title: Stau1_KnockDown_PAS-Seq_BiolReplica#2

city: Worcester

first: Alper

last: Kucukural

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description: Sample 27

data_processing:
library strategy: RIPSeq; RNASeq; RiboSeq; PAS-Seq
The libraries mapped using tophat2 after ribosomal reads were removed.
Following parameters were used for tophat mappings; -p 8 -g 1 --no-coverage-search
For PAS_Seq data, bowtie used with following parameters;-p 8 -v 2 -a --strata --best -m 1
The biological replicas were merged for Sonication_Formaldehyde libraries.
The alignment files are converted to bigWig files.
Genome_build: hg18
Supplementary_files_format_and_content: bw; bigWig files were generated from bam and bed format alignments using bedtools coverage and wigToBigWig tools.

growth_protocol: HEK293 Flp-IN T-REx cells (Life Technologies) were grown in DMEM (+ Pyruvate) and 10% FBS and passed (1/10 dilution) every 3 days for a maximum of 15 passages.

extract_protocol:
For RIP-Seq experiments, cells were lysed in hypotonic lysis buffer and sonicated before the IP was performed. For Ribosome footprinting and RNA-Seq experiments, cells were lysed to only obtain the cytoplasmic fraction. For PAS-Seq libraries, cells were lysed in TRIZOL and RNAs extracted.
Ligation of an adaptor to the 3' end of RNA followed by Reverse-Trascription using an adaptor specific primer. After Reverse-Transcription, cDNAs are circularized and PCR amplified using Illumina's PE 1.0 and 2.0 primers.

treatment_protocol: Expression of Stau1-WT and Mutant proteins was induced using doxycyclin 16 hours prior to cell lysis. For formaldehyde crosslinking RIP-Seq experiments, cells we fixed with formaldehyde for 10 minutes and the reaction quenched for 5 minutes prior to cell lysis. For Ribosome footprinting experiments, cells were incubated with Cycloheximide for 10 minutes prior to cell lysis.

tag: protein expressed

value: Poly(A) selected RNA


title: Stau1_Overexpression_PAS-Seq_BiolReplica#2

status: Public on Nov 25 2013

type: SRA

state: MA

country: USA

description: Sample 29

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: Flag-Stau1-WT (65KDa Isoform)

tag: molecule subtype


title: H3K9ac ChIPSeq HAHA_cohort1

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description: H3K9ac ChIPSeq HAHA_cohort1

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm8 genome assembly using Bowtie version 0.12.8 with the following configurations: -n 1 -l 30 -m 1.
Peaks were called using HOMER v4.2 with FDR 0.1%.
Genome_build: mm8
Supplementary_files_format_and_content: BigWig files were preduced by HOMER v4.2 using default parameters.

molecule: genomic DNA

organism: Mus musculus

source_name: H3K9ac ChIPSeq HAHA_cohort1

growth_protocol: Adult male HDAC3 floxed mice were intravenously injected with adeno-associated virus (AAV) expressing Cre along with AAV expressing the indicated HDAC3 mutants.

extract_protocol:
Whole cell lysates were prepared from cross-linked livers. After sonication, histone-DNA complexes were immunoprecipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Seq DNA Sample Prep Kit (Illumina IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mice were fed ad libum and euthanized at 2-weeks after injection at 5 pm (ZT10).

tag: strain

tag: antibody

value: H3K9ac Millipore 06-942 lot#1973414

tag: tissue

value: liver


title: MXB 3DAP

status: Public on Nov 26 2013

city: Tucson

first: Xiangfeng

last: Wang

address: 1140 E. South Campus Drive, Marley Building 541C

department: School of Plant Sciences

institute: University of Arizona

data_processing:
Illumina RTA software used for basecalling.
Raw sequence reads were processed into clean full-length reads using the BGI small RNA pipeline. First, all low-quality reads were removed from the raw sequence, and the 3' adapter reads, 5' adapter contaminants, sequences containing the polyA tail and those smaller than 18 nt were also discarded. The remaining high-quality sequences were counted, and the unique sequences with their associated read counts were mapped to the maize genome to infer siRNA loci.
Genome_build: ZmB73_RefGen_v2.tar.gz
Supplementary_files_format_and_content: Compressed tab-delimited text files include counts and length for each sequence

organism: Zea mays

source_name: maize

growth_protocol: Maize B73 and Mo17 inbred lines were grown under greenhouse conditions. Reciprocal crosses and self-pollination were performed as follows: the ears were bagged before silking; when the silks grew to approximately 2 to 3 cm long, the ears were cut at 2cm from the top and the tassels were bagged. Pollination was conducted on the next day using the corresponding pollen. The un-pollinated kernels (0-DAP) and the kernels from the reciprocal crosses of B73 and Mo17 at 3, 5, 7, 10, and 15-DAP were harvested. Endosperm tissues from the 7, 10, and 15-DAP kernels were manually isolated. The endosperm and kernel were harvested from three different ears as three biological replicates and were immediately frozen in liquid nitrogen.

extract_protocol:
The total RNA was isolated from the 36 (12 samples × 3 replicates) groups of plant material using the Trizol method according to the manufacturer’s instructions.
18-30 nts RNAs were gel-purified from total RNA sample, Illumina 5’ and 3’ RNA adapter were sequentially ligated to the RNA fragments and the ligated products were size-selected on denaturing polyacrylamide gels. The adapter-linked RNA was reverse transcribed with small RNA RT primers and amplified with 15 cycles of PCR using small RNA PCR primer 1 and 2 (Illumina). The libraries were sequenced with the Illumina Genome Analyzer.

value: kernel

tag: age

tag: genotype/variation


title: Stau1_KnockDown_PAS-Seq_BiolReplica#1

description: Sample 26


title: CHIP_DL23_4OHT_4h_H3

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin, 2009). Non-uniquely placed reads were discarded.
Cisgenome v2.0 software package was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes.
Genome_build: hg19
Supplementary_files_format_and_content: alignment file (chr;start;end;strand)

source_name: DL23 cell line with pcDNA3-HA-FOXO33-ER

growth_protocol: DLD1 and DLD1-F3 cells were grown on RPMI-1640 medium with 10% FCS and standard supplements

extract_protocol:
Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD sequencer to produce 50-bp long reads.
4-hydroxy-tamoxifen (4OHT) from Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with PKB inhibitor VIII (Santa Cruz) at a concentration of 10uM. Cells were grown in the absence or 4 hour presence of 4OHT or PKB inhibitor. Three independent batches of chromatin were obtained for all three conditions and mixed, with a total of 80x106 cells per IP. IPs were performed for 16h with the following antibodies: 2.5 ug of H3K4me1, H3K4me3 and H3K27ac and total H3 from Abcam (ab8895, ab8580 and ab4729, ab1791) and 16ug of αFOXO3 (Santa Cruz, H144) for the FOXO3-ER (2) ChIP-seq. The second H3K27ac(2) ChIP-seq was performed on an independent fourth batch of chromatin.

value: DL23 cell line with pcDNA3-HA-FOXO33-ER

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: CHIP_DL23_VIII_4h_H3K27ac


title: Stau1_Overexpression_RibosomeFootprinting_BiolReplica#2

description: Sample 23

value: Ribosome footprint mRNA


title: HEK293_Control_PAS-Seq_BiolReplica#1

description: Sample 24


title: Stau1_Overexpression_RibosomeFootprinting_BiolReplica#1

description: Sample 22


title: Stau1_KnockDown_RibosomeFootprinting_BiolReplica#1

description: Sample 20


title: H3K9ac ChIPSeq YF_cohort2

description: H3K9ac ChIPSeq YF_cohort2

source_name: H3K9ac ChIPSeq YF_cohort2


title: Stau1_KnockDown_RibosomeFootprinting_BiolReplica#2

description: Sample 21


title: HEK293_Control_RibosomeFootprinting_BiolReplica#2

description: Sample 19


title: MN_Mit_pat1.114

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

description: Mononucleosomal DNA

data_processing:
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Matlab “Wavelet Toolbox”, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.
For all the genomic analyses, we have used as a reference the S. pombe genome version of 23/08/07 (http://www.pombase.org/ , ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/).

organism: Schizosaccharomyces pombe

source_name: Mononucleosomal DNA

growth_protocol: For the Mei0h, Mei3h and Mei5h, cells were grown in Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen and 0,05 g/l leucine for 14 h after which NH4Cl was added to 0.5 g/l and leucine concentration was increased to 0,1 g/l.  Samples were taken at 0h, 3h and 5h after transfer to 34 ºC to induce synchronous meiosis. For the Mit sample, cells were grown in rich medium (YES) at 32ºC until OD595=0.8. For the Mit_pat1.114, cells were grown in Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC until OD595=0.8

extract_protocol:
Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (Fermentas #ENO181) to a final concentration of 180 units/ml for 40 minutes at 37 ºC to yield about 90% mononucleosomes. After reverting crosslink DNA of mononucleosomal size was purified from agarose gels.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture type

value: Asynchronous mitosis


title: MN_Mit

description: Mononucleosomal DNA


title: HEK293_Control_RibosomeFootprinting_BiolReplica#1

description: Sample 18


title: Stau1_Overexpression_PAS-Seq_BiolReplica#1

description: Sample 28


title: H3K9ac ChIPSeq KA_cohort1

description: H3K9ac ChIPSeq KA_cohort1

source_name: H3K9ac ChIPSeq KA_cohort1


title: MN_Mei3h

description: Mononucleosomal DNA

value: Synchronous meiosis

tag: time

value: 3 hours


title: MN_Mei5h

description: Mononucleosomal DNA

value: 5 hours


title: Stau1_Overexpression_RNASeq_BiolReplica#2

description: Sample 17

value: Cytoplasmic Poly(A) RNA


title: MN_Mei0h

description: Mononucleosomal DNA

value: 0 hours


title: HEK293_Control_PAS-Seq_BiolReplica#2

description: Sample 25


title: Stau1_KnockDown_RNASeq_BiolReplica#2

description: Sample 15


title: HEK293_Control_RNASeq_BiolReplica#2

description: Sample 13


title: HEK293_Control_RNASeq_BiolReplica#1

description: Sample 12


title: Stau2-WT_RNaseI_Footprinting

description: Sample 10

value: Flag-Stau2-WT (65KDa Isoform)

value: Stau2 associated RNAs


title: Stau1-MUT_Sonication_Formaldehyde_BiolReplica#2

description:
Sample 7
Biological replicates merged in the processed files (Stau1-MUT_Sonication_Formaldehyde.bw)

value: Flag-Stau1-Mutant (65KDa Isoform)

value: Stau1 associated RNAs


title: Stau2-MUT_Rnase_Footprinting

description: Sample 11

value: Flag-Stau2-Mutant (65KDa Isoform)


title: Stau1-MUT_Sonication_Formaldehyde_BiolReplica#1

description:
Sample 6
Biological replicates merged in the processed files (Stau1-WT_Sonication_Formaldehyde.bw)


title: Stau1-WT_Sonication_Formaldehyde_BiolReplica#1

description:
Sample 4
Biological replicates merged in the processed files (Stau1-WT_Sonication_Formaldehyde.bw)

value: Flag-Stau1-WT (65KDa Isoform)


title: Stau1-WT_RNaseI_Footprinting_BiolReplica#2

description: Sample 2


title: Stau1_KnockDown_RNASeq_BiolReplica#1

description: Sample 14


title: Stau1-WT_Sonication_Formaldehyde_BiolReplica#2

description:
Sample 5
Biological replicates merged in the processed files (Stau1-MUT_Sonication_Formaldehyde.bw)


title: Stau1-WT_RNaseI_Footprinting_BiolReplica#1

description: Sample 1


title: MCF-7_E2_50U_200-300bp

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

country: Canada

institute: UNIVERSITY HEALTH NETWORK

description: DNase-seq

data_processing:
Illumina Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.0.0
MACS2 was used to call peaks and generate bigwiggle file
Genome_build: hg19
Supplementary_files_format_and_content: mapped bed file

source_name: Breast cancer cell line MCF-7

growth_protocol: The prostate cancer cell line LNCaP and breast cancer cell line MCF7 were obtained from the American Type Culture Collection. LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin. MCF-7 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
LNCaP and MCF-7 cells were harvested by trypsinization followed by nuclei extraction. Entact nuclei were treated with Dnase I for desired time.
Libraries were prepared according to Rubicon's instructions accompanying the ThruPLEX-FD kit.

