title: TR Progeny 2 [small RNA-seq]

city: Lethbridge

first: Igor

last: Kovalchuk

address: 4401 University Drive

country: Canada

institute: UofL

description:
processed data file: progeny.result.txt.gz
treated progeny

data_processing:
Basecalling and demultiplexing was performed using CASAVA 1.8.1 with default settings
Adapter trimming was performed using cutadapt software httverision 0.9.5p://code.google.com/p/cutadapt/ () with options specified to search for adapters anywhere in the read sequence and retain only sequences longer than 17 nucleotides, quality trimming was performed with sanger quality score cutoff of 20.
Collapsing reads into unique tags using fastx toolkit: # convert to fasta: cat trimmed.fastq | perl -e '$i=0; while(<>) {if(/^\@/&&$i==0) {s/^\@/\>/;print;} elsif ($i==1) {print;$i=-3} $i++;}' > trimmed.fasta  # collapser: fastx_collapser -i trimmed.fasta -ogrouped_reads.txt
Fraction of reads aligning to the genome was estimated using bowtie (0.12.7): bowtie -v 2 --best -p 4 -y -m 1 -a --strata --al unique_aligned --un unaligned --max multiple <indexed_genome> <trimmed.fastq>
Novel miRNA prediction: All of the reads from every library that could be aligned to the reference genome were pooled together. MiRDeep-P software (version 1.3) http://faculty.virginia.edu/lilab/miRDP/ was used for novel miRNA discovery. Filtering step in miRDeep-P was performed using gene annotation from http://brassicadb.org, positions of known miRNA were extended by 100 bp in both directions and added to the gff files containing Brassica gene annotation.
Prediction of phased loci, likely producing ta-siRNAs, was performed using ta-si prediction tool from java implementation of UAE small RNA toolkit httversion 2.3.2p with default parameters://srna-workbench.cmp.uea.ac.uk/ ()
Analysis of library compositions was performed by aligning trimmed sequencing reads to various known and predicted classes of small RNAs. The alignments were perfomed using bowtie: bowtie -n 2 -l 17 --best -p 4
Assessing mapping to highly repetitive sequences: The idea was look at the fraction of reads mapping to highly repetitive regions of the genome (simple, low complexity repeats etc.). Chosen cutoff was 50 or more matching loci. Exact bowtie command was: bowtie -v 2 --best -m 50 -p 4 -S
Genomic alignment: bowtie -v 2 --best -m 50 -p 4 -S  <index> trimmed.fastq aligned.sam
Statistical comparisons between control and treated groups were performed using DESeq (version 1.9.5) with default settings.
Genome_build: Brapa_1.0 (Wang X, Wang H et al; Brassica rapa Genome  Sequencing Project Consortium; PMID: 21873998)
Supplementary_files_format_and_content: All of the standard output produced by cuffmerge and cuffdiff; details included in 'README.txt'

organism: Brassica rapa

source_name: treated progeny

growth_protocol: Seeds obtained from a single unstressed plant were germinated on All purpose potting soil (Plant Etc; Lethbridge, AB, Canada) mixed in the proportion 4:1 with vermiculite (The Professional Gardener Co LTD, AB, Canada) in 4x4 inch square pots. The soil mixture was pre-soaked once with Miracle-Gro fertilizer (Scotts Canada Ltd., Mississauga, ON, Canada) and was maintained constantly moist with tap water. Rapid-cycling B. rapa parental plants (30 plants per group) and their progeny were cultivated in biochambers (BiofootTM, model GC-20, Winnipeg, MB, Canada) under continuous high-intensity cold light illumination (200 µmol m-2 s-1) provided by fluorescent lamps and a 60% relative humidity at 22°C as described previously (Daugherty and Musgrave 1994; Tel-Zur and Goldman 2007). The cultivation of plants under constant light did not affect their phenotypic appearance as compared to plants grown under a long-day photoperiod (16 h day, 8 h night).

extract_protocol:
All tissue samples harvested from control and treated plants were subjected to total RNA isolation using the Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. Two independent RNA samples per every tissue were prepared. Total RNA was further purified and concentrated using the RNA Clean-Up and Concentration Kit (Norgen Biotek Corp., Ontario, Canada). The quality and concentration of every sample were quantified using the NanoDrop 2000C spectrophotometer (Thermo Fisher Scientific Inc.) and the absorption ratios at 260/280 and 260/230 nm wavelengths. Agarose gel electrophoresis was performed to verify RNA sample integrity.
Small non-coding RNA libraries were generated from 16 samples of total RNA in 2 biological replicates for most of the tissues using the TruSeq small RNA library construction kit according to the manufacturer’s protocol (Illumina, San Diego, CA, U.S.A.). Briefly, the 3΄ and 5΄ adapters were ligated to small RNAs from the total RNA sample followed by reverse-transcription PCR amplification. PCR was performed with two primers that annealed to the ends of adapters and contained indexes. Subsequently, the libraries with unique indexes were pooled together; the cDNA was gel-purified using a TBE PAGE gel and then concentrated by ethanol. Following a successful library quality control by qPCR, flow cell cluster generation was performed using a cBot. Single-end multiplexed sequencing was done using the Illumina GAIIx platform with the total of 36 cycles.

treatment_protocol: Two weeks post germination, before the appearance of apical inflorescence shoots, plants from the treated group were exposed to 42°C for 3h per day for 7 days in a row. Subsequently, plants from both control and treated groups and their progeny were grown in continuous light at 22°C.

tag: line

value: R-o-18 a rapid-cycling self-compatible inbred line of Brassica rapa var. trilocularis (Roxb.) Hanelt (yellow sarson)

tag: exposed to

value: 42°C for 3h per day for 7 days

tag: days post germination when tissue was collected

value: Leaves


title: CT Progeny 2 [small RNA-seq]

status: Public on Dec 01 2014

type: SRA

description:
processed data file: progeny.result.txt.gz
control progeny

library_source: transcriptomic

molecule: total RNA

source_name: control progeny

value: 22°C (control)

tag: tissue


title: TR Progeny 1 [small RNA-seq]


title: CT Progeny 1 [small RNA-seq]


title: DamID_gfp Male

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

description:
C. elegans (+contaminating E.coli)
DamID reads

library_source: genomic

data_processing:
DamID adapter sequences were cut from raw reads using cutadapt with following parameters:  -g CGCGGCCGAG -e 0.15
Cut reads were mapped to ce10 C. elegans genome with bowtie, using -m 1 -- best parameters
sam file converted to bam using samtools before import into R
genomic intervals from bowtie were imported to R, intervals not starting with GATC were removed (plus strand) as well as intervals not ending with GATC (minus strand). Number of reads per 100 kb regions was then counted (file: GATC_read_counts_per_100kb_bin.tab)
GATC counts per 100 kb bin was normalized to the total number of GATC reads. For all intervals, the ratio between lmn-1/mel-28 and gfp frequency was calculated (file:Ratios_per_100kb_bin.tab)
Genome_build: ce10
Supplementary_files_format_and_content: GATC_read_counts_per_100kb_bin.tab DamID read counts per 100 kb bin for all strains (males and hermaphrodites, summed for repeats)
Supplementary_files_format_and_content: Ratios_per_100kb_bin.tab Ratio between localized dam (lmn-1/mel-28) and free dam (gfp) for males and hermaphrodites, per 100 kb bin

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Entire animals (20)

growth_protocol: Worm were grown at 25°C on a E. coli bacterial lawn

extract_protocol:
PCR product was purified on a Qiaquick column following the instructions of the manufacturer, except that an additional 35% guanidine hydrochloride was introduced before the PE washes
PCR fragments were end-repaired using End-It (Epicentre), A-tailed using Klenow fragment and ligated to Y-shaped library primers. Indexed primers were used to amplify (6 cycles) the library.

treatment_protocol: 10 worms were pooled together in a single PCR tube containing 1ul of lysis buffer (10 mM Tris-Ac, 10 mM MgAc, 50 mM KAc, 0.67% Tween20, 0.67% NP40), snap-frozen in liquid nitrogen. Frozen worms were thawed and 2 ul of lysis buffer with ProtK (final concentration in 3 ul 0.67 mg/ml) was added. Worms were then digested for 4 hours at 42°C, ProtK was inactivated at 80°C for 10'. Lysates were then digested with 0.1 ul DpnI restriction enzyme, together with 7 ul One-Phor-All buffer (10 mM TrisAc pH7.5, 50 mM KAc, 10 mM MgAc), 6 hours at 37°C. ds DamID adapters (0.2 ul 50 uM) were then ligated at 16°C overnight (hybridized 5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA and 5’-TCCTCGGCCGCG) with 0.5 ul T4 ligase and 2 ul T4 ligase buffer in a total volume of 20 ul. Ligated fragments were then PCR amplified using 5’-NNNNGTGGTCGCGGCCGAGGATC.

tag: genotype

value: Strain expressing a fusion between DNA adenine methyltransferase (dam) and gfp, under transcriptional control of the uninduced hsp-16.41 promoter

tag: gender

value: Male

tag: developmental stage

value: L4 stage


title: TR Endosperm 2 [small RNA-seq]

description:
processed data file: endosperm.result.txt.gz
treated endosperm

source_name: treated endosperm

tag: tissue collection

value: Endosperm dissected from fully-developed green seeds

value: Endosperm


title: DamID_gfp Hermaphrodite

value: Hermaphrodite


title: TR Endosperm 1 [small RNA-seq]


title: CT Endosperm 2 [small RNA-seq]

description:
processed data file: endosperm.result.txt.gz
control endosperm

source_name: control endosperm


title: CT Endosperm 1 [small RNA-seq]


title: NCI H660 + E2 [ERα_ChIP-Seq]

city: NEW YORK

first: Dimple

last: Chakravarty

state: NY

address: Belfer Research Building 413 E 69 St., New York

department: Pathology

country: USA

institute: Weill Cornell Medical College

data_processing:
Sequencing reads were aligned to the reference genome (hg18) using Illumina GERALD (both NCI H660 cell lines and VCaP + E2) or CASAVA 1.8 (VCaP and VCaP ERα) using default parameters
Peak detection for all ChIP-seq experiments was performed with ChIPseeqer (Giannopoulou and Elemento, 2011), using the same parameters for all datasets (i.e., p-value threshold for peaks=10-5, minimum distance between peaks=100bp). For details, please go to: http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_use
Genome_build: hg18
Supplementary_files_format_and_content: BED files of the ERa binding sites locations for the different cell lines

organism: Homo sapiens

source_name: NCI H660 cell line

growth_protocol: Prostate cell lines were maintained in appropriate medium. VCaP and VCaP ERa expressing cells were maintained in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin streptomycin. NCI-H660 cells were grown in RPMI 1640 supplemented with 0.005 mg/ml insulin, 0.01 mg/ml transferrin, 30 nM sodium selenite, 10 nM hydrocortisone, 10 nM 17 beta estradiol, 5% FBS and an extra 2 mM of L-glutamine (for a final concentration of 4 mM).

extract_protocol:
Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Brandson), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq Sample Kit (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 from 200-300 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 for VCaP + E2 and NCI H660 + E2  were sequenced on the Genome Analyzer  II  and for VCaP cells, VCaP ERa + E2 and Sample Input  in a HiSeq 2000.

