title: nunsigfp.fastq.gz

city: BOSTON

first: NELSON

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: Sample 16

data_processing:
fastx_clipper from fastx_toolkit-0.0.13.2 to remove the 3' adapter sequence with paramaters "-M 9 -n -l 20"
Genome_build: Drosophila melanogaster, BDGP R5/dm3; http://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/
Supplementary_files_format_and_content: tab delimited text format. 1st column: sequence (after trimming adapters), 2nd column: frequency

source_name: OSS_siGFP_nascent transcript

growth_protocol: OSS cells were cultured in Shield and Sang M3 media that was supplemented with 10% FBS,  10ug/ml insulin, 0.6mg/ml Glutathione, and 10% fly extract.  Cells were incubated in a humified chamber at standard atmospheric oxygen at 27C and were split by pipetting into new media every 4 days.

extract_protocol:
Whole cell lysates for CLIP were generated by lysting in Q-column buffer (20mM Hepes-KOH pH 7.9; 10% glycerol; 0.1 M KOAc; 0.2 mM EDTA; 1.5 mM MgCl2; 0.5 mM DTT; 1X Roche Complete EDTA-free Protease Inhibitor Cocktail; 0.5% NP40), dounced with 50 strokes and sonicated 2 rounds for 30 secs.  mRNA was CLIP RNA fragments were extracted with Trizol. mRNAs were further isolated by the Magnetrac Atail selection kit. The two antibodies used are not sold from a manufacturer but were custom made.  The mouse monoclonal antibody against Piwi was obtained from the Siomi lab (Saito et al. Genes Dev. 2006 Aug 15;20(16):2214-22.) while the rabbit polyclonal antibody against Piwi was generated by the Lau lab with a peptide antigen to the N terminal 12 amino acids of the Piwi gene.
CLIP tags and one set of mRNA sequencing libraries were generated with custom protocol for constructing small RNA libraries (Robine et al, Curr Bio 2009).  All other mRNA libraries were constructed with the ScriptSeq version 1 and version 2 kits from Epicenter Biotech.

treatment_protocol: For CLIP, cells were irradiated with 254nm UV light with 0.9j/cm2 of energy.  For mRNA-Seq experiments, cells were treated with 100 pmoles of small interfering RNAs per 10cm dish of OSS cells via a nucleofection with the Amaxa V kit using program D013.

value: Ovary somatic sheet cells  (OSS)

value: ovarian follicle cell

tag: treated with

value: siGFP

tag: molecule subtype

value: nascent transcript


title: nunsipiwi.fastq.gz

status: Public on Sep 15 2014

type: SRA

middle: C

country: USA

description: Sample 17

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster

source_name: OSS_siPiwi_nascent transcript

tag: cell line

tag: cell type

value: siPiwi


title: nucpsipiwi.fastq.gz

description: Sample 15

source_name: OSS_siPiwi_nucleoplasmic RNA

value: nucleoplasmic RNA


title: siPIWI0125.fastq.gz

description: Sample 21

value: mRNA


title: osssipiwi.fastq.gz

description: Sample 19


title: siGFP0125.fastq.gz

description: Sample 20


title: macroH2A1 KD replicate 1

city: Bronx

first: Matthew

middle: Jon

last: Gamble

state: NY

address: 1300 Morris Park Ave / Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Sample 4

data_processing:
Base calls performed using CASAVA version 1.7
The sequencing reads were trimmed of barcodes and aligned to the human genome (hg19) using GSNAP version 2012-07-12
The reads were then binned into genes (Ensemble ens67) using HTSeq version v0.5.3p3 (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html).
Identification of differential gene expression for protein coding genes with at least 20 reads across all replicates was performed with DESeq (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: processed data files include uniquely mapping read counts for each gene
Supplementary_files_format_and_content: DESeq output consists of tab separated values for baseMean, baseMeanA(Luc KD), baseMeanB(macroH2A1 KD), foldChange, log2FoldChange, pval, padj.

organism: Homo sapiens

source_name: IMR90_macroH2A1 KD

growth_protocol: IMR90 (ATCC, CCL-186) primary human fetal lung fibroblast cells were cultured in MEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Tripure Isolation Reagent (Roche).
RNA samples were treated with RNase-free DNaseI and purified by using the RNeasy Mini Kit (QIAGEN). The resulting RNA was depleted of ribosomal RNA by using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicentre). The rRNA-depleted RNA was used to synthesize the first strand cDNA using SuperScript® III First-Strand Synthesis System (Invitrogen) according to the manufacturers instructions. Subsequently, the second strand was generated by using E. coli DNA ligase (Invitrogen), E. coli DNA polymerase (Invitrogen), and dUTP, dCTP, dATP, and dGTP set (10 µmol each, Promega), in the Second Strand Buffer (Invitrogen). Then the cDNA were sheared with Covaris to roughly 300bp. After fragmentation, samples were purified with MinElute columns (Qiagen).  And the protruding 3’ and 5’ ends of the fragments were repaired using T4 DNA Polymerase (NEB) and T4 DNA Polynucleotide kinase (NEB) in T4 DNA ligase buffer (NEB). Next, dA ends were generated by employing Klenow Fragment (3’->5’ exo-, NEB), in Buffer 2 (NEB). Adapter ligation reactions were then set up using indexed adapters and Quick Ligase (NEB). The products were used as the template for UNG (Fermentas) treatment and PCR amplification using Phusion High-Fidelity DNA Polymerase (NEB). The libraries were visualized on 2% E-Gel® General Purpose Agarose Gels (Invitrogen). The barcoded libraries were sequenced on a single lane of a HiSeq2500 (Illumina).

