title: GSC-0827 Day 23  Rep 1

description:
sgRNA
827231


title: GSC-0131 Day 23  Rep 1

status: Public on Feb 15 2016

type: SRA

city: Seattle

first: Patrick

last: Paddison

state: WA

address: 1100 Fairview Ave N, C3-187

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
sgRNA
131231

library_source: genomic

data_processing:
Base calling was performed using Illumina's RTA software, v1.17.21.3
Bcl to fastq conversion was conducted using Illumina's CASAVA v1.8.2
Demultiplexing of in line indices was performed using fastx-toolkit
Reads were aligned to the GECKO v1 human sgRNA reference via bowtie 1.0.0, allowing for 0 mismatches
Normalization and significance testing were done using the Bioconductor package edgeR
Genome_build: GECKO v1 human sgRNAs
Supplementary_files_format_and_content: tab delimited text file with annotation and raw counts for each sgRNA across all samples

molecule: genomic DNA

organism: Homo sapiens

source_name: GBM stem-like cells

growth_protocol: GSC and NSC lines were grown in N2B27 neural basal media (StemCell Technologies) supplemented with EGF and FGF-2 (20ng/mL each) (Peprotech) on laminin (Sigma) coated polystyrene plates and passaged as previously described.  Cells were detached from their plates using Accutase (Millipore).  Cells were split every 3-4 days.

extract_protocol:
Genomic DNA was extracted using QiaAmp blood purification Midi kit (Qiagen).
A two-step PCR procedure was employed to amplify sgRNA sequences (first PCR:12 cycles) and then to incorporate deep sequencing primer sites onto sgRNA amplicons (second PCR:20 cycles).  For the first PCR, the amount of genomic DNA for each sample was calculated in order to achieve 500-fold coverage over the library (~6.6 μg of gDNA for 106 cells), which resulted in ~213 μg DNA per sample. For each sample, ~100 separate PCR reactions were performed with 2 μg genomic DNA in each reaction using Herculase II Fusion DNA Polymerase (Agilent). Afterwards, a second PCR was performed to add on Illumina adaptors and to barcode samples, using 5ul of the product from the first PCR. We used a primer set to include both a variable 1-6 bp sequence to increase library complexity and 6 bp Illumina barcodes for multiplexing of different biological samples. Resulting amplicons from the second PCR were column purified using the combination of PureLink PCR purification kit (Life Technologies) and MinElute PCR purification kit (Qiagen) to remove genomic DNA and first round PCR product. Purified products were quantified, and mixed.

treatment_protocol: For large-scale transduction, ~ 220 million GSC or NSC cells were plated into T225 flasks at an appropriate density per biological replicate.  Each replicate was transduced such that ~500 fold representation of the library was achieved (at MOI~1 and 30% infection efficiency).  2 days after transduction, puromycin was added (1-4μg/ml) and maintained for 3 days.  A portion of cells were harvested as Day 0 time point.  The remaining cells were then passaged into T225 flasks maintaining 500 fold representation and cultured for an additional 21-23 days or ~8-10 cell doublings.

tag: isolate

tag: time

value: Day 23

tag: cell type

value: GBM stem-like cells

tag: source

value: Primary patient-derived isolates

tag: age

value: Adult

tag: gbm subtype

value: Mesenchymal


title: CB-003  PND 2N

city: New Brunswick

first: Caroll

last: Bagnell

state: New Jersey

address: 59 Dudley Road

department: Animal Sciences

institute: Rutgers University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed using bcl2fastq conversion software v1.8.3 (Illumina, Inc., San Diego, CA, USA) with default settings. Raw reads were mapped to the latest pig Sscrofa10.2 build (NCBI). Further, downstream analysis was done on the Avadis NGS (Strand Scientifics) platform.
Mapped reads were filtered based on their read quality (Quality threshold > 30, Alignment score threshold > 95, Mapping quality threshold > 40) and then on duplicates. Quantification was accomplished using TMM normalization.
Genome_build: NCBI Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include TMM normalized Expression values for each Sample.

molecule: total RNA

organism: Sus scrofa

source_name: nursed_PND 2_uterus

extract_protocol:
Total RNA was isolated using Rneasy kit (Qiagen) following the manufacturer's protocol.  RNA quality was assessed using Agilent Bioanalyzer and Qbit Fluorometer.
RNA libraries were prepared for sequencing using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA) according to the manufacturer's instructions

treatment_protocol: Pigs were euthanized within 1 h of birth (PND 0) or at 50 h of age (PND 2N and PND 2R).  Uteri were trimmed of connective tissue, immersed in RNALater and stored at -80C until RNA extraction.

tag: breed

value: Crossbred (Landrace, Yorkshire, Duroc, Hampshire)

tag: feeding

value: nursed

tag: age (days)

value: PND 2

tag: tissue

value: uterus


title: MDAMB231 Glutamine starvation batch7 RP

status: Public on Feb 14 2016

city: Amsterdam

first: Koos

last: Rooijers

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
ribosome profiling
adapter sequence (3'): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.7) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: MDA-MB-231 cell line

growth_protocol: All breast cancer cell lines were grown in DMEM supplemented with 10% FBS in 5% CO2 at 37°C.

extract_protocol:
Approximately 30e6 cells were treated with chloramphenicol (100μg/ml) for 15 minutes and cycloheximide (100μg/ml) for 5 minutes. Cells were lysed in buffer B (20 mM Tris-HCl, pH 7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml chloramphenicol, 100 μg/ml cycloheximide, 1x Complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7% - 47%) using the SW- 41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in mito-monosomes and cytosolic monosomes were identified by western blotting, pooled and treated with proteinase K (Roche) in 1% SDS. Released RPFs were purified using Trizol reagent (Invitrogen) following the manufacturer’s instructions.
RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30-33 nucleotides was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England Biolabs Inc. Beverly, MA, USA) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England Biolabs Inc. Beverly, MA, USA) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.

treatment_protocol: For starvation experiments, cells were culture for 48hrs in glutamine-free DMEM (Life Technologies) supplemented with 10% dialyzed FBS in 5% CO2 at 37°C.

tag: cell line


title: CB-002  PND 2N


title: MCF10A starvation RP

data_processing:
Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.6) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: MCF10A cell line

growth_protocol: MCF10A cells were cultured in DMEM/F12 1:1 medium supplemented with 5% horse serum, EGF (10 ng/ml), insulin (10 μg/ml), cholera toxin (100 ng/ml), and hydrocortisone (500 ng/ml) in 5% CO2 at 37°C.

treatment_protocol: For inhibition of mTOR and nutrient starvation experiments, MCF10A cells were treated either with 250 nM of Torin 1 (Tocris Bioscience, Bristol, UK) or with EBSS medium (Sigma) for 2 hours, respectively.

tag: adapter sequence (3')


title: MCF7 Glutamine starvation batch7 RP

source_name: MCF7 cell line


title: Hs578t Glutamine starvation batch7 RP

source_name: Hs578t cell line


title: GSC-0131 Day 0 Rep 1

description:
sgRNA
131001

value: Day 0


title: 01-23_V1

city: San Francisco

first: Charles

last: Chiu

state: CA

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
reads were mapped to hg19 Refseq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: PBMCs

extract_protocol:
PBMCs were isolated from fresh whole blood using Ficoll (Ficoll-Paque Plus, GE Healthcre) and total RNA was extracted from 10e7 PBMCs using TRIzol reagent (Life Technologies).  Messenger RNA was isolated with Oligotex mRNA mini kit (Qiagen)
Scriptseq RNA-seq library preparation kit (Epicentre) was used to generate the RNA-seq libraries according to the manufacturer's protocol.

tag: individual

value: patient 01-23

tag: disease state

value: Lyme disease

value: acute Lyme pre-treatment (V1)

value: PBMC


title: T47D Glutamine starvation batch7 RP

source_name: T47D cell line


title: CB-001  PND 2N


title: T47D control batch7 RP


title: Sample_FP3

city: Wuhan city

first: Hongyuan

last: zhang

state: Hubei Provinve, P.R. China

address: Wuhan Academy of Agricultural Sciences, Hanshi Road, Huangpi District, Wuhan,430065, Hubei Province, China

country: China

institute: Wuhan Academy of Agricultural Sciences

description: small RNA profiling

data_processing:
Automated base calling of the raw sequence and vector removal were performed with PHRED and CROSS MATCH programs
All unique sequences were aligned to the rice genome (MSU 7, ftp://ftp.plant biology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/) using SOAP for mapping.
Sequences that mapped to rice rRNA, tRNA, scRNA, snRNA or snoRNA were removed based on National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/) and Rfam RNA family databases.
Known miRNA were identified through a BLAST search against miRNA database miRBase release 20 (http://mirbase.org/)
Novel miRNAs were used to predict  MIREAP (http://so urceforge.net/projects/ mireap/).
Genome_build: MSU 7
Supplementary_files_format_and_content: Tab-delimited text files include mature miRNA counts from known hairpins.

organism: Oryza sativa Indica Group

source_name: Young panicles

growth_protocol: WXS rice were grown in the field in Huazhong Agricultural University, Wuhan, Hubei province (30°28′ N, 114°21′ E) from May 2014 to August 2014. When the panicle length was approximately 1 cm, then transferred sixty plants of these WXS into cooling pond to treat them with low temperature for 2 weeks. At the permissive temperature (22 °C), these rice plants was converted to a normal male-fertile line, named WXS (F). In the same time, WXS developed into no pollen male sterile rice in natural ecological rice paddy, named WXS (S). Young panicles were collected under the two different conditions at pollen mother cell formation stages and pollen meiosis stage. Rice panicles at different developmental stages, including: SP2, SP3, FP2 and FP3, were collected.

extract_protocol:
Total RNA was extracted from rice young panicle at the pollen mother cell formation stages and meiosis stage using the Trizol reagent (TaKaRa, Dalian, China) according to the manufacturer’s instructions.
Small RNAs ranging 18-30nt were size fractionated from 15% polyacrylamide gel electrophoresis (PAGE), isolated from the gel and ligated with the 5’ and 3’ RNA adaptors using T4 ligase. The resulting products were reverse transcribed and amplified using 15 PCR cycles to produce sequencing libraries.