treatment_protocol: LNCaP and MCF-7 cells were starved in phenol-red-free medium supplemented with 10% charcoal stripped FBS for 3 days before hormone stimulation.

tag: passage

tag: digestion level

tag: fragment size


title: Stau1-MUT_RNaseI_Footprinting

description: Sample 3


title: L_D_50U_50-300bp_1

description: DNase-seq

source_name: Prostate cancer cell line LNCaP

value: LNCaP


title: L_D_50U_50-300bp_2

description: DNase-seq


title: MCF-7_E2_50U_100-200bp

description: DNase-seq


title: L_V_50U_200-300bp

description: DNase-seq


title: Stau1-MUT_Sonication_Native

description:
Sample 9
Only raw data reported


title: L_D_100U_50-100bp

description: DNase-seq


title: L_V_50U_100-200bp

description: DNase-seq


title: Stau1_Overexpression_RNASeq_BiolReplica#1

description: Sample 16


title: L_D_100U_200-300bp

description: DNase-seq


title: L_D_75U_50-100bp

description: DNase-seq


title: L_D_100U_100-200bp

description: DNase-seq


title: Stau1-WT_Sonication_Native

description:
Sample 8
Only raw data reported


title: L_D_50U_100-200bp

description: DNase-seq


title: L_V_50U_50-100bp

description: DNase-seq


title: L_D_50U_200-300bp

description: DNase-seq


title: Dp1_ChIPSeq_replicate_1

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Chromatin IP against Dp1

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the Drosophila melanogaster genome dm3 (April 2006, BDGP R5/dm3)) using BOWTIE aligner program (version 0.11.3) (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained. Parameter used: --best --strata -m 1 -v 2. Peak calling: Aligned replicate data were merged. Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/), version 1.4.1; and parameter used: --shiftsize=90 --gsize=dm --tsize=36 --bw=450 --wig --single-profile.

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: S2R+ cells were grown in Schneider's Drosophila Medium (Gibco) containing 10% fetal bovine serum (FBS).

extract_protocol: ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101), except that AMPure XP Beads (Beckman Coulter #A63881) were used for purification of DNA fragments as described in TruSeq DNA sample preparation v2 guide (Illumina).

tag: cell type

value: embryonic cells

value: rabbit anti-Dp1


title: Dp1_ChIPSeq-replicate2

description: Chromatin IP against Dp1

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the Drosophila melanogaster genome dm3 (April 2006, BDGP R5/dm3)) using BOWTIE aligner program (version 0.11.3) (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained. Parameter used: --best --strata -m 1 -v 2


title: input DNA

description: input DNA


title: L_D_25U_50-100bp

description: DNase-seq


title: L_D_50U_50-100bp

description: DNase-seq


title: L_D_5U_100-200bp

description: DNase-seq


title: L_D_25U_100-200bp

description: DNase-seq


title: L_D_5U_200-300bp

description: DNase-seq


title: MCF-7_E2_50U_50-100bp

description: DNase-seq


title: L_D_75U_200-300bp

description: DNase-seq


title: L_D_5U_50-100bp

description: DNase-seq


title: SV40 tAg BS-seq Rep1

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: Bisulphite sequencing of cells bypassing senescence

data_processing:
Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to hg18 whole genome using bismark v0.5.1 (bowtie v0.12.7) with directional setting and chunkmbs set to 256.  Remaining default settings.
Multiple reads where both ends of the fragment align to the same genomic positions on the same strand were reduced to a single instance.  Reads with more than 3 methylated cytosines in non-CpG contexts are discarded.
Reads are summarised on a per-CpG basis.
DMRs are computed by filtered to CpGs binomial meth call <= 0.01FDR.  A sliding window was used (2kb) starting at CpG and ending at most distant CpG within 2kb of the start position.  Total G, Pooled G and Heterogenous G (difference between Total G and Pooled G) are calculated for each window and converted to P-values using the chi-square distribution.  P-values are FDR corrected and adjacent windows merged where corrected P-values <= 0.05.  Regions smaller than 5kb are discarded and heterogeneous regions are subtracted from the Pooled G regions.  Resulting Pooled G regions are reported as DMRs.
Genome_build: hg18
Supplementary_files_format_and_content: Summary files represent the number of reads supporting methylated/unmethylated bases at each CpG sequenced in that sample (Format is: chr <tab>  position  <tab>  methylated reads  <tab>   unmethylated reads).  bigWig files represent the percentage methylation at a given CpG (filtered to exclude CpGs with low coverage on a per replicate basis – >=10 reads in at least one sample & >=3 read in the other) and generated using UCSC wigToBigWig.  peak files represent differentially methylated regions at 5% FDR.

source_name: cells bypassing senescence

growth_protocol: IMR-90 cells (Coriell) were grown in Dulbecco’s Modified Eagle Medium, high glucose (Life Technologies) supplemented with 20% Fetal Bovine Serum (FBS), 2mM L-glutamine and 100ug/ml penicillin-streptomycin (Life Technologies) and incubated at 37˚C with 3% (v/v) O2 and 5% (v/v) CO2.

extract_protocol:
DNA was extracted with phenol-chloroform method.
Libraries were prepared by BGI, Shenzhen.  Briefly, DNA is fragmented and methylated adapters are ligated to DNA fragments.  DNA is bisulphite treated and sequenced on Illumina GAIIx/HiSeq platforms as per manufacturers instructions.

treatment_protocol: For Proliferating and Senescent cells no treatment was performed outside the library construction.  To achieve senescence bypass in near senescent IMR90 a SIN human immunodeficiency virus I (lenti) vector expressing the early region (encoding Large and small T-antigen) of Simian virus 40 (SV40) from the CMV-promoter and the gene encoding aminoglycoside phosphotransferase (Neomycin resistance), driven by the SV40 early promoter was generated. After infection IMR90 were cultured in the presence of 500µg/ml G418-sulphate (Invitrogen) for one week, to select for SV40 T-antigen expressing cells.. (encoding Large and small T-antigen) of Simian virus 40 (SV40) from the CMV-promoter and the gene encoding aminoglycoside phosphotransferase (Neomycin resistance), driven by the SV40 early promoter was generated.


title: Senescent BS-seq Rep2

description: Bisulphite sequencing of senescent cells

source_name: senescent cells


title: Proliferating BS-seq Rep3

description: Bisulphite sequencing of proliferating cells

source_name: proliferating cells


title: Proliferating BS-seq Rep2


title: L_D_75U_100-200bp

description: DNase-seq


title: SV40 tAg BS-seq Rep2


title: SV40 tAg BS-seq Rep3


title: Proliferating BS-seq Rep1


title: Senescent BS-seq Rep3


title: Senescent BS-seq Rep1


title: un-induced whiteflies

status: Public on Nov 24 2013

city: Hangzhou

first: Xiaowei

address: 866 Yuhangtang Road

department: Insect Sciences

country: China

institute: Zhejiang University

description: Control

data_processing:
Basecalls performed using BclConverter-1.9.0
Clean tags were generated after removing adaptor sequences, low quality sequences, empty reads and tags with a copy number of <2 using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
A database containing all possible CATG+17 nucleotide tag sequences were created for the transcriptome of the MED species of whitefly using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
Sequencing tags were mapped to the whitefly transcriptome reference database with no more than one nucleotide mismatch using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
The number of unambiguous clean tags for each gene was calculated for gene expression analysis and TPM (number of transcripts per million tags) were used to normalize the data according to the method described by t' Hoen et al (Nucleic Acids Res. 36, e141).
Genome_build: Read alignment was performed against the Mediterranean whitefly transcriptome reference database (BMC Genomics, 11:400. PMID: 20573269).
Supplementary_files_format_and_content: Tab-delimited text files include TPM (number of transcripts per million tags) values for each tag.

organism: Bemisia tabaci

source_name: Adults

growth_protocol: Culture of whiteflies was maintained on cotton plants. Beauveria bassiana spores were harvested after cultivating for nearly 7 days in 27°C, 95% relative humanity and diluted to 10^10 spores/ml using sterile distilled water containing 0.05% Tween-80.

extract_protocol: For each sample, approximately 6 ug mRNA was purified with magnetic oligo (dT) and double strand cDNA were synthesized. The bead bound cDNA was subsequently digested with NlaIII which recognizes the CATG sites. Magnetic beads were used to purify the 3' end cDNA fragments and Illumina adapter 1 was added to their 5' ends. The purified cDNA fragments were digested using MmeI which cuts 17bp downstream of the CATG site thus producing tags with adapter 1. Then, Illumina adaptor 2 was added to the 3’ ends of the tag. After 15 cycles of PCR amplification, 6% TBE polyacrylamide gel electrophoresis was used to purify the tags. After digestion, single strand molecules were added to the Illumina sequencing flowcell and fixed.

treatment_protocol: Nearly 10000 whitefly adults on cotton leave were placed in a Petri dish and spore solution was used to give a spray with Automatic Potter Spray Tower. Nearly 1,000 of control whiteflies, 48h fungal-induced whiteflies and 72h fungal-induced whiteflies were collected, respectively

tag: group

value: Mediterranean (MED, commonly known as Q biotype)

tag: growth protocol

value: maintained on cotton plants

tag: infection

value: no infection

value: control


title: L_D_25U_200-300bp

description: DNase-seq

tag: cell line


title: 72h fungal-induced whiteflies

value: Beauveria bassiana

value: 72 hours


title: 48h fungal-induced whiteflies

value: 48 hours


title: A13P

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

institute: ZheJiang University

data_processing: All alignments were performed using a tool package SOAP2, a program specially designed for next-generation sequencing analysis, allowing up to 2 mismatches. Sequenced reads were respectively aligned to human transcript reference sequences from ENSEMBL database (build 55) for expression evaluation at the level of gene or exon. Reads that unable to be mapped to transcriptome were also aligned to novel exon-exon junction database that was previously developed by our group for detection of new alternative splicing events.After alignment to the transcriptome, the expression level of genes was determined based on the value of RPKM (reads per kilobase per million), which was calculated as the number of reads mapped to the transcripts of one gene divided by the transcript length and the number of total mapped reads in one sample. The expression level of each exon or exon-exon junction was also evaluated by RPKM, similarly calculated as the number of reads mapped to unique exon divided by the exon length and the number of total mapped reads in one sample. Three kinds of statistical analyses were applied to estimate the significance of expression difference, including paired t-test and paired wilcoxon signed rank test based on RPKM value, and a recently proposed software package edgeR (a program specifically designed for analyzing RNA-seq data ) based on read count. The difference with P <0.05 for t test and wilcoxon signed rank test and FDR<0.05 for edgeR was considered as significant. To assess the distribution of DEGs at different expression abundance levels, MA-plot was made.