value: human primary lung fibroblasts

tag: genotype/variation

value: expressing shRNA directed against macroH2A1


title: nucpsigfp.fastq.gz

description: Sample 14

source_name: OSS_siGFP_nucleoplasmic RNA


title: mRNA-siPiwi-srna.fastq.gz

description: Sample 13


title: cytosipiwi.fastq.gz

description: Sample 9

source_name: OSS_siPiwi_cytoplasmic RNA

value: cytoplasmic RNA


title: clip-piwi-block.fastq.gz

description: Sample 7

value: negative control of Piwi associated RNA fragments


title: mRNA-siGFP-srna.fastq.gz

description: Sample 11


title: clip-piwi-SiomiAb1.fastq.gz

description: Sample 6

tag: clip antibody

value: mouse monoclonal antibody against Piwi

value: Piwi associated RNA fragments


title: WT_NR

city: Philadelphia

first: Shelley

middle: L

last: Berger

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Departments of Cell & Developmental Biology; Biology; Genetics

institute: University of Pennsylvania

library_source: genomic

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to sacCer3 using bowtie2 -t --phred33-quals -k1 -N 1 --n-ceil 0,0.15 -p 20 -x -U -S
Aligned reads normalized by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalized by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT Saccharomyces cerevisiae

growth_protocol: 30 degrees celcius; synthetic complete media; NR - 2% glucose, CR - 0.05% glucose

extract_protocol:
QIAGEN Blood and Cell Culture DNA Kit
NEBNext DNA Library Prep Master Mix Set for Illumina

treatment_protocol: Cell walls were digested with zymolyase followed by digestion of chromatin with MNase and ExoIII

tag: treatment

value: Mnase-treated DNA

tag: strain

value: WT

tag: growth protocol

value: Non-restricted


title: mRNA-siGFP-scriptseq.fastq.gz

description: Sample 10


title: clip-piwi-LauAb1.fastq.gz

description: Sample 3

value: rabbit polyclonal antibody against Piwi


title: osssigfp.fastq.gz

description: Sample 18

value: Ovary somatic sheet cells  (OSS)


title: clip-piwi-LauAb2.fastq.gz

description: Sample 4

value: ovarian follicle cell


title: Nun-siPiwi.fastq.gz

description: Sample 2


title: BMMC_dbdb

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description:
CGATGT_s_3_1_sequence
CGATGT_s_3_2_sequence

data_processing:
Illumina RTA 1.13.48 was used for basecalling.
Masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using tophat 1.2.0 with parameter -g 10
Abundance measurement of each gene is represented by TMM normalized (using EdgeR bioconductor package)  reads located in each gene.
Genome_build: mm9

organism: Mus musculus

source_name: Bone marrow macrophages

growth_protocol: Bone marrow cells were cultured in 10 ng/ml of MCSF (BMMC) or 20 ng/ml of GM-CSF (BMGM) for 7-8 days

extract_protocol:
Total RNA was extracted using miRNeasy columns with on column DNAse digestion as described by the manufacturer (Qiagen, Vlencia, CA)
Total RNA was depleted of Ribosomal RNA using RiboMinus kit (Life Technologies, Carlsbad, CA) according to manufacturer’s protocols. Paired End libraries were prepared, size selected, gel purified and sequenced on Illumina HiSeq2000 platform following the manufacturer’s protocols (Illumina Inc, San Diego, CA).

value: Bone marrow macrophages

tag: phenotype

value: Type 2 Diabetic


title: RD2

status: Public on Sep 14 2014

city: New York

first: Yanwen

last: Jiang

institute: Weill Cornell Medical College

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads were aligned to human hg19 using STAR aligner (Dobin et al, Bioinformatics, 2012)
Read counts and differential expression were accessed by edgeR (Robinson et al, Bioinformatics, 2010)
Genome_build: hg19
Supplementary_files_format_and_content: reads count in .txt format

source_name: DLBCL cell line

growth_protocol: IMDM + 10% FBS + 1% HEPES

extract_protocol:
Cells were dissolved in Trizol and total RNA was extracted according to the Trizol protocol (Life Technologies, Cat. No. 15596-018).
Libraries were constructed according to the Illumina Truseq RNA sample preparation guide.

treatment_protocol: Transfected with siRNA against BCL6, then etopic expression of either WT BCL6 or BCL6 RD2 mutant

tag: genotype

value: siBCL6;etopic expression of BCL6 RD2 mutant

value: DLBCL


title: Scer

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

country: France

institute: Univ. Bordeaux

data_processing:
Raw reads were filtered to obtain only reads with an average quality > 20 using the approach described by Sasson and Michael (2010) then mapped to whole genomes using bowtie v0.12.7 with parameters -v 2 -m 1, splice junctions were found by TopHat with default parameters and defined intron size -i 49 -I 1050.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, the number of reads falling in each intron were counted and normalized by the size of intron and by the size of the library. For genes reads falling in the exons only were counted and normalized as above.
Genome_build: sacCer3
Supplementary_files_format_and_content: *_comp.txt: tab-delimited text files include intron RPKM values for each Sample; *_introns.bed: TopHat junction output for each Sample

source_name: whole cells

growth_protocol: YPD media, 30 ºC, 200 rpm

extract_protocol:
Cells were collected at absorbance of 0.5 at 600 nm. RNA extraction was performed using Trizol (Invitrogen, UK), RNA was precipitated in LiCl (Ambion, UK), washed with 70 % ethanol and resuspended in water. Ten μg of total RNA was processed with the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen) to deplete the rRNA.
cDNA libraries were constructed using the SOLiD 4.0 System from Life Technologies according to the standard manufacturer's protocol.