treatment_protocol: For estrogen treatment experiment,  VCaP and NCI-H660 cells were hormone starved for 48 hours prior to treatment with 10nM of 17 b estradiol (E2) for 14 hours

tag: cell line

value: Prostate cancer cell line

tag: agent

tag: passages

value: 4 to 5

tag: chip antibody

value: ERα (diagenode, AC-066-100, lot # 001)


title: h_BrainA8_MBD_M

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Library strategy: MBD-Seq
Library selection: MeCP2 protein methyl-CpG binding domain
Sequenced reads were mapped to hg18 genome using MAQ with parameters -n 2 -m 0.001 -e 70 -a 250
Reads with a poor mapping score were filtered out using bamtools with the paramater -mapQuality ">=20"
BAM files were converted into wig format using bedtools
Genome_build: hg18
Supplementary_files_format_and_content: Merged files containing the combined read data for all replicates for that sample. Columns represent: chromosome, start position, stop position & read_coverage. A single header row provides additional information for the browser.

source_name: Pons

extract_protocol:
DNA was extracted and sheared to approximately 400 bp using sonication and then ligated to Illumina's adapters. Methylated DNA was purified by two step MBD Affinity Purification as described in Skene et al., 2010.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating fragmented DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was ethanol precipitated and then reconstituted in running buffer prior to MAP-purification. Purified DNA was PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

tag: individual

value: A

tag: age

tag: neuropathological status

value: Control

value: Pons


title: DamID_lmn-1 Hermaphrodite

value: Strain expressing a fusion between DNA adenine methyltransferase (dam) and lmn-1, under transcriptional control of the uninduced hsp-16.41 promoter


title: VCaP + E2 [ERα_ChIP-Seq]

source_name: VCaP cell line

value: 3 to 4


title: TR Embryo 1 [small RNA-seq]

description:
processed data file: embryo.result.txt.gz
treated embryo

source_name: treated embryo

value: R-o-18 a rapid-cycling self-compatible inbred line of Brassica rapa var. trilocularis (Roxb.) Hanelt (yellow sarson)

value: 42°C for 3h per day for 7 days

value: Embryos dissected from fully-developed green seeds

value: Embryo


title: TR Embryo 2 [small RNA-seq]


title: DamID_lmn-1 Male

value: Male


title: h_BrainA4_MBD_M

source_name: Temporal

value: Temporal


title: CT Embryo 1 [small RNA-seq]

description:
processed data file: embryo.result.txt.gz
control embryo

source_name: control embryo

value: 22°C (control)


title: TR Fert. Ovules 27 [small RNA-seq]

description:
processed data file: pol_ov.result.txt.gz
treated fertlized ovules

source_name: treated fertlized ovules

value: Fertilized ovules


title: TR Fert. Ovules 1 [small RNA-seq]


title: CT Fert. Ovules 24 [small RNA-seq]

description:
processed data file: pol_ov.result.txt.gz
control fertilized ovules

source_name: control fertilized ovules


title: h_BrainA1_MBD_M

source_name: Frontal

value: Frontal


title: CT Fert. Ovules 23 [small RNA-seq]


title: TR Unf. Ovules 26 [small RNA-seq]

description:
processed data file: unpol_ovules.result.txt.gz
treated unfertilized ovules

source_name: treated unfertilized ovules

value: Unfertilized ovules


title: TR Unf. Ovules 25 [small RNA-seq]


title: CT Unf. Ovules 22 [small RNA-seq]

description:
processed data file: unpol_ovules.result.txt.gz
control unfertilized ovules

source_name: control unfertilized ovules


title: CT Unf. Ovules 1 [small RNA-seq]


title: TR Inf. Meristem 16 [small RNA-seq]

description:
processed data file: appical_meristem.result.txt.gz
treated inflourescence meristem

source_name: treated inflourescence meristem

value: Inflorescence meristem


title: CT Pollen 18 [small RNA-seq]

description:
processed data file: pollen.result.txt.gz
control pollen

source_name: control pollen

value: Pollen


title: CT Pollen 17 [small RNA-seq]


title: TR Leaves 2 [small RNA-seq]

description:
processed data file: leaves.result.txt.gz
treated leaves

source_name: treated leaves

value: Leaves


title: CT Inf. Meristem 13 [small RNA-seq]

description:
processed data file: appical_meristem.result.txt.gz
control inflourescence meristem

source_name: control inflourescence meristem


title: CT Leaves 1 [small RNA-seq]

description:
processed data file: leaves.result.txt.gz
control leaves

source_name: control leaves


title: TR Leaves 1 [small RNA-seq]


title: TR Progeny 2 [RNA-seq]

description:
treated progeny
processed data file: progeny_diff_out.tar.gz

data_processing:
Basecalling using CASAVA 1.6 with default parameters
Demultiplexing was done using novobarcode (NovoCraftV2.08) with default settings
Read quality check using FastQC
Read alignment using Tophat2 v. 2.04: tophat2 --solexa1.3-quals -p 4 --library-type fr-unstranded --b2-sensitive <index> <reads_fastq>
Transcript assembly using Cufflinks v 2.0.2: cufflinks -o cuff_out -p 4 --frag-bias-correct <genome_fasta> --multi-read-correct --library-type fr-unstranded <bam>
Assemblies were merged using cuffmerge with default settings
Statistical comparisons between samples were done using cuffdiff: cuffdiff -o <genome.fasta> -p 4 -L CT,TR -u <gtf>  <ct_file1>,<ct_file2> <tr_file1>,<tr_file2>
Genome_build: Brassica rapa v.1.2
Supplementary_files_format_and_content: All of the standard output produced by cuffmerge and cuffdiff; details included in 'README.txt'
Supplementary_files_format_and_content: cuffmerge_out.tar.gz; cuffmerge output files containing the results of transcript assembly

source_name: Leaves

extract_protocol:
All tissue samples harvested from control and treated plants were subjected to total RNA isolation using the Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. Two independent RNA samples per every tissue were prepared. Total RNA was further purified and concentrated using the RNA Clean-Up and Concentration Kit (Norgen Biotek Corp., Ontario, Canada). The quality and concentration of every sample were quantified using the NanoDrop 2000C spectrophotometer (Thermo Fisher Scientific Inc.) and the absorption ratios at 260/280 and 260/230 nm wavelengths. Agarose gel electrophoresis was performed to verify RNA sample integrity.
The mRNA libraries were prepared from 16 samples of total RNA in 2 biological replicates according to the TruSeq RNA sample Prep v2 LS protocol (Illumina, San Diego, CA, U.S.A.). Briefly, mRNA was purified from the total RNA samples using poly-T oligo-attached magnetic beads followed by mRNA fragmentation, first- and second-strand cDNA synthesis. Later, the overhangs resulting from the fragmentation of double-stranded (ds) cDNA were repaired to form blunt ends. A single ‘A’ nucleotide was added to the 3΄ ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. Multiple indexing adapters were ligated to the ends of ds cDNA to prepare them for hybridization onto a flow cell followed by a PCR amplification step. The libraries were quantified using the qPCR technique and analyzed on a Bioanalyzer 2100 (Agilent Technologies) using a DNA specific chip. Subsequently, the libraries were normalized and pooled together followed by flow-cell cluster generation using a cBot fully automated clonal cluster generation system for Illumina sequencing. Single-end multiplexed sequencing was done using the Illumina GAIIx platform with the total of 100 cycles.

tag: treatment


title: CT Progeny 1 [RNA-seq]

description:
control progeny
processed data file: progeny_diff_out.tar.gz


title: CT Progeny 2 [RNA-seq]


title: TR Endosperm 2 [RNA-seq]

description:
treated endosperm
processed data file: endosperm_diff_out.tar.gz

source_name: Endosperm

value: Endosperm dissected from fully-developed green seeds


title: CT Leaves 2 [small RNA-seq]


title: TR Progeny 1 [RNA-seq]


title: CT Embryo 2 [small RNA-seq]


title: TR Endosperm 1 [RNA-seq]


title: CT Endosperm 2 [RNA-seq]

description:
control endosperm
processed data file: endosperm_diff_out.tar.gz


title: CT Endosperm 1 [RNA-seq]


title: CT Embryo 1 [RNA-seq]

description:
control embryo
processed data file: embryo_diff_out.tar.gz

source_name: Embryo


title: CT Embryo 2 [RNA-seq]


title: TR Fert. Ovules 2 [RNA-seq]

description:
treated fertlized ovules
processed data file: polinated_ovules_diff_out.tar.gz

source_name: Fertilized ovules


title: TR Fert. Ovules 1 [RNA-seq]


title: CT Fert. Ovules 2 [RNA-seq]

description:
control fertilized ovules
processed data file: polinated_ovules_diff_out.tar.gz


title: TR Pollen 20 [small RNA-seq]

description:
processed data file: pollen.result.txt.gz
treated pollen

source_name: treated pollen


title: TR Embryo 2 [RNA-seq]

description:
treated embryo
processed data file: embryo_diff_out.tar.gz


title: TR Pollen 19 [small RNA-seq]


title: CT Inf. Meristem 14 [small RNA-seq]


title: TR Unf. Ovules 1 [RNA-seq]

description:
treated unfertilized ovules
processed data file: unpollinated_ovules_diff_out.tar.gz

source_name: Unfertilized ovules


title: CT Unf. Ovules 1 [RNA-seq]

description:
control unfertilized ovules
processed data file: unpollinated_ovules_diff_out.tar.gz


title: TR Pollen 1 [RNA-seq]

description:
treated pollen
processed data file: pollen_diff_out.tar.gz

source_name: Pollen


title: CT Pollen 1 [RNA-seq]

description:
control pollen
processed data file: pollen_diff_out.tar.gz


title: TR Inf. Meristem 2 [RNA-seq]

description:
treated inflourescence meristem
processed data file: appical_diff_out.tar.gz

source_name: Inflorescence meristem


title: TR Inf. Meristem 1 [RNA-seq]


title: TR Embryo 1 [RNA-seq]


title: TR Leaves 2 [RNA-seq]

description:
treated leaves
processed data file: leaves_diff_out.tar.gz


title: CT Leaves 2 [RNA-seq]

description:
control leaves
processed data file: leaves_diff_out.tar.gz


title: TR Leaves 1 [RNA-seq]


title: CT Leaves 1 [RNA-seq]


title: 24h Pseudomonas-treated whiteflies

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

country: China

institute: Zhejiang University

description: 24 hours after infection with Pseudomonas

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.

molecule: polyA RNA

organism: Bemisia tabaci

source_name: Adults

growth_protocol: Culture of whiteflies was maintained on cotton plants in climate chambers at 27 ± 1 °C, 14 h light/10 h darkness with 70 ± 10% relative humidity (RH).