tag: line

value: WXS(F)

tag: developmental stage

value: pollen mother cell meiophase

tag: phenotype

value: Fertility


title: 01-20_V1

value: patient 01-20


title: Kidney tumor tissue 4 tumor 2 RP

data_processing:
(Ribosome profiling data only) Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.7) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: Kidney tissue

value: kidney


title: Sample_SP2

description: small RNA profiling

value: WXS(S)

value: pollen mother cell formation stage

value: Sertility


title: MCF7 control batch7 RP


title: MCF7 IP150 RP

description: ribosome profiling

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS

extract_protocol:
MCF7 GFP-RPL10a cells were treated with cycloheximide at a final conc of 10ug/m for 5 min. Cells were washed with cold PBS, scraped, and pelleted. Cell pellet was lysed with 1ml of NP40 lysis buffer (20mM Tris-HCl pH 7.8, 10mM MgCl2, 150mM KCl, 1% NP40, 2 mM DTT, 1X Complete protease Inhibitors, 100 ug/ml CHX) for 15 min, centrifuged for 10 min at 1300 g and 1ml of supernatant recovered. IP samples: (50ul/100ul) GFP-Trap_M beads (Chromotek) were washed for 3 times in 1ml of NP40 lysis buffer, resuspended in 3 ml of NP40 lysis buffer. 1ml of cleared lysate (cell line or tumor) was added to the beads and digested with RNAse I (100U/ul) for 1hr at RT under constant rotation. Beads were washed 3 times with of NP40 Lysis buffer and 3 times with NP40 wash buffer (20mM Tris-HCl pH 7.8, 10mM MgCl2, 350mM KCl, 1% NP40, 2 mM DTT, 1X Complete protease Inhibitors, 100 ug/ml CHX). Beads were resuspended in 300 ul of lysis buffer with 1% SDS and 15 ul of Proteinase K (Roche) and incubated for 1hr at 45C. Supernatant was recovered and resuspended in TriSure. RNA was isolated and libraries prepared according to the RP protocol.
RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30-33 nucleotides was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England Biolabs Inc. Beverly, MA, USA) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England Biolabs Inc. Beverly, MA, USA) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.

tag: protocol


title: Sample_FP2

description: small RNA profiling


title: Hs578t control batch7 RP


title: Kidney tumor tissue 3 tumor 2 RP


title: MCF7 IP50 RP

description: ribosome profiling


title: MCF7 SG RP

description: ribosome profiling

value: sucrose gradient


title: Kidney normal tissue 2 tumor 2 RP


title: Kidney tumor tissue 2 tumor 2 RP


title: Kidney normal tissue 1 tumor 2 RP


title: Kidney tumor tissue tumor 4 RP

value: tumor


title: Kidney tumor tissue tumor 3 RP


title: Kidney tumor tissue 4 RNAseq

molecule: polyA RNA

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.


title: MDAMB231 control batch7 RP


title: Sample_SP3

description: small RNA profiling


title: Kidney tumor tissue 1 RNAseq


title: Kidney normal tissue 2 RNAseq


title: SUM159PT in vivo 2 repl2 RP

description: Ribosome profiling

growth_protocol: SUM159PT cells were cultured in DMEM/F12 1:1 medium supplemented with 5% FBS, insulin (5μg/ml), and hydrocortisone (1μg/ml).

extract_protocol:
SUM-159 GFP-RPL10a cells were treated with cycloheximide at a final conc of 10ug/m for 5 min. Cells were washed with cold PBS, scraped, and pelleted. Cell pellet was lysed with 1ml of NP40 lysis buffer (20mM Tris-HCl pH 7.8, 10mM MgCl2, 150mM KCl, 1% NP40, 2 mM DTT, 1X Complete protease Inhibitors, 100 ug/ml CHX) for 15 min, centrifuged for 10 min at 1300 g and 1ml of supernatant recovered.     For tumors preparation, each tumor was lysed in 1ml of NP40 lysis buffer in a tissue homogenizer. Tumor lysate was centrifuged at 1300g for 10 min and the supernatant was incubated with the beads.    85 ul per condition of GFP-Trap_M beads (Chromotek) were washed for 3 times in 1ml of NP40 lysis buffer, resuspended in 3 ml of NP40 lysis buffer. 1ml of cleared lysate (cell line or tumor) was added to the beads and digested with  RNAse I (100U/ul) for 1hr at RT under constant rotation. Beads were washed 3 times with of NP40 Lysis buffer and 3 times with NP40 wash buffer (20mM Tris-HCl pH 7.8, 10mM MgCl2, 350mM KCl, 1% NP40, 2 mM DTT, 1X Complete protease Inhibitors, 100 ug/ml CHX). Beads were resuspended in 300 ul of lysis buffer with 1% SDS and 15 ul of Proteinase K (Roche) and incubated for 1hr at 45C. Supernatant was recovered and resuspended in TriSure. RNA was isolated and libraries prepared according to the RP protocol.
RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30-33 nucleotides was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England Biolabs Inc. Beverly, MA, USA) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England Biolabs Inc. Beverly, MA, USA) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.


title: SUM159PT in vitro 2 repl2 RP

description: Ribosome profiling


title: Kidney normal tissue tumor 3 RP

value: normal


title: Kidney tumor tissue 1 tumor 2 RP


title: SUM159PT in vitro 1 repl2 RP

description: Ribosome profiling


title: SUM159PT in vivo 2 repl1 RP

description: Ribosome profiling


title: SUM159PT in vivo 1 repl1 RP

description: Ribosome profiling


title: Kidney tumor tissue 3 RP

source_name: Kidney tumor tissue 3 RP

value: Kidney


title: SUM159PT in vitro 2 repl1 RP

description: Ribosome profiling


title: Kidney tumor tissue 2 RP

source_name: Kidney tumor tissue 2 RP


title: SUM159PT in vitro 1 repl1 RP

description: Ribosome profiling


title: Kidney normal tissue 1 RP

source_name: Kidney normal tissue 1 RP


title: Kidney normal tissue tumor 4 RP


title: PC3 ASNase 1 batch2 RP

description: ribosome profiling

source_name: PC3 cell line

growth_protocol: PC3 cells were cultured in RPMI medium supplemented with 10% FBS

treatment_protocol: For samples which were ASNase treated: PC3 cells were treated with L-Asparaginase (Sigma) at 1U/ml for 48hrs in RPMI supplemented with 10% dialyzed FBS

tag: agent

value: L-Asparaginase


title: Kidney normal tissue 2 RP

source_name: Kidney normal tissue 2 RP


title: Kidney tumor tissue 1 RP

source_name: Kidney tumor tissue 1 RP


title: Kidney tumor tissue 3 RNAseq


title: Kidney tumor tissue 2 RNAseq


title: SUM159PT in vivo 1 repl2 RP

description: Ribosome profiling


title: PC3 ASNase batch1 RP

description: ribosome profiling


title: PC3 control batch2 RP

description: ribosome profiling


title: SUM1315 harringtonine RP

description:
Ribosome profiling
adapter sequence (3'): TCGTATGCCGTCTTCTGCTTG

source_name: SUM1315 harringtonine RP

growth_protocol: SUM1315 cells were culture in DMEM:F12 (1:1) medium supplemented with 5% FCS, EGF (10 ng/ml), and Insulin (5μg/ml)

treatment_protocol: Cells were treated with of harringtonine (2 μg/ml) for 5 min.


title: MCF10A control RP

description:
adapter sequence (3'): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
ribosome profiling

data_processing:
(Ribosome profiling data only) Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.6) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: MCF10A control RP


title: Kidney normal tissue 1 RNAseq


title: MCF10A torin RP

source_name: MCF10A torin RP


title: Kidney tumor tissue 4 RP

source_name: Kidney tumor tissue 4 RP


title: PC3 control batch1 RP

description: ribosome profiling


title: SUM1315 control RP

source_name: SUM1315 control RP


title: Enteric NC, biological rep 2 of 3

status: Public on Feb 12 2016

city: New York

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat v1.3.3 with these parameters: -p8 -r 180 --library-type fr-unstranded --no-coverage-search --no-novel-juncs
Analysis with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with DESeq output with fold change compared to CNS samples are provided.

source_name: embryonic stem cells

extract_protocol:
RNA was extracted with Trizol and cleaned up using a Qiagen RNEasy column
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: differentiation day

value: day 12


title: Melanocyte biased NC, biological rep 3 of 3


title: Melanocyte biased NC, biological rep 2 of 3


title: Enteric NC, biological rep 1 of 3


title: Melanocyte biased NC, biological rep 1 of 3


title: Enteric NC, biological rep 3 of 3


title: "default" NC, biological rep 2 of 3


title: PC3 ASNase 2 batch2 RP

description: ribosome profiling


title: "default" NC, biological rep 3 of 3


title: "default" NC, biological rep 1 of 3


title: Pol2 Ser2_C42_sieRNA.rep2

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Pol2 differential binding was analyzed by edgeR(v3.6.8)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file

source_name: Pol2 Ser2_C42_sieRNA

growth_protocol: Prostate cancer cells were cultures (typically 2-3 × 10^6 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: The cells were cultures with charcoal-stripped (steroid depleted) serum medium for 48 hours and then treated with ethanol or 10 nmol/l of mibolerone (BIOMOL, Plymouth Meeting, PA). For PSA eRNA knocking down, the cells were transfected with control siRNA or PSA si-eRNA for 48 hours and two roundly.

tag: cell type

value: prostate cancer cell line

tag: transfected with

value: PSA si-eRNA

tag: chip antibody

value: Pol II H5

tag: chip antibody vendor

value: Covance

tag: chip antibody cat. #


title: Pol2 Ser2_C42_sieRNA.rep1


title: CCNT1_LNCaP_rep2

value: LNCaP

value: Santa Cruz


title: Pol2 Ser2_C42_NS_rep2

source_name: Pol2 Ser2_C42_NS

value: control siRNA


title: Pol2 Ser2_C42_NS_rep1


title: CCNT1_C42_sieRNA_rep2


title: CCNT1_C42_NS_rep2


title: CCNT1_LNCaP_rep1


title: CCNT1_C42_sieRNA_rep1


title: CCNT1_C42_NS_rep1


title: AR_LNCaP_Mib_rep3

tag: treated with

value: 10 nmol/l of mibolerone


title: AR_LNCaP_EtOH_rep3

value: ethanol


title: AR_LNCaP_Mib_rep2


title: AR_C42_Mib_rep2


title: AR_C42_Mib_rep3


title: AR_C42_EtOH_rep3


title: AR_LNCaP_EtOH_rep2


title: AR_C42_EtOH_rep2


title: LNCaP_Mib

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedGraph

source_name: prostate cancer cell

growth_protocol: Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).