title: BMGM_db+

description:
GATCAG_s_3_1_sequence
GATCAG_s_3_2_sequence

value: Control


title: RD3


title: clip-piwi-LauAb3.fastq.gz

description: Sample 5


title: BMGM_dbdb

description:
TAGCTT_s_3_1_sequence
TAGCTT_s_3_2_sequence


title: Nun-siGFP.fastq.gz

description: Sample 1

value: siGFP

value: nascent transcript


title: cytosigfp.fastq.gz

description: Sample 8

source_name: OSS_siGFP_cytoplasmic RNA

value: cytoplasmic RNA


title: RD1


title: BMMC_db+

description:
ATCACG_s_3_1_sequence
ATCACG_s_3_2_sequence


title: WT2

value: siBCL6;etopic expression of WT BCL6


title: mRNA-siPiwi-scriptseq.fastq.gz

description: Sample 12

value: siPiwi

value: mRNA


title: totRNA_ink128

status: Public on Sep 13 2014

city: Emeryville

first: Claudia

middle: Ani

last: Rubio

address: 5300 Chiron Way

department: Oncology

institute: Novartis Institutes for Biomedical Research

description: RNAseq of total RNA from cells treated with 200 nM INK128 for 2 hours

data_processing:
Basecalls were performed with Casava v1.8.1 or 1.8.3
Sequence reads were trimmed for adapter and polyA sequences and mapped to the hg19 genome, as well as UCSC KnownGene canonical transcripts, using Bowtie v2 (no more than 2 mismatches, -a –m -16)
Alignments were merged and uniquely mapped reads were counted to calculate the reads per kilobase per million (RPKM), or fragments per kilobase million (FPKM; INK128 data).  Genomic positions with non-uniquely aligned reads as well as positions that overlapped with more than one KnownGene canonical transcript were excluded from the RPKM calculation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Excel files containing RPKM (Silvestrol) or FPKM (INK128) data for each sample.

source_name: Breast cancer cells

growth_protocol: MDA-MB-231 cells were grown in culture at a density of 1-7 x 106 cells/ml in RPMI supplemented with 10% Fetal Calf Serum

extract_protocol:
Extraction protocol was carried out as described by Ingolia et al. Nat Protoc 2012, 7:1534–50.
Library construction was performed as described by Ingolia et al. Nat Protoc 2012, 7:1534–50.

treatment_protocol: Cells were treated in culture with fresh media containing vehicle (DMSO) or drug for 1-2 hours before harvesting

value: Ductal breast carcinoma

tag: passage #

value: 200 nM INK128 for 2 hours


title: totRNA_dmso

description: RNAseq of total RNA from cells treated with DMSO for 2 hours

value: DMSO for 2 hours


title: FP_ink128

description: RNAseq of ribosome footprints from cells treated with 200 nM INK128 for 2 hours


title: FP_dmso

description: RNAseq of ribosome footprints from cells treated with DMSO for 2 hours


title: mRNA_silvestrol_2hr

description: RNAseq of mRNA from cells treated with 25 nM Silvestrol for 2 hours

value: 25 nM Silvestrol for 2 hours


title: FP_silvestrol_1hr

description: RNAseq of ribosome footprints from cells treated with 25 nM Silvestrol for 1 hour

value: 25 nM Silvestrol for 1 hour


title: FP_dmso_1hr

description: RNAseq of ribosome footprints from cells treated with DMSO for 1 hour

value: DMSO for 1 hour


title: FP_dmso_2hr


title: FP_silvestrol_2hr_br

description: RNAseq of ribosome footprints from cells treated with 25 nM Silvestrol for 2 hours; biological replicate


title: S_L1.2

status: Public on Sep 12 2014

city: Ithaca

first: Michael

last: Scanlon

address: Emerson Hall, Room 140

institute: Cornell University

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: sheath; Repeat:2

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to the reference genome Agpv2 using the software Tophat v2.0.10.
Raw read counts per sample per gene as calculated by cuffdiff, using working set genes of Agpv2 (gff file: ZmB73_5a_WGS.gff).
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuffdiff ( v2.1.1).
Genome_build: B73_Refgenv2
Supplementary_files_format_and_content: ligule_count.txt is a tab delimited text file with raw read counts per sample as provided by cuffdiff (cuffdiff output file: genes.read_group_tracking).
Supplementary_files_format_and_content: ligule_fpkm.txt is a tab-delimited text files include FPKM values for each Sample.

molecule: polyA RNA

organism: Zea mays

growth_protocol: Plants for LM were grown in growth chambers with a cycle of 15 h light at 25°C and 9 h dark at 20°C.

extract_protocol:
Total RNA was isolated from the collected cells using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). DNaseI treatment was performed during the RNA isolation using Qiagen DNaseI. RNA amplification was performed using the TargetAmp 2-Round aRNA Amplification Kit 2.0 (Epicentre Biotechnologies). The Bioanalyzer 2100 (Agilent Technologies) was used to determine the quality of the amplified RNA.
The cDNA libraries were prepared using the standard Illumina mRNA-seq sample prep kits (revision D) and paired-end adaptors.

treatment_protocol: For analysis of wild-type leaf domains, plants were sectioned along the lateral axis, perpendicular to the midrib-margin axis. Tissue was microdissected from P7 primordia. For the ligule region, a 100μm high rectangle centred on the preligule band was selected. Pre-blade and pre-sheath tissue was taken from similar sized rectangles 50μm above and below the ligule region respectively. For the analysis of lg1-R and wild-type siblings, tissue between 400-900μm  from the base of P6 primordia was selected. Three replicates of 5-6 plants each were taken for each tissue type.