source_name: Liver tissues, Non-cancerous adjacent

extract_protocol: Total RNAs were extracted from about 60 mg of tissues for each of the 10 paired samples using the mirVana™ miRNA Isolation Kit (Ambion Inc.) according to the manufacturer’s instruction. The RNA yields were quantified by NanoDrop ND1000 (Thermo- Fisher Scientific, Waltham, MA) and the RNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). The RNA integrity number (RIN) of every RNA sample used for sequencing was more than 8. The cDNA libraries for 10 paired samples were constructed using mRNA-Seq Sample Prep Kit based on the Illumina Inc.’s guide. In brief, polyA-containing mRNA was purified using oligo-dT beads from 10ug of total RNAs for each sample and fragmented into small fragments using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed into first strand cDNA using random primers (Invitrogen Inc.), followed by second-strand cDNA synthesis. After end-repair processing, a single ‘A’ base was added to cDNA fragments at 3' end. The cDNAs were then ligated to adapters, purified by 2% agrose gel, and then enriched by PCR to create the final cDNA library.

tag: paired sample id

tag: tissue type

value: Non-cancerous

tag: virus infection

value: HBV


title: A82P


title: A39P


title: A39C

source_name: Liver tissues, Cancer

value: Cancer


title: A60P


title: A63C


title: A63P


title: A13C


title: A82C


title: A60C


title: A57C


title: A35P


title: A35C


title: A31P


title: A05P


title: A19P


title: A05C


title: AY6

status: Public on Nov 23 2013

city: Pittsburgh

first: Andrew

last: Georgiadis

address: 203 Craft Ave.

institute: UPMC

description: Sample 2

data_processing:
Reads from each sample were mapped using Tophat 2.0.6  mapper with Bowtie aligner (Langmead et al. , 2009, Trapnell et al. , 2009) to the most updated reference sequence (hg19).
Expression representation was determined as length-based average coverage values using our in-house software RNASeqnator (Sethi & Lyons-Weiler, personal communication). RNASeqnator renders a ‘gene-level’ analysis for all exons reported under any NCBI identifier to co-occur in an mRNA transcript.  This is conducted as a ‘superset’, and we therefore refer to that measurement as a “supertranscript”, or ST, analysis. ST measurements were compared between groups using methods selected by Efficiency Analysis (Jordan et al. , 2008).  Efficiency analysis points to transformation and normalization methods, and to tests for difference, that are optimally reproducible using a re-sampling scheme.
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing cube root normalized coverage; Efficiency analysis indicated that median/mean normalization followed by cube root transformation was highly reproducible (internally consistent) compared to other methods for studying differential expression.

source_name: semen

extract_protocol:
For improved total RNA isolation, the ejaculate was incubated at 37⁰C or immediately washed with an equal volume of Sperm Washing Medium, at 37⁰C (SWM, Irvine, Santa Ana, CA). SWM contains 21 mM HEPES buffer, 4 mM Sodium Bicarbonate, and 5 mg/mL Bovine Serum Albumin.  The cell mixture was spun at 680 x g for 12 minutes. Supernatant was removed and the sperm pellet was resuspended in the residual liquid. The samples were subjected to minimal mixing and spinning in order to preserve RNA. Cell suspensions were completely homogenized by vigorous vortexing and used for RNA isolation with warmed (37⁰C) TRIzol reagent (Life Technologies, Carlsbad, CA).  RNA was isolated according to the manufacturer (Invitrogen) and the RNA pellet was resuspended in RNase-free water. Total RNA was DNase treated and purified using an RNeasy Mini Kit spin column (Qiagen) and diluted in RNase-free water.
Ribosomal RNA reduction was carried out via the RiboMinus Eukaryote Kit for RNA-Seq (Life Technologies). 500 ng of ribosomal-free RNA and random primers were used for whole transcriptome library preparation in total RNA-Seq protocol (Life Technologies). Final libraries were quantified using qPCR NGS Library Quantification Kit (AB SOLiD, Life Technologies).  Equimolar amounts of each cDNA library were pooled and ePCR was performed using the EZBead system (Life Technologies). Enriched templated beads were applied to AB SOLiD flow cell and 75 bp sequencing reads were collected using the Solid 5500xl sequencer (Life Technologies).

tag: tissue

value: whole semen

tag: phenotype

value: Normozoospermic

tag: molecule subtype

value: rRNA depleted total RNA


title: A31C


title: Asia II 3

description: ZHJ1 biotype

data_processing:
Basecalls performed using BclConverter-1.9.0
Clean tags were generated after removing adaptor sequences, low quality sequences, empty reads and tags with a copy number of <2 using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
The common tags of MEAM1, MED and Asia II 3 species were filtered out using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
To get the orthologous genes, all common tags were mapped to the transcriptome reference database of MEAM1, MED and Asia II 3 and allowed no mismatch using a custom written Perl program developed by Beijing Genome Institute (BGI, Shenzhen, China).
The number of unambiguous clean tags for each gene was calculated for gene expression analysis and TPM (number of transcripts per million tags) were used to normalize the data according to the method described by t' Hoen et al (Nucleic Acids Res. 36, e141).
Genome_build: Read alignment was performed against the MEAM1, MED and Asia II 3 whitefly transcriptome reference database (BMC Genomics, 11:400; BMC Genomics, 12:458; BMC Genomics, 13:529).
Supplementary_files_format_and_content: Tab-delimited text files include TPM (number of transcripts per million tags) values for each tag.

source_name: Asia II 3 species (previous known as ZHJ1 biotype)

growth_protocol: To prepare pure whitefly cultures, a pair of virgin adult whiteflies of MEAM1, MED or Asia II 3 was separately released onto cotton plant to oviposit and develop for five generations.

extract_protocol:
Total RNA was isolated using SV total RNA isolation system (Promega) and mRNA was purified from 6 µg of the total RNA from each of the samples with magnetic oligobeads.
For each sample, approximately 6 mg mRNA was purified with magnetic oligo (dT) and double strand cDNA were synthesized. The bead bound cDNA was subsequently digested with NlaIII which recognizes the CATG sites. Magnetic beads were used to purify the 3' end cDNA fragments and Illumina adapter 1 was added to their 5' ends. The purified cDNA fragments were digested using MmeI which cuts 17bp downstream of the CATG site thus producing tags with adapter 1. Then, Illumina adaptor 2 was added to the 3’ ends of the tag. After 15 cycles of PCR amplification, 6% TBE polyacrylamide gel electrophoresis was used to purify the tags. After digestion, single strand molecules were added to the Illumina sequencing flowcell and fixed.

treatment_protocol: To prepare whitefly samples, approximately 3,000 newly emerged whiteflies from each species were released onto the leaves of two cotton plants in different cages. After feeding for 24 h, approximately 500 female adults were separately collected for each species.

tag: strain

value: Whole body

tag: growth condition

value: maintained on cotton

tag: developmental stage

value: Adults


title: MEAM1

description: B biotype

source_name: Middle East Asia Minor 1 species (previous known as B biotype)


title: AY4

description: Sample 1


title: MED

description: Q biotype

source_name: Mediterranean species (previous known as Q biotype)


title: Polysomal_stress2

city: Chatujak

first: Piyada

last: Juntawong

state: Bangkok

address: 50 Ngamwongwan rd.

department: Genetics

country: Thailand

institute: Kasetsart University

description: Immunoprecipitated (TRAP)-polysomal mRNA, poly(A)+ selected.

data_processing:
Base calling performed with Illumina CASAVA version 1.8.
R/Bioconductor (version 2.15.1) and ShortRead package (Morgan et al., 2009) were used in short read preprocessing steps (demultiplexing FASTQ files, adaptor trimming, quality assessment and filtering of reads).
The processed short reads were mapped to the Arabodopsis genome (Version TAIR10) using TopHat v1.3.1 (Trapnell et al., 2009) with command "tophat -p 8 -g 1 --segment-length 15 -i 30 -I 3000 -G".
Read count data in terms of RPKM (reads per kilobase per million) were calculated for each specific mRNA feature.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include abundance measurements (RPKM values) for each mRNA feature (uniquely mapped and multi-mapped).

organism: Arabidopsis thaliana

source_name: 7 d.o. whole seedlings, 2 hr. hypoxia, immunoprecipitate (TRAP)-polysomal mRNAs

growth_protocol: Seedlings were grown on solid media containing 0.43% (w/v) Murashigi Skoog salts, 1% (w/v) sucrose, and 0.6% (w/v) phytagel, pH 5.7-5.8 in a growth chamber (Percival) at 23 °C under 16 h light (80 μE m-2 sec-1) and 8 h dark cycle for 7 d.