extract_protocol:
Total RNA was purified with SV total RNA isolation kit (Promega) according to the manufacturer’s instructions. RNA quality was assessed by Nanodrop 2000 (Thermo Scientific) and 2100 Bioanalyzer.
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: The infection solution was obtained from an overnight Pseudomonas culture. The density of bacteria was adjusted to 1×108 CFU/ml in 10% sucrose solution. The same sucrose solution without P. aeruginosa was used as control.  About 1,500 newly emerged adult whiteflies were collected for each treatment. The control and 24 h treatment groups were fed, respectively, with sucrose and bacterial solution. After 18 h, the 6 h treatment group was fed with bacteria. At 24 hours post-infection (hpi), approximately 1,000 whiteflies were collected from the control, 6 and 24 hpi treatments, respectively.

tag: species

value: Mediterranean (MED)

tag: growth protocol

value: maintained on cotton

tag: infection

value: Pseudomonas

tag: time

value: 24 hours


title: CT Fert. Ovules 1 [RNA-seq]

tag: line

value: R-o-18 a rapid-cycling self-compatible inbred line of Brassica rapa var. trilocularis (Roxb.) Hanelt (yellow sarson)

tag: days post germination when tissue was collected


title: 6h Pseudomonas-treated whiteflies

description: 6 hours after infection with Pseudomonas

value: 6 hours


title: un-treated whiteflies

description: no infection (control)

value: no infection

value: control


title: Celf2heart_7dy_101203_A6837

city: Gainesville

first: Eric

middle: T

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Reads were aligned to the mm9 mouse genome and splice junctions using tophat/bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values in matrix format (Entrez IDs as gene identifiers).

organism: Mus musculus

extract_protocol:
Mice between 14 and 16 weeks old were fed 2 g/kg doxycycline to induce Celf2 expression in heart.  All food was removed from cages 2-3 hours prior to addition of dox food.  At the indicated time point, the mouse was sacrificed, and the heart was dissected.  Blood was removed by washing with PBS.  The atria were removed, and small portion of the apex was removed.  The remaining ventricle tissue was frozen in liquid nitrogen. Total RNA from the ventricle tissue was prepared by lysis in guanidium isothiocyanate, followed by phenol/chloroform extraction, and prepared for RNA sequencing.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.

tag: strain background

value: FVB

value: 14 -16 weeks

tag: genotype/variation

value: containing tet-inducible Celf1 cassette

tag: fed with

value: 2 g/kg doxycycline

tag: time point

value: 7 days

tag: tissue

value: heart (ventricle)


title: Celf2heart_ctl_101129_A6743

value: MHCrtTA

value: 72 hours


title: Celf2heart_7dy_101203_A6836


title: Celf2heart_ctl_101117_A6897


title: Celf2heart_ctl_101129_A6747


title: Celf2heart_72h_101117_A6835


title: Celf2heart_72h_101203_A6750


title: WRR−

city: Guangzhou

first: OuYang

last: Hongjia

state: Guangdong

address: Wushan street 483

department: College of Animal Science

institute: South China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences, low quality reads (Sanger bases quality < 20), and contaminant reads were removed with the Fastx-Toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/).
Sequenced reads were mapped to chicken genome to annotate the location in the chromosomes using Bowtie (http://bowtie-bio.sourceforge.net /index.shtml).
Genome_build: Gallus_gallus.Galgal4.73

organism: Gallus gallus

source_name: Spleen

extract_protocol:
Total RNA was extracted from each spleen using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: strains

value: Recessive White Rocks

tag: disease state

value: Uninfected Recessive White Rocks

value: 140 day old


title: Celf2heart_72h_101117_A6834


title: Celf2heart_7dy_101117_A6838


title: WRR+

value: J subgroup avian leukosis virus (ALV-J) infected Recessive White Rocks


title: CT Inf. Meristem 2 [RNA-seq]

description:
control inflourescence meristem
processed data file: appical_diff_out.tar.gz


title: CT Inf. Meristem 1 [RNA-seq]


title: Celf2heart_24h_101129_A6749

value: 24 hours


title: Celf2heart_24h_101129_A6748


title: Celf2heart_12h_101129_A6740

value: 12 hours


title: TBP ChIP-nexus (Human K562 cells) Rep 1

status: Public on Dec 02 2014

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

description:
hsap_k562_tbp_chipnexus_01
Illumina multiplex barcode: ACAGTG
ChIP-nexus

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome Build:
hsap_k562_tbp_chipnexus_01_positive.bw: UCSC hg19
hsap_k562_tbp_chipnexus_01_negative.bw: UCSC hg19

source_name: Homo sapiens_K562 cells

growth_protocol: grown at 37C, 5% CO2 w/ humidity in Iscove's DMEM media with 10% fetal bovine serum

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then dounced to bread down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp.  300 ul soluble chromatin from ~ 10 million cells was used
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

treatment_protocol: no treatment, only fixation by formaldehyde

tag: cell line

value: K562 cells

tag: chip antibody

value: anti-TBP rabbit polyclonal, Santa Cruz Technology, catalog # sc-204X (ChIP-grade), lot # C-0513


title: Celf2heart_24h_101117_A6744

tag: age


title: Celf2heart_12h_101129_A6741


title: Celf2heart_12h_101117_A6742


title: Celf1muscle_ctl_A4374

extract_protocol:
Mice between 20 and 22 weeks old were fed 2 g/kg doxycycline to induce Celf1 expression in muscle  All food was removed from cages 2-3 hours prior to addition of dox food.  At the indicated time point, the mouse was sacrificed, and the gastrocnemius muscles were dissected.  Samples were frozen in liquid nitrogen prior to RNA extraction. Total RNA from the ventricle tissue was prepared by lysis in guanidium isothiocyanate, followed by phenol/chloroform extraction, and prepared for RNA sequencing.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.

value: 20-22 weeks

value: MDAFrtTA

value: control

value: gastrocnemius muscle


title: Celf1muscle_ctl_A4393

value: FVB

value: 2 g/kg doxycycline


title: Celf1muscle_ctl_A3559


title: Celf1muscle_7dy_A4411

value: containing tet-inducible Celf1 cassette

value: 7 days


title: TR Inf. Meristem 15 [small RNA-seq]

description:
processed data file: appical_meristem.result.txt.gz
treated inflourescence meristem

value: R-o-18 a rapid-cycling self-compatible inbred line of Brassica rapa var. trilocularis (Roxb.) Hanelt (yellow sarson)

tag: exposed to

value: 42°C for 3h per day for 7 days

value: Inflorescence meristem


title: Celf1muscle_7dy_A4387


title: Celf1muscle_7dy_A4380


title: Celf1muscle_72h_A3561

value: 72 hours


title: Celf1muscle_72h_A4408


title: Celf1muscle_24h_A4414


title: Celf1muscle_72h_A4372


title: Celf1muscle_24h_A4404


title: Celf1muscle_12h_A4346


title: Celf1muscle_12h_A4331


title: 1144N0007

first: Matthew

middle: Francis

last: Nolan

state: UK

address: Hugh Robson Building

department: Centre for Integrative Physiology

institute: University of Edinburgh

data_processing:
Base-calling: Raw data were processed using Casava 1.8 (completed by Ark-Genomics)
Sequenced fragments were aligned using TopHat v2.0.8. (completed by Ark-Genomics)
Relative RNA abundance and differential expression were computed using Cuffdiff 2 software (Nov 2013) on the output BAM files (default settings) (Trapnell et al. 2012)
Genome_build: Ensembl 73- mus musculus
Supplementary_files_format_and_content: genes_exp.diff.txt: Tab sep file containing differential expression data; RawFPKM: Tab sep file containing Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) for each gene, reformatted from read_group_tracking; genes.fpkm_tracking.txt: Tab sep file containing group mean and var FPKM for each gene; genes.read_group_tracking.txt: Tab sep file containing read and FPKM data for each sample for each gene

source_name: Dorsal MEC acute slices

extract_protocol:
We compared RNA from dorsal and ventral MEC of 4 groups of mice. To minimize the effects of inter-animal variability and variability in the dissection, whilst maintaining sufficient power to detect dorsoventral differences, samples were pooled with 3 or 4 mice in each group. RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen Cat:74804).  RNA integrity was assessed using a Agilent 2100 Bioanalyzer. All sample RINs were between 7.1 and 8.5.
cDNA was synthesized and amplified using the Ovation RNA-Seq System V2 (NuGEN Cat:7102) using 120 ng of starting material for each sample. The samples were fragmented and sequenced by the Ark-Genomics facility using Illumina HiSeq with multiplexed paired-end analysis on two lanes.

treatment_protocol: Brains were rapidly extracted from 13 male 8-week-old C57Bl/6JolaHsd mice and maintained in modified oxygenated artificial cerebrospinal fluid (ACSF) of the following composition (mM): NaCl 86, NaH2PO4 1.2, KCl 2.5, NaHCO3 25, CaCl2 0.5, MgCl2 7, glucose 25, sucrose 75), at approximately 4ºC. One 400 µm thick sagittal slice containing the right MEC was cut from each brain using a Leica Vibratome VT1200 system. Dorsal and ventral regions were microdissected under a dissection microscope, with care taken to avoid inclusion of ventral entorhinal cortical regions, parasubicular or postrhinal regions and subicular regions. Tissue sections were collected into separate RNase-free eppendorf tubes before being quickly frozen on dry ice. Frozen tissue was stored at -80ºC for several weeks before RNA extraction.

tag: strain

tag: gender

value: male

value: Brain

tag: mec region

value: dorsal

value: 8 weeks


title: 1144N0008

source_name: Ventral MEC acute slices

value: ventral


title: 1144N0006


title: Celf1muscle_24h_A4349

value: 20-22 weeks

value: 24 hours


title: 1144N0004


title: WT_0L_Mock

city: Kunming

first: Jinsong

last: Wu

address: Lanhei Road 132

institute: Kunming institute of Botany, the Chinese Academy of Sciences

description: mock 1 d

data_processing:
Basecalls performed using filter_fq (BGI Internal software)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then transcriptome de novo assembly is carried out with short reads assembling program - Trinity, the parameter is --seqType fq --min_contig_length 100   --min_glue 3 --group_pairs_distance 250   --path_reinforcement_distance 85 --min_kmer_cov 3
Unigene expression difference analysis by Reads Per Kilobase of exon per Megabase of library size (RPKM), and SOAP with parameter -m 0 -x 500 -s 40 -l 35 -v 5 -r 1

organism: Nicotiana attenuata

source_name: Source-sink transition leaves

extract_protocol:
RNA was extracted with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A. alternata infection according to Sun et al. 2014 in Plant Pathology

value: leaf

tag: genotype

value: WT

tag: developmental stage

value: 35-day-old rossette staged plants


title: WT_0L_Infection

description: Alternaria alternata infection 1 d


title: 1144N0002


title: 1144N0003


title: 1144N0005


title: 1144N0001


title: RNA110714RH_64

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

data_processing:
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection; Trimmed 10 base-pairs from 5' end and 5 base-pairs for 3' end from read sequences.
Bowtie 0.12.7 was used for read alignment with the following parameters: v=2 (2 mismatches allowed), trim3=10, trim5=5, k=1, m=1 (report only unique alignments), p=5
Normalization: Gene and exon expression data were imported into the R (version 3.0.2 - Linux) application environment and samples were normalized using the upper-quartile normalization factor generated for each sample by the edgeR (version 3.4.2) Bioconductor package. Following normalization, genes which had zero expression in more than half of the samples were filtered from the analysis and exons with zero expression in more than half of the samples were set to 0.
Genome_build: mm9
Supplementary_files_format_and_content: RNA110714RH_normalizedGeneCounts.txt: first column has the ENSEMBL Gene ID, subsequent 60 columns provide the normalized reads for each sample for each gene
Supplementary_files_format_and_content: RNA110714RH_normalizedExonCounts.txt: first column has the ENSEMBL 'Gene ID_start location' (i.e. the ensemble gene id has the exon start location after the "underscore --> "_"), subsequent 60 columns provide the normalized reads for each sample for each gene exon;

source_name: Dissected Tissue - Striatum (Brain)

extract_protocol:
Brain striatum region was hand-dissected and frozen. Total RNA was harvested by using manual homogenization using Trizol reagent (Invitrogen), mortar and pestle. It was then precipitated using sodium acetate after isolation.
RNA libraries were prepared for sequencing using TruSeq PolyA Illumina protocol: PolyA(+) RNA was recovered from 1 ug of total RNA using oligo-dT attached to magnetic beads. PolyA(+) RNA was chemically fragmented. Double stranded DNA was made from the fragmented RNA using random hexamers. All ends were repaired.  A single A was added to each of the 3’ ends of each fragment. Illumina adaptors were ligated to the fragments.  Concentration was determined by real time PCR. Samples were mixed for multiplexing. Samples were diluted to target 180 million templates per lane on the flow cell

tag: behavioral phenotype

tag: Sex

value: Male


title: RNA110714RH_63

value: Female


title: Sox2 ChIP-exo

city: Ashburn

first: Zhe

last: Liu

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

description: ChIP-exo-enriched genomic DNA.