tag: cultivar

value: wild type

tag: tissue

value: P7 leaf primordia adaxial L1 sheath


title: S_L1.1

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: sheath; Repeat:1


title: S_L1.3

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: sheath; Repeat:3


title: KU1-21-RNA_C

city: Kingston upon Thames

first: Sabrina

last: Roberts

state: Surrey

address: Penryhn Road

department: Life Sciences

country: United Kingdom

institute: Kingston University

description:
Raw data file: R_2012_07_24_09_46_36_user_KU1-21-RNA-C.basecaller.bam
Raw data file: R_2012_07_24_09_46_36_user_KU1-21-RNA-C.unaligned.basecaller.bam

data_processing:
Ion Torrent Software was used for base calling
RNA-Seq reads were aligned to reference genome NCCP11945 (GCA_000020105.1)  using NextGENe v2.3.4.2
Genome_build: GCA_000020105.1
Supplementary_files_format_and_content: post processing tables, expression report, sat infor, parameters

organism: Neisseria gonorrhoeae

source_name: Bacteria

growth_protocol: N. gonorrhoeae strain NCCP11945 was grown in standard conditions on GC agar (Oxoid) at 37°C in and incubator with 5% CO2 overnight.

extract_protocol:
Bacterial samples stored in RNALater were removed and extracted using Rneasy Kit (Qiagen)
Libraries were prepared using the Ion Torrent protocols for use with the Ion Torrent  RNA-Seq Kit (Life Technologies)


title: KU1-20-RNA_A

description:
Raw data file: R_2012_07_24_05_52_06_user_KU1-20-RNA-A.basecaller.bam
Raw data file: R_2012_07_24_05_52_06_user_KU1-20-RNA-A.unaligned.basecaller.bam


title: L_L1.2

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: ligule; Repeat:2

value: P7 leaf primordia adaxial L1 ligule


title: WT1

value: DLBCL


title: WT3


title: mRNA_dmso_2hr

description: RNAseq of mRNA from cells treated with DMSO for 2 hours

value: untreated


title: B_L1.3

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: blade; Repeat:3

value: P7 leaf primordia adaxial L1 blade


title: B_L1.2

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: blade; Repeat:2


title: FP_dmso_2hr_br

description: RNAseq of ribosome footprints from cells treated with DMSO for 2 hours; biological replicate


title: L_L1.1

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: ligule; Repeat:1


title: B_L1.1

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: blade; Repeat:1


title: wtL-3

description: Wild-type tissue from P6 leaf primordia (all cell layers). Repeat 3

value: P6 leaf primordia


title: lg1-1

description: lg1 mutant tissue from P6 leaf primordia (all cell layers). Repeat 1


title: wtL-2

description: Wild-type tissue from P6 leaf primordia (all cell layers). Repeat 2


title: wtL-1

description: Wild-type tissue from P6 leaf primordia (all cell layers). Repeat 1


title: S-5

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: sheath; Repeat:5

value: P7 leaf primordia sheath


title: lg1-3

description: lg1 mutant tissue from P6 leaf primordia (all cell layers). Repeat 3


title: FP_untreated

description: RNAseq of ribosome footprints from untreated cells


title: S-4

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: sheath; Repeat:4


title: S-3

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: sheath; Repeat:3


title: L-5

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: ligule; Repeat:5

value: P7 leaf primordia ligule


title: L_L1.3

description: Tissue captured from P7 leaf primordia (only adaxial L1 tissue was captured). Tissue: ligule; Repeat:3


title: L-4

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: ligule; Repeat:4


title: L-3

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: ligule; Repeat:3


title: B-4

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: blade; Repeat:4

value: P7 leaf primordia blade


title: Pdr_2_AB_CTL

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

data_processing:
Illumina software version CASAVA 1.8.2
Alignment using bowtie2 v 2.1.0
PeakCalling using SPP v 1.10.1
Genome_build: Candida glabrata strain CBS138

organism: Nakaseomyces glabratus CBS 138

source_name: 2nd Ab control for pdr

growth_protocol: All strains were grown to mid-log phase in rich YPD medium prior to isolation of chromatin.

extract_protocol:
Chromatin immunoprecipitation was done as described in http://labs.fhcrc.org/hahn/Methods/mol_bio_meth/hahnlab_ChIP_method.html [ http://mcb.asm.org/content/31/4/818.long ] with the following modifications. Briefly, 100 ml cell cultures were grown to an A600 of 0.8 to 1 in YPD medium at 30°C. Cells were lysed in ChIP lysis buffer in the presence of 0.5 mm glass beads (BioSpec Products Inc.) for 4 x 5 min with 2 min pauses in between in a Vortex Genie 2 at speed setting of 10 in multiple 1.5 ml microfuge tubes. Shearing of chromatin was done in an E220 Focused-ultrasonicator [Covaris] under following conditions: Peak Incident Power (W): 175; Duty Factor: 10%; Cycles per burst: 200; Treatment Time: 420 sec; Temperature: 7oC; Sample volume: 130 ml. An AFA Fiber Pre-Slit Snap-Cap [6 x 15mm] microTUBE [Covaris] was used for the shearing. For immunoprecipitation, 2mg of TAP polyclonal antibody (Thermo Scientific; Product # CAB1001; Lot # NH77071) or CgPdr1 specific polyclonal antibody (described above) was used.
The library preparation of ChIP-ed DNA was done on the Nugen Mondrian SP Workstation: http://www.nugen.com/nugen/index.cfm/products/msp/products/workstation-plus/ with the Ovation SP Ultralow DR Multiplex System: http://www.nugen.com/nugen/index.cfm/products/msp/products/ultralow/

value: rho+ pdr1D

tag: chip antibody

value: IgG


title: lg1-2

description: lg1 mutant tissue from P6 leaf primordia (all cell layers). Repeat 2