treatment_protocol: The cells were cultures with charcoal-stripped (steroid depleted) serum medium for 48 hours and then treated with ethanol or 10 nmol/l of mibolerone (BIOMOL, Plymouth Meeting, PA).

value: LNCaP cell

tag: chip antibodies

value: Androgen Receptor (Santa Cruz, N-20)

value: 0 nmol/l of mibolerone


title: LNCaP_input

tag: cell line


title: LNCaP_rep1

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with parameters "-p 4 --keep-fasta-order --keep-tmp -z0 --no-coverage-search --bowtie1 --library-type fr-unstranded --max-multihits 20".
Raw count and RPKM were calcualted using RSeQC (v2.3.6) with parameters "-d '1+-,1-+,2++,2--' -r hg19.refseq.bed12"
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed files are Tab separated plain text files. Each file contains 10 columns:Chromosome, transcript start position, transcript end position, RefSeq accession number, score (0), transcript strand, read count calculated from reads mapped to forward strand, read count calculated from reads mapped to reverse strand, RPKM calculated from reads mapped to forward strand, RPKM calculated from reads mapped to reverse strand.

source_name: prostate cancer cell (LNCaP)

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Rneasy Plus Mini Ki t(Qiagen). Ribo-zero rRNA remove Kit was used. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: passages

value: Primary PC


title: C4-2_EtOH

value: C4-2 cell


title: C4-2_Mib


title: C4-2_rep1

source_name: prostate cancer cell (C4-2)

value: CRPC


title: LNCaP_rep2


title: C4-2_input


title: Pol II N20_C42_siPSA-eRNA_rep2

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MACS2 (v2.0.10)
Pol2 differential binding was analyzed by edgeR(v3.6.8)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file

growth_protocol: Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped serum (CSS).

treatment_protocol: The cells were cultures with charcoal-stripped (steroid depleted) serum medium for 48 hours and then were transfected with siRNAs. For PSA eRNA knocking down, the cells were transfected with control siRNA or PSA si-eRNA for 48 hours and two roundly.

value: Santa Cruz Pol II (N-20) sc-899


title: Pol II N20_C42_siPSA-eRNA_rep1


title: C4-2_rep2


title: Pol II N20_C42_NS_rep2


title: Pol II 8WG16_C42_siPSA-eRNA_rep1

value: Covance Pol II 8WG16 MMS-126R


title: Pol II 8WG16_C42_siPSA-eRNA_rep2


title: Pol II N20_C42_NS_rep1


title: Pol II 8WG16_C42_NS_rep2


title: Pol II 8WG16_C42_NS_rep1


title: AR_C42_NS_rep2

value: Santa Cruz AR (N-20) sc-816


title: AR_C42_siPSA-eRNA_rep1


title: spinal cord meninges 2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina BaseCaller software to bcl files, which were demultiplexed to fastq files with CASAVA (version 1.8.2).
Sequences were aligned to the genome reference sequence of Rattus norvegicus (RGSC assembly v5.0). Alignment was performed using the STAR alignment software (Dobin et al., 2012; version 2.3.0e) allowing for 2 mismatches within 45 bases.
Conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting was conducted with SAMtools (Li et al., 2009, version 0.1.18) and HTSeq (Anders et al., 2014, version 0.6.1p1).
Data was preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (Anders and Huber, 2010, version 1.2.10). Candidate genes were filtered to a minimum of 2-fold change and FDR-corrected p-value < 0.05.
Gene annotation was performed using Rattus norvegicus entries from Ensembl v78 (www.ensembl.org) via the biomaRt package (Durinck et al., 2005, version 2.18.0).
Genome_build: rnor5
Supplementary_files_format_and_content: abundance measurements from htseq-count

organism: Rattus norvegicus

source_name: CD4+ Tmbp cells

extract_protocol:
MBP-specific T cells expressing GFP were isolated from blood, CSF, spinal cord meninges and parenchyma by FACS-sorting at 4°C and stored in Trizol.
RNA libraries were prepared for sequencing using Illumina TruSeq protocols for messenger RNA

tag: strain

value: Lewis

tag: genotype

value: wild type

tag: tissue

value: spinal cord meninges

value: CD4+ Tmbp cells


title: spinal cord meninges 3


title: CNS parenchyma 3

value: CNS parenchyma


title: AR_C42_NS_rep1


title: CNS parenchyma 2


title: CSF 3

value: CSF


title: AR_C42_siPSA-eRNA_rep2


title: CSF 2


title: CNS parenchyma 1


title: LNCaP_EtOH


title: blood 3

value: blood


title: CSF 1


title: blood 2


title: blood 1


title: MAO8

city: University of California Santa Barbara

first: Michelle

middle: A

last: O’Malley

address: Engineering 2 Bldg

department: Chemical Engineering

institute: UC Santa Barbara

data_processing:
Assembled De-novo Transcriptome using Trinity (v2012-10-05) and parameters --jaccard-clip option
Aligned all conditions to output fasta and got expression estimates of transcripts using RSEM (v1.2.6)
Genome_build: De novo
Supplementary_files_format_and_content: all_samples.isoforms.fpkm.txt

organism: Piromyces finnis

source_name: Whole Organism

growth_protocol: Cultures grown in ~ 9 ml Medium C (Davies et. al, J Gen Microbiol. 1993 Jun;139 Pt 6:1395-400.) at 39°C to mid-log phase (P≥5 psi)

extract_protocol:
Qiagen RNEasy Mini Kit (Plant/Fungi Protocol)
RNA libraries were prepared for sequencing using standard Illumina protocols Samples1-2, Shishkin protocol (http://guttmanlab.caltech.edu/protocols.php) Samples3-38

tag: energy substrate

value: Avicel


title: MAO9

value: Glucose


title: MAO4

value: Reed Canary Grass


title: MAO3


title: MAO6


title: MAO7

value: Cellobiose


title: spinal cord meninges 1


title: MAO5

value: Filter Paper


title: MAO13


title: MAO12


title: CNS, biological rep 2 of 4

value: day 12


title: CNS, biological rep 3 of 4


title: MAO11


title: CNS, biological rep 4 of 4


title: CNS, biological rep 1 of 4


title: MAO10


title: B23

value: Fructose


title: Reed Canary Grass


title: MAO1


title: B22


title: WT CD4 Input

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. For the Histone Marks ChIP-Seq, according to the sequencing quality, we trimmed 5 bases in 3' end for the 51 bases read length ChIP-Seq libraries and trimmed 10 bases in 5' end and 25 bases in 3' end for the 101 bases read length ChIP-Seq Libraries. For the Tcf1 ChIP-Seq libraries, no sequence trimming was necessary. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Histone Marks ChIP-Seq libraries, SICER (v1.1, Zang et al., Bioinformatics) was used to identify islands. In each library, islands were identified with false discovery rate (FDR) of less than 1E-4 and island-filtered tags were used for downstream analysis.
For Tcf1 ChIP-Seq libraries, MACS (v1.4.2, Zhang et al., Genome Biol) was used for peak calling. We used the criteria of enrichment of four-fold or more, a P value of <1E-5 and false-discovery rate of <5% and thus identified TCF-1 binding peaks. The top 1000 TCF-1 peaks (ranked by P value) identified were analyzed with the MEME-ChIP suite of motif-based sequence-analysis tools (v4.10.1, Bailey., Nucleic Acids Research) to define consensus DNA-binding motifs.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with islands or peaks

organism: Mus musculus

source_name: CD4 T cells

extract_protocol:
Mature CD4 or CD8 thymocytes were sort-purified for WT or Tcf1/Lef1-deficient mice, the cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with antibodies against H3K4me3, H3K27me3, H3K27Ac, H3K9Ac, or Tcf1, which were then properly washed and immunoprecipitated DNA extracted.
Splenic CD8 T cells were sort-purified for WT or Tcf1-deficient mice, the cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with a Tcf1 antiserum, which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform. For Histone Marks: ChIPseq, single end, 51 nucleotide sequencing. For several samples we did the high throughput sequencing for a second time to improve the coverage, and the other sequencing strategy is: ChIPseq, single end, 101 nucleotide sequencing. For Tcf1: ChIPseq, single end, 50 nucleotide sequencing.

value: mature thymocytes

tag: cell phenotype

value: TCRbeta high, CD69–, CD24–, CD8+


title: WT CD8 Tcf1 ChIP-Seq

source_name: CD8 T cells

value: splenic T cells

value: TCRbeta high, CD8+


title: Glucose


title: Tcf1-deficient CD8 Tcf1 ChIP-Seq

description: No processed data available for this sample which  was used as the control for the sample: WT CD8 Tcf1 ChIP-Seq


title: B21

value: Reed Canary Grass w/ Glucose Spike

tag: time after glucose spike (min)


title: B20


title: WT CD4 H3K27Ac ChIP-Seq

value: wild type


title: WT CD4 H3K9Ac ChIP-Seq


title: B19


title: WT CD4 H3K27Me3 ChIP-Seq


title: MAO2


title: B17


title: WT CD4 H3K4Me3 ChIP-Seq


title: Tcf1/Lef1-deficient CD8 Input


title: Tcf1/Lef1-deficient CD8 H3K9Ac ChIP-Seq


title: B18


title: B14


title: B13


title: Tcf1/Lef1-deficient CD8 H3K27Ac ChIP-Seq


title: Tcf1/Lef1-deficient CD8 H3K27Me3 ChIP-Seq


title: Tcf1/Lef1-deficient CD8 H3K4Me3 ChIP-Seq


title: B11


title: B24


title: WT CD8 Input


title: B10


title: B9


title: WT CD8 H3K27Me3 ChIP-Seq


title: WT CD8 H3K9Ac ChIP-Seq


title: B7


title: B8


title: WT CD8 H3K4Me3 ChIP-Seq


title: B6


title: B16


title: Tcf1/Lef1-deficient CD8 rep2

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The RNA-Seq libraries were then processed by RSEM (v1.2.21, Li et al., BMC Bioinformatics) to estimate expression levels of all genes. The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.  UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
EBSeq (v1.5.4, Leng et al., Bioinformatics), as an integral component of RSEM package, was used to identify differentially expressed genes (FDR = 0.01).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample ...