data_processing:
Reads mapping - Bowtie2.
Strand separation - Customized.
Strand-sensitive peak calling - GeneTrack.
Peak pairing - Customized.
Thresholding - R.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Bed file containing the genomic localizations of ChIP-exo mapped peak-pairs.

source_name: ES cells treated with TSA, Sox2 ChIP

growth_protocol: Regular mouse ES cell culturing protocol.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to "Rhee, H.S., and Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419" with custom-made Illumina adapters. Single-end 50bp reads.

treatment_protocol: Embryonic stem cells were treated with 50nM TSA (Sigma: T8552) for 8 hours prior to ChIP-exo mapping.

tag: cell type

value: embryonic stem cells

tag: treatment

value: 50nM trichostatin A (TSA) for 8hrs

value: anti-Sox2 (R&D Systems, Cat. # AF2018, Lot # KOY0112011)


title: RNA110714RH_62


title: RNA110714RH_59


title: RNA110714RH_60


title: RNA110714RH_58


title: RNA110714RH_61


title: Celf1muscle_12h_A4403

tag: strain background

value: FVB

tag: genotype/variation

value: containing tet-inducible Celf1 cassette

tag: fed with

value: 2 g/kg doxycycline

tag: time point

value: 12 hours

value: gastrocnemius muscle


title: RNA110714RH_57


title: RNA110714RH_55


title: RNA110714RH_54


title: RNA110714RH_53


title: RNA110714RH_51


title: RNA110714RH_48


title: RNA110714RH_52


title: RNA110714RH_50


title: RNA110714RH_49


title: RNA110714RH_47


title: RNA110714RH_42


title: RNA110714RH_45


title: RNA110714RH_41


title: RNA110714RH_46


title: RNA110714RH_43


title: RNA110714RH_40


title: RNA110714RH_44


title: RNA110714RH_39


title: RNA110714RH_37


title: RNA110714RH_56


title: RNA110714RH_33


title: RNA110714RH_38


title: RNA110714RH_35


title: RNA110714RH_32


title: RNA110714RH_31


title: RNA110714RH_28


title: RNA110714RH_30


title: RNA110714RH_27


title: RNA110714RH_26


title: RNA110714RH_25


title: RNA110714RH_24


title: RNA110714RH_23


title: RNA110714RH_19


title: RNA110714RH_20


title: RNA110714RH_21


title: RNA110714RH_22


title: RNA110714RH_18


title: RNA110714RH_17


title: RNA110714RH_15


title: RNA110714RH_36


title: RNA110714RH_34


title: RNA110714RH_16


title: RNA110714RH_13


title: RNA110714RH_7


title: RNA110714RH_14


title: RNA110714RH_12


title: RNA110714RH_29


title: RNA110714RH_3


title: RNA110714RH_4


title: RNA110714RH_2


title: celf1_clip_muscle

data_processing:
library strategy: CLIP-seq
Reads were trimmed of adapters, and aligned to the mm9 mouse genome and splice junctions using tophat/bowtie.
CLIP clusters were identified as described in Yeo et al, NSMB 2009. Briefly, overlapping reads were combined and tested to assess whether their density is consistent with a null model in which reads would be distributed according to a poisson distribution.  These bed files contain only clusters found within Entrez gene boundaries.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of CLIP clusters

source_name: muscle

extract_protocol:
CLIP was performed using 254 nm UV irradiation as previously described (PMID 19272451), using heart tissue or muscle tissue of 16-week-old mice or cultured C2C12 mouse myoblasts.
Tissue was ground to a powder using liquid nitrogen-cooled mortar and pestle prior to UV irradiation. The dry powder was placed into a 10 cm2 tissue culture dish, sitting on ice, and crosslinked 3 x 400 mJ/cm2.  In between each round of cross-linking, the dish was shaken from side to side, to redistribute the tissue powder and provide maximum opportunity for all tissue particles to be cross-linked. The tissue was then lysed in RIPA buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% sodium deoxycholate, 1% NP-40, 0.5% SDS). The lysate was treated with DNase and RNase If (NEB) for 10 minutes at 37 degrees, with dilutions of 1:10,000 and 1:50,000 providing optimal RNA fragment lengths for downstream purification. Immunoprecipitation was performed using the 3B1 antibody clone against CELF1 (Millipore) and protein A beads (Invitrogen).  The beads were washed twice with RIPA and twice with RIPA containing 1M NaCl. The 3' adapter was pre-adenylated with ImpA (Hafner et al., 2008) and ligated while the RNA-protein complexes were on beads using T4 RNA ligase (Rnl2 truncation) in the absence of ATP (NEB). The complexes were run on SDS-PAGE gel, transferred to nitrocellulose, and isolated from membrane as previously described (Wang et al., 2009). The protein was digested by proteinase K, and RNA was precipitated, and ligated to the 5' adapter using T4 RNA ligase (NEB). Two nucleotide-long barcode sequences were used at the 3' end of the 5' adapter, to allow for censoring of CLIP read PCR duplications (Adapter and primer sequences (5' to 3') are provided in the CLIP-seq_readme.txt). Ligated products were resolved by electrophoresis on TBE-urea polyacrylamide gels, isolated, and subjected to RT-PCR using Superscript III enzyme (Invitrogen) and Phusion polymerase (NEB). PCR primers contained indexes for sequence multiplexing, but for these experiments no samples were multiplexed.

tag: cell/tissue type

value: muscle

tag: ip antibody

value: anti-cugbp1 antibody clone 3B1

tag: ip antibody vendor

value: Millipore

tag: ip antibody cat. #


title: celf1_clip_heart

source_name: heart (ventricle)

value: heart (ventricle)


title: 70Z3 RNA-Seq Replicate 2

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

institute: Insititut de Recherches Cliniques

data_processing:
ChIP-Seq reads were aligned to mm10 using Bowtie2 v2.10; Reads were processed and duplicates were removed using Samtools and a genome coverage file was generated and scaled to reads per million reads (RPM) obtained for each sample using Bedtools. For Miz1 ChIP-Seq, peaks were called using Macs.
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10; Reads were processed with Samtools and countfiles were generated by mapping reads to Ensembl genes using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: .bw files contain normalized RPM (Reads Per Million reads) scores of genomic coverage. *peakcall_peaks.txt files contain called peaks from Macs. txt files are tab-delimited text files containing counts on GRCm38 Ensembl genes

source_name: 70Z3 RNA-Seq

extract_protocol:
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies)
For ChIP-Seq experiments, sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS. For RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS

tag: cell line

value: lymphoblast

tag: development stage

value: Pre-B


title: 70Z3 RNA-Seq Replicate 3


title: celf1_clip_c2c12

source_name: C2C12 myoblast

value: C2C12 myoblast


title: 70Z3 ChIP-Seq H3K27Ac

source_name: 70Z3 ChIP-Seq H3K27Ac

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: 70Z3 RNA-Seq Replicate 1


title: 70Z3 ChIP-Seq H3K9Ac

source_name: 70Z3 ChIP-Seq H3K9Ac


title: 70Z3 ChIP-Seq H3K4Me3

source_name: 70Z3 ChIP-Seq H3K4Me3


title: P6D4 RNA-Seq Replicate 1

source_name: P6D4 RNA-Seq

value: SCID.adh murine thymic lymphoma


title: P6D4 RNA-Seq Replicate 2


title: P6D4 RNA-Seq Replicate 3


title: 70Z3 ChIP-Seq Miz1

source_name: 70Z3 ChIP-Seq Miz1

value: rabbit anti-Miz-1

value: Santa Cruz Biotechnology


title: 70Z3 ChIP-Seq Input

source_name: 70Z3 ChIP-Seq Input


title: P6D4 ChIP-Seq H3K27Ac

source_name: P6D4 ChIP-Seq H3K27Ac


title: P6D4 ChIP-Seq H3K9Ac

source_name: P6D4 ChIP-Seq H3K9Ac


title: P6D4 ChIP-Seq H3K4Me3

source_name: P6D4 ChIP-Seq H3K4Me3


title: MEF NEAT1 KO [RNA-Seq]

description: poly-A+ RNA-sequencing

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were mapped to the genome and a splice junction library based on RefSeq and UCSC knownGenes for MEF and VCaP respectively. Casava 1.8 was used with default parameters. The splice junction library was generated via RSEQtools (Habegger et al. Bioinformatics) using createSpliceJunctionLibrary program. Mm10 or hg18 were used as genome references for MEF and VCAP, respectively.
Reads Per Kilobase of exon per million of library size (RPKM) were calculated using RSEQtools (Habegger et al., Bioinformatics 2011) In short, exons from all isoforms of a gene were merged to create one composite gene model. The number of nucleotides falling in the exons of this composite gene model were counted and normalized by the size of the gene model (per kilobase) and by the size of the library (mapped nucleotides per million)
Genome_build: mm10 for MEFs
Genome_build: hg18 for VCaP experiments
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each sample. For MEF, the corresponding human gene is reported if found. For details see Chakravarty et al. (submitted manuscript: The Estrogen receptor alpha regulated NEAT1 long non-coding RNA promotes prostate cancer progression)

source_name: MEF cell line

growth_protocol: Prostate cell lines were maintained in appropriate medium. VCaP and VCaP ERa expressing cells were maintained in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin streptomycin. NEAT1 WT and KO MEFs were cultured in 1:1 mixture of DMEM and HamF12 supplemented with 10% FCS and 1% penicillin streptomycin

extract_protocol:
MEF cell lines as well as  the VCaP and VCaP ERa cell lines were subjected to RNA extraction using Trizol reagent.
RNA libraries for the MEF cell lines were prepared for sequencing using standard Illumina protocols. In VCaP and VCaP ERa cell lines, Ribo-Zero rRNA removal kit (RZH1046, Epicentre Biotechnologies, Madison, WI) was used to remove ribosomal RNA from 1 ug of total RNA followed by incorporation of deoxy-UTP during second strand cDNA synthesis. Subsequently the uridine containing strand was destroyed and that enabled identification of the transcript orientation.