extract_protocol:
Polysome extraction was performed using 5 mL of pulverized frozen tissue homoginized in 10 mL Polysome Extraction Buffer (PEB: 200 mM Tris-HCl [pH 9.0], 200 mM KCl, 36 mM MgCl2, 25 mM EGTA, 5 mM DTT, 1 mM phenylmethanesulfonylfluoride, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol, 1% (v/v) Triton X-100, 1% (v/v) polyoxyethylene (23) lauryl ether, 1% (v/v) Tween-40, 1% (v/v) Nonidet P-40, 1% (v/v) Polyoxyethylene 10 tridecyl ether). After removal of cell debris by centrifugation at 16,000g at 4 °C for 15 min, the crude cell supernatant (S16 fraction) was filtered through sterilized Miracloth (Calbiochem, La Jolla, CA) and 500 μL was saved for extraction of total RNA. The pass-through supernatant was added to EZview Red ANTI-FLAG M2 Affinity Gel (clone M2, Sigma, cat# F2426) (500 μL) that was pre-washed twice with Wash Buffer (WB: 200 mM Tris-HCl [pH 9.0], 200 mM KCl, 36 mM MgCl2, 25 mM EGTA, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). Binding of FLAG-epitope-tagged ribosome-mRNA complexes was by incubation at 4 °C for 2 h with gentle rocking. The supernatant was removed and the gel were washed 4 times by resuspension in 10 mL WB buffer and centrifuged to discard the wash solution. Ribosome-mRNA complex elution was performed by incubation of the washed gel in 1 mL WB buffer with addition of 200 ng/μL 3xFLAG peptide (Sigma) and 20 U/mL of SUPERase·In (Ambion) RNase inhibitor at 4 °C for 30 min. Total and immunopurified polysomal RNA were extracted by use of TRIzol reagent (Invitrogen) according to manufacturer's instruction. Two methods were used for ribosome footprint isolation. First, ribosome footprints (RFs) were generated from ribosomes obtained by differential centrifugation. In the second, RFs were obtained by TRAP. For isolation of RFs by differential centrifugation, approximately 15 mL pulverized frozen tissue and 30 mL PEB were used to obtain the S16 fraction. The S16 fraction was layered on top of a 1.75 M sucrose cushion (400 mM Tris-HCl [pH 9.0], 200 mM KCl, 30 mM MgCl2, 1.75 M sucrose, 5 mM DTT, 50 μg/mL chloramphenicol, 50 μg/mL cycloheximide) and centrifuged at 170,000g for 18 h at 4°C in a 70Ti rotor (Beckman) to obtain a polysome pellet (P170). The P170 fraction was resuspended in 300 μL of RNase I Digestion buffer (RNID: 20 mM Tris-HCl [pH 8.0], 140 mM KCl, 35 mM MgCl2, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). The optical density (Absorbance at 260 nm) was determined by use of a Nanodrop1000 (Thermo Scientific). Approximately 2000 OD units of polysome were used in a nuclease digestion to obtain RFs, by use of 10 U of RNase I (Ambion) per 100 units of polysomes. Digestion was carried out for 2 h at room temperature with gentle mixing. The reaction was stopped by addition of 50 U SUPERase·In. The sample was loaded on top of a 20-60% sucrose gradient (Kawaguchi et al., 2005) which was centrifuged at 4°C in a SW55Ti rotor (Beckman) at 250,000g for 1.5 h. The UV absorbance profile of the gradient was evaluated by use of a model UA-5 ISCO UV detector (Teledyne ISCO, Lincoln, NE). Fractions corresponding to 80S monosome region, containing the ribosomes produced by digestion, were collected and RNA was isolated by use of TRIzol reagent according to manufacturer's instruction. As a control, a mock digested sample and untreated samples were fractionated on sucrose density gradients in the same manner. For isolation of ribosome complexes obtained by TRAP, approximately 5 mL pulverized frozen tissue and 10 mL PEB were used to obtain the S16 fraction. The immunopurification procedure was carried out as described previously with an exception that WB was replaced by RNID. In-gel RNase I digestion was performed by resuspension of the washed gel in 400 uL RNID buffer with addition of 250 U RNase. The mixture was incubated for 2 h at room temperature with gentle rocking. RFs were extracted by use of TRIzol reagent according to manufacturer's protocol.
For the construction of ribosome footprint libraries, the oligo-dT tailing method described by Ingolia et al. (2009, 2010) was used with some adaptations for plant samples. Small RNA fragments (<200nt) including RFs were obtained by size-selection. RNA was resuspended in 500 μL RNase-free water with 30 unit SUPERase·In and purified by passage through Ultra-4 centrifugal filters at 750g for 30 min at 4°C. The flow-through was recovered and RNA was precipitated with isopropanol. The RFs were further separated on 17% 7 M urea denaturing polyacrylamide gel electrophoresis in 0.5x TBE and stained with SYBR Gold (Invitrogen). The gel region corresponding to nucleotide fragments of 25-35 nt was excised and the nucleic acid eluted from the gel pieces by crushing and soaking in 300 mM NaOAc [pH 5.2], 1 mM EDTA, 0.1 unit SUPERase·In overnight at 4 °C. After removal of the gel pieces, RNAs were precipitated with isopropanol method with addition of 20 μg glycogen (Ambion). RNA samples were resuspended in 10 μL RNase-free water, heated for 2 min at 75 °C, and quickly chilled on ice. The dephosphorylation of the 3' terminus was carried out in a 30 μL reaction containing 1x T4 polynucleotide kinase buffer, 10 units SUPERase·In, and 15 units T4 polynucleotide kinase (NEB) at 37 °C for 1 h. RNAs were precipitated and resuspened in 11.25 μL RNase-free water. Resuspended RNAs were heated at 75 °C for 2 min and kept on ice. The polyadenylation of the 3' end was preformed in 25 μL poly(A) tailing reaction containing 1x poly(A) polymerase buffer, 0.5 mM ATP, 6 units SUPERase·In and 1.5 units poly(A) polymerase (NEB) at 37 °C for 10 min. The reaction was quenched by addition of 1.3 μL 250 mM EDTA. RNAs were precipitated with isopropanol, resuspended in 11 μL RNAse-free water and used for cDNA synthesis with oligo-dT linker (oNTI225: 5' phos-GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCCGTATCATT/internalSpacer18/CACTCA/internalSpacer18/CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3'). In brief, poly(A) tailed RNAs were mixed with 1 μL of 10 mM (each) dNTPs and 1 μL of 2 pM oNTI225 linker heated at 5 min at 65 °C to denature and quickly chilled on ice. To the reaction, 4 μL 5X First Strand Buffer, 1.0 μL SUPERase·In, 1.0 μL 100 mM DTT, and 1.0 μL SuperScript III (Invitrogen) were added and incubated 30 min at 48 °C. The reaction was heat-inactivated for 15 min at 98 °C, separated on a 10% 7M urea denaturing polyacrylamide gel in 0.5x TBE, and stained with SYBR Gold. The region corresponded to nucleotide fragments of 130 nt was excised, eluted from the gel by use of a crushing and soaking method, and precipitated as described previously. The cDNA pellets were resuspended in 15 μL RNase free water and subjected to single strand DNA circularization. The circularization reaction (20 μL) contained 1x CircLigase buffer, 1 μL of 1 mM ATP, 1 μL of 50 mM MnCl2, and 1 μL (100 units) of CircLigase enzyme (Epicentre Biotechnologies). The reaction was incubated at 60 °C for 1 h and heat-inactivated at 80 °C for 10 min. Contaminating rRNA fragments were partially removed by subtractive hybridization. This was performed with biotinylated oligos corresponding to rRNA fragments abundant in initial RF libraries: (rRNA1 (AT2g01020, AT3G41768) 5'/5BioTEG/CATAAACGATGCCGACCAGGGATCAGCGG-3'; rRNA2: (AT3G41768) 5'-/5BioTEG/TTTATTAGATAAAAGGTCGACG-3'). We have subsequently done subtraction with oligonucleotides antisense to additional contaminating rRNA and tRNA fragments, further reducing background sequences in libraries. Briefly, 5 μL of the circularization reaction was combined with 1 μL of 20x SSC, 1 μL of 200 μM subtraction pool (combination of rRNA1 and rRNA2 biotinylated oligos), and 3 μL water, denatured at 100 ° C for 90 sec, and annealed to 37 °C in a thermal cycler. The biotinylated oligo/rRNA hybrids were recovered using Dynabeads MyOne Streptavidin C1 (Invitrogen) using 0.25 mg beads/sample according to manufacturer's instructions. The RFs of the subtracted libraries were precipitated as described above and resuspended in 20μL water. PCR amplification of libraries was performed in an 83.5 μL reaction that consisted of 1x Phusion HF buffer, 1.7 μL of 10 mM (each) dNTPs, 0.8 μL of 50 mM (each) library primers (oNTI200: 5'-CAAGCAGAAGACGGCATA3-'; oNTI201: 5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3'), 58.4 μL water, 0.8 μL Phusion HF polymerase (NEB), and 5 μL rRNA subtracted circularized template. Amplification was performed as follows: 30 sec at 98 °C; 15 cycles of 10 sec at 98 °C, 10 sec at 60 °C, and 5 sec at 72 °C. PCR products were separated on a 3 % low melting agarose gel in 1x TAE. The amplified RF library (~120-125 bp) was excised and subjected to gel purification by use of the Qiagen MinElute Gel Extraction Kit (Qiagen). For construction of total and polysomal mRNA Fragment Libraries, polyadenylated mRNAs were extracted from total and polysomal RNAs (15 - 80 μg) by Oligo-dT DynaBead (Invitrogen) purification according to manufacturer's instructions. Purified RNAs were eluted in 20 μL RNase-free water and subjected to partial alkaline hydrolysis according to Ingolia et al. (2009) with slight modification. One volume of poly(A) mRNA was combined with an equal volume of 2x fragmentation buffer (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3), incubated 40 min at 95 °C, and quenched immediately on ice. Randomly fragmented mRNAs were precipitated by the isopropanol method and resuspended in 10 μL RNase-free water. RNAs were size-selected on 17% of 7 M urea denaturing polyacrylamide gel in 0.5x TBE. The regions corresponded to 25-35 nt were cut and RNAs were eluted from gel pieces as described previously. The fragmented RNAs were subjected to 3' end dephosphorylation and 5' end phosphorylation, respectively. Dephosphorylation was performed as described previously. The phosphorylation reaction contained 1x T4 polynucleotide kinase buffer, 10 units SUPERase·In, 15 nM ATP, and 15 units T4 polynucleotide kinase (NEB) at 37 °C for 1 h following by RNA precipitation and resuspension in 4.1 μL RNase-free water. Sequencing libraries were constructed by use of NEXTflex Small RNA Sequencing Kit (Bioo Scientific) and NEXTflex Small RNA Barcodes – Set A (Bioo Scientific) according to manufacturer's protocols. Libraries were subjected to quality control runs by evaluation of RF size and quantity on an Agilent 2100 Bioanalyzer. Total and polysomal mRNA-seq libraries were combined in equal molar amounts for library multiplexing.

treatment_protocol: Hypoxia treatment was started at the end of the day in a plexiglass chamber supplemented with 99.99% (v/v) argon for 2 hr under low light (7 μE m-2 sec-1). Normoxia samples were kept in air under the same light and humidity conditions.

tag: ecotype/background

tag: line

value: transgenics 35S:HF-RPL18B line 12-2-4

tag: age

value: 7 days

value: whole seedlings

tag: treatment

value: 2 hr. hypoxia

tag: replicate

tag: adaptor

value: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC


title: A57P


title: Polysomal_no_stress2

source_name: 7 d.o. whole seedlings, 2 hr. normoxia, immunoprecipitate (TRAP)-polysomal mRNAs

value: 2 hr. normoxia


title: A19C


title: Polysomal_no_stress1


title: Total_stress2

description: Total mRNA, poly(A)+ selected.

source_name: 7 d.o. whole seedlings, 2 hr. hypoxia, total mRNAs


title: Polysomal_stress1


title: Total_no_stress2

description: Total mRNA, poly(A)+ selected.

source_name: 7 d.o. whole seedlings, 2 hr. normoxia, total mRNAs


title: Total_no_stress1

description: Total mRNA, poly(A)+ selected.


title: IP_RS_NoStress

description: Ribosome footprint of ribosomes obtained by immunoprecipitation (TRAP), taking advantage of the RPL18-FLAG incorporated into ribosomes in this genotype.

data_processing:
Library strategy: Ribo-Seq
Base calling performed with Illumina CASAVA version 1.8.
R/Bioconductor (version 2.15.1) and ShortRead package (Morgan et al., 2009) were used in short read preprocessing steps (demultiplexing FASTQ files, adaptor trimming, quality assessment and filtering of reads).
The processed short reads were mapped to the Arabodopsis genome (Version TAIR10) using TopHat v1.3.1 (Trapnell et al., 2009) with command "tophat -p 8 -g 1 --segment-length 15 -i 30 -I 3000 -G".
Read count data in terms of RPKM (reads per kilobase per million) were calculated for each specific mRNA feature.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include abundance measurements (RPKM values) for each mRNA feature (uniquely mapped and multi-mapped).

source_name: 7 d.o. whole seedlings, 2 hr. normoxia, immunoprecipitate (TRAP)-ribosome footprints


title: RS_NoStress3

description: Ribosome footprint of ribosomes obtained by sucrose gradient centrifugation.

source_name: 7 d.o. whole seedlings, 2 hr. normoxia, ribosome footprints


title: RS_Stress1

source_name: 7 d.o. whole seedlings, 2 hr. hypoxia, ribosome footprints


title: RS_NoStress2


title: Total_stress1

description: Total mRNA, poly(A)+ selected.