extract_protocol:
Mature CD8 thymocytes were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol


title: B5


title: Tcf1/Lef1-deficient CD8 rep1


title: WT CD8 H3K27Ac ChIP-Seq


title: B3


title: Tcf1-deficient CD8 rep2


title: B2


title: B12


title: WT_border_1

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

country: France

institute: INRA

data_processing:
default parameters to Torrent Suite Software version 4.0.2
Mapping with Bowties2 on messager RNA TAIR 10 reference (parameters : no MultiHit, local reads mapping, TAIR 10 refrence with one gene model)
Genome_build: Arabidopsis thaliana TAIR 10
Supplementary_files_format_and_content: The processed data files contain 3 comment lines corresponding to the time of processing, the number of reads parsed and the number of reads mapped. An example is shown below:
#sam2pkm :2014-02-14 11:16:22.632693
#total read parsed : 34170794
#total read mapped : 28674853
Then the column headers;
"id" = the locus identifier (Arabidopsis Genome Initiative code)
"len" = the length of the gene model in nt
"nb_single" = the number of reads mapped on the gene model

organism: Arabidopsis thaliana

source_name: WT_leaf border

extract_protocol:
extraction_ARN_Trizol
RNA libraries were prepared for sequencing using standard LifeTechnologies protocols for Ion Torrent Proton (4476286_Ion Total RNA-Seq Kit v2_UG_RevE.pdf)
RNA Seq in Stranded Single End, sizing 230bp, ribo RNA dépletion (ribo-zero-rrna-removal-kit-(plant-leaf).pdf)

treatment_protocol: no treatment

tag: stock

tag: developmental stage

tag: genotype/variation

value: rosette_young leaf border (green)


title: FLV_border_2

source_name: FLV_leaf border

value: FLV mutants

value: rosette_young leaf border (white)


title: WT CD8 rep2


title: B4


title: B1


title: FLV_border_1


title: WT_center_2

source_name: WT_leaf center

value: rosette_young leaf center


title: Ovule

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed reads with 3′ adapter reads, 5′ adapter contaminants, the poly-A tail, and sequences <18 nt. After this preprocessing, the sequenced raw data were transferred into clean reads. Modified sequences from 18 nt to 30 nt were used for further analyses.
Further analysis began with SOAP 2.0 software (Li et al. 2009) to map the clean reads from mature G. biloba ovules onto entries in the Michigan State University transcriptome database. The GenBank and Rfam (version 10.1) databases were used to annotate the rRNA, scRNA, snoRNA, snRNA, and tRNA in the sRNA library (Gardner et al. 2011). the remaining sRNA sequences were retained for miRNA identification.
Previously known miRNAs were identified in these sRNA sequences by alignment to sequences in miRBase (Release 20.0) with no mismatches (Griffiths-Jones et al. 2008).
Reads remaining without annotation were used to predict potentially novel miRNAs using MIREAP software, followed by a prediction of secondary structure using MFOLD  software (Zuker 2003)
We used the Web-based psRNATarget program to identify putative targets for conserved and novel miRNAs.
Genome_build: G. biloba mRNA transcriptome database [Genbank: SRP051312]
Supplementary_files_format_and_content: The compressed files include miRNA read counts (.fa) and targets (.txt).

organism: Ginkgo biloba

source_name: Ovule

growth_protocol: Mature ovules (before pollination) were obtained from healthy G. biloba trees (approximately 30 years old) growing under natural conditions in the Institute of Botany, Chinese Academy of Sciences.

extract_protocol:
Samples were collected in April 2012. Total RNAs of ovules were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: Ovule

value: Mature

tag: sex type

value: Female tree


title: WT_border_2


title: WT_center_1


title: Tcf1-deficient CD8 rep1


title: Gata4_TKO_CM_Average_Footprints

status: Public on Feb 11 2016

city: SAN FRANCISCO

first: Benoit

middle: G.

last: Bruneau

address: 1650 OWENS STREET

institute: GLADSTONE INSTITUTES

data_processing:
Library strategy: ChIP-Exo
Barcoded libraries were single-end 50bp sequenced on an Illumina HiSeq 2500 instrument. Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using bowtie2 (ChIP-seq, ChIP-exo) (Langmead and Salzberg, 2012). Samtools was then used to retain reads that had a mapq score of 30 or greater (Li et al., 2009), thereby ensuring that each mapped uniquely to the genome assembly. The 5'-most position of reads that mapped to the reference strand and the 3'-most position of reads that mapped to the non-reference strand were identified for each read as the actual edges of each exonuclease-treated fragment. The genome was divided into 20bp genomic bins and a normalized tag density was calculated for each genomic bin 'i' as follows:
tag density(i)=([#tags within 75bp of i] X [total# genomic bins])/(total #of tags)
To identify broad regions of binding, bins with tag densities of greater than 100 were merged to generate a peak list for each sample. Within 1kb of each region, strand-specific single-base-resolution tag densities were calculated for each dataset by dividing each region into 1bp bins, then counting the number of tags within 5bp of each bin. For each region of binding, the footprint for each bound region was defined as the span from the peak position of '+' strand binding to the peak position of '-' strand binding as seen from the high-resolution tag densities. For subsequent analyses, any overlapping footprint for replica/factor/stage/genotype was merged to generate an average footprint list. Only average footprints present in at least two replicas of the same factor, stage and genotype were considered (Final Average Footprints).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and bed files

source_name: Differentiated Cardiomyocytes

growth_protocol: We used a directed differentiation system to generate cardiac precursors (CP) and cardiomyocytes (CM) from WT ES cells, and ES cells in which Tbx5 and/or Nkx2-5 have been deleted.

extract_protocol:
ChIP-exo was performed according to methods published previously (Boyer et al., 2005; Serandour et al., 2013; Wamstad et al., 2012) using specific antisera to TBX5 (sc-17866 XS, lot no. B1213), NKX2-5 (sc-8697 XS, lot no. B1213), and GATA4 (sc-1237 XS, lot no. B1213) on chromatin isolated from 10 mill. cells. Re-ChIP-exo was performed from 40 mill cells, combining methods published previously (Serandour et al., 2013; Shankaranarayanan et al., 2011).
ChIP-exo libraries were prepared  according to (Serandour et al., 2013)

tag: cell type

value: ES-derived  Cardiomyocytes

value: Tbx5 knockout

tag: chip antibody


title: Gata4_NKO_CP_Average_Footprints

source_name: Cardiac Precursors

value: ES-derived Cardiac Precursors

value: Nkx2-5 knockout


title: Tbx5_NKO_CM_Average_Footprints


title: Tbx5_WT_CM_Average_Footprints

value: WT


title: Nkx2-5_TKO_CP_Average_Footprints


title: Nkx2-5_TKO_CM_Average_Footprints


title: Gata4_TKO_CP_Average_Footprints


title: ΔBCHL-R rep1

city: Ithaca

first: Martin

last: Wiedmann

address: 341 Stocking Hall

department: Food Science

institute: Cornell University

description: Total RNA was treated with Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input for removal of 16S and 23S ribosomal RNA

data_processing:
Raw data was generated by the Illumina pipeline software v1.8
the sequence reads were aligned to a 10403S genome using the BWA-MEM with default settings.The output was a SAM files for each sample. Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from BWA and convert them to BAM format. BAM files were converted to strand-specific base count files. Coverage at each base position along the chromosome was calculated by enumerating the number of reads that aligned to a given base for each DNA strand separately.
Differential expression of genes in different strains was statistically assessed using the BaySeq method implemented in the BaySeq 2.2.0 package available from Bioconductor. Genes were considered differentially expressed if they showed a false discovery rate (FDR) < 0.05 and a fold change (FC) ≥ 2.0 (meaning genes were upregulated on Prha-sigH) or FC ≤ 0.5 (meaning genes were downregulated on Prha-sigH).
Sliding window analysis: the 10403S genomes was divided into windows of 51 nt (window size) with 25 nt overlap (window sliding) and the RNA-Seq coverage was obtained for each of the 116,123 resulting windows. Bayseq version 2.2.0 was then used, as described above, to identify windows with significant differential expression between the ΔBCHL::Prha-sigH strain and the ΔBCHL::Prha strain. Fold change was also calculated as described above and windows presenting an FDR < 0.05 and FC > 2.0 were considered for further analysis. Windows matching the required thresholds were then sorted and overlapping windows were considered as being part of the same fragment. Fragments that were mapped to the same gene or operon were considered as being part of the same transcriptional unit (TU). The 5’ end of significant TUs were then manually scanned for promoter sequences, as described above.
Genome_build: 10403S genome (genebank accession number: NC_017544), assembly ASM16869v2
Supplementary_files_format_and_content: An excel spreadsheet (.xlsx) file: Raw count data and normalized count data (from BaySeq output) for each coding gene in 10403S. BaySeq result (likelihood of being differentially expressed and False Discovery Rate). Fold Changes (ΔBCHL-RH/ΔBCHL-R) and whether the Fold Changes are above or below the thresholds (< 0.5 or > 2.0) are provided. And a text (.txt) file containing the output from BaySeq with normalized coverage for each 51 nt window and Fold Changes (ΔBCHL-RH/ΔBCHL-R)

organism: Listeria monocytogenes 10403S

source_name: BHI broth

growth_protocol: strains were streaked from frozen BHI stock, stored at -80°C in 15% glycerol, onto a BHI agar plate, followed by incubation at 37°C for 24 h. A single colony was subsequently inoculated into 5 ml of BHI broth in 16 mm tubes, followed by incubation at 37oC with shaking (230 rpm) for 18 h (Series 25 Incubator, New Brunswick Scientific, Edison, NJ). After 18 h, 50 μl BHI culture was inoculated into fresh 5 ml BHI broth and grown to OD600 0.4-0.5 at 37°C.

extract_protocol:
Total RNA was extracted by using RNA protect, proteinase K, and lysozyme, followed by Tri reagent with bead-beating. Total RNA was incubated with DNase in the presence of RNasin to remove remaining DNA.
Preparation of cDNA fragment libraries was performed using the ScriptSeqTM Complete Kit (Bacteria)-Low Input (Epicentre, Madison, WI), which is composed of Ribo-ZeroTM rRNA Removal Reagents (Bacteria)-Low Input, Magnetic Core Kit-Low Input, and ScriptSeqTM v2 RNA-Seq Library Preparation Kit.