title: Pdr_R+

source_name: R+ with pdr Ab pulldown

value: rho+


title: Pdr_AB_CTL

source_name: Ab control for Pdr pulldown


title: Pdr_2_R0

source_name: 2nd R0 with pdr Ab pulldown


title: Pdr_R0

source_name: R0 with pdr Ab pulldown


title: R0_TAP

source_name: R0 treatment with TAP ab

value: rho0 strain with TAP-PDR1 on chromosome

value: TAP


title: B-3

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: blade; Repeat:3


title: TAP_AB_ctrl

source_name: Ab control for TAP

value: rho0 strain with with TAP-PDR1 on chromosome


title: ngn3-nega

city: Shenzhen

first: ilmen

last: zhang

state: Guangdong Province

address: Beishan Industrial Zone,Yantian District

country: China

institute: BGI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity
RNA-seq reads were aligned to the hg19 reference using bowtie version 12.7 and tophat version 2.0 with the default configurations
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.  using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads and RPKM values for each Sample

source_name: NGN3-eGFP Negative  cells were purified at stage 4

growth_protocol: Human embryonic stem cell (hESC) lines were cultured in DMEM/F12 (Life Technologies) supplied with 20% (vol/vol) KnockOut Serum Replacement (KSR, Life Technologies), 1% (vol/vol) MEM Non-Essential Amino Acids Solution (NEAA, Life Technologies), 1% (vol/vol) GlutaMAX Supplement (Life Technologies), 1% penicillin-streptomycin (PS, HyClone), 0.05 mM 2-mercaptoethanol (2-ME, Life Technologies) and 25 ng/ml basic fibroblast growth factor (bFGF, OriGene) on mitomycin-C (Sigma-Aldrich, or Roche)-treated mouse embryonic fibroblast (MEF) feeder layers. The medium was changed daily. Cultures were normally passaged by Dispase II (Roche) at a 1:4-1:6 split ratio every 4-6 days.

extract_protocol:
2ug Total RNAs were extracted from cells with RNeay Plus Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A five-stage differentiation protocol was used for directed differentiation, including definitive endoderm (which was treated with a high concentration of Activin-A for 4 days), primitive gut tube (which was treated with KGF and SB525334 for 3 days), posterior foregut (which was treated with RA, Noggin and SANT-1 for 4 days), pancreatic and endocrine progenitors (which were treated with Noggin and TPB for 3-5 days), and hormone-producing cells (which were treated with human LIF and Alk5 inhibitor II for more than 5 days).

value: NGN3-eGFP Negative  cells

tag: origin

value: hES-derived pancreatic non-endocrine assosiated cells


title: nSR100-iCLIP-mm

status: Public on Sep 11 2014

first: Bushra

last: Raj

address: 421 Curie Boulevard

description: iCLIP barcode: NNCGCCNNN.  Antibody: anti-FLAG

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
PAR-iCLIP/iCLIP: Reads were collapsed, and the barcode and adaptor sequences were trimmed from the 5' and 3' ends respectively. Tags longer than 20 nucleotides were mapped to the human reference geneome hg19 or mouse reference genome mm9 using Bowtie by allowing a maximum of 2 mismatches, and only tags with less than or equal to five mapped locations were kept. Bedgraphs were generated using the BEDtools (v2.17.0) tool: genomecov
mm9, hg19
Genome_build: Bedgraphs of individual PAR-iCLIP/iCLIP tag densities are provided

source_name: N2A, dox-inducible

growth_protocol: N2A and 293T cell lines were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), sodium pyruvate, and non-essential amino acids. N2A and 293T cells that were transduced with lentiviruses were additionally cultured in the presence of 2ug/mL puromyocin to maintain selection.

extract_protocol:
iCLIP was performed as described in Huppertz et. al, 2014, Methods.
iCLIP libraries were generated as described in Huppertz et. al, 2014, Methods

treatment_protocol: A stable cell line was established by transducing cells with dox-inducible lentiviruses expressing Flag-nSR100 and selection with 2 ug/mL puromycin. For iCLIP experiments, cells were crosslinked (0.15 J/cm2) at 254 nm in a Stratalinker 1800

tag: antibody

value: FLAG

tag: construct


title: OTI-TRM+gBpep_rep2_sample1

city: Amsterdam

first: silvia

last: ariotti

address: Plesmanlaan 121

country: Netherlands

institute: NKI

description:
datarun 2760_3 MiSeq!
Sample 17

data_processing:
All samples were aligned using Tophat and readcounts were calculated with Htseq-count
Sample 1-6 were aligned using Tophat version 1.3.1 based on ensembl version 64 with parameters  --library-type fr-unstranded -G
Sample 7-10,29-36 were aligned using Tophat version 1.4.0 based on ensembl version 66 with parameters  --library-type fr-unstranded -G --transcriptome-index
Sample 11-28,37-45 were aligned using Tophat version 2.0.6 based on ensembl version 66 with parameters --bowtie 1 --library-type fr-unstranded  -no-coverage-search -M -transcriptome-index
Genome_build: mm9
Supplementary_files_format_and_content: The file genecounts_all.txt contains the absolute readcounts as a result from Htseq-count. Genes that have 0 readcounts across all samples were removed.

source_name: full-thickness skin

extract_protocol:
Skin harboring tissue resident memory T cells was injected with virus or peptide. 9 hours later, the mouse was sacrificed, full-thickness skin collected and snap-frozen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were tattoo-vaccinated in the hind legs with 2µg DNA TTFC carrier protein plus the indicated peptide in order to induce a population of skin-resident memory T cells. Mice were used for experiments at least three weeks after vaccination (memory phase).

