ribo-shMbnl12

description:
Mbnl12-ribo
RNA-Seq, single end
Ribosome footprints
Processed data file: myoblast_ribo_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 and Mbnl2 depleted, ribosomal fraction

extract_protocol:
C2C12 mouse myoblasts were grown in DMEM with 20% FBS. Ribosomes were isolated by pelleting cell lysate through a sucrose cushion. RNA was isolated by guanidium isothiocyanate, followed by ethanol precipitation.
Ribosome footprinting libraries were prepared as previously described (Ingolia et al., Science 2009 (PMID 19213877)) using small RNA Illumina adapters.

tag: shRNA

value: Mbnl1, Mbnl2

tag: subcellular fraction

value: ribosomes


title: Tumor from mouse model 9 of pancreatic cancer

description:
MPANC_9.Tumor
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.


title: C2C12ribo-control

description:
LKO-ribo
RNA-Seq, single end
Ribosome footprints
Processed data file: myoblast_ribo_RPKM.txt

source_name: C2C12 mouse myoblast, control, ribosomal fraction

value: control


title: CLIP-B6Muscle

description:
B6Muscle
CLIP-Seq
Total RNA
Processed data file: B6Muscle_clusters.bed

data_processing:
Library strategy: CLIP-Seq
Reads were aligned to the mm9 mouse genome and splice junctions using Bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
For CLIP-seq data, adapters were trimmed prior to mapping.
CLIP clusters were defined as previously described (Yeo et al., NSMB 2009 (PMID 19136955)).
For ribosome footprinting data, polyA tails were trimmed prior to mapping.
Genome_build: mm9
Supplementary_files_format_and_content: tissue_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: fly_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_ribo_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: B6Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: 129Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Heart_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Muscle_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: C2C12_clusters.bed: Bed file of CLIPseq clusters.

source_name: vastus lateralis, WT, Mbnl CLIP

extract_protocol:
Brain, heart, and muscle (vastus) were isolated from 16-week-old C56BL/6 or 129SVJ male mice. Tissue was dissociated and UV irradiated.
CLIP-seq libraries were prepared as previously described (Wang et al., Methods 2009 (PMID 19272451)), using small RNA Illumina adapters.

value: wildtype

tag: age

value: 16 weeks

tag: gender

value: male

value: skeletal muscle (vastus lateralis)

tag: clip antibody

value: Mbnl polyclonal


title: blood from healthy human donor 3 processed by IgG CTC-Chip

description:
HD_3.IgG
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: healthy donor, blood, IgG CTC-Chip

tag: donor

value: healthy donor 3

value: healthy

tag: cell type


title: Exposed to Aplanochytrium s_7

city: Ithaca

first: Colleen

last: Burge

address: 215 Tower Road/E343 Corson Hall

department: Department of Ecology and Evolutionary Biology

institute: Cornell University

description: Pool n=12

data_processing:
CLC Genomics workbench used for trimming sequencing with the following parameters :  all sequences were trimmed based on quality scores of 0.05 and the number of ambiguous nucleotides (>2 on ends). Sequences smaller than 20 bp were also removed.
CLC Genomics Workbench v4.0 (CLC Bio) was used to map the reads to the assembled transcriptome and to obtain raw counts of sequencing reads using following parameters: unspecific match limit = 5, maximum number of mismatches = 2, minimum number of reads = 10.
Statistical comparisons of count data between the control and Aplanochytrium exposed libraries was carried out using DESeq
Genes were considered differentially expressed in a given library when the adjusted p-value was less than or equal to 0.05.  All genes described had respective e-values of less than 1E-6 except for selected immune related genes. For these genes, nucleotide sequences were translated using ORF finder and compared to the Swiss-Prot database using a p-blast, psi-blast, and pfam-searches. Only sequences with significant protein domain similarity were considered.
Genome_build: NA: transcriptome to be submitted to TSA
Supplementary_files_format_and_content: Tab deliminted files include RFKM values and unique genes for each sample

organism: Gorgonia ventalina

source_name: whole organism

growth_protocol: Sea fans were collected from the field and held for two days before moving to the lab where they were held in aquariums for 3 days.

extract_protocol: For each treatment, samples were pooled (n=12) using 900 ng of total RNA from each sea fan. RNA quality was assessed using an Agilent BioAnalyzer 2100 at the Cornell University Life Sciences Core Laboratory Center (CLC). Library preparation was done at the Cornell Microarray facility using the mRNA-Seq 8-Sample Prep Kit (Illumina, San Diego, California) followed by sequencing preparation using the standard cluster generation kit and 36 cycle Illumnia sequencing kit (Illumina, San Diego, California) at the Cornell University CLC. Each library was sequenced in its own individual lane where 86 bp reads were captured using an Illumina/Solexa Genome Analyzer at the Cornell University CLC.