treatment_protocol: 250 μl 1M rhamnose stock solution was added to 5 ml OD600 0.4-0.5 bacterial cultures (for a final concentration of 50 mM rhamnose), followed by incubation at 37°C for an additional 30 min.

value: 10403S::deltaBCHL Prha

tag: growth stage

value: log phase

tag: induction

value: Rhamnose addition


title: Gata4_DKO_CM_Average_Footprints

value: Tbx5;Nkx2-5 double knockout


title: ΔBCHL-RH rep2

value: 10403S::deltaBCHL Prha-sigH


title: Tbx5_WT_CP_Average_Footprints


title: Gata4_DKO_CM_Average_Density


title: Tbx5_NKO_CP_Average_Footprints


title: ΔBCHL-RH rep1


title: ΔBCHL-R rep2


title: Gata4_DKO_CP_Average_Footprints


title: Nkx2-5_WT_CM_Average_Footprints


title: Gata4_WT_CP_Average_Footprints


title: Gata4_NKO_CM_Average_Footprints


title: ΔBCHL-RH rep3


title: rnaseq replicate 2

city: Darlinghurst

first: Erin

last: Heyer

state: NSW

address: 384 Victoria Street

department: Genomics & Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description:
mRNA fragments 20-45 nts
Sequencing of mRNA fragments

data_processing:
Files were demultiplexed by 5' barcode, trimmed to remove 3' adaptor sequence (TGGAATTCTCGGGTGCCAAGG), and filtered by length.
Reads were aligned to a library of noncoding RNA genes; those not matching were retained for further analysis.
Reads were aligned to the genome in a splice-aware manner using TopHat parameters '-N 2 -g 20 --segment-length 12 --coverage-search --library-type fr-secondstrand --bowtie1 --max-intron-length 1500 --max-segment-intron 1500 --max-coverage-intron 1500'
RiboSeq reads ≥25 nts and RNASeq reads ≥22 were used for further analysis.
Counts per gene were calculated from mapped reads using HTSeq-count with parameters ' --stranded=yes --type=exon --idattr=gene_id --mode=union'
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed .csv file contains a matrix (with columns: gene name, total ribosome footprint counts and total mRNA counts for all libraries, DESeq2 output comparing monosome to polysome counts) for all annotated genes.

organism: Saccharomyces cerevisiae

source_name: whole cells

growth_protocol: YEPD @ 30°C, cells harvested at OD600 of 0.6

extract_protocol:
Total RNA was extracted from clarified lysate and depleted of ribosomal RNAs using RiboZero.  Remaining RNAs were fragments and size selected.
Collected cells were resuspended in lysis buffer and lysed by vortexing with glass beads.
RNAs were ligated to a preadenylated DNA linker and reverse transcribed.  cDNAs were gel purified, circularized, and PCR amplified.

treatment_protocol: Cells were treated with 100 ug/ml cycloheximide for 2 min, then rapidly collected by vacuum filtration

tag: 5' barcode

value: TCTACCC


title: Nkx2-5_WT_CP_Average_Footprints


title: Gata4_DKO_CP_Average_Density


title: ΔBCHL-R rep3


title: rnaseq replicate 1

value: ATTCACC


title: Gata4_WT_CM_Average_Footprints


title: Gata4_NKO_CM_Average_Density


title: Tbx5_NKO_CM_Average_Density


title: Gata4_NKO_CP_Average_Density


title: Nkx2-5_TKO_CM_Average_Density


title: Gata4_TKO_CM_Average_Density


title: Nkx2-5_TKO_CP_Average_Density


title: Tbx5_WT_CP_Average_Density


title: Tbx5_WT_CM_Average_Density


title: Nkx2-5_WT_CP_Average_Density


title: Gata4_WT_CP_Average_Density


title: Nkx2-5_WT_CM_Average_Density


title: Gata4_TKO_CP_Average_Density


title: Gata4_WT_CM_Average_Density


title: RNA_DKO_CM.2

data_processing:
Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using tophat2 (RNA-seq) (Kim et al., 2013). For each gene, reads were counted, and counts-per-million (CPM) calculated using featureCounts (Liao et al., 2014). Finally, edgeR was used to perform differential expression analyses (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

extract_protocol:
Ttotal RNA was isolated from 3 mill cells using TRizol Reagent.
Libraries were prepared according to NuGEN Ultralow V2 kit and paired-end 100bp sequenced on an Illumina HiSeq 2500 instrument.


title: Input EB replicate2

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using option of --best -v 2 --strata -m 1
We used Homer tool to pool the two replicates and allowed only one tag per base by using an option -tbp 1.
Two replicates were merged.  Homer was used for peak calling for the corresponding input control
Genome_build: mm9
Supplementary_files_format_and_content: .bedGraph and HOMER Peaks .bed

source_name: EB

growth_protocol: CCE mESCs were grown on gelatin-coated plates in DMEM containing 15% fetal bovine serum (Hyclone), 1 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 1X penicillin-streptomycin, and 1X ESGRO/2i (Life Technologies).

extract_protocol:
Nuclei were isolated, mononucleosomes were subsequently obtained from CCE mESCs and CCE EBs. Cells were lysed in hypotonic TMSD buffer to isolate nuclei, which were then digested with micrococcal nuclease. The resulting mononucleosomes were immunoprecipitated with Protein AG beads (Pierce) bound to either anti-Brd4 (Abcam) or anti-acetyl-H4 (Millipore).
Washed beads from ChIP were then treated with RNase A followed by Proteinase K. Samples were cleaned up using DNA Clean & Concentrator-5 (Zymogen)
The ChIP library was prepared using the multiplexed ChIP-Seq sample preparation protocol available on the University of Pennsylvania Functional Genomics Core website (http://fgc.genomics.upenn.edu/)
anti-Brd4 (Abcam 128874 and anti-acetyl-H4 (Millipore 06-866)

treatment_protocol: CCE EBs were formed by growing CCE mESCs in suspension in media lacking ESGRO/2i.

value: EB

tag: replicate

tag: antibody

value: Input


title: RNA_DKO_CP.2

tag: genotype


title: RNA_DKO_CM.1


title: RNA_DKO_CM.3


title: RNA_DKO_CP.3


title: Input mESC replicate2

source_name: mESC

value: mESC


title: CRY1 ChIP-seq

city: Lausanne

first: Laura

last: Symul

state: Station 15

address: EPFL SV IBI UPNAE, AAB 039

department: SV-IBI

country: Switzerland

institute: EPFL

data_processing:
Data were processed using the Illumina Pipeline Software v1.40
Sequenced DNA reads (Illumina, 36 bases long reads) were mapped to the human genome (Homo Sapiens Genome Reference Consortium Human Build 37 [GRCh37/hg19; Feb. 2009]) using Bowtie with maximally two mismatches and only one hit allowed on the genome. For BMAL1 ChIPs, the reads from sample 1-3 were merged together.
Only one tag per genomic position was kept.
Detection of enriched regions with MACS  (Zhang et al, 2008) with the following parameters: shift = 70 bp (BMAL1), 90 bp (CLOCK) and 100 bp (CRY1), bandwidth = 2 x shift, genome size = 2.16 Gb.
A refined estimate of the binding site location in each of these regions was then obtained by a deconvolution algorithm that models the expected distribution of tags on the positive and negative strands (Rey et al, 2011).
Local maxima in the deconvoluted signal were used as the center positions of the binding sites. The deconvolution methods also provides a goodness of fit score that quantifies whether the plus and minus tag distributions fit the expected patterns (Rey et al, 2011). This score was used to reject spurious sites.
Genome_build: GRCh37/hg19; Feb. 2009
Supplementary_files_format_and_content: bedGraph of the shifted and merged strands. Each line is the number of tags in this region. The shifts are 70 bp  for BMAL1, 90 bp for CLOCK and 100 bp for CRY1.

growth_protocol: U2OS cells were grown to confluence at 37°C with 5% CO2. Cells were cultured in growth medium, containing DMEM (Dulbecco's modified Eagles medium) with 4.5 g/L glucose, which was supplemented with 10% (v/v) FCS (Fetal Calf Serum) and Penicillin/Streptomycin (Final conc.1x). All chemicals were obtained from PAA.

extract_protocol:
ChIP was performed as described previously (Rey et al, 2011; doi:10.1371/journal.pbio.1000595) with adjustments specific to mammalian cell culture.
Libraries were prepared with the ChIP-Seq Sample Preparation Kit (Illumina) and samples were quantified using a Qubit fluorometer (Invitrogen).

tag: entrainment

value: confluent, desynchronized

tag: cell line


title: CLOCK ChIP-seq

value: CLOCK


title: Input mESC replicate1


title: RNA_NKO_CM.3


title: Tbx5_NKO_CP_Average_Density


title: RNA_NKO_CM.2


title: Brd4 EB replicate2


title: Brd4 EB replicate1


title: RNA_NKO_CM.1

value: ES-derived  Cardiomyocytes


title: RNA_NKO_CP.3

value: Tbx5 knockout


title: RNA_NKO_CP.2


title: RNA_DKO_CP.1

value: ES-derived Cardiac Precursors


title: Input EB replicate1


title: RNA_NKO_CP.1


title: H4ac EB replicate1

value: anti-acetyl-H4 (Millipore 06-866)


title: RNA_TKO_CM.1


title: BMAL1 ChIP-seq


title: H4ac mESC replicate1


title: RNA_TKO_CP.3


title: RNA_TKO_CM.3


title: H4ac EB replicate2


title: Brd4 mESC replicate1


title: RNA_TKO_CP.2


title: RNA_TKO_CP.1


title: RNA_WT_CM.1

value: WT


title: RNA_WT_CP.3


title: RNA_WT_CP.2


title: RNA_WT_CM.3


title: RNA_WT_CP.1


title: RNA_WT_CM.2


title: Brd4 mESC replicate2


title: global riboseq replicate 1

description:
ribosome-protected RNA 26-32 nts
Ribosome footprint profiling from all ribosomes

extract_protocol:
Clarified lysate was digested with RNase I and separated on a sucrose gradient.  Monosome fractions were collected and the RNA was extracted and size selected for ribosome footprints.
Collected cells were resuspended in lysis buffer and lysed by vortexing with glass beads.
RNAs were ligated to a preadenylated DNA linker and reverse transcribed.  cDNAs were gel purified, circularized, and PCR amplified.