title: MeiosisReleaseIME4plus90min_IP

status: Public on Nov 22 2013

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Reads were initially mapped against all SK1 ribosomal RNA (rRNA) sequences using Bowtie (version 0.12.7), and all reads aligning to the rRNA were discarded. All remaining reads were aligned against the SK1 genome using Tophat (version 1.4.1). Parameters used were ‘--max-multihits 1 –prefilter-multihits’ and ‘–transcriptome-index’, for which we assigned a pre-indexed version of the SK1 transcriptome. An in-house script was then used to cast all reads aligning to the genome upon the SK1 transcriptome. Only reads fully matching a transcript structure, as defined by the transcriptome annotation, were retained. Such reads were computationally extended in transcriptome space from the beginning of the first read to the end of its mate, and coverage in transcriptome-space was calculated for each nucleotide across all transcripts.
Peak detection within genes. To search for enriched peaks in the m6A IP samples,   we scanned each gene using sliding windows of 100 nucleotides with 50 nucleotides overlap. Each window was assigned a score, corresponding to the fold of the mean coverage in the window over the median coverage across the gene. Windows with scores greater than 4 (i.e. greater than 4-fold enrichment) and with a mean coverage >10 reads were retained. Overlapping windows were merged together, and for each disjoint set of windows in transcriptome space we recorded its start, end, and peak position (corresponding to the position with the maximal coverage across the window), and its peak score (corresponding to the fold-change of enrichment in coverage over the median gene level).
Ensuring that peaks were absent in input. We repeated the same steps for the input sample. We eliminated from all subsequent analysis all windows that were detected in both step 1 and in step 2.
Comparison of multiple samples. To identify peaks that were robustly present across multiple replicates of wild-type samples but absent in the ime4∆/∆ negative control samples, we applied the following strategy. We first merged the coordinates of all windows from all samples passing step 1 and 2, to define a set of disjoint windows passing these filters in at least one of the samples. For each such window, we recalculated the peak start, end, and peak position and peak score across each of the samples using the approach in step 1. To identify IME4 dependent peaks in S. cerevisiae, we required that (i) the peak is detected in at least two of three replicates, (ii) the distribution of peak scores across the wild-type samples is significantly different from its counterpart in the ime4∆/∆ samples (Student’s t-test, P value < 0.05), and (iii) the mean peak score across the WT replicates is at least 3-fold greater than the mean peak score in the ime4∆/∆ samples.
Genome_build: yeast sk1
Supplementary_files_format_and_content: bed

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Time Course Meiosis ReleaseIME4plus90min IP

growth_protocol: To induce synchronous meiotic entry, cells were pre-selected on 1% yeast extract, 2% peptone, 3% glycerol, 2% agar for 24 hours at 30°C, grown for 24 hr in 1% yeast extract, 2% peptone, 4% dextrose at 30°C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 hr at 30°C, 300 rpm. Cells were then washed once with water and re-suspended in SPO (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30°C at 190 rpm. Cells were isolated from SPO at the indicated times, collected by centrifugation, re-suspended in pre-warmed 1% yeast extract, 2% peptone, 2% dextrose and incubated at 30°C at 190 rpm. For ectopic expression of the MIS complex, cells were collected after 150 minutes of mitotic growth in the presence of cupric sulfate, induced with 100 µM CuSO4 in rich complete synthetic media (2% glucose).

extract_protocol:
RNA was extracted from cells using a standard hot acid phenol protocol. Briefly, cell pellets were resuspended in equal volumes of acid phenol:chloroform 5:1 pH 4.3-4.7 (Sigma), buffer AE (50 mM sodium acetate, 10mM EDTA 1% SDS) and glass beads. This mixture was vortexed for 15 minutes, followed by a 15 minute incubation at 65°C. Samples were centrifuged for 10 minutes (12,000g, 4°C); the supernatant isolated, re-extracted with phenol:chloroform::5:1, and precipitated with sodium acetate and isopropanol. Enrichment of polyadenylated RNA (polyA+ RNA) from total RNA was performed using Oligo(dT) dynabeads (Invitrogen) according to the manufacturer’s protocol. The mRNA was chemically fragmented into ~80-nt-long fragments using RNA fragmentation reagent (Ambion). The sample was then subjected to Turbo DNAse treatment (Ambion), followed by a phenol-chloroform extraction, and resuspension in 20 μl of  IPP buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5). 25 μl of protein-G magnetic beads were washed and resuspended in 200 μl of IPP buffer, and tumbled with 3 μl of affinity purified anti-m6A polyclonal antibody (Synaptic Systems) at room temperature for 30 minutes. Following 2 washes in IPP buffer, RNA was added to the antibody-bead mixture, and incubated for 2 h at 4°C. The RNA was then washed twice in 200 μl of IPP buffer, twice in low-salt IPP buffer (50 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5), and twice in high-salt IPP buffer (500 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5), and eluted in 30 μl RLT (Qiagen). To purify the RNA, 20 μl MyOne Silane Dynabeads (Life Technologies) were washed in 100 μl RLT, resuspended in 30 μl RLT, and added to the eluted RNA. 60 μl 100% ethanol was added to the mixture, the mixture attached to the magnet and the supernantant discarded. Following two washes in 100 μl of 70% ethanol, the RNA was eluted from the beads in 160 μl IPP buffer. Eluted RNA was subjected to an additional round of IP, by re-incubating it with protein-A magnetic beads coupled to anti-m6A antibody, followed by washes, elution from the protein-A beads and purification as above, followed by elution from the MyOne silane dynabeads in 10 μl H20.
Strand-specific m6A RNA-seq libraries were generated as described in (Engreitz et al., 2013). Briefly, RNA was first subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3’ ligation of an RNA adapter using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed using AffinityScript Multiple Temperature Reverse Transcriptase (Agilent), and the cDNA was subjected to a 3’ ligation with a second adapter using T4 ligase. The single-stranded cDNA product was then amplified for 9-14 cycles in a PCR reaction. Libraries were sequenced on Illumina Miseq, HiSeq 2000 and/or HiSeq 2500 platforms generating paired end reads (25 or 30 bp from each end, depending on the platform).

tag: strain info

tag: antibody

value: anti-m6A (synaptic sytems)


title: RS_Stress3


title: IP_RS_Stress

source_name: 7 d.o. whole seedlings, 2 hr. hypoxia, immunoprecipitate (TRAP)-ribosome footprints


title: MeiosisReleaseIME4plus105min_IP

source_name: Time Course Meiosis ReleaseIME4plus105min IP


title: MeiosisReleaseIME4plus60min_input

source_name: Time Course Meiosis ReleaseIME4plus60min input


title: MeiosisReleaseIME4plus105min_input

source_name: Time Course Meiosis ReleaseIME4plus105min input


title: MeiosisReleaseIME4plus30min_input

source_name: Time Course Meiosis ReleaseIME4plus30min input


title: MeiosisReleaseIME4plus60min_IP

source_name: Time Course Meiosis ReleaseIME4plus60min IP


title: MeiosisReleaseIME4plus0min_IP

source_name: Time Course Meiosis ReleaseIME4plus0min IP


title: MeiosisReleaseIME4plus30min_IP

source_name: Time Course Meiosis ReleaseIME4plus30min IP


title: WTrep2_IP

source_name: WT Replicate 2 IP


title: KAN1 negative 2

city: Tuebingen

first: Felix

last: Ott

address: Spemannstr. 35-39

country: Germany

institute: Max Planck Institute for Developmental Biology

data_processing:
Base calling: Illumina SCS/RTA version 2.8
Demultiplexing, read filtering and trimming: SHORE import version 0.8 (shore.sf.net). Filtering parameters: “-n 10% -c -k 32”
Read mapping: SHORE mapflowcell version 0.8 (shore.sf.net) utilizing GenomeMapper version 0.4.4 (http://1001genomes.org/software/genomemapper.html). mapflowcell alignment parameters “-n 4 --select=10,11,12,13 --restrict=on”
Peak calling: SHORE peak version 0.8 (shore.sf.net). Simultaneous peak calling on both replicates using default peak calling parameters, TAIR10 genome annotation file provided via “-a”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text table (see README.txt)

source_name: KAN1 negative 2

growth_protocol: 10 days in liquid culture

extract_protocol:
Brandt et al., Plant Journal 2012
Illumina ChIP-Seq multiplex

treatment_protocol: 45 minutes DEX treatment

tag: ecotype

value: input


title: KAN1-FLAG replicate 2

source_name: KAN1-FLAG replicate 2

value: Sigma anti-FLAG magnetic beads (Product No. A2220)


title: KAN1 negative 1

source_name: KAN1 negative 1


title: EarlyMeiosisIME4plus1hr_IP

source_name: Time Course Early MeiosisIME4plus1hr IP


title: EarlyMeiosisIME4plus3hr_input

source_name: Time Course Early MeiosisIME4plus3hr input


title: MeiosisReleaseIME4plus90min_input

source_name: Time Course Meiosis ReleaseIME4plus90min input


title: RNA-seq-PFG

city: Stanford

first: Kyle

middle: M.

last: Loh

state: CA

address: 265 Campus Drive

department: Department of Developmental Biology

institute: Stanford University School of Medicine

data_processing:
For RNA-seq, sequenced read were aligned using Tophat  and FPKM (fragments per kilobase of exon per million mapped reads) calculated using Cufflinks
Genome_build: hg19

source_name: hESC derived anterior foregut (PFG)

growth_protocol: Most hESC lines employed in this study were originally cultured on irradiated mouse embryonic fibroblast (MEF) feeder layers. To adapt hESC lines to feeder-free culture, MEF-grown hESCs were initially transferred onto Matrigel-coated plates and propagated in MEF-conditioned medium (CM). hESCs were continually passaged on Matrigel-coated plates in MEF-CM until they efficiently could plate on Matrigel (in lieu of a feeder layer) and until residual irradiated MEFs were eliminated after serial passaging to prevent feeder carryover into future defined culture conditions.All hESC and hiPSC lines were propagated feeder-free in mTeSR1. Differentiation was conducted feeder-free in fully-defined. Prefacing differentiation, confluent hPSC cultures were passaged as small clumps with collagenase IV (typically 1:3 split ratio) onto new plates coated with either human fibronectin or Matrigel. After 1-2 days of recovery in mTeSR1, hPSCs were washed with F12 (Gibco) to evacuate all mTeSR1 and then were treated for 24 hours with Activin A (100 ng/mL, R&D Systems), CHIR99021 (2 μM, Stemgent), and PI-103 (50 nM, Tocris) in CDM2 to specify APS. Afterwards, cells were washed (F12), then treated for 48 hours with Activin A (100 ng/mL), LDN-193189/DM3189 (250 nM, Stemgent), and optionally, also FGF2 (10 ng/mL, Invitrogen) in CDM2 to generate DE by day 3. Media was refreshed every 24 hours. Day 3 DE was patterned into AFG, PFG, or MHG by 4 days of continued differentiation in CDM2. DE was washed (F12), then differentiated as follows: AFG, A-83-01 (1 μM, Tocris) and DM3189 (250 nM); PFG, RA (2 μM, Sigma) and DM3189 (250 nM); MHG, BMP4 (10 ng/mL, R&D Systems), CHIR99021 (3 μM), and FGF2 (100 ng/mL), yielding day 7 anteroposterior domains.

extract_protocol:
For RNA-seq, RNA was harvested from adherent cells grown in individual wells of a 12-well plate by  the addition of 350 μL of RLT Buffer for several minutes. RNA could be indefinitely  frozen at -80 °C or could be directly extracted. RNA extraction was conducted with the  RNeasy Micro Kit (Qiagen) generally as per the manufacturer’s recommendations,  however with an intermediate 1 hour on-column DNase digestion to eliminate residual  genomic DNA, and RNA was finally eluted from the column in 30 μL H2O.
RNA-seq library construction was conducted with the TruSeq RNA Library Preparation Kit (Illumina) as per the manufacturer’s instructions.