treatment_protocol: One piece of each sea fan (n=12) was injected three times with a solution of a 5 day culture of an Aplanochytrium previously isolated from a sea fan [19].  Complementary clonal pieces (n=12) were injected with QPX media only [44] to serve as a control.  After 24 hours an area including each of the three injection points was collected from each sea fan and flash frozen in liquid nitrogen and subsequently stored at -80 C.  Sea fan samples were shipped on dry ice overnight to Cornell University and stored at -80 C until sample preparation.

value: whole organism

tag: treatment

value: exposed to Aplanochytrium parasite


title: CLIP-B6Heart

description:
B6Heart
CLIP-Seq
Total RNA
Processed data file: B6Heart_clusters.bed

source_name: whole heart, WT, Mbnl CLIP

value: whole heart


title: CLIP-B6Brain

description:
B6Brain
CLIP-Seq
Total RNA
Processed data file: B6Brain_clusters.bed

source_name: whole brain, WT, Mbnl CLIP

value: whole brain


title: CLIP-129Brain

description:
129Brain
CLIP-Seq
Total RNA
Processed data file: 129Brain_clusters.bed


title: C2C12-shMbnl12

description:
Mbnl12-100825
RNA-Seq, paired end
PolyA RNA
Processed data file: myoblast_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 and Mbnl2 depleted

extract_protocol:
C2C12 mouse myoblasts were grown in DMEM with 20% FBS, and infected with lentiviral shRNAs against Mbnl1 and/or Mbnl2. RNA was isolated by Trizol, followed by RNeasy columns.
Ribosomal RNA was depleted by Ribozero (Epicentre) and libraries were prepared using paired end Illumina adapters.


title: untreated MCF7 H3K4me2 ChIP-Seq

city: Lebanon

first: xiaoyang

last: zhang

address: 1 Medical Center Driver

institute: Dartmouth Medical School

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 were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: untreated MCF7 H3K4me2

growth_protocol: MCF7 cells were maintained in DMEM (Invitrogen) supplemented with 10% FBS

extract_protocol: Library preparation for next-generation sequencing was performed according to manufacturerâs instruction starting with 5 ng of material (Illumina Inc.).

treatment_protocol: 10-8M E2 treatment 45mins

value: untreated

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot#


title: E2 treated MCF7 H3K4me2 ChIP-Seq

source_name: E2 treated MCF7 H3K4me2

tag: cell line

value: 10-8M E2 for 45 minutes


title: C2C12-shMbnl2

description:
Mbnl2-100825
RNA-Seq, paired end
PolyA RNA
Processed data file: myoblast_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl2 depleted


title: control s_6

description: Pool n=12


title: CLIP-C2C12

description:
C2C12
CLIP-Seq
Total RNA
Processed data file: C2C12_clusters.bed

source_name: C2C12 mouse myoblast, Mbnl CLIP


title: C2C12-shMbnl12-ins

description:
Mbnl-ins
RNA-Seq, paired end
Insoluble RNA
Processed data file: myoblast_fractionation_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 and Mbnl2 depleted, insoluble fraction

extract_protocol:
C2C12 mouse myoblasts were grown in DMEM with 20% FBS, and infected with lentiviral shRNAs against Mbnl1 and Mbnl2. Cytosolic, membrane, and insoluble fractions were isolated using 0.015% digitonin, 0.5% Triton X-100, and 1 M NaCl, respectively. RNA was isolated by guanidium isothiocyanate, followed by ethanol precipitation and RNeasy cleanup.
Ribosomal RNA was depleted by Ribozero (Epicentre) and libraries were prepared using paired end Illumina adapters.

value: Mbnl1, Mbnl2

value: insoluble


title: C2C12-shMbnl1

description:
Mbnl1-100825
RNA-Seq, paired end
PolyA RNA
Processed data file: myoblast_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 depleted


title: C2C12-shMbnl12-mem

description:
Mbnl-mem
RNA-Seq, paired end
Membrane RNA
Processed data file: myoblast_fractionation_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 and Mbnl2 depleted, membrane fraction

value: membrane


title: C2C12-shMbnl12-cyto

description:
Mbnl-cyto
RNA-Seq, paired end
Cytosolic RNA
Processed data file: myoblast_fractionation_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 and Mbnl2 depleted, cytosolic fraction

value: cytosolic


title: C2C12-control-ins

description:
LKO-ins
RNA-Seq, paired end
Insoluble RNA
Processed data file: myoblast_fractionation_RPKM.txt

source_name: C2C12 mouse myoblast, control, insoluble fraction

value: control


title: Blood from mouse model 10 of pancreatic cancer processed by EpCAM CTC-Chip

description:
MPANC_10.EpCAM
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: mouse pancreatic cancer model, blood, EpCAM CTC-Chip