value: TGACTCC


title: polysome riboseq replicate 2

description:
ribosome-protected RNA 26-32 nts
Ribosome footprint profiling from polysomes

extract_protocol:
Clarified lysate was separated on a sucrose gradient.  Polysome fractions were pooled, digested with RNaseI, and separated on a 2nd sucrose gradient.  Monosome fractions were collected and the RNA was extracted and size selected for ribosome footprints.
Collected cells were resuspended in lysis buffer and lysed by vortexing with glass beads.
RNAs were ligated to a preadenylated DNA linker and reverse transcribed.  cDNAs were gel purified, circularized, and PCR amplified.


title: global riboseq replicate 2


title: polysome riboseq replicate 1

value: TAGCCCC


title: monosome riboseq replicate 2

description:
ribosome-protected RNA 26-32 nts
Ribosome footprint profiling from monosomes

extract_protocol:
Clarified lysate was separated on a sucrose gradient.  Monosome fractions were pooled, digested with RNaseI, and separated on a 2nd sucrose gradient.  Monosome fractions were collected and the RNA was extracted and size selected for ribosome footprints.
Collected cells were resuspended in lysis buffer and lysed by vortexing with glass beads.
RNAs were ligated to a preadenylated DNA linker and reverse transcribed.  cDNAs were gel purified, circularized, and PCR amplified.

value: ACAAGCC


title: monosome riboseq replicate 1

value: CGGGACC


title: H4ac mESC replicate2


title: mRNA-EtOH_30min

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

data_processing:
RNA-seq reads were aligned and mapped to the Drosophila reference genome (BDGP Release 5) using SOAPaligner/SOAP2, allowing no more than 5 bp mismatches. Low-quality reads (containing adapters or high content of unknown bases) were filtered out.
Expression levels for genes were calculated using RPKM (reads per kilobase transcriptome per million mapped reads) method (Mortazavi et al., 2008) using the CLC Genomics Workbench (CLC bio, Boston, MA).
Genome_build: DM3
Supplementary_files_format_and_content: text files include RPKM values for each sample, and differential expression between the two samples

organism: Drosophila melanogaster

source_name: heads

growth_protocol: All flies were maintained on a standard cornmeal/molasses/agar medium under 12:12 light:dark conditions

extract_protocol:
Approximately 180 adult female flies were used per sample. Flies were transferred to a 50 ml conical tube and snap frozen in liquid nitrogen. Heads were snapped off from the body by briefly vortexing the tubes. The frozen heads were sorted from the bodies using a series of cooled metal mesh sieves. Total RNA was isolated from the heads using the guanidinium thiocyanate single-step method (Ausubel, 1994). After isolation, RNA was treated with DNAse I (Life Technologies, Grand Island, NY) and purified by acid-phenol/chloroform extraction and ethanol precipitation. RNA concentration and quality was assessed using a 2100 Bioanalyzer RNA 6000 Pico Chip (Agilent Technologies, Inc., Santa Clara, CA). RIN values for the control and ethanol-treated samples were 6.80 and 6.40, respectively.
Poly(A)+ RNA was prepared from an aliquot of each total RNA sample with magnetic oligo-(dT) beads (Dynabeads® Oligo (dT), Life Technologies, Grand Island, NY). cDNA synthesis and Illumina library construction were performed with the TruSeq RNA Library Preparation Kit using standard Illumina protocols

treatment_protocol: The ethanol treated group was exposed to an ethanol-saturated air stream until all flies were sedated (15 minutes), followed by a 30 minute ethanol-free air stream. For the untreated control group, flies were exposed to an ethanol-free air stream for the entire 45 minutes.

tag: strain

value: Canton-S

value: Adult (3-5 days)

tag: treatment

value: 15 min ethanol vapor, 30 minute air


title: mRNA-control

value: control


title: RNA_TKO_CM.2


title: P.vivax_normalized_RNAseq_1

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

data_processing:
sequencing reads were aligned to P.vivax Sal-I genome using Tophat2 version2.0.7 with default parameters and reads mapped to r(t)RNA genes were removed from further steps
remained sequencing reads were aligned to P.vivax Sal-I genome using Tophat2 vesion2.0.0 with parameters: --mate-inner-dist 0 --mate-std-dev 80 -i 10 -I 10000 --library-type fr-unstranded --min-segment-intron 10 --max-segment-intron 10000 -N 4 --read-edit-dist 4
only properly paired and uniquely mapped reads used in further analysis
Fragments Per Kilobase of coding exon per Million fragments mapped (FPKM) were estimated using Cufflinks by forcing the software to use P.vivax genome annotations only and --frag-bias-correct was applied.
Genome_build: P. vivax genome plasmodb version 8.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Plasmodium vivax

source_name: Asexual stages

growth_protocol: Time point samples of two P.vivax isolates were collected from Northwesterm Thailand. The details were described as PNAs 2008 [Bozdech et al. PNAs 2008].

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: all mixed

tag: isolate

value: mixed


title: P.vivax_normalized_RNAseq_3

tag: developmental stage


title: P.vivax_smru2_RNAseq_36hr

value: early schizont

tag: time point (hours)


title: P.vivax_smru2_RNAseq_42hr

value: late schizont


title: P.vivax_smru2_RNAseq_48hr


title: P.vivax_smru2_RNAseq_30hr


title: P.vivax_smru2_RNAseq_24hr

value: Trophozoite


title: P.vivax_normalized_RNAseq_4


title: P.vivax_smru2_RNAseq_12hr


title: P.vivax_normalized_RNAseq_2


title: P.vivax_smru2_RNAseq_6hr

value: late ring


title: P.vivax_smru1_RNAseq_48hr


title: P.vivax_smru1_RNAseq_42hr


title: HBRR

city: Milwaukee

first: Wenli

last: Li

state: Wisconsin

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

data_processing:
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Genome_build: UCSC hg19

source_name: HBRR-AmpliSeq

extract_protocol:
Total RNA was extracted per manufacturer’s recommendations using total RNA Purification 96-Well Kit (Norgen Biotek Corp.).
Proton RNA-seq libraries were prepared for sequencing using standard ribosomal RNA depletion method for Proton RNA-seq. For library preparation of AmpliSeq whole transcriptome a barcoded cDNA library is first generated with SuperScript® VILO™ cDNA Synthesis kit from 10ng of total RNA. Then cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Amplified cDNA Libraries were evaluated for quality and quantified using Agilent Bioanalyzer High sensitivity chip. Libraries were then diluted to 100pM and pooled equally, with eight individual samples per pool.

treatment_protocol: The hiPSC-CMs were stimulated with endothelin-1 (ET-1) to induce a hypertrophic response following our established CM hypertrophy protocol (Aggarwal et al., 2014. Plos One.)

tag: reference

value: Ambion FirstChoice® Human Brain Reference Total RNA


title: UHRR

source_name: UHRR-AmpliSeq

value: Agilent Universal Human Reference RNA


title: P.vivax_smru1_RNAseq_36hr


title: EBs D8 rep 1

city: Heraklion, Crete

first: Christiana

last: Hadjimichael

address: Nikolaou Plastira 100

department: Institute of Molecular Biology and Biotechnology (IMBB)

country: Greece

institute: Foundation for Research and Technology - Hellas (FORTH)

description: EBs D8 rep 1

data_processing:
Basecalls performed using CLC Genomics Workbench.The methods and tools developed for CLC Genomics Workbench are inspired by the findings and methods described in [Creighton et al., 2009], [Wyman et al., 2009], [Morin et al.,2008] and [Stark et al., 2010].
Sequenced reads were trimmed for adaptor sequence. Then, they were annotated using miRBase Rel.2.1 and we specified how the alignment of the tags against the annotation sources should be performed. The tag was allowed to extend or miss the annotated mature region at the 5' or 3' end 2 bases. The maximum mismatches were 2 (default).
Samples were then normalized using quantile normalization and subsequently transformed to log2 values to normalize variation across orders of magnitude. Differential expression was calculated on the basis of a paired t-test and corrected for multiple hypotheses under an FDR of 5%.
Genome_build: miRbase Release 2.1
Supplementary_files_format_and_content: file includes Original, normalized and transformed values for each sample. The average values for ESCs D0 and EBs D8 as well as the fold change and the p-value.

source_name: Embryonic stem cells

growth_protocol: The murine feeder-independent ES cell line CGR8 was cultured in gelatin-coated flasks in Glasgow minimal essential medium (GMEM; Gibco,) supplemented with 100 U/ml leukemia inhibitory factor (LIF; ESGRO-Millipore,), 2mM L-glutamine (Gibco) 100μM beta-mercaptoethanol (Sigma Aldrich, USA) and 10% heat-inactivated HyClone fetal bovine serum (FBS; GE Healthcare Life Sciences).

extract_protocol:
Small RNAs (smRNAs) were extracted from ES cells and EBs D8 using mirVana™ miRNA Isolation Kit (Ambion, Life Technologies). The concentrations of smRNAs were determined using a NanoDrop ND-1000 Spectrophotometer and the size and purity were assesed using the Bioanalyzer 2100 (Agilent Technologies).
Approximately 100ng of miRNA was used for library constructions following the protocol for the Ion Torrent Total RNA-Seq Kit. Briefly, the smRNAs were hybridized and ligated with Ion Adaptor mix, a reverse transcription was performed and the cDNAs were purified using the Nucleic Acids Binding Beads. The amplification of cDNAs was performed by PCR using the Ion 5’ PCR primer and the Ion 3’ PCR primer and the amplified DNA was purified using the Nucleic Acids Binding Beads. Final libraries were used for sequencing analysis on the Ion Torrent PGM instrument using 316 chips.

treatment_protocol: For EB formation, cells were trypsinized and diluted in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) supplemented with 2mM L-glutamine (Gibco) 100μM beta-mercaptoethanol (Sigma Aldrich, USA) and 20% heat-inactivated HyClone fetal bovine serum (FBS; GE Healthcare Life Sciences), to a final concentration of 1000 cells/20μl. Twenty microliter drops were plated on the lids of 140-mm plates, which were carefully inverted over the petri-dishes filled with approximately 10 ml PBS. EBs were cultured without LIF as hanging drops for 2 days and then were collected and cultured in suspension for 6 more days.