value: Fibroblast cell line generated from E13.5 embryos of NEAT1 KO mice

tag: strain

tag: passages

value: 2 to 3


title: P6D4 ChIP-Seq Miz1

source_name: P6D4 ChIP-Seq Miz1

tag: cell type


title: P6D4 ChIP-Seq Input

source_name: P6D4 ChIP-Seq Input


title: RNA110714RH_5

source_name: Dissected Tissue - Striatum (Brain)

tag: behavioral phenotype

tag: Sex

value: Female


title: MEF WT [RNA-Seq]

description: poly-A+ RNA-sequencing

value: Fibroblast cell line generated from E13.5 embryos of WT mice


title: RNA110714RH_6

value: Male


title: RNA110714RH_1


title: VCaP [RNA-Seq]

description: poly-A-, stranded RNA-sequencing

source_name: VCaP cell line

value: Prostate cancer cell line

value: 5 to 6


title: si-REST-003-2

city: Los Angeles

middle: Sook

last: Lee

state: California

address: 1501 San Pablo St.

department: Biomedical Engineering

institute: University of Southern California

data_processing:
Bcl conversion: Illumina bcl2Fastq ver 1.8.4  to convert from bcl format to fastq.gz raw reads file
Alignment and read counting done with GT-FAR ver 0.1 using gencode19 annotation.
A second alignment was done with Tophat ver 1.4.0 using hg19_ucsc reference and parameter -G hg19_ucsc.gtf (optional reference annotation)
Cuffdiff/Cufflinks was used for the Tophat alignment
DESeq was run with cases vs. Controls using the GT-FAR read counts
Functional Analysis using DAVID was run on cuffdiff and DESeq data.
Genome_build: hg19_ucsc
Supplementary_files_format_and_content: text files containing analysis of all samples together. Some files will have separate columns for each sample; details in the 'README_2.txt'

growth_protocol: MDA-MB-231 cancer cell lines were maintained in a modified complete medium (RPMI, 10% FBS, 10mM HEPES, 2 mM L-glutamine, 1mM sodium-pyruvate, 0.05mM 2-mercaptoethanol, 11 mM D-glucose).

extract_protocol:
Total RNAs were isolated from cell lines using Trizol (Invitrogen) and digested with Turbo DNase (Ambion) to remove genomic DNA, according to the manufacturer’s instructions.
Libraries from rRNA-depleted samples were prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina) following the recommended protocol starting from the RNA fragmentation stage.  Purification of polyadenylated RNA was omitted.  Libraries were pooled (4 samples per pool), clustered on cBOT (Illumina), and sequenced on HiSeq2000, each pool in one lane.  We performed single-end 100 bp reads.  Reads were mapped using TopHat followed by data analysis using Cufflinks and Cuffdiff software, as well as our own pipeline.

treatment_protocol: For siRNA transfection, we used DharmaFect (Thermo Scientific) or RNAiMax (Invitrogen) according to the manufacturer’s instructions.

value: Breast cancer cell line

value: highly invasive

tag: transfected with

value: REST-003 siRNA


title: si-REST-003-1


title: VcaP ERa [RNA-Seq]

description: poly-A-, stranded RNA-sequencing

source_name: VCaP ERa cell line

value: Prostate cancer cell line overexpressing ERa

value: 4 to 5


title: si-Control-2

value: control siRNA


title: si-Control-1


title: 6nor

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

data_processing:
Basecalls performed with Illumina Pipeline 1.8
Alignment of paired-end reads (FASTQ) to human genome build 19 (hg19) was performed using Genentech’s Genomic Short-Read Nucleotide Alignment Program (GSNAP v. 2012-06-25) (Wu and Watanabe, 2005;Wu and Nacu, 2010; Grant et al., 2011) using known splice-sites (splicesites19) provided by RefGen through the UCSC Genome Browser and the parameters –m 2 –B 5 –N 1 –t 24 –d hg19 --gunzip –s splicesites19 –A sam –-quality-protocol=sanger --trim-mismatch-score=0 --terminal-threshold=100 --ambig-splice-noclip --query-unk-mismatch=1 --npaths=1
Conversion of SAM to BAM file format for compatibility with downstream analysis was performed using SAMtools (Li et al., 2009)
Aligned reads were filtered to remove unaligned reads and reads with >1 match.
Annotations for mRNAs from theRefSeq database and for lincRNAs from Cabili, et al. (Cabili et al., 2011) were used to generate the raw read counts with HTSeq-count program. DESeq (Anders and Huber, 2010) was chosen for normalization to produce normalized counts that were used for statistical analysis.  FPKM values were calculated based on the raw read counts, total number of mapped reads and the length of genes.
Genome_build: hg19
Supplementary_files_format_and_content: 4 tab-delimited text files containing: 1) normalized read counts for genes and 2) normalized read counts for lincRNAs; 3) FPKM values of genes; 4) FPKM values of lincRNAs

source_name: Normal cells

extract_protocol:
4-micron thickness sections on PEN membrane slides were prepared under RNAase free conditions.  Laser capture microdissection of distinct areas of normal lung, pure BAC and invasive adenocarcinoma was performed using the Applied Biosystems Arcturus Veritas Microdissection System (Life Technologies, Grand Island, NY). Total RNA was isolated using the Ambion RecoverAll kit (Life Technologies, Grand Island, NY) according to manufacturer’s protocol.
Sequencing libraries were prepared using the Ovation RNA-Seq FFPE (7150-08) and Encore NGS Library System 1 kits (300-08; sans multiplexing) according to manufacturer’s protocol (NuGEN Technologies, Inc., San Carlos, CA).
Non-multiplexed sequencing of 100 bp paired-end reads was performed using the Illumina GAIIx (Illumina, Inc., San Diego, CA) according to manufacturer’s protocols

treatment_protocol: Samples were formalin-fixed and paraffin-embedded.

tag: patient id

tag: tissue source

value: laser micro-dissected archival FFPE tissue specimens

tag: tissue type

value: surrounding normal lung (nor)


title: 6inv

source_name: Tumor cells

value: invasive lung carcinoma (inv)


title: 4inv


title: 6ais

value: non-invasive adenocarcinoma in situ (ais)


title: 5nor


title: 5inv


title: 4ais


title: 3nor


title: 1nor


title: 2nor


title: 3inv


title: 2inv


title: 3ais


title: 5ais


title: 1inv


title: 4nor


title: wt-REST

data_processing:
Bcl conversion: Illumina bcl2Fastq ver 1.8.4 to convert from bcl format to fastq.gz raw reads file
Alignment and read counting done with GTFAR ver 0.1 using gencode19 annotation.
A second alignment was done with Tophat ver 1.4.0 using hg19_ucsc reference and parameter -G hg19_ucsc.gtf (optional reference annotation)
Transcript abundance estimation on the second alignment done with Cufflinks ver 1.0.1 using parameters -u (for multi-read-correct), -b hg19_ucsc.fa (for bias detection and correction) and -G hg19_ucsc.gtf (for optional reference annotation)
Genome_build: hg19_ucsc
Supplementary_files_format_and_content: tab-delimited text files from GT-FAR runs and Cufflinks runs which include RPKM values for each sample and isoform counts for each sample; more details in the 'README_1.txt'

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 and MCF-7 cancer cell lines were maintained in a modified complete medium (RPMI, 10% FBS, 10mM HEPES, 2 mM L-glutamine, 1mM sodium-pyruvate, 0.05mM 2-mercaptoethanol, 11 mM D-glucose).

extract_protocol:
Total RNAs were isolated from cell lines using Trizol (Invitrogen) and digested with Turbo DNase (Ambion) to remove genomic DNA, according to the manufacturer’s instructions.
Libraries from rRNA-depleted samples were prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina) following the recommended protocol starting from the RNA fragmentation stage. Purification of polyadenylated RNA was omitted. Libraries were pooled (4 samples per pool), clustered on cBOT (Illumina), and sequenced on HiSeq2000, each pool in one lane. We performed single-end 100 bp reads. Reads were mapped using TopHat followed by data analysis using Cufflinks and Cuffdiff software, as well as our own pipeline.

treatment_protocol: Lipofectamine 2000 (Invitrogen) was used for mt- or wt-REST cDNA plasmid transfection experiments. For siRNA transfection, we used DharmaFect (Thermo Scientific) or RNAiMax (Invitrogen) according to the manufacturer’s instructions.

value: wt-REST

tag: genotype/variation

value: overexpression of wild type REST


title: 2ais


title: si-REST_1

value: weakly invasive

value: si-REST

value: Downregulation of REST


title: EGFP

value: EGFP (control)

value: EGFP control


title: mt-REST

value: mt-REST

value: overexpression of mutant REST


title: si-REST_2


title: 1ais


title: Drought stressed soybean leaves; line LD003309, rep 1d

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: library strategy: PARE-seq

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the soybean genome.
PARE-seq: the adapter sequences were trimmed from raw sequence reads, and then the PARE sequences were trimmed to the lengths between 18 and 21 nucleotides. PARE reads were mapped to the soybean genome.
Genome_build: The Soybean (Glycine max) genome; JGI Glyma1
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Glycine max

source_name: soybean leaves

extract_protocol: Small RNA libraries were constructed from total RNA isolated from soybean using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). The libraries were sequenced on an Illumina HiSeq 2000 at the Delaware Biotechnology Institute (Newark, DE). Degradome libraries (PARE) constructed from total RNA isolated from soybean using Plant RNA Reagent (Invitrogen, Life Technologies, USA). The libraries were constructed as previously described (Zhai et al. 2009 PMID: 23810899). The libraries were sequenced on an Illumina HiSeq 2000 at the Delaware Biotechnology Institute (Newark, DE).

tag: tissue

value: soybean leaves

tag: line

tag: treatment

value: drought stressed


title: si-Gapdh

tag: cell line

value: si-GAPDH (control)

value: control


title: NEB_hRRP40

city: Aarhus

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

data_processing:
Basecalls were done using CASAVA from Illumina
Paired-end reads were mapped to hg19 using the STAR mapping pipeline (Dobin et al. 2013)
RPM values were calculated using the rpkmforgenes.py script (Ramsköld et al. 2009)
RP10M values were calculated and normalized to control knock-down (NEB_GFP) and log2 ratios calculated and plotted as shown in Figure 6E (custom R script)
Genome_build: hg19
Supplementary_files_format_and_content: tab-deliminated RP10M (reads per ten million mapped reads) values for snoRNAs and their flanking regions;
Figure6E_RNAseq_DataTable_PlottedValues.txt; Average RP10M (reads per ten million mapped reads) values and RP10M ratios for all samples and regions analyzed
Figure6E_RNAseq_DataTable_RP10Mvalues.txt; RP10M values for all samples and regions analyzed

source_name: HeLa cells

growth_protocol: HeLa cells were grown in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% Penicilin/Streptavidin, at 37°C, 5% CO2.