tag: cell type

value: hESC derived anterior foregut (PFG)


title: RNA-seq-AFG

source_name: hESC derived anterior foregut (AFG)

value: hESC derived anterior foregut (AFG)


title: RNA-seq-APS

source_name: hESC derived anterior primitive streak (APS)


title: EarlyMeiosisIME4plus2hr_IP

source_name: Time Course Early MeiosisIME4plus2hr IP


title: EarlyMeiosisIME4plus3hr_IP

source_name: Time Course Early MeiosisIME4plus3hr IP


title: EarlyMeiosisIME4plus2hr_input

source_name: Time Course Early MeiosisIME4plus2hr input


title: EarlyMeiosisIME4plus1hr_input

source_name: Time Course Early MeiosisIME4plus1hr input


title: ChIP-seq-MHG-H3K27ac

data_processing:
For chip-seq, sequenced reads were mapped to the hg19 human reference genome using Bowtie, allowing up to 3 bp mismatches and discarding reads mapping to more than 1 genomic locus.
Chip-seq peak detection was done using DFilter (Kumar et al., Nature biotechnology, 2013)
The Chip-seq wiggle tracks were made using MACS and visualization was performed using the Integrative Genomics Viewer from the Broad Institute.
Genome_build: hg19

source_name: hESC derived anterior foregut (MHG)

extract_protocol:
For Chip-seq, Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.  Antibodies were eluted from beads and formaldehyde cross-linking was reversed overnight by mild heating (65 °C),  and chromatin was sequentially treated with RNase and Proteinase K before final  column purification.
Illumina sequencing libraries were generated using the TruSeq ChIP Sample Preparation Kit (Illumina). Briefly, 10 ng of ChIP-enriched DNA was end-repaired, 3’ adenylated, ligated with Illumina adapters, and amplified through 15 cycles of PCR amplification with Phusion High Fidelity DNA polymerase (Finnzymes) with primers directed against the adapters.

value: hESC derived anterior foregut (MHG)

tag: chip antibody

value: H3K27ac (abcam, ab4729)


title: EarlyMeiosisIME4plus45min_IP

source_name: Time Course Early MeiosisIME4plus45min IP


title: EarlyMeiosisIME4plus30min_IP

source_name: Time Course Early MeiosisIME4plus30min IP


title: RNA-seq-H7-ESC

source_name: H7-Embryonic stem cell

value: H7 - Embryonic stem cell


title: RNA-seq-DE

source_name: hESC derived definitive endoderm cells

value: hESC derived definitive endoderm cells


title: ChIP-seq-MHG-H3K27me3

value: H3K27me3 (Millipore/upstate , 07-449 )


title: EarlyMeiosisIME4plus30min_input

source_name: Time Course Early MeiosisIME4plus30min input


title: ChIP-seq-MHG-H3K4me3

value: H3K4me3 (abcam, ab8580)


title: ChIP-seq-MHG-H3K4me2

value: H3K4me2(abcam, ab32356)


title: KAN1-FLAG replicate 1

source_name: KAN1-FLAG replicate 1


title: MeiosisReleaseIME4plus0min_input

source_name: Time Course Meiosis ReleaseIME4plus0min input


title: ChIP-seq-MHG-input

source_name: hESC derived posterior foregut (MHG)

value: hESC derived posterior foregut (MHG)


title: EarlyMeiosisIME4plus15min_input

source_name: Time Course Early MeiosisIME4plus15min input


title: ChIP-seq-PFG-H3K27me3

source_name: hESC derived anterior foregut (PFG)


title: EarlyMeiosisIME4plus15min_IP

source_name: Time Course Early MeiosisIME4plus15min IP


title: ChIP-seq-PFG-H3K27ac


title: EarlyMeiosisIME4plus0min_input

source_name: Time Course Early MeiosisIME4plus0min input


title: EarlyMeiosisIME4plus0min_IP

source_name: Time Course Early MeiosisIME4plus0min IP


title: ChIP-seq-PFG-input

source_name: hESC derived posterior foregut (PFG)

value: hESC derived posterior foregut (PFG)


title: ChIP-seq-AFG-H3K4me2

source_name: hESC derived anterior foregut (AFG)


title: IME4delrep3_input

source_name: IME4 deletion  Replicate 3 input


title: ChIP-seq-AFG-input


title: ChIP-seq-DE-H3K27me3


title: ChIP-seq-AFG-H3K27ac


title: IME4delrep3_IP

source_name: IME4 deletion  Replicate 3 IP


title: ChIP-seq-DE-input


title: IME4cat_IP

source_name: IME4 catalytic mutant IP


title: IME4cat_input

source_name: IME4 catalytic mutant input


title: ChIP-seq-DE-H3K27ac


title: ChIP-seq-DE-H3K4me2


title: MISminus_input

source_name: MIS inducible strains, without induction input


title: MISminus_IP

source_name: MIS inducible strains, without induction,IP


title: ChIP-seq-APS-H3K4me3

source_name: hESC derived anterior primitive streak (APS)


title: ChIP-seq-APS-H3K27ac

value: hESC derived anterior primitive streak (APS)


title: PointMutPosContRep2_input

source_name: Positive Control 2 for point mutations, using an ash1 deletion strain


title: PointMutPosContRep2_IP


title: ChIP-seq-PFG-H3K4me2


title: ChIP-seq-AFG-H3K27me3


title: EarlyMeiosisIME4plus45min_input

source_name: Time Course Early MeiosisIME4plus45min input


title: ChIP-seq-APS-H3K4me2


title: ChIP-seq-APS-input


title: ChIP-seq-AFG-H3K4me3


title: ChIP-seq-PFG-H3K4me3


title: MISplus_IP

source_name: MIS induction IP


title: ChIP-seq-H7-ESC-H3K27ac

source_name: H7-Embryonic stem cell


title: ChIP-seq-H7-ESC-H3K4me2


title: ChIP-seq-H7-ESC-H3K4me3


title: ChIP-seq-H7-ESC-input


title: PointMutNam8_IP

source_name: Point Mutation Nam8 IP


title: ChIP-seq-DE-H3K4me3

source_name: hESC derived definitive endoderm cells


title: PointMutIME2_input

source_name: Point Mutation IME2 input


title: IME4delVeg_input

source_name: IME4 deletion Veg input


title: ZR-75-1

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

description: Sample 8

data_processing:
Illumina's Genome Analyzer system software programs for base-calling
the 50bp paired end reads were aligned using BWA 0.6.2
the input files were the fastq files of the two ends, and the out put files were the SnowShoes-FTD called fusion transcripts
Genome_build: hg19
Supplementary_files_format_and_content: The .txt file reports fusion transcripts identified using SnowShoes-FTD version 2.0

source_name: breast cancer cell line

growth_protocol: Standard cell line growth

extract_protocol:
RNA was extracted by Qiagen Mini RNeasy Kit (Qiagen)
TruSeq RNA sample preparation kit (Illumina)

tag: cell line

tag: disease state

value: breast cancer


title: PointMutNam8_input

source_name: Point Mutation Nam8 input


title: PointMutIME2_IP

source_name: Point Mutation IME2 IP


title: MDA-MB-231

description: Sample 5


title: MDA-MB-468

description: Sample 6


title: MISplus_input

source_name: MIS induction input


title: WTVeg_IP

source_name: WT Veg IP


title: WTVeg_input

source_name: WT Veg input


title: T47D

description: Sample 7


title: ChIP-seq-H7-ESC-H3K27me3


title: MCF7

description: Sample 4


title: BT-20

description: Sample 3


title: MCF10A

description: Sample 2

source_name: Normal breast cell line

value: Normal breast


title: IME4delrep2_input

source_name: IME4 deletion  Replicate 2 input


title: PointMutMEI5_IP

source_name: Point Mutation MEI5 IP

value: anti-m6A (synaptic sytems)


title: ChIP-seq-APS-H3K27me3

source_name: hESC derived anterior primitive streak (APS)


title: IME4delrep2_IP

source_name: IME4 deletion  Replicate 2 IP


title: IME4delVeg_IP

source_name: IME4 deletion Veg IP


title: IME4delrep1_input

source_name: IME4 deletion  Replicate 1 input


title: PointMutZip1_input

source_name: Point Mutation Zip1 input


title: mRNA_HITS-CLIP

first: Ying

last: Chen

state: PA

address: 423 Guardian Drive

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt.
Reads from both libraries were mapped to the human genome (USSC hg19 assembly) using a previously described analysis pipeline (Li et al.; Zheng et al.).
Potential miRNA-target pairs were predicted using the miRanda program (v3.3a) with non-default parameter as “–en -10”.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for miRNAs and CLIP contigs on mRNAs.

source_name: pancreatic islet

extract_protocol:
Both the miRNA library and mRNA library were sequenced on Illumina HiSeq 2000 following standard protocols
HITS-CLIP library prepared as described in Chi et al (2009) Nature and McKenna et al (2010) Gastroenterology.

tag: hits-clip antibody

value: Argonaute antibody 2A9 (Zissimos Mourelatos lab)

tag: tissue

value: islets


title: miRNA_HITS-CLIP

value: Argonaute antibody 2A8 (Zissimos Mourelatos lab)


title: PointMutMEI5_input

source_name: Point Mutation MEI5 input

tag: strain


title: PointMutZip1_IP

source_name: Point Mutation Zip1 IP


title: IME4delrep1_IP

source_name: IME4 deletion  Replicate 1 IP


title: WTrep3_IP

source_name: WT Replicate 3 IP


title: PointMutPosContRep1_IP

source_name: Positive Control 1 for point mutations, using an ash1 deletion strain


title: PointMutNegCont_input

source_name: Negative control for meiosis progression, performed using an IME2 deletion strain


title: PointMutYNL195C_IP

source_name: Point Mutation YNL195C IP


title: PointMutYSP3_input

source_name: Point Mutation YSP3 input


title: PointMutPosContRep1_input


title: PointMutYSP3_IP

source_name: Point Mutation YSP3 IP


title: WTrep3_input

source_name: WT Replicate 3 input


title: PointMutMus81_IP

source_name: Point Mutation Mus81 IP


title: BT-474

description: Sample 1

source_name: breast cancer cell line


title: PointMutNegCont_IP


title: Mayotte Natural medium

city: Gif-sur-Yvette

first: François

last: Wurmser

address: Bât 13, avenue de la Terrasse

department: INEE

country: France

institute: CNRS UPR9034

data_processing:
Base Calls using CASAVA
Data cleaning was done using seqclean software with adapter cleaning (-v ) and shortquality trimming (-l 32). Other options set were for screening adapter sequences -y 7 and -x 90.
Mapping was done using ELAND software supplied by Illumina using 32 kmer and allowing upto 2 mismatches (6.25% error rate). Successively on D. melanogaster and D. simulans reference genome. (Flybase)
Orthology of D. simulans FB Ids were reconstructed using a home made pipeline.
Normalisation RPKM
Genome_build: Drosophila melanogaster and Drosophila simulans (FlyBase reference genomes, April 2010)
Supplementary_files_format_and_content: Table of normalised counts per sampe per gene

organism: Drosophila simulans

source_name: NM whole body

growth_protocol: We grew a hundred males for 7 days, each from a hundred different female collected in the wild

extract_protocol:
RNA extraction was performed using Macherey-Nagel Nucleospin RNA II kit, with 4 extraction per samples, that were then pooled. Quality and quantity were checked with an Experion (Biorad)
RNA samples were precipitated and the pellets dissolved in water. The total RNAs were analysed for their integrity by capillary electrophoresis. From the total RNA samples poly(A)+ RNA was prepared which was used for cDNA synthesis. cDNA was synthesized using an oligo(dT)-linker primer and M-MLV H- reverse transcriptase for first strand synthesis. The reaction conditions were chosen such that the length of the first-strand cDNAs was limited to about 100 – 500 nt. Finally, the cDNAs were PCR amplified using a high fidelity DNA polymerase. For Solexa sequencing the cDNAs in the size range of 250 – 450 bp were eluted from preparative agarose gels. Aliquots of the size fractionated cDNAs were analyzed by capillary electrophoresis.