tag: background strain

tag: donor strain

tag: passages


title: ESCs D0 rep2

description: ESCs D0 rep2


title: P.vivax_smru1_RNAseq_24hr


title: EBs D8 rep 2

description: EBs D8 rep 2


title: P.vivax_smru1_RNAseq_6hr


title: P.vivax_smru1_RNAseq_18hr


title: NLFK_input DNA

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

data_processing:
Quality metrics were gathered with FastQC version 0.11.2
Reads were filtered with cutadapt version 1.4.2
Reads were aligned with Bowtie2 version 2.2.3
Genome_build: ICGSC Felis_catus 6.2, Canine parvo virus NCBI Reference Sequence NC_001539.1
Supplementary_files_format_and_content: Processed files are the aligned files. Alignment to CPV genome in infected and non-infected cells yields the information in the results.

organism: Felis catus

source_name: Kidney cells

extract_protocol:
Lysates were sonicated and precipitated with specific antibodies against H3K27ac.
Guidelines from the NEBnext Ultra DNA-library preparation kit for Illumina were used. DNA range 150-350 bp was gel-purified and library quantified by Agilent bioanalyzer and subjected to 50 bp single-end read sequencing with Illumina Hiseq 2000 at EMBL Genecore, Heidelberg.

value: NLFK

tag: cell type

value: feline kidney cells

tag: infected with

tag: chip antibody

value: none (input DNA)


title: ESCs D0 rep1

description: ESCs D0 rep1


title: NLFK_CPV-infected_H3K27ac_ChIPSeq

value: canine parvovirus (CPV)

tag: time point

value: 24 h post infection

value: H3K27ac (Abcam; ab4729)


title: AB02-F

status: Public on Feb 10 2016

city: Shenyang

first: Chang

last: Liu

address: Dongling street

institute: Shenyang agriculture university

data_processing:
Illumina software used for basecalling.
After sequencing, the base calling step was repeated to eliminate any unwanted raw reads .
clean reads were mapped to reference sequences using the TopHat
The gene expression level was calculated by using RPKM method
Genome_build: B. rapa (Chiifu-401)' (available at  ftp://bradata:zhl410ivf@brassicadb.org/Brassica_rapa/)
Supplementary_files_format_and_content: processed data file include RPKM values for genes in each Sample.

organism: Brassica rapa subsp. pekinensis

source_name: Chinese cabbage_fertile

growth_protocol: The seeds were sowed in the greenhouse after vernalization.

extract_protocol:
Total RNA was extracted with Trizol, according to the manufacturer’s instructions.The quality and purity were attained using Agilent 2100 Bioanalyzer and 1.0% agarose gel electrophoresis.
RNA libraries were prepared for sequencing using Illumina protocols

tag: gender

value: male

value: fertile

tag: tissue

value: bud


title: NLFK_non-infected_H3K27ac_ChIPSeq


title: P.vivax_smru2_RNAseq_18hr


title: HEPG2 mRNA heat shock 4h IP

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

data_processing:
Library strategy: m1A-seq
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome or S.pombe genome version ASM294v2.29 or S.cerevisea genome version S288C. Aligment was done using tophat version 2.0.12 with parameters - -M -p 3 --no-novel-juncs -g 5 and the relevant gff transcriptome annotation
Enriched intervals were identified using MACS2,in IP over input. FC>=2, FDR<=0.05
Peak middle was determined for peaks that appeared in both replicates.if no replicates were avialable FC>=4 was taken.
For PARSseq samples reads were trimmed using cutadapt and aligned to the human transcriptome (knownCanonical transcripts from UCSC) using bowtie2 (--local).
Only uniquely aligned reads were used for downstream analysis
For each position in the transcriptome number of read start at each base were counted. For this step only reads with more than 5 nts matching the transcript at the start of the read were counted
PARS-scores were calculted for each position in the transcriptome as described in Wan et al. 2014.
Genome_build: hg19 for human ,S.pombe genome version ASM294v2.29 , S.cervisea genome version S288C
Supplementary_files_format_and_content: Peak lists in excel format include peak middle coordinates for each cell type

source_name: HEPG2 cell line

growth_protocol: in the Glucose starvation experiments cells were grown on glucose free medium for 4 hours before harvest. In S.Pombe Cells were grown in either EMM-N medium for 4 hours or in malt mating medium for 5 hours

extract_protocol:
Total RNA of the indicated cell types was extracted using 5PRIME RNA purification kit. Where indicated mRNA enriched RNA was purified by oligo dT selection.
Fragmentation was carried out using Ambion fragmentation reagents in 70ºc.Competetive elution was carried out using free m1A nucleoside  (330 microMolar m1A in 10 mM Tris pH 7.4 ,375 mM NaCl 0.1% NP-40.
Immunoprecipitation was done using MBL anti-m1A antibody D345-3 mAb.Dimmroth rearrangment was performed by heating the samples to either 50ºC or 60ºC for 1H under pH 10.4 conditions.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).

treatment_protocol: in the heat shock experiments cells were incubated at 43 degrees celsius for 4 hours prior to harvesting.


title: HEPG2 total RNA Untreated input replicate


title: HEPG2 mRNA heat shock 4h input


title: HEPG2 total RNA Untreated IP replicate


title: AB02-S

source_name: Chinese cabbage_sterile

tag: genotype

value: sterile


title: RNA-Seq_MDA-MB-231_R3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim 10bp from 5'end. (FASTQ Trimmer 1.0.0)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v21). Genes with very low expression (<3  counts) were removed from the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the counts from the HTSeq-count quantification.

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF-7 cells and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271) + 10% (v/v) FBS (Atlanta Biologicals) Pen/Strep (Life Technologies)  Glutamine (Life Technologies)  .

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini kit (Qiagen #74134).
RNA libraries were prepared for sequencing using standard Illumina protocols using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina #RS-122-2301). Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and pellets stored at -80C.

value: breast

value: metastatic site derived

tag: neoplasia type

value: adenocarcinoma

tag: cell line


title: WT CD8 rep1

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The RNA-Seq libraries were then processed by RSEM (v1.2.21, Li et al., BMC Bioinformatics) to estimate expression levels of all genes. The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.  UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
EBSeq (v1.5.4, Leng et al., Bioinformatics), as an integral component of RSEM package, was used to identify differentially expressed genes (FDR = 0.01).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample ...

source_name: CD8 T cells

extract_protocol:
Mature CD8 thymocytes were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: wild type

value: mature thymocytes

tag: cell phenotype

value: TCRbeta high, CD69–, CD24–, CD8+


title: HEPG2 mRNA Glucose starvation 4h IP replicate B


title: RNA-Seq_MDA-MB-231_R1


title: HEPG2 mRNA Glucose starvation 4h input replicate B


title: RNA-Seq_MDA-MB-231_R2


title: P.vivax_smru1_RNAseq_30hr

value: early schizont

tag: isolate


title: RNA-Seq_MCF7_R3


title: HEPG2 mRNA Glucose starvation 4h IP replicate A


title: HEPG2 mRNA Glucose starvation 4h input replicate A


title: RNA-Seq_MCF7_R2


title: HEPG2 mRNA untreated input replicate E


title: RNA-Seq_MCF7_R1


title: HEPG2 mRNA untreated IP replicate E


title: RNA-Seq_MCF10A_R3

value: luminal ductal cells

value: fibrocystic disease


title: RNA-Seq_MCF10A_R2


title: HEPG2 mRNA untreated input replicate D


title: RNA-Seq_MCF10A_R1


title: HEPG2 mRNA untreated input replicate C


title: HEPG2 mRNA untreated IP replicate D


title: HEPG2 mRNA untreated input replicate B


title: HEPG2 mRNA untreated IP replicate B


title: MDA231_H3K4ME3_R2

description:
MDA-231 SAMPLE 4
H3K4me3 ChIP
processed data file: MDA231_H3K4ME3_logFE.bw

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Concatenate replicates.
Align reads with STAR v2.4, splicing disabled with '--alignIntronMax 1'.
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF-7 cells and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red) + 10% (v/v) FBS (Atlanta Biologicals).

extract_protocol:
Nuclei were isolated using a modification of the Dignam method (Dignam et al Nucleic Acids Res. 1983) and pellets were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin ranging from 200-800 bp with an average peak size of 500 bp.  For immunoprecipitation, 30 μg of sheared chromatin was incubated with 10 ug of anti H3K4me3 (Abcam, ab1012 lot#GR80367-1) or H3K4ac (Active Motif -39382 lot#29108001) overnight at 4°C and then incubated with 50 μl Protein-G Dynabeads (Life Technologies 10004D lot#123085320) for 4 h at 4°C.
Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range.
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and crosslinked with 0.8% formaldehyde (Thermo Scientific Cat no. 28908) in PBS for 10 minutes at room temperature with continuous shaking

value: mammary gland/breast epithelial cell

tag: atcc id

value: adenocarcinoma; ATCC HTB-26

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: MDA231_H3K4AC_R1

description:
MDA-231 SAMPLE 1
H3K4AC ChIP
processed data file: MDA231_H3K4AC_logFE.bw

value: Active Motif


title: MDA231_input_R2

description:
MDA-231 SAMPLE 6
genomic DNA control


title: MDA231_H3K4AC_R2

description:
MDA-231 SAMPLE 2
H3K4AC ChIP
processed data file: MDA231_H3K4AC_logFE.bw


title: MDA231_H3K4ME3_R1

description:
MDA-231 SAMPLE 3
H3K4me3 ChIP
processed data file: MDA231_H3K4ME3_logFE.bw


title: HEPG2 mRNA untreated IP replicate C


title: MDA231_input_R1

description:
MDA-231 SAMPLE 5
genomic DNA control


title: Kasumi1_RN-1_1uM_24h_R2

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
Sequencing was performed on an Illumina HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold. Samples with fewer than 10 reads FPKM are replaced with the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene. Genes were further filtered to include only protein-coding, IG* and TR* Ensembl gene categories.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19
Supplementary_files_format_and_content: Gene FPKM, sample annotations, gene annotations (all text format)

growth_protocol: Cells were propaged in RPMI media supplemented with 20% FCS (Kasumi-1) or 10% FCS + 10 ng/mL GM-CSF (SKNO-1).

extract_protocol: RNA was isolated following Trizol lysis as per the manufacturer's protocol (Life Technologies) or using Qiagen RNeasy Plus mini kits and sequenced at Ocean Ridge Biosciences.