extract_protocol:
Cells were harvested on day six and RNA was extracted using TRIzol reagent.
5ug of total RNA was rRNA depleted using RIBOZERO (Epicentre) and cDNA libraries were generated with NEBNext Small RNA Library kit (NEB) according to the manufacturer’s instructions.

treatment_protocol:
For RNAi assays, cells were seeded at low confluence (approximately 3300 cells/cm2) and grown for 24 hr before the first transfection. Transfections were performed using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions and siRNA at a final concentration of 15 nM of each siRNA;
Target  Sense (5 -3 )
eGFP: GACGUAAACGGCCACAAGUdTdT
hRRP40: CACGCACAGUACUAGGUCAdTdT
hRRP6: CCAGUUAUACAGACCUAUAdTdT
hDIS3: AGGUAGAGUUGUAGGAAUAdTdT
hDIS3L: CGUAAAGACUUGAGGAAAAdTdT
48 hr after the first transfection, media was changed and the transfection was repeated. At least five hours after each transfection, media was replaced with fresh media. Cells were harvested 24-48 hr after the second transfection, preventing plates from being more than 90% confluent.

value: HeLa S2

value: hRRP40 siRNA

tag: molecule subtype

value: rRNA-depleted total RNA


title: Drought stressed soybean leaves; line IA3023, rep 1d

description: library strategy: PARE-seq


title: Well-watered soybean leaves (control for drought); line LD003309, rep 1d

description: library strategy: PARE-seq

value: well watered


title: NEB_GFP

value: GFP siRNA control


title: Opened flowers, the first day of flowering, rep 1

description: library strategy: PARE-seq

source_name: soybean opened flower

value: soybean opened flower

tag: sample time

value: first day of flowering


title: Opened flowers, the first day of flowering, rep 2

description: library strategy: PARE-seq


title: Well-watered soybean leaves (control for drought); line IA3023, rep 1d

description: library strategy: PARE-seq


title: S-001167506

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed based on evidence of adaptor contamination then mapped to hg19 whole genome using tophat v.2.0.8 with parameters -G [hg19_ERCC_gtf] --no-novel-juncs --transcriptome-only
For each sample, Cufflinks (v.2.1.1) was used to quantify External RNA Controls Consortium (ERCC) Spike-In and hg19 transcripts based on reads that mapped to the provided hg19 and ERCC reference files.
Differential expression of genes and transcripts for all paired samples passing QC and that had been treated with vitamin D or left untreated was obtained using Cuffdiff (v.2.1.1) with the quantified transcripts computed by Cufflinks (v.2.1.1), while applying bias correction. Options: -p 12 --min-outlier-p 0.05 -b [hg19_reference_index] -u [hg19_gtf] Control_Baseline,Asthma_Baseline,Control_Albuterol,Asthma_Albuterol,Control_Vitamin-D,Asthma_Vitamin-D  [List of accepted_hits.bam for each sample sorted by condition]
CummeRbund R package (v.2.0.0) was used to create FPKM matrix of all samples and this was merged with cuffdiff output genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample that passed QC (ALL_Sample_FPKM_Matrix.txt) and gene-based differential expression results for pairs of samples that passed QC under baseline and vitamin D treatment conditions (cuffdiff output: asthma_control_vitD_gene_exp.diff)

source_name: airway smooth muscle cells

growth_protocol: Primary ASM cells were isolated from white aborted lung transplant donors with fatal asthma or no chronic illness. Passages 4 to 7 ASM cells maintained in Ham's F12 medium supplemented with 10% FBS were used in all experiments.

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA).

treatment_protocol: Cells from each donor were treated with 100 nM vitamin D,  1 μM albuterol, or control vehicle for 18 h.

tag: disease

value: Control

value: Albuterol

tag: donor

value: human airway smooth muscle cells


title: S-001167504


title: S-001167505


title: S-001167502

value: Asthma


title: S-001167500


title: S-001167503


title: Unopened flowers, 1 day before flowering, rep 2

description: library strategy: PARE-seq

source_name: soybean unopened flower

value: soybean unopened flower

value: 1 day before flowering


title: S-001167501


title: Unopen flowers, 1 day before flowering, rep 1

description: library strategy: PARE-seq


title: Ovaries, dissected from unopened flowers, rep 1

description: library strategy: PARE-seq

source_name: soybean ovaries

value: soybean ovaries


title: S-001167499


title: S-001167498


title: Nodules, 25 days post-inoculation, dissected from roots

description: library strategy: PARE-seq

source_name: soybean nodules

value: soybean nodules

value: 25 days post-inoculation


title: Ovaries, dissected from unopened flowers, rep 2

description: library strategy: PARE-seq


title: Anthers, dissected from unopened flowers, rep 1

description: library strategy: PARE-seq

source_name: soybean anthers

value: soybean anthers


title: Nodules, 30 days post-inoculation, dissected from roots

description: library strategy: PARE-seq

value: 30 days post-inoculation


title: Anthers, dissected from unopened flowers, rep 2

description: library strategy: PARE-seq


title: S-001167496


title: NEB_DIS3_DIS3L_hRRP6

value: HeLa S2

value: DIS3, DIS3L and hRRP6 siRNA (triple knock-down)


title: Nodules, 15 days post-inoculation, dissected from roots

description: library strategy: PARE-seq

value: 15 days post-inoculation


title: S-001167495


title: Nodules, 10 days post-inoculation, dissected from roots

description: library strategy: PARE-seq

value: 10 days post-inoculation


title: Nodules, 20 days post-inoculation, dissected from roots

description: library strategy: PARE-seq

value: 20 days post-inoculation


title: S-001167497


title: S-001167493


title: Nodules, 30 days post-inoculation, dissected from roots, rep 2


title: S-001167494


title: Nodules, 30 days post-inoculation, dissected from roots, rep 1


title: Nodules, 25 days post-inoculation, dissected from roots, rep 2


title: S-001167492


title: Nodules, 25 days post-inoculation, dissected from roots, rep 1


title: S-001167489


title: Nodules, 25 days post-inoculation, dissected from roots, rep 3


title: S-001167487

description:
All_Sample_FPKM_Matrix.txt
asthma_control_vitD_gene_exp.diff

value: Baseline


title: S-001167491

value: Control


title: Nodules, 20 days post-inoculation, dissected from roots, rep 2


title: Nodules, 20 days post-inoculation, dissected from roots, rep 1


title: Nodules, 20 days post-inoculation, dissected from roots, rep 3


title: Nodules, 15 days post-inoculation, dissected from roots, rep 3


title: S-001167490

value: Albuterol


title: S-001167485

value: human airway smooth muscle cells


title: S-001167486


title: S-001167484

value: Asthma


title: S-001167482


title: S-001167481


title: Nodules, 30 days post-inoculation, dissected from roots, rep 3


title: S-001167479


title: S-001167488


title: Nodules, 10 days post-inoculation, dissected from roots, rep 2


title: S-001167476


title: “Bent” leaf, rep 2

value: soybean leaves


title: Nodules, 10 days post-inoculation, dissected from roots, rep 1


title: Vinton leaves (flagellin treated 30 minutes), rep 1

tag: cultivar

value: Vinton

value: flagellin treated 30 minutes


title: Nodules, 10 days post-inoculation, dissected from roots, rep 3

value: soybean nodules


title: “Bent” leaf, rep 1


title: S-001167483


title: S-001167474


title: S-001167477


title: Nodules, 15 days post-inoculation, dissected from roots, rep 2


title: Vinton leaves (flagellin treated 30 minutes), rep 2


title: S-001167472


title: Vinton leaves (Control of flagellin treated: water 30 minutes), rep 1

value: water 30 minutes


title: Vinton leaves (Control of flagellin treated: water 30 minutes), rep 2


title: Nodules, 15 days post-inoculation, dissected from roots, rep 1


title: Dassel leaves (flagellin treated 30 minutes), rep 1

value: Dassel


title: S-001167471


title: S-001167478


title: S-001167480


title: Williams 82 leaves (flagellin treated 30 minutes), rep 2

tag: variety

value: Williams 82


title: S-001167470

value: Vitamin-D


title: Dassel leaves (Control of flagellin treated: water 30 minutes), rep 2


title: Dassel leaves (Control of flagellin treated: water 30 minutes), rep 1


title: S-001167468


title: Williams 82 leaves (flagellin treated 30 minutes), rep 1


title: S-001167475


title: S-001167473


title: S-001167467


title: S-001167466


title: Williams 82 leaves (Control of flagellin treated: water 30 minutes), rep 2


title: S-001167465


title: Victon leaves (Chitin treated 30 minutes), rep 2

value: Victon

value: Chitin treated 30 minutes


title: Victon leaves (Chitin treated 30 minutes), rep 1


title: S-001167464


title: Williams 82 leaves (Control of flagellin treated: water 30 minutes), rep 1


title: Dassel leaves (flagellin treated 30 minutes), rep 2


title: S-001167462


title: Victon leaves (Control of chitin treated: water 30 minutes), rep 2


title: S-001167463


title: Dassel leaves (Chitin treated 30 minutes), rep 1


title: Victon leaves (Control of chitin treated: water 30 minutes), rep 1


title: S-001167461


title: S-001167469


title: S-001167458


title: Dassel leaves (Control of chitin treated: water 30 minutes), rep 1


title: S-001167456


title: S-001167457


title: S-001167460


title: Williams 82 leaves (Chitin treated 30 minutes), rep 1

value: William 82


title: Williams 82 leaves (Chitin treated 30 minutes), rep 2


title: S-001167453


title: S-001167455


title: Williams 82 leaves (Control of chitin treated: water 30 minutes), rep 2


title: Williams 82 leaves (Control of chitin treated: water 30 minutes), rep 1


title: Drought stressed soybean leaves; line LD003309, rep 3

value: drought stressed


title: Dassel leaves (Chitin treated 30 minutes), rep 2


title: Lactimidomycin treated HCT116

city: Ghent

first: Gerben

last: Menschaert

address: Coupure Links 653

country: Belgium

institute: Ghent University, Faculty of BioScience Engineering

description:
RIBO-seq
HCT116_LTM_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligning the reads was done using STAR (2.3.0e_r291). The STAR based workflow sequentially aligns the reads to STAR indices composed of the following sequences (a) the PhiX bacteriophage genome, (b) Homo sapiens rRNA (obtained using BioMart, filtered on Mt_rRNA and rRNA gene types) and (c) Homo sapiens complete genome (obtained from the corresponding IGenome repository). The STAR internal clipping function was used to clip the 3’ adaptor, two mismatches were allowed for the alignment, the option seedSearchStartLmaxOverLread was set to 0.5 and no introns were allowed for the alignment against the PhiX genome. Reads where mapped allowing both uniquely and multi-mapping reads (up to 15 locations).
Only reads with a length between 26 and 34 bases (i.e. only the relevant ribosome protected fragments (RPFs)) were retained for further genomic coordinate mapping. RPF alignments were assigned to a specific P site nucleotide based on the length of the fragment. The offset from the 5’ end of the alignment was +12, +13 and +14 respectively for alignment of less than or equal to 30 bases long, 31–33 bases long, and greater than or equal to 34 bases long.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files where created using the PROTEOFORMER pipeline, data values represent the number of mapped RPF fragments.