value: whole body

tag: origin

value: Mayotte (Comores, France)


title: Gotheron Natural medium

source_name: NG whole body

value: Gotheron (France)


title: Gotheron Corn medium

source_name: CG whole body


title: mCherry_cntr2

city: Oakland

first: Ravi

last: Sachidanandam

address: 2945 Webster St

institute: Girihlet Inc.

data_processing:
Illumina CASAVA version 1.7 used for basecalling
Mapped to the Danio rerio genome build Zv9/danRer7
Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non-zero expression
Values were quantile-normalized allowing comparisons of the two sets using custom-built software and algorithms as described (Aravin et al., 2008; Olson et al., 2008; Tam et al., 2008)
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: Tab-delimted text file includes genes and their quantile normalized frequencies.

organism: Danio rerio

source_name: Zebrafish 5 dpf liver

extract_protocol:
Total RNA was extracted using Trizol and mRNA was purified using poly-A beads
The mRNA was chemically fragmented,and Hi-seq compatible, bar-coded adapters were ligated to both ends.

tag: genotype/variation

value: liver

tag: developmental stage

value: 5 dpf


title: UHRF1_hi_A


title: Parkinson's Disease (PD) patient, post-DBS following 1 hour off electrical stimulation (OFF-Stim), sample 12

status: Public on Nov 21 2013

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

data_processing:
Prior to alignment, all of the reads were subjected to trimming of the 15 end-terminal base pairs using home-made software.
The adapter and primer sequences were further trimmed. These included trimming of the 5' small RNA adapter, discarding of the SOLiD miRNA reverse primer, trimming of the 3' small RNA adapter and removal of the 5' end-terminal nucleotide using CLC bio Genomics Workbench software version 4.0 beta. Of a total of 166,746,207 sequence reads, 71,939,833 were left post-filtering, average length: 21 bp.
The remaining sequence reads were subjected to alignment to miRBase (version 15) human sequences through CLC bio Genomics Workbench software version 4.0 beta.
The reads were further subjected to alignment to the human filter reference sequence database (Ambion, Inc.) of 764 small RNA sequences including snoRNA, tRNA, spliceosomal RNA, etc.
Genome_build: 1) miRBase version 15;  2) human filter reference sequences database (Ambion, Inc.)
Supplementary_files_format_and_content: 1) grouped_miRBase.txt: counts grouped by miRNA name and form (including * forms and sequence); 2) grouped_on_mature_miRBase.txt: counts grouped only by mature miRNA name; 3) unannotated.txt: unannotated sequences identified in the sample; 4) grouped_filter_seq_DB.txt: counts grouped by RNA molecule name (other than miRNA).

source_name: Blood leukocytes, PD, post-DBS, off electrical stimulation

growth_protocol: Leukocytes were filtered from total blood samples (collected with EDTA vacutainer tubes) with Ambion Inc. LeukoLOCK™ filters within 10 minutes of blood extraction.

extract_protocol: RNA was harvested using the alternative protocol for extraction of RNA from cells captured on LeukoLOCK™ Filters Using TRI Reagent®. The amount of ethanol was adjusted to include the small RNA fraction. Libraries for deep sequencing were prepared from total leukocyte RNA with the manufacturer's SREK (Small RNA Expression Kit) protocol (Applied Biosystems, Foster City, CA, USA). The DNA libraries were tested using a DNA 1000 Lab Chip on Bioanalyzer 2100. Briefly, the total RNA samples were hybridized with Adaptor Mix A, which is a set of oligonucleotides with a single-stranded degenerate sequence at one end and a defined sequence required for SOLiD sequencing at the other end. The Adaptor Mix A constrains the orientation of the RNA in the ligation reaction such that hybridization with it yields template for SOLiD sequencing from the 5' end of the sense strand. After hybridization, the adaptors are ligated to the small RNA molecules using Ligation Enzyme Mix, which is a mixture of an RNA Ligase and other components. Ligation requires an RNA molecule with a 5'-monophosphate and a 3'-hydroxyl end; therefore, most small RNAs can participate in this reaction, and intact mRNA molecules with a 5' cap structure are excluded. Next, the small RNA population with ligated adaptors was reverse transcribed for each sample, to generate a cDNA library. This was followed by treatment with RNase H to digest the RNA from RNA/cDNA duplexes and to reduce the concentration of unligated adaptors and adaptor by-products. The cDNA libraries were amplified using bar-coded primer sets and 15-18 cycles of PCR. The amplified cDNA library was cleaned up and size selected from gel - PCR products ~105–150 bp are isolated, corresponding to inserts derived from the small RNA population. These contained 90 base pairs of primers and adapter sequences each. The amplified cDNA libraries generated with the SOLiD Small RNA Expression Kit were thereafter ready for attachment to beads at the emulsion PCR step of the SOLiD sample preparation workflow. The slides were analyzed on an Applied Biosystems SOLiD System 3.0 (V3.5). The Applied Biosystems SOLiD sequencer generated 50-base read sequences as .csfasta files and the corresponding quality control (.QUAL) files.

treatment_protocol: The captured leukocytes were treated with RNAlater immediately after filtration of the blood and were maintained frozen until RNA extraction.

value: blood leukocytes

value: Parkinson's disease

tag: treatment state

value: post-deep brain stimulation following 1 hour off electrical stimulation

tag: gender

value: male


title: Parkinson's Disease (PD) patient, post-DBS following 1 hour off electrical stimulation (OFF-Stim), sample 9


title: UHRF1_hi_B


title: Mayotte Corn medium

source_name: CM whole body


title: PointMutMus81_input

source_name: Point Mutation Mus81 input


title: Healthy control (HC) volunteer, sample 3

source_name: Blood leukocytes, healthy control

value: healthy


title: Healthy control (HC) volunteer, sample 2


title: Parkinson's Disease (PD) patient, post-DBS following 1 hour off electrical stimulation (OFF-Stim), sample 6


title: C.g_∆pacC

first: Gilgi

last: Friedlander

address: Hertzel st

institute: Weizmann Institute of Science

data_processing:
Basecalls performed using CASAVA 1.8.1 (use only Illumin'a passed filter)
Only reads that passed Illumina's chasitity filter were used. No further filtering was done.
Reads were aligned to Colletotrichum gloeosporioides contigs (SUB133583, PRJNA176412) using TopHat V1.3.0 with the option --segment-mismatches 1
Transcripts were defined using cufflinks 1.1.0; the gtf transcript file was submitted with the data
Quantify transcripts using Partek Genomics Suite V6.6 beta (the output of RPKM and counts are in the excel file Cgl_WT_pacC_RNAseq.xlsx)
Transcripts were annotated using blast2go. The annotations are in the excel file (Cgl_WT_pacC_RNAseq.xlsx)
Genome_build: Colletotrichum gloeosporioides contigs (SUB133583, PRJNA176412)
Supplementary_files_format_and_content: excel file including read counts and RPKM; gtf file of transcripts

organism: Colletotrichum gloeosporioides

source_name: ∆pacC_In vitro liquid pH7 Mycelia

growth_protocol: C. gloeosporioides WT and ∆pacC were incubated on M3S (Tu, 1985) at 24°C in shaking at 150 rpm for 3 days and were filtrated and washed twice with 40 ml of DDW. The washed mycelia were resuspended in 40 ml of fresh SM containing (per liter): 4 g K2HPO4, 2 g MgSO4•7H2O, 0.3 g CaCl2•2H2O, 10 mg FeCl3, 50 mM KNO3 and 50 mM glucose buffered with 50 mM phthalate-hydroxide buffer (Sigma) to pH 7.0. Mycelia were harvested 1, 3, 6, 12 and 19 hours after.

extract_protocol:
RNA was extracted using Tri-reagent standard protocol followed by Qiagen RNeasy mini kit clean-up and treated with RNase free DNase set (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: delta-pacC

value: mycelia

tag: incubation time at secondary media (ph 7)

value: A pool of 1, 3, 6, 12 and 19 hours


title: RNA_delta_Rv3263

city: College Station

first: Thomas

middle: R

last: Ioerger

state: TX

address: Interdisciplinary Life Sciences Building

department: Computer Science

institute: Texas A&M University

data_processing:
Base-calling  by OLB Version 1.9.3
Read mapping using in-house software (mapper, 2011-07-09)
Reads per gene counted and normalized as RPKM.
Differential expression p-values and q-values calculated using DESeq R package. (see Anders and Huber (2010))
Genome_build: NC_000962.2
Supplementary_files_format_and_content: .wig files contain depth of coverage  for both + strand and – strand; spreadsheet contains gene expression levels (RPKM) for each condition, log of fold-change, and P-values calculated by....(NegBinom? Ref? Rockhopper?)

organism: Mycobacterium tuberculosis H37Rv

source_name: In vitro cell culture

growth_protocol: Cultures were grown to log phase in roller bottles in 7H9 media supplemented with tween, glycerol, and OADC

extract_protocol:
Cell pellets were disrupted by bead-beating in Trizol followed by extraction and clean-up with an RNeasy kit.
Strand-specific RNA-seq libraries were constructed using the dUTP method to preserve strand specificity essentially as described in: Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., et al. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Research, 37(18), e123–e123. doi:10.1093/nar/gkp596.

value: knockout  (delta_Rv3263)


title: RNA_H37Rv_SS1

value: wildtype (H37Rv_SS1)


title: Parkinson's Disease (PD) patient, post-DBS on electrical stimulation (ON-Stim), sample 8

source_name: Blood leukocytes, PD, post-DBS, on electrical stimulation

value: post-deep brain stimulation on electrical stimulation


title: mCherry_cntr1


title: C.g_WT

source_name: WT_In vitro liquid pH7 Mycelia

value: WT


title: WTrep1_input

source_name: WT Replicate 1 input

tag: strain info


title: PointMutYLR149C_IP

source_name: Point Mutation YLR149C IP

tag: antibody

value: anti-m6A (synaptic sytems)


title: n2a-paupar-R1

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

data_processing:
library strategy:  Capture Hybridisation Analysis of RNA Targets (CHART)-seq
alignment: 50bp, paired-end reads were mapped to the mouse genome (mm9) using bowtie with the options “-m1 –v2 –best –strata –a”
peak-calling: Peak calls were made using the MACS2 algorithm (Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137) (https://github.com/taoliu/MACS/blob/master/README) with the options “--mfold 10 30 --gsize=2.39e9 --qvalue=0.01”. Peak calls were then filtered such that only peak calls with a -log10 qvalue > 5 were retained (FDR < 0.001%). Peaks were called seperately for  (i) Paupar1 (treatment) vs LacZ1 (control), (ii) Paupar2 (treatment) vs LacZ2 (control), (iii) Paupar1 (treatment) vs input1 (control), (iv) Paupar2 (treatment) vs Input1 (control).
construction of final peak set: The final peakset comprises of peaks common to all four individual comparisions. Overlapping peaks were merged in this analysis.
Genome_build: mm9
Supplementary_files_format_and_content: A single bed file containing the final paupar peak set. The average MACS2 peak score is reported in the score column.

extract_protocol:
CHART Enrichment and RNase H Mapping experiments were performed as previously described (Simon, 2013, Capture hybridization analysis of RNA targets (CHART). Curr Protoc Mol Biol Chapter 21: Unit 21 25). CHART extract was prepared from approximately 8 x 107 N2A cells per pull down and hybridized with 810 pmol biotinylated oligonucleotide cocktail overnight with rotation at room temperature. Complexes were captured using 250ml MyOneC1 streptavidin beads (Invitrogen) overnight at room temperature with rotation. Bound material was extensively washed and eluted using RNase H (New England Biolabs) for 30 min at room temperature. Samples were treated with Proteinase K and cross-links were reversed. DNA was sheared to an average fragment size of 150-300 bp using a Bioruptor (Diagenode).
Fragmented DNA was end-repaired, A-tailed and adapter-ligated before size selection and amplification. The prepared libraries were QC’ed and multiplexed before paired end sequencing over one lane of a Illumina HiSeq flow cell. For more information contact the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford.

treatment_protocol: None.

value: neuro 2A (N2A)

value: neuroblastoma

tag: molecule subtype

value: genomic DNA associated with endogenous Paupar transcripts


title: n2a-paupar-R2

tag: cell type


title: n2a-input-R1

value: input DNA sample


title: PointMutYNL195C_input

source_name: Point Mutation YNL195C input


title: n2a-lacZ-R2

value: genomic DNA associated with a control oligonucleotide (corresponding to the E.coli LacZ sequence)


title: Parkinson's Disease (PD) patient, post-DBS on electrical stimulation (ON-Stim), sample 5

value: blood leukocytes

value: Parkinson's disease


title: n2a-lacZ-R1


title: 13289-100mers-GM12878-243-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78339)

city: Pasadena

first: Diane

middle: E

last: Trout

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

department: Biology

institute: California Institute of Technology

description:
****************************
GSM1087891 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78339
****************************

data_processing: Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on.   Only the first read was used for the few libraries that were sequenced as paired end.