treatment_protocol: Cells in culture were treated with either 0.1% DMSO or 1 uM RN-1 or GSK690 for 72 hours (Kasumi) or 4 days (SKNO-1)

tag: agent


title: Kasumi1_GSK690_1uM_24h_R1


title: Kasumi1_GSK690*_1uM_24h_R2


title: Kasumi1_GSK690*_1uM_24h_R1


title: MCF7_input_R1

description:
MCF7 SAMPLE 5
genomic DNA control

value: adenocarcinoma; ATCC HTB-22


title: MCF7_H3K4ME3_R2

description:
MCF7 SAMPLE 4
H3K4me3 ChIP
processed data file: MCF7_H3K4me3_logFE.bw


title: Kasumi1_DMSO_1uM_24h_R1

value: DMSO


title: MCF7_H3K4ME3_R1

description:
MCF7 SAMPLE 3
H3K4me3 ChIP
processed data file: MCF7_H3K4me3_logFE.bw


title: MCF7_H3K4AC_R2

description:
MCF7 SAMPLE 2
H3K4AC ChIP
processed data file: MCF7_H3K4AC_logFE.bw


title: MCF7_H3K4AC_R1

description:
MCF7 SAMPLE 1
H3K4AC ChIP
processed data file: MCF7_H3K4AC_logFE.bw


title: SKNO1_GSK690*_1uM_24h_R2


title: MCF10A_H3K4ME3_R2

description:
MCF10A SAMPLE 4
H3K4me3 ChIP
processed data file: MCF10A_H3K4ME3_logFE.bw

value: fibrocystic disease; ATCC CRL-10317


title: SKNO1_RN-1_1uM_24h_R2


title: MCF10A_H3K4ME3_R1

description:
MCF10A SAMPLE 3
H3K4me3 ChIP
processed data file: MCF10A_H3K4ME3_logFE.bw


title: SKNO1_GSK690_1uM_24h_R1


title: Kasumi1_GSK690_1uM_24h_R2


title: Kasumi1_DMSO_1uM_24h_R2


title: SKNO1_DMSO_1uM_24h_R2


title: MCF7_input_R2

description:
MCF7 SAMPLE 6
genomic DNA control


title: MCF10A_H3K4AC_R1

description:
MCF10A SAMPLE 1
H3K4AC ChIP
processed data file: MCF10A_H3K4AC_logFE.bw


title: 8-6321-F08-8

city: Los Angeles

first: Jacqueline

middle: Gire

last: O'Rourke

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

data_processing:
fastq reads were alignd to the mouse genome (mm9) with tophat v2.0.8b with parameters -G --no-novel-juncs
bam files were annotated in using Partek software to generate RPKM numbers for each Refseq annotated gene
Genome_build: mm10 (brain) and mm9 (spinal cord)

source_name: brain

growth_protocol: Mouse brains and spinal cords were collected at 6 month

extract_protocol:
Brain and spinal cords were flash frozen on dry ice, and RNA was harvested using Trizol. Total RNA isolated using the PureLink™ RNA Mini Kit (Catalog # 12183018A) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Iontorrent (brain) or Illumina (spinal cord) protocols.  RNA sequencing libraries were constructed with the TruSeq RNA Sample Prep Kits v2 from Illumina. 12 RNA samples were indexed with different adapters and pooled for sequencing.

tag: strain

value: cortex


title: 11-6324-F112-11


title: SKNO1_RN-1_1uM_24h_R1


title: 10-6317-F112-10


title: SKNO1_GSK690_1uM_72h_R2


title: SKNO1_RN-1_1uM_72h_R2


title: SKNO1_GSK690*_1uM_24h_R1


title: SKNO1_GSK690*_1uM_72h_R2


title: 7-6320-F08-7


title: 6-6319-F08-6


title: Kasumi1_RN-1_1uM_24h_R1


title: 5-6318-F08-5


title: 4-6327-NTg-4

value: nontransgenic (NTg)


title: SKNO1_DMSO_72h_R1


title: 3-6326-NTg-3


title: SKNO1_RN-1_1uM_72h_R1


title: MCF10A_H3K4AC_R2

description:
MCF10A SAMPLE 2
H3K4AC ChIP
processed data file: MCF10A_H3K4AC_logFE.bw

tag: cell type


title: Kasumi1_GSK690_1uM_72h_R2


title: SKNO1_DMSO_1uM_24h_R1


title: 1-6322-NTg-1


title: 2-6323-NTg-2


title: 9-6316-F112-9


title: Kasumi1_GSK690*_1uM_72h_R2


title: Kasumi1_DMSO_72h_R2


title: Kasumi1_RN-1_1uM_72h_R2


title: SKNO1_DMSO_72h_R2


title: Kasumi1_GSK690*_1uM_72h_R1


title: Kasumi1_GSK690_1uM_72h_R1


title: Kasumi_GSK690_input

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files and corresponding TDF files suitable for visualization using the Integrative Genomics Viewer (IGV) available from the Broad Institute.

extract_protocol:
Treated cells in culture were cross-linked with 1% formaldehyde for 10 minutes and then queched with glycine.  Washed cells were lysed and sonicated, followed by antibody immunoprecipitation.
DNA libraries for ChIP-seq were prepared using Ovation Ultralow DR Multiplex System kits (0330-32, NuGEN) followed by Illumina sequencing at the MIT BioMicro Center.

value: 72 hours


title: Kasumi1_RN-1_1uM_72h_R1


title: Kasumi_DMSO_input


title: Kasumi_GSK690_H3K4me2

value: Millipore

tag: chip antibody vendor id


title: Kasumi_RN-1_input

tag: chip antibody


title: Kasumi1_DMSO_72h_R1

tag: time point


title: Kasumi_RN-1_H3K4me2


title: SKNO1_GSK690_1uM_72h_R1


title: SKNO1_GSK690*_1uM_72h_R1


title: Kasumi_RN-1_KDM1A

value: Bethyl


title: Kasumi_DMSO_H3K4me2


title: Kasumi_GSK690_KDM1A


title: SKNO1_GSK690_1uM_Day4_Input

value: 4 days


title: Kasumi_DMSO_KDM1A


title: SKNO1_RN-1_1uM_Day4_Input


title: SKNO1_GSK690_1uM_Day4_KDM1A


title: SKNO1_DMSO_Day4_Input


title: HepG2 PARSseq S1 replicate B

data_processing:
Library strategy: PARS-seq
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 or hg19 whole genome using tophat version 2.0.12 with parameters - -M -p 3 --no-novel-juncs -g 5
Enriched intervals were identified using MACS2,in IP over input. FC>=2, FDR<=0.05
Peak middle was determined for peaks that appeared in both replicates.
For PARSseq samples reads were trimmed using cutadapt and aligned to the human transcriptome (knownCanonical transcripts from UCSC) using bowtie2 (--local).
Only uniquely aligned reads were used for downstream analysis
For each position in the transcriptome number of read start at each base were counted. For this step only reads with more than 5 nts matching the transcript at the start of the read were counted
PARS-scores were calculted for each position in the transcriptome as described in Wan et al. 2014.
Genome_build: hg19 for human, mm10 for mouse
Supplementary_files_format_and_content: Peak lists include peak middle coordinates for each cell type

extract_protocol:
Total RNA of the indicated cell types was extracted using 5PRIME RNA purification kit. Where indicated mRNA enriched RNA was purified by oligo dT selection.
Fragmentation was carried out using Ambion fragmentation reagents in 70ºc.Competitive elution was carried out using free m1A nucleoside  (330 microMolar m1A in 10 mM Tris pH 7.4 ,375 mM NaCl 0.1% NP-40.
Immunoprecipitation was done using MBL anti-m1A antibody D345-3 mAb.Dimmroth rearrangement was performed by heating the samples to either 50ºC or 60ºC for 1H under pH 10.4 conditions.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).


title: HepG2 PARSseq V1 replicate A


title: SKNO1_DMSO_Day4_KDM1A


title: SKNO1_GSK690_1uM_24h_R2


title: SKNO1_RN-1_1uM_Day4_KDM1A


title: HepG2 PARSseq S1 replicate A


title: HEK293 total RNA input replicate B

data_processing:
Library strategy: M1A-seq
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 or hg19 whole genome using tophat version 2.0.12 with parameters - -M -p 3 --no-novel-juncs -g 5
Enriched intervals were identified using MACS2,in IP over input. FC>=2, FDR<=0.05
Peak middle was determined for peaks that appeared in both replicates.
For PARSseq samples reads were trimmed using cutadapt and aligned to the human transcriptome (knownCanonical transcripts from UCSC) using bowtie2 (--local).
Only uniquely aligned reads were used for downstream analysis
For each position in the transcriptome number of read start at each base were counted. For this step only reads with more than 5 nts matching the transcript at the start of the read were counted
PARS-scores were calculted for each position in the transcriptome as described in Wan et al. 2014.
Genome_build: hg19 for human, mm10 for mouse
Supplementary_files_format_and_content: Peak lists include peak middle coordinates for each cell type

source_name: HEK293T cell line


title: HepG2 PARSseq V1 replicate B


title: HEK293 total RNA input replicate A


title: HEK293 total RNA IP replicate A


title: HEPG2 total RNA Untreated input competitive elution


title: HEPG2 total RNA rearranged at 60c IP


title: HEPG2 total RNA Untreated IP competitive elution


title: HEK293 total RNA IP replicate B


title: HEPG2 total RNA rearranged at 50c IP


title: HeLa mRNA input replicate B

source_name: HeLa cell line

value: HeLa


title: HeLa mRNA input replicate A


title: HEPG2 total RNA rearranged at 50c input


title: HEPG2 total RNA rearranged at 60c input


title: HeLa mRNA IP replicate A


title: T11-548A

city: Gaithersburg

first: Dong

last: Shen

state: MD

address: MedImmune Way

department: Translational Science

institute: Medimmune

data_processing:
Illumina
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human genome reference hg19  via Bowtie
Data were normalized using DESeq in R.
Genome_build: hg19
Supplementary_files_format_and_content: TSV file with normalized read counts for each sample.

source_name: tumor

extract_protocol:
Tumor and normal samples  were removed, flash frozen on dry ice, and RNA was harvested.  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease status

value: small cell lung cancer


title: T12-1866A