source_name: Colorectal carcinoma cell line

growth_protocol: HCT116 cells were cultivated in McCoy's 5A (Modified) Medium (Gibco) supplemented with 10% fetal bovine serum, 2 mM alanyl-L-glutamine dipeptide (GlutaMAX, Gibco), 50 units/ml penicillin and 50 µg/ml steptamycin at 37°C and 5% CO2.

extract_protocol:
100 µl of the clarified HCT116 cell lysate (equivalent to 4 × 106 cells) was used as input for ribosome footprinting. The A260 absorbance of the lysate was measured with Nanodrop (Thermo Scientific) and for each A260, 5 units of ARTseq Nuclease (Epd icentre) were added to the samples. The nuclease digestion proceeded for 45 min at room temperature and was stopped by adding SUPERase.In Rnase Inhibitor (Life Technologies). Next, the ribosome protected fragments (RPFs) were isolated using Sephacryl S400 spin columns (GE Healthcare) according to the procedure described in ‘ARTseq Ribosome Profiling Kit, Mammalian’ (Epicentre). The RNA was extracted from the samples using acid 125 phenol:24 chloroform:1 isoamyl alcohol and precipitated overnight at -20°C by adding 2 μl glycogen, 1/10th volume of 5 M ammonium acetate and 1.5 volumes of 100% isopropyl alcohol. After centrifugation at 18,840 × g and 4°C for 20 min, the purified RNA pellet was resuspended in 10 μl nuclease free water.
The HCT116 libraries were created according to the guidelines described in the ARTseq Ribosome profiling Kit, Mammalian protocol (Epicentre). The RPFs were initially rRNA depleted using the Ribo-Zero Magnetic Kit (Human/Mouse/Rat, Epicentre), omitting the 50°C incubation step. Cleanup of the rRNA depletion reactions was performed through Zymo RNA Clean & Concentrator-5 kit (Zymo Research) using 200 μl binding buffer and 450 μl absolute ethanol. The samples were separated on a 15% urea-polyacrylamide gel and footprints of 26 to 34 nucleotides long were excised. RNA was extracted from the gel and precipitated. The pellet was resuspended in 20 μl nuclease-free water. Next, RPFs were end polished, 3’ adaptor ligated, reverse transcribed and PAGE purified. 5 μl of circularized template DNA was used in the PCR reaction and amplification proceeded for 11 cycles. The libraries were purified with AMPure XP beads (Beckman Coulter) and their quality was assessed on a High Sensitivity DNA assay chip (Agilent technologies). The concentration of the libraries was measured with qPCR and they were single end sequenced on a Hiseq (Illumina) for 50 cycles.

treatment_protocol: Cultures at 80-90% confluence were treated with 50 µM LTM or 100 µg/ml CHX (Sigma, USA) for 30 min at 37°C. Subsequently, cells were washed with PBS, harvested by trypsin-EDTA, suspended and washed again with PBS and recovered by 5 min of centrifugation at 1,500 × g, all in the presence of CHX to maintain the polysomal state. Cell pellets were resuspended in ice-cold lysis buffer, formulated according to Guo et al. (2010)3 (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2 mM dithiothreitol (DTT), 100 mg/ml CHX, 1 × complete and EDTA-free protease inhibitor cocktail (Roche)), at a concentration of 40 × 106 cells/ml. After 10 min of incubation on ice with periodic agitation, lysed samples were passed through QIAshredder spin columns (Qiagen) to shear the DNA. Subsequently, the flow-throughs were centrifuged for 10 min at 16,000 × g and 4°C. The recovered supernatant was aliquoted, snap-frozen in liquid nitrogen and stored at -80°C for subsequent ribosome footprint recovery and cDNA library generation.

tag: cell type

value: Colorectal carcinoma derived cell line

tag: treated with

value: 50 µM lactimidomycin for 30 min at 37°C

value: Ribosome protected fragments


title: Drought stressed soybean leaves; line LD003309, rep 1


title: Drought stressed soybean leaves; line IA3023, rep 3


title: mu_total4arep3

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

description:
mmdiff_GENE_DE-total4a-totalcontrol.out
mmdiff_GENE_DOD-poly4a-polycontrol-total4a-totalcontrol.out
mmdiff_GENE_DOD-poly4a-total4a-polycontrol-totalcontrol.out
mmdiff_GENE_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_GENE_DOD-sub4a-total4a-subcontrol-totalcontrol.out
mmdiff_TRANSCRIPT_DE-total4a-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-poly4a-polycontrol-total4a-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-poly4a-total4a-polycontrol-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-total4a-subcontrol-totalcontrol.out
mmdiff_5UTRGENE_DE-total4a-totalcontrol.out
mmdiff_5UTRGENE_DOD-poly4a-polycontrol-total4a-totalcontrol.out
mmdiff_5UTRGENE_DOD-poly4a-total4a-polycontrol-totalcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-total4a-subcontrol-totalcontrol.out

data_processing:
Base caller: Illumina RTA 1.13.48
Bustard version 1.9.4
Demultiplexing (internal processing)
The RNA-seq reads were aligned to version 68 of the Ensembl human reference cDNA and ncRNA sequences using Bowtie 1.
The MMSEQ gene expression analysis software (38) was then used to estimate transcript expression levels.
The marginal posterior mean and standard deviation of the log expression parameter corresponding to each transcript or set of transcripts (i.e. gene or probe) was then used as the outcome in a Bayesian model selection algorithm implemented in the MMDIFF software.
Genome_build: Ensembl 68
Supplementary_files_format_and_content: Normalised count values start with suffix mu_*
Supplementary_files_format_and_content: MMSEQ and MMDIF output table
All the output is described in the following website:
https://GitHub.com/eturro/mmseq

growth_protocol: MCF7 cells were grown in DMEM 10% FBS under standard cell culture conditions.

extract_protocol:
Total RNA was extracted using TRIAZOL reagent. Subpolysomal and polysomal RNA was extracted using Guanidine HCl-ethanol precipitation, followed by LiCl precipitation. All samples were then repurified using miRNeasy kit (Qiagen).
Processing of total RNA following Illumina's standard TruSeq® RNA Sample Prep Kit-v2 protocol.

treatment_protocol: Control ON-TARGETplus Non-targeting Pool and ON-TARGETplus SMART pool siRNAs targeting eIF4A1 were transfected into cells according to manufacturer's instructions (Thermo Scientific). DharmaFECT1 Transfection Reagent was used.


title: mu_total4arep4


title: S-001167459

value: human airway smooth muscle cells


title: Drought stressed soybean leaves; line IA3023, rep 2


title: mu_total4arep2


title: mu_total4arep1


title: Drought stressed soybean leaves; line IA3023, rep 1


title: mu_sub4arep1

description:
mmdiff_GENE_DE-sub4a-subcontrol.out
mmdiff_GENE_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_GENE_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_GENE_DOD-sub4a-total4a-subcontrol-totalcontrol.out
mmdiff_TRANSCRIPT_DE-sub4a-subcontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-total4a-subcontrol-totalcontrol.out
mmdiff_5UTRGENE_DE-sub4a-subcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_5UTRGENE_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-total4a-subcontrol-totalcontrol.out


title: Well-watered soybean leaves (control for drought); line LD003309, rep 3

value: well-watered


title: mu_sub4arep3


title: mu_sub4arep4


title: Well-watered soybean leaves (control for drought); line LD003309, rep 2

value: soybean leaves


title: mu_sub4arep2

description:
mmdiff_GENE_DE-sub4a-subcontrol.out
mmdiff_GENE_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_GENE_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_GENE_DOD-sub4a-total4a-subcontrol-totalcontrol.out
mmdiff_TRANSCRIPT_DE-sub4a-subcontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_5UTRGENE_DE-sub4a-subcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_5UTRGENE_DOD-sub4a-subcontrol-total4a-totalcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-total4a-subcontrol-totalcontrol.out


title: Well-watered soybean leaves (control for drought); line LD003309, rep 1


title: Well-watered soybean leaves (control for drought); line IA3023, rep 3


title: mu_poly4arep4

description:
mmdiff_GENE_DE-poly4a-polycontrol.out
mmdiff_GENE_DOD-poly4a-polycontrol-total4a-totalcontrol.out
mmdiff_GENE_DOD-poly4a-total4a-polycontrol-totalcontrol.out
mmdiff_GENE_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_TRANSCRIPT_DE-poly4a-polycontrol.out
mmdiff_TRANSCRIPT_DE-poly4a-polycontrol.out
mmdiff_TRANSCRIPT_DOD-poly4a-polycontrol-total4a-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-poly4a-total4a-polycontrol-totalcontrol.out
mmdiff_TRANSCRIPT_DOD-sub4a-subcontrol-poly4a-polycontrol.out
mmdiff_5UTRGENE_DE-poly4a-polycontrol.out
mmdiff_5UTRGENE_DOD-poly4a-polycontrol-total4a-totalcontrol.out
mmdiff_5UTRGENE_DOD-poly4a-total4a-polycontrol-totalcontrol.out
mmdiff_5UTRGENE_DOD-sub4a-subcontrol-poly4a-polycontrol.out


title: mu_poly4arep1


title: Well-watered soybean leaves (control for drought); line IA3023, rep 2


title: Well-watered soybean leaves (control for drought); line IA3023, rep 1


title: Dassel leaves (Control of chitin treated: water 30 minutes), rep 2


title: Drought stressed soybean leaves; line LD003309, rep 2


title: Cycloheximide treated HCT116

description:
RIBO-seq
HCT116_CHX_1

value: 100 µg/ml cycloheximide for 30 min at 37°C


title: mu_poly4arep2


title: Opened flowers, rep 2

value: soybean opened flower


title: mu_totalcontrolrep2


title: mu_totalcontrolrep3


title: Unopened flower, rep 2

value: soybean unopened flower


title: Opened flowers, rep 1


title: mu_totalcontrolrep4


title: mu_totalcontrolrep1


title: mu_subcontrolrep1


title: Ovaries, rep 1

value: soybean ovaries


title: Anthers, rep 2

value: soybean anthers


title: mu_subcontrolrep3


title: Anthers, rep 1


title: mu_polycontrolrep4


title: mu_polycontrolrep3


title: mu_polycontrolrep1


title: mu_poly4arep3


title: mu_polycontrolrep2


title: CDK13sh1

first: Joan

last: Conaway

institute: Stowers Institute

description: RNAseq after CDK13 RNAi

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Ensembl 67 GTF human annotations using TopHat v2.0.10 and Bowtie v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches.
UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: bigWig format (http://genome.ucsc.edu/goldenPath/help/bigWig.html)

growth_protocol: HCT116 cells were grown in DMEM medium (Sigma D6429) with 10% FBS (Sigma).