value: skin

value: wild type


title: OTI-TRM+OVApep_rep2_sample1

description:
datarun 2760_1 MiSeq!
Sample 15


title: nSR100-PAR-iCLIP-mm_rep2

description: PAR-iCLIP barcode: NNTTAANNN. Antibody: anti-FLAG

extract_protocol:
PAR-iCLIP was performed as described in Huppertz et. al, 2014, Methods.
PAR-iCLIP libraries were generated as described in Huppertz et. al, 2014, Methods

treatment_protocol: A stable cell line was established by transducing cells with dox-inducible lentiviruses expressing Flag-nSR100 and selection with 2 ug/mL puromycin. For PAR-iCLIP experiments, cells were treated with 2 ug/mL dox, 100 uM 4-thiouridine, and crosslinked (0.15 J/cm2) at 365 nm in a Stratalinker 1800


title: OTI-TRM+OVApep_rep2_sample2

description:
datarun 2760_2 MiSeq!
Sample 16


title: OTI-TRM+gBpep_rep2_sample2

description:
datarun 2760_4 MiSeq!
Sample 18


title: nSR100-PAR-iCLIP-mm_rep1

description: PAR-iCLIP barcode: NNTATTNNN. Antibody: anti-FLAG

value: dox-inducible lentiviruses expressing Flag-nSR100


title: Lib67PUDC0h_input

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Reads were mapped against the yeast genome (sacCer3) using Bowtie (version 0.12.7), with the following parameters: ‘-k 8 --best --strata --sam --maxins 50000’. Reads were mapped against the human (hg19) genome using Tophat (version 1.4.1), with the parameters ‘--max-multihits 1 –prefilter-multihits’ and ‘–transcriptome-index’, for which we assigned a pre-indexed version of the relevant transcriptomes, based on the UCSC Known Genes set of annotations. An in-house script was then used to project all reads aligning to the genome to yeast and human transcriptomes. Only read pairs fully matching a transcript structure, as defined by the ‘UCSC Known Genes’ transcriptome annotation, were retained. Each read pair was computationally extended in transcriptome space from the beginning of the first read to the end of its mate, whereupon, for each nucleotide, we recorded both the number of ‘left’ reads initiating at each position (corresponding to the last position traversed by reverse transcriptase) and the number of overall reads covering each position.  In addition, to facilitate examination of sites in rRNA and snRNAs, we used Bowtie to directly align reads against a transcriptomic database, harboring these two classes of RNA. These alignments were processed as above, to record the number of reads starting and overlapping each position.
Putative Ψ sites were identified using the following approach: (1) For each treated or non-treated sample, a Ψ-ratio was calculated, corresponding to the number of reads beginning at the position divided by the overall number of reads covering it (Figure 1B). A pseudocount of 1 was added to both the numerator and denominator to stabilize the ratio and avoid division by 0. (2) Log2 fold changes of Ψ ratios in the treated versus non-treated samples were generated, to yield the Ψ-fold change. All positions with a Ψ-ratio >0.1, a Ψ-fc >3 (corresponding to 8 fold enrichment) and with >5 reads beginning at the position were considered putative pseudouridylated sites. (3) To allow comparison across multiple conditions/perturbations, we first merged from all samples the positions of all windows passing step (2), to define a set of all unique sites passing the filters in at least one condition. For each such site, we then calculated a Ψ-ratio and Ψ-fc in each sample. We then calculated a median Ψ-ratio and median Ψ-fc across all samples, and considered all sites in which these values exceeded 0.1 and 3, respectively (unless explicitly otherwise stated). (4) As identical genes are often present in the genome in multiple copies (e.g. rRNA and tRNA), we demanded that each sequence of 21 nucleotides surrounding the putative pseudouridylated position in the dataset be unique; All redundancies were filtered out. Finally, we also filtered out sites in positions other than immediately following ‘U’.
Genome_build: sacCer3. hg19, mm9
Supplementary_files_format_and_content: text tables with putative pseudouridylation sites. Each tables contains genomic coordinates of the site, along with information pertaining to the PSI ratios and fold changes calculated for each site across the different experiments. Also the underlying raw data in terms of read counts is provided for each site, including the number of reads beginning and overlapping each position in the treated and input samples.

extract_protocol:
Enrichment of polyadenylated RNA (polyA+ RNA) from total RNA was performed using one round of enrichment using Oligo(dT) dynabeads (Invitrogen) according to the manufacturer’s protocol. CMC-treatment was performed essentially as described in (Bakin and Ofengand, 1993; Bakin and Ofengand, 1998). Specifically, pelleted polyA+ RNA was resuspended in 30 mL of 0.17M CMC in BEU buffer (50mM bicine, pH 8.3, 4 mM EDTA, and 7M urea) or in 30 mL of BEU buffer as input at 37°C for 20 min. Reaction was stopped with 100 mL of 0.3M NaOAc and 0.1 mM EDTA, pH 5.6 (Buffer A), 700 mL of EtOH, and 1 mL of glycogen. After chilling for 5 min in dry ice, the pellet was recovered, washed with 70% EtOH, dissolved in 100 mL of Buffer A, and reprecipitated with 300 mL of EtOH and 1 mL of glycogen. After washing as above, the pellet was dried, dissolved in 40 mL of 50 mM sodium bicarbonate, pH 10.4, and incubated at 37°C for 3 hours. The RNA was precipitated by addition of 100 mL of Buffer A, 700 mL EtOH, and 1 mL of glycogen. The pellet was washed with 70 % EtOH and then dissolved with water for subsequent library preparation.
The mRNA was chemically fragmented into ~80-150 nt-long fragments by performing a short fragmentation (30 seconds) using RNA fragmentation reagent and stop solution (Ambion). RNA was subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3’ ligation of an RNA adapter using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed using AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) or SuperScript III (Life Technologies), and the cDNA was subjected to a 3’ ligation with a second adapter using T4 ligase. The single-stranded cDNA product was then amplified for 9-12 cycles in a PCR reaction. Libraries were sequenced on Illumina HiSeq 2500 platforms generating paired end reads (30 bp from each end).