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

tag: labexpid


title: Parkinson's Disease (PD) patient, pre-DBS, sample 7

source_name: Blood leukocytes, PD, pre-DBS

value: pre-deep brain stimulation

value: male


title: 13302-100mers-GM12878-256_100cells-TopHat-1.4.1-GENCODE-V13

tag: cell line


title: 13303-100mers-GM12878-257_100cells-TopHat-1.4.1-GENCODE-V13


title: 13291-100mers-GM12878-245-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78421)

description:
****************************
GSM1087893 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78421
****************************


title: 13290-100mers-GM12878-244-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78451)

description:
****************************
GSM1087892 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78451
****************************


title: 13285-100mers-GM12878-238-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78307)

description:
****************************
GSM1087887 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78307
****************************


title: 13283-100mers-GM12878-236-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78308)

description:
****************************
GSM1087885 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78308
****************************


title: 13301-100mers-GM12878-255_11cells-TopHat-1.4.1-GENCODE-V13


title: 13279-100mers-GM12878-207-TopHat-1.4.1-GENCODE-V13


title: 13282-100mers-GM12878-235-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78311)

description:
****************************
GSM1087884 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78311
****************************


title: 13275-100mers-GM12878-10ng_2-TopHat-1.4.1-GENCODE-V13


title: 13276-100mers-GM12878-100pg_1-TopHat-1.4.1-GENCODE-V13


title: 13277-100mers-GM12878-100pg_2-TopHat-1.4.1-GENCODE-V13


title: 13274-100mers-GM12878-10ng_1-TopHat-1.4.1-GENCODE-V13


title: Healthy control (HC) volunteer, sample 1

tag: disease state

value: healthy


title: 13287-100mers-GM12878-240-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78312)

description:
****************************
GSM1087889 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78312
****************************


title: 13286-100mers-GM12878-239-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78310)

description:
****************************
GSM1087888 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78310
****************************


title: 12820-100mers-GM12878_208-TopHat-1.4.1-GENCODE-V13


title: 13300-100mers-GM12878-254_10cells-TopHat-1.4.1-GENCODE-V13


title: 13288-100mers-GM12878-242-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78309)

description:
****************************
GSM1087890 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78309
****************************


title: 12818-100mers-GM12878_200-TopHat-1.4.1-GENCODE-V13


title: 12819-100mers-GM12878_205-TopHat-1.4.1-GENCODE-V13


title: 12543-100mers-GM12878_195-TopHat-1.4.1-GENCODE-V13


title: 12542-100mers-GM12878_194-TopHat-1.4.1-GENCODE-V13


title: 13278-100mers-GM12878-204-TopHat-1.4.1-GENCODE-V13


title: 13284-100mers-GM12878-237-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78313)

description:
****************************
GSM1087886 record metadata submitted on Feb 25 2013 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE78313
****************************


title: 12540-100mers-GM12878_192-TopHat-1.4.1-GENCODE-V13


title: 12536-100mers-GM12878_188-TopHat-1.4.1-GENCODE-V13


title: 12538-100mers-GM12878_190-TopHat-1.4.1-GENCODE-V13


title: 12537-100mers-GM12878_189-TopHat-1.4.1-GENCODE-V13


title: 12535-100mers-GM12878_187-TopHat-1.4.1-GENCODE-V13


title: 12539-100mers-GM12878_191-TopHat-1.4.1-GENCODE-V13


title: PointMutYLR149C_input

source_name: Point Mutation YLR149C input


title: 12524-100mers-GM12878_185-TopHat-1.4.1-GENCODE-V13


title: 12523-100mers-GM12878_184-TopHat-1.4.1-GENCODE-V13


title: 12520-100mers-GM12878_10B_10-TopHat-1.4.1-GENCODE-V13


title: 12519-100mers-GM12878_10A_12-TopHat-1.4.1-GENCODE-V13


title: 12518-100mers-GM12878_30B-TopHat-1.4.1-GENCODE-V13


title: 12517-100mers-GM12878_30A-TopHat-1.4.1-GENCODE-V13


title: 12516-100mers-GM12878_100B-TopHat-1.4.1-GENCODE-V13


title: 12541-100mers-GM12878_193-TopHat-1.4.1-GENCODE-V13


title: 12515-100mers-GM12878_100A-TopHat-1.4.1-GENCODE-V13


title: nodular fasciitis (STT6061_NF)

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

description: Experiment type: 3SEQ

data_processing:
Sequenced Reads after filtered by quality, were re-filtered by fastx, and then were mapped to the transcriptome (refMrna, downloaded from the UCSC genome browser, www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches
Total numbers of sequenced reads for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix. The library size was then normalized to one million reads (TPM).
The sequencing depth for each library was determined with the estimation of library saturation for transcriptome detection, which showed that our sequencing depths were deep enough to detect almost all of the known mRNAs expressed.
The distances between sequencing reads and 3’end of mRNAs were measured to be around 100-200nt as we expected.
Genome_build: hg19
Supplementary_files_format_and_content: 10groups.fibrous.tumor.transcriptome_RPM_round.txt expressional matrix with sample by column and gene by row (linked as supplementary file on Series record).

source_name: NF

extract_protocol:
Multiple 2mm-diameter cores were taken from diagnostic FFPE material for RNA isolation. Then, total RNA was extracted by using of RecoverAll Total Nucleic Acid Isolation Kit (Ambion).
Poly(A)+RNA was selected and enriched with oligo(dT) using the Oligotex mRNA mini Kit (Qiagen).  The Poly(A) RNA was heat sheared to 100~200nt fragments. The sheared RNA was then subjected to first and second strand cDNA synthesis, followed by additional steps of library construction as described previously. The libraries were sent to the Stanford Genomic Center to be sequenced for the first 36bp at the 5’end of mRNA fragments with Illumina GA IIx machines.

treatment_protocol: Clinical tissue samples were formalin-fixed and paraffin-embedded (FFPE).

value: Soft Tissue

tag: tissue archive method

value: FFPE

tag: stromal signature

value: NF signature

tag: prognosis

value: UNCLEAR


title: fibroma of tendon sheath (STT6068_FOTS)

description: Experiment type: 3SEQ

source_name: FOTS

tag: tissue

value: FOTS signature

value: BAD


title: nodular fasciitis (STT6060_NF)

description: Experiment type: 3SEQ


title: nodular fasciitis (STT6059_NF)

description: Experiment type: 3SEQ


title: nodular fasciitis (STT5636_NF)

description: Experiment type: 3SEQ


title: fibroma of tendon sheath (STT5784_FOTS)

description: Experiment type: 3SEQ


title: fibroma of tendon sheath (STT6065_FOTS)

description: Experiment type: 3SEQ


title: 12534-100mers-GM12878_186-TopHat-1.4.1-GENCODE-V13


title: 12522-100mers-GM12878_183-TopHat-1.4.1-GENCODE-V13


title: nasopharyngeal angiofibroma (STT5806_NPAF)

description: Experiment type: 3SEQ

source_name: NPAF

value: NPAF signature


title: nodular fasciitis (STT6063_NF)

description: Experiment type: 3SEQ


title: nasopharyngeal angiofibroma (STT5788_NPAF)

description: Experiment type: 3SEQ


title: fibroma of tendon sheath (STT5782_FOTS)

description: Experiment type: 3SEQ


title: nasopharyngeal angiofibroma (STT5786_NPAF)

description: Experiment type: 3SEQ


title: nodular fasciitis (STT6062_NF)

description: Experiment type: 3SEQ


title: palmar fibromatosis (STT5642_PF)

description: Experiment type: 3SEQ

source_name: PF

value: PF signature


title: palmar fibromatosis (STT5643_PF)

description: Experiment type: 3SEQ


title: palmar fibromatosis (STT6056_PF)

description: Experiment type: 3SEQ


title: palmar fibromatosis (STT5781_PF)

description: Experiment type: 3SEQ


title: nasopharyngeal angiofibroma (STT5793_NPAF)

description: Experiment type: 3SEQ


title: infantile digital fibromatosis (STT5777_IF)

description: Experiment type: 3SEQ

source_name: IF

value: IF signature


title: infantile digital fibromatosis (STT5652_IF)

description: Experiment type: 3SEQ


title: nasopharyngeal angiofibroma (STT5792_NPAF)

description: Experiment type: 3SEQ


title: nasopharyngeal angiofibroma (STT5787_NPAF)

description: Experiment type: 3SEQ


title: elastofibroma (STT6051_EF)

description: Experiment type: 3SEQ

source_name: EF

value: EF signature

value: GOOD


title: palmar fibromatosis (STT6058_PF)

description: Experiment type: 3SEQ


title: elastofibroma (STT5999_EF)

description: Experiment type: 3SEQ


title: elastofibroma (STT6000_EF)

description: Experiment type: 3SEQ


title: collagenous fibroma (STT5994_FC)

description: Experiment type: 3SEQ

source_name: FC

value: FC signature


title: infantile digital fibromatosis (STT5644_IF)

description: Experiment type: 3SEQ


title: collagenous fibroma (STT6070_FC)

description: Experiment type: 3SEQ


title: palmar fibromatosis (STT5650_PF)

description: Experiment type: 3SEQ


title: elastofibroma (STT6052_EF)

description: Experiment type: 3SEQ


title: WTrep1_IP

source_name: WT Replicate 1 IP

tag: strain

value: anti-m6A (synaptic sytems)


title: collagenous fibroma (STT6073_FC)

description: Experiment type: 3SEQ


title: palmar fibromatosis (STT6057_PF)

description: Experiment type: 3SEQ


title: collagenous fibroma (STT6071_FC)

description: Experiment type: 3SEQ


title: solitary fibrous tumor (STT6077_SFT)

description: Experiment type: 3SEQ

source_name: SFT

value: SFT signature


title: solitary fibrous tumor (STT5388_SFT)

description: Experiment type: 3SEQ