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and residual DNA was digested with RNase-free DNase I (NEB).
Total RNA was depleted of rRNA with Ribo-zero (Illumina) and libraries were made with the Tru-Seq mRNA kit (Illumina)

treatment_protocol: HCT116 cells were infected with  lentivirus for 24 hrs and then selected with 2 ug/ml Puromycin for 48 hrs before harvest.

value: human colon cancer cell

value: CDK13 knockdown

tag: shRNA

value: ATCAGCTTCTTTATCTTCAGG

value: Ribosomal RNA-depleted total RNA


title: CDK13sh2

description: RNAseq after CDK13 RNAi

value: TAAATCAGCAAGAAGACATCG


title: CDK12sh2

description: RNAseq after CDK12 RNAi

value: CDK12 knockdown

value: AACAATCTCCTCTTTCAGTGC


title: Ovaries, rep 2


title: Unopened flowers, rep 1


title: CDK9sh2

description: RNAseq after CDK9 RNAi

value: CDK9 knockdown

value: TGATTGAGATTTGTCGAACCA


title: CDK9sh1

description: RNAseq after CDK9 RNAi

value: CTACTACATCCACAGAAACAA


title: GFPsh1

description: RNAseq after non-targeting-RNAi

value: GFP (non-targeting) control

value: GCAAGCTGACCCTGAAGTTCA


title: GFPsh2

description: RNAseq after non-targeting-RNAi


title: CDK12sh1

description: RNAseq after CDK12 RNAi

value: TTCAGAGTTATAGAGCCGAGC


title: VCaP200

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

data_processing:
Base calling was performed using the software provided with the Illumina HiSeq 2000
Sequences of the first mates were trimmed 8 bp upstream and of the second mates 7 bp upstream using FastX toolkit 0.0.13
InFusion v0.6.1 (http://bitbucket.org/kokonech/infusion) was applied for chimeric RNA detection using Ensembl v68 data and the following configuration: --library RF --allow-intergenic --allow-non-coding --min-split-reads 2 --min-span-pairs 0 --min-fragments 3 --min-unique-split-reads 0 --min-unique-alignment-rate 0.08
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited reports listing fusions discovered with InFusion v0.6.1

source_name: VCaP cells

growth_protocol: VCaP was cultured in Dulbecco’s modified Eagle medium (Life Technologies, Darmstadt, Germany) supplemented with 2mM L-glutamine, 1mM sodium pyruvate and 10% of fetal bovine serum (Biochrom, Berlin, Germany);  LNCap was cultured in RPMI1640 (Life Technologies) supplemented with 10% fetal bovine serum (Biochrom).

extract_protocol:
From each cell line, 700,000 cells were extracted using the SPLIT RNA extraction kit (Lexogen GmbH, Vienna, Austria).
Strand-specific NGS libraries were prepared from 500 ng RNA using the SENSE mRNA-Seq library preparation kit (Lexogen GmbH, Vienna, Austria).

value: VCaP

value: Prostate cancer cell line

tag: passage


title: LNCaP200

source_name: LNCaP cells

value: LNCaP


title: VCaP500


title: LNCaP500


title: mu_subcontrolrep2


title: mu_subcontrolrep4


title: Femoral plaque 159

city: Kuopio

first: Einari

last: Aavik

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: library strategy: MethylCap

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired end sequencing reads (51 bp) were mapped to human genome hg19 using Bowtie v0.12.9 software.3 The Bowtie parameters were set to 0 mismatches in the seed (first 28 nucleotides).
Only unique reads were retained and both fragments must be located within 400 bp of each other on the human reference genome hg19
Multiple paired reads with the exact same location in one sample were discarded, as these are most likely amplified from the same sequence
Methylated regions were annotated using Homo Sapiens Ensembl database v56.
Methylated regions were binned to promoter (from -2000 to +500 from transcription start site), exon (with exon number), intron and intergenic compartments
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: bed files, counts represent the highest number of overlapping reads observed in defined genomic locus. Length of loci varies from ~500 bp to ~3000 bp.

source_name: Femoral artery atherectomy

extract_protocol:
Purified chromosomal DNA was sonicated, methylated fragments captured by MethylCap kit (Diagenode AF-100-0048, Belgium) and sequenced
Multiplexed paired end ChIP protocol’ (Illumina): Sample Prep Master Mix Set 1 (NEB E6040) was used in combination with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001) on Apollo 324 with PrepX-DNA Library Kit (IntegenX Cat# 400040)

value: athersclerotic human artery

tag: gender

value: female

tag: age


title: Femoral plaque 152

description: library strategy: MethylCap


title: Femoral plaque 79

description: library strategy: MethylCap

value: male


title: Femoral plaque 232

description: library strategy: MethylCap


title: Femoral plaque 21

description: library strategy: MethylCap


title: Femoral plaque 258

description: library strategy: MethylCap


title: Femoral plaque 148

description: library strategy: MethylCap


title: Mammary artery 052

description: library strategy: MethylCap

source_name: Mammary artery

value: healthy human artery


title: sRNAs_Illumina

city: Paterna

first: Regis

middle: Lopes

last: Correa

state: Valencia

address: CL. Catedrático Agustín Escardino 9

country: Spain

data_processing:
Base-calling by HiSeq Control Soft. 1.4.8 and CASAVA 1.7.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then separeted in diffrent files according to their sizes.
The unique reads ranging from 16 to 26 nt were extracted from files using locally developed perl scripts.
Unique sequences were used to BLAST against the miRBASE database (release 19). Only sequences having 100% ID and no gaps were retrieved.
Unique sequences were aligned to coffee ESTs using the SOAP2 software.
Genome_build: miRBASE release 19
Supplementary_files_format_and_content: Tab-delimited table with the number of reads mapping to known and new microRNA sequences.

organism: Coffea canephora

source_name: Leaves

growth_protocol: Plant were harvested from field plantations

extract_protocol:
Total RNAs were extracted with Concert™ Plant RNA Reagent (Invitrogen)
Libraries were prepared according to Illumina's instructions. Procedures were: Acrylamide gel purification of the small RNA fragments; Single-stranded ligation of 3’ adapter; Single-stranded ligation of 5’ adapter; Acrylamide gel purification; Reverse transcription and PCR amplification to generate the DNA Colonies Template Library; Library quantification and dilution at 10 nM.

value: Leaves

tag: strain

value: Conilon

tag: developmental stage

value: Flowering plants


title: Mammary artery 056

description: library strategy: MethylCap

tag: tissue


title: Femoral plaque 99

description: library strategy: MethylCap


title: Mammary artery 021

description: library strategy: MethylCap


title: Mammary artery 015

description: library strategy: MethylCap


title: Mammary artery 017

description: library strategy: MethylCap


title: NS#4_A

city: Basel

first: Julien

last: Roux

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

description: control

data_processing:
Cutadapt (version 1.2.1) was used to trim adapter sequences from RNA-seq reads. Tophat (version 2.0.6) was used to perform gapped alignments of reads to the human reference genome (Ensembl, release 69, October 2012). Ensembl gene model annotations (GFF) were supplied to guide the initial alignment step. Only uniquely mapped reads with less than 3 mismatches to the genome sequence were retained.
The script htseq-count from the package HT-Seq (http://www-huber.embl.de/users/anders/HTSeq/) was used to calculate the number of reads mapped to human genes in each sample (with the options –s no, -m union and -t exon). Gene models were downloaded from the Ensembl database (release 69, October 2012). Gene lengths were downloaded from the Ensembl database (release 69, October 2012), and used to calculate Reads Per Kilobase of exon per Megabase of library size (RPKM).
Genome_build: human reference genome (Ensembl, release 69, October 2012)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: lymphoblastoid cell line

growth_protocol: The human cell line GM19238 was cultured at 5% CO2 and 37°C in RPMI 1640 medium supplemented with 2mM L-glutamine and 15% fetal bovine serum, per Coriell’s recommendations (http://ccr.coriell.org/Sections/Support/Global/Lymphoblastoid.aspx?PgId=213). The medium was also supplemented with 100 IU/mL penicillin and 100 μg/mL streptomycin. Cells were counted and split three times a week to 350,000 cells/mL.

extract_protocol:
RNA from both time points was extracted using the RNeasy Plus 96 kit (Qiagen). The quality and concentration of all RNA samples were measured using the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfections were performed with the Lonza 96-well nucleofector system, using transfection solution SF and transfection program DN-100. On-Target SmartPool siRNAs from Dharmacon were used to knockdown target genes. For each transfection, one million cells were transfected with 50 pmol siRNA. Five independent transfections (biological replicates) were performed for each splicing factor. After transfection, cells were plated in 1 mL of medium in 96‐well plates and incubated for 48 hours. After 48 hours, 500 μL of cell culture were removed for RNA extraction for qPCR, 100 μL of fresh medium was added to each well and plates were incubated for an additional 24 hours. After a total of 72 hours of incubation, the remaining culture was pelleted for RNA extraction for RNA-sequencing library preparation. The control siRNAs consisted of a pool of four siRNAs specifically designed not to target any human or mouse gene. All transfections were conducted in one phase on three separate 96-well plates.

value: lymphoblastoid cell line

tag: hapmap individual

tag: condition

value: control

tag: percentage knockdown (qpcr after 48h)

tag: rin score

tag: multiplexing index sequence

value: TTAGGC

tag: multiplexing index number


title: NS#1_A

description: control

value: AGTCAA


title: NS#2_C

description: control

value: TAGCTT


title: NS#1_B

description: control

value: ATCACG


title: NS#2_A

description: control

value: TGACCA


title: 40_PCBP2_G

value: knockdown

tag: splicing factor targeted

tag: splicing factor targeted (ensembl id)


title: 42_RNPS1_E

tag: cell type

value: GGCTAC


title: 40_PCBP2_D

value: CGATGT


title: 40_B


title: 37_D

value: CGTACG


title: 37_SRP46_C


title: 42_D

value: GAGTGG


title: 42_H

value: CAGATC


title: 37_A


title: 35_C

description: HNRPF

value: HNRPF

value: GTTTCG


title: 35_HNRPF_A

description: HNRPF

value: GATCAG


title: 32_HNRPK_C

description: HNRPK

value: HNRPK


title: 33_B

value: lymphoblastoid cell line


title: 33_HNRPH1_D

value: GCCAAT


title: NS#4_C

description: control

value: control


title: 33_C

value: GTGGCC


title: 32_A

description: HNRPK


title: 32_D

description: HNRPK


title: NS#3_B

description: control

value: CTTGTA


title: 29_C

description: ADAR

value: ADAR


title: 29_D

description: ADAR


title: 29_ADAR_A

description: ADAR


title: 26_RBMX_A

description: RBMX

value: RBMX

value: ACAGTG


title: 26_D

description: RBMX

value: knockdown


title: 26_B

description: RBMX

value: TTAGGC


title: 25_D

value: CGATGT


title: 24_SFRS1_C

value: ATCACG


title: 25_SFRS10_A

value: ACTTGA


title: 25_C


title: 24_A


title: 24_B


title: 22_D

description: SYNCRIP

value: SYNCRIP

value: GTGAAA


title: 21_B


title: 22_C

description: SYNCRIP


title: 21_RNPC2_E


title: 35_B

description: HNRPF

value: HNRPF


title: 20_C


title: 19_C

description: HNRPR

value: HNRPR

value: GATCAG