tag: knockdown

tag: knockout

tag: tissue/cell line

value: Bone marrow derived dendritic cells

value: input


title: Pdr_2_R+

source_name: 2nd R+ with pdr Ab pulldown


title: U2af65-PAR-iCLIP_nSR100-KD

description: PAR-iCLIP barcode: NNTGGCNNN. Antibody: anti-U2af65

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
PAR-iCLIP: Reads were collapsed, and the barcode and adaptor sequences were trimmed from the 5' and 3' ends respectively. Tags longer than 20 nucleotides were mapped to the human reference geneome hg19 using Bowtie by allowing a maximum of 2 mismatches, and only tags with less than or equal to five mapped locations were kept. Bedgraphs were generated using the BEDtools (v2.17.0) tool: genomecov
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript. Bedgraphs of individual (PTBP1, U2af65) and pooled (nSR100, 3 biological replicates) PAR-iCLIP tag densities are provided

source_name: N2A, nSR100 depleted

treatment_protocol: Cells were transduced with lentiviruses expressing shRNAs targeting nSR100. Stable populations were selected using 2 ug/mL puromycin. For PAR-iCLIP experiments, cells were treated with 100 uM 4-thiouridine, and crosslinked (0.15 J/cm2) at 365 nm in a Stratalinker 1800

tag: cell line

tag: shRNA/sirna

value: shRNA against 3'UTR of nSR100


title: U2af65-PAR-iCLIP_Ctrl-KD

description: PAR-iCLIP barcode: NNGGCGNNN. Antibody: anti-U2af65

source_name: N2A, control

treatment_protocol: Cells were transduced with lentiviruses expressing shRNAs targeting GFP. Stable populations were selected using 2 ug/mL puromycin. For PAR-iCLIP experiments, cells were treated with 100 uM 4-thiouridine, and crosslinked (0.15 J/cm2) at 365 nm in a Stratalinker 1800

value: control shRNA against GFP


title: E11.5 heart total RNA-Seq

city: Berkeley

first: Han

last: Wu

state: California

address: 1 Cyclotron Road, Mail Stop 84-171

department: Genomics Division

institute: Lawrence Berkeley National Lab

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were identified by using a sliding window method EnrichedRegionMaker module from USEQ
Enriched regions overlapping with refGene, mouse mRNA or ESTs were removed
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mappable reads and RPKM values for enriched region

source_name: E11.5 mouse heart tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols after ribosomal RNAs depletion

value: heart

tag: age

value: embryonic day 11.5


title: E11.5 limb total RNA-Seq

source_name: E11.5 mouse limb tissue

value: limb

tag: strain


title: B-5

description: Tissue captured from P7 leaf primordia (all cell layers). Tissue: blade; Repeat:5

value: P7 leaf primordia blade


title: N2A_siPtbp1_KD_b

source_name: N2A, Ptbp1 depleted

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich).
For RNA-Seq, standard Illumina mRNA-Seq libraries were prepared according to the manufacturer.

treatment_protocol: Cells were transfected with ON-TARGETplus siRNA pool (Thermo Scientific-Dharmacon) using RNAiMax reagent (Life Technologies), as recommended by the manufacturer. A non-targeting siRNA pool was used as a control. Cells were harvested 48 hours post transfection

value: siRNA pool against Ptbp1


title: R+_TAP

source_name: R+ with TAP Ab pulldown

value: rho+ strain with TAP-PDR1 on chromosome

value: TAP


title: FP_silvestrol_2hr

description: RNAseq of ribosome footprints from cells treated with 25 nM Silvestrol for 2 hours

source_name: Breast cancer cells

tag: cell type

value: Ductal breast carcinoma

tag: treatment

value: 25 nM Silvestrol for 1 hour


title: N2A_siCtrl_KD_b

value: control siRNA pool


title: N2A_Ctrl_KDshGFP-2

description:
Similar to N2A_Ctrl_KDshGFP-1, but different read lengths.  Runs were combined for downstream analyses
MmumRNA-50-CL_N2A_nSR100_Cont_exprRPKM.txt

treatment_protocol: Cells were transduced with lentiviruses expressing shRNAs targeting GFP. Stable populations were selected using 2 ug/mL puromycin


title: N2A_siU2af65_KD_a

source_name: N2A, U2af65 depleted

value: siRNA pool against U2af65


title: N2A_siCtrl_KD_a


title: FemalePN_APH_3

city: Beijing

first: Xianlong

last: Li

address: 5, Yiheyuan Rd., Haidian District

department: Biodynamic Optical Imaging Center, College of Life Sciences

institute: Peking University

data_processing:
Base calling is performed by CASAVA_v1.8.2
Alignment is performed by Bismark v0.7.6
Convert alignment results to information of each base of reference sequence, using SAMTools mpileup v0.1.18 (r982:295)
Identification of individual demethylated CpG site using the threshold, i.e. one-tail Fisher exact test with P < 0.05, Benjamini-Hochberg false discovery rate (FDR) < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: SingleCmet format files which records each covered cytosine's information like genomic coordinates, base read in reference genome, strand assignment, total depth, methylated and unmethylated reads occurrence, methylation level, cytosine context in reference and cytosine type (i.e., CpG, CHG or CHH).