tag: background/strain

value: FVB

tag: mouse model

value: MPANC 10

value: pancreatic cancer

value: blood

value: EpCAM CTC-Chip

value: circulating tumor cell (CTC)


title: C2C12ribo-shMbnl2

description:
Mbnl2-ribo
RNA-Seq, single end
Ribosome footprints
Processed data file: myoblast_ribo_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl2 depleted, ribosomal fraction

value: ribosomes


title: Input_async_ChIPseq

description:
Rescued subline of G1E expressing a Gata1-estrogen receptor (ER) transgene; recapitulates erythroid differentiation after induction by estradiol treatment for 24hr.
Chomatin IP input, GSM453998

source_name: asynchrnous G1E-ER4+E2 cells

tag: strain

tag: developmental stage

value: Rescued subline of G1E  expressesing a Gata1-estrogen receptor (ER) transgene; recapitulates erythroid differentiation after induction by estradiol treatment for 24hr.


title: Input_mitotic_ChIPseq

description:
Rescued subline of G1E expressing a Gata1-estrogen receptor (ER) transgene; recapitulates erythroid differentiation after induction by estradiol treatment for 24hr.
Chomatin IP input

source_name: mitotic G1E-ER4+E2 cells


title: C2C12-control-mem

description:
LKO-mem
RNA-Seq, paired end
Membrane RNA
Processed data file: myoblast_fractionation_RPKM.txt

source_name: C2C12 mouse myoblast, control, membrane fraction

tag: shRNA


title: C2C12ribo-shMbnl1

description:
Mbnl1-ribo
RNA-Seq, single end
Ribosome footprints
Processed data file: myoblast_ribo_RPKM.txt

source_name: C2C12 mouse myoblast, Mbnl1 depleted, ribosomal fraction

tag: subcellular fraction


title: GATA1_mitotic_ChIPseq

description:
Rescued subline of G1E expressing a Gata1-estrogen receptor (ER) transgene; recapitulates erythroid differentiation after induction by estradiol treatment for 24hr.
Chromatin IP against GATA1

value: GATA1 (Santacruz,clone N6, sc-265)


title: C2C12-control-cyto

description:
LKO-cyto
RNA-Seq, paired end
Cytosolic RNA
Processed data file: myoblast_fractionation_RPKM.txt

source_name: C2C12 mouse myoblast, control, cytosolic fraction


title: MBNL2 KO, biological rep3

status: Public on Aug 16 2012

first: Ranjan

last: Batra

state: California

address: 2880 Torrey Pines Scenic Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
ΔE2/ΔE2_Hippocampus-3
2011-03-22_8_1.fastq & 2011-03-22_8_2.fastq files are technical repliates of 2011-03-22_7_1.fastq & 2011-03-22_7_2.fastq.

data_processing:
Raw sequence reads were mapped back to the mouse reference genome (mm9) together with a comprehensive database of annotated exon junctions compiled from mouse, human, and rat mRNA/EST data.  The program tophat (v1.3.2) with bowtie (v3.4.6) was used for alignment (parameters: -a 5 -F 0.05 -r 150 -j <junction.hmr.raw>)
After read mapping, transcript structure between the sequenced ends could be ambiguous due to alternative splicing, and if this occurs, the structure was inferred using a bayes method by modeling the size distribution of cDNA fragments
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format, with the four columms representing chromosome, start (0-based), end (1-based), and normalized read coverage (FPKM)

source_name: MBNL2 ΔE2/ΔE2 hippocampus

growth_protocol: Hippocampi dissected from MBNL2 ΔE2/ΔE2 mice or WT female mice, 2-3 months of age

extract_protocol: Mice were genotyped and hippocampii were dissected from 3 mutant and 3 wild-type animals. Total RNA was extracted using Trizol and samples were purified with RNeasy™  Kit (Qiagen). Sequencing libraries were prepared after PolyA RNA isolation using mRNA-sequencing kit (Illumina).

tag: strain background

value: C57BL/6 and 129 SvlmJ mixed

tag: genotype/variation

tag: age

value: 2-3 months

value: female

tag: tissue

value: hippocampus


title: MBNL2 KO, biological rep2

tag: gender


title: MBNL2 KO, biological rep1


title: Ascites from mouse model 9 of pancreatic cancer

description:
MPANC_9.Ascites
mRNA
Helicos Digital Gene Expression pipeline. See Pubmed ID 19581875.

source_name: mouse pancreatic cancer model, ascites

value: MPANC 9

tag: disease state

value: ascites from pancreatic tumor


title: WT, biological rep3

source_name: wild-type hippocampus

value: WT


title: WT, biological rep2


title: WT, biological rep1


title: C2C12-control

description:
LKO-100825
RNA-Seq, paired end
PolyA RNA
Processed data file: myoblast_RPKM.txt

source_name: C2C12 mouse myoblast, control

value: control