source_name: Aphidicolin treated female pronuclei

extract_protocol:
Approximately 100-130 pronuclei in each treatment were harvested, and lysed in 5  μl lysis buffer (20 mM Tris, 2 mM EDTA, 20 mM KCl, 0.3% Triton-X 100, 1 mg/ml QIAGEN protease) at 50°C for 3h. Protease was inactivated at 75°C for 30 min.
Genomic DNA from pronuclei was digested by 10 U TaqI (NEB) for 3 h at 65°C. Then the digested DNA was end-repaired and dA-tailed with exonuclease-deficient Klenow Fragment (Fermentas) in the presence of 40 μM dATP, 4 μM dGTP and 4 μM dCTP. Next the Illumina TruSeq adapters were ligated to the DNA fragments with concentrated T4 DNA ligase (Fermentas) overnight. After that, bisulfite conversion of the library was performed using MethylCode DNA Methylation Kit (Invitrogen). Then bisulfite-converted DNA was amplified by 20 cycles of PCR using PfuTurboCx polymerase (Agilent Technologies), and purified by AMPure XP beads (Beckman). Finally an extra round of PCR amplification was performed to increase the amount of DNA to about 500 ng with Phusion HF Master Mix (NEB), and the 200~500 bp DNA fragments were selected on a 12% polyacrylamide gel. The size distribution of the final library was analyzed by Fragment Analyzer (Advanced Analytical Technologies) and the libraries were sequenced on Illumina HiSeq 2000 or 2500.

treatment_protocol: One-cell zygotes were collected 7.5-8 hrs after ICSI. Their pronuclear stages were further determined based on microscope observation of the size of the two pronuclei and the distance between them. Zygotes [Tet3 mat∆/ +] deficient in maternal Tet3 were obtained using Zp3-Cre conditional knockout female mice as previously described. In experiments with the inhibition of pronuclear DNA replication, zygotes in culture after ICSI were incubated with 0.2 µg/ml of aphidicolin until the extraction of pronuclei.

tag: gender

value: female

value: pronuclei


title: N2A_Ctrl_KDshGFP-1

description:
Similar to N2A_Ctrl_KDshGFP-2, but different read lengths. Runs were combined for downstream analyses
MmumRNA-50-CL_N2A_nSR100_Cont_exprRPKM.txt


title: N2A_nSR100_KDshL4-1

description:
Similar to N2A_nSR100_KDshL4-2, but different read lengths.  Runs were combined for downstream analyses
MmumRNA-50-CL_N2A_nSR100_KD_exprRPKM.txt

treatment_protocol: Cells were transduced with lentiviruses expressing shRNAs targeting nSR100. Stable populations were selected using 2 ug/mL puromycin


title: ngn3-pos

source_name: NGN3-eGFP Positive  cells were purified at stage 4

value: NGN3-eGFP Positive  cells

value: hES-derived pancreatic endocrine assosiated cells


title: FemalePN_APH_2


title: N2A_nSR100_KDshL4-2

description:
Similar to N2A_nSR100_KDshL4-1, but different read lengths.  Runs were combined for downstream analyses
MmumRNA-50-CL_N2A_nSR100_KD_exprRPKM.txt

value: shRNA against 3'UTR of nSR100


title: FemalePN_Tet3KO_4

source_name: maternally Tet3 KO female pronuclei


title: Lib67PUDC0h_CMC_treatment

value: Bone marrow derived dendritic cells


title: FemalePN_WT_3

source_name: WT female pronuclei


title: 293T_Ctrl

source_name: 293T, control

treatment_protocol: A stable cell line was established by transducing cells with dox-inducible lentiviruses expressing Flag-nSR100 and selection with 2 ug/mL puromycin. nSR100 expression was induced with 1 ug/mL dox for 48 hours.


title: FemalePN_WT_2


title: Oocyte_1

source_name: MII oocytes

value: oocyte


title: Oocyte_2


title: 293T_nSR100

source_name: 293T, nSR100 overexpression


title: NIL5 RNA-seq at 30°C

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: Sample 5

data_processing:
Rice genome sequences and annotated gene models were downloaded from TIGR6.1 (http://rice.plantbiology.msu.edu/). The single end 86nt reads with strand direction were aligned to TIGR6.1 genome sequence using TopHat (Trapnell et al., 2009) allowing up to two mismatches. Splice junction sequences required at least four bases on each side of the junction. Reads mapped to multiple locations as well as only uniquely mapped reads were used and compared with each other to avoid the improper deletion of reads for subsequent analysis. The gene expression levels were measured in reads per kilobase of exon model per million mapped reads (RPKM), which indicated that the total exons of a gene were detected when they met the criterion of more than 3 RPKM (Mortazavi et al., 2008). The differential expressed genes were identified using DEGseq (Wang et al., 2010). Genes with more than 2 fold change and p-value < 0.01 were regarded as differential expressed genes.
Genome_build: Orazy TIGR6.1
Supplementary_files_format_and_content: Wig files were generated using MACS program

organism: Oryza sativa

source_name: NIL5 RNA-seq at 30°C

growth_protocol: Rice plants used in the study were Orazy sativa spp. indica cv. 93-11, NIL5 (near-isogenic line 5 of Zhu1s in the 93-11 background) and NIL8 were planted in phytotrons at DAT of 22°C and 30°C (Koithtron S-153w, Japan) at the China National Rice Research Institute, Hangzhou.

extract_protocol: Total RNAs were extracted from ~10cm panicles of 93-11, NIL5 and NIL8 using TRIzol Reagent (15596–026; Invitrogen). Polyadenylated RNAs were isolated using Dynabeads® mRNA Purification Kit (Invitrogen). The RNA-Seq libraries were prepared using Illumina Directional mRNA-Seq Library Prep. v1.5 protocol and sequenced on Illumina GAII to generate high-quality single-end reads of 80 nt in length.

treatment_protocol: All plants were grown in phytotrons at DAT of 22°C, 24°C, 26°C, 28°C and 30°C (Koithtron S-153w, Japan) at the China National Rice Research Institute, Hangzhou.

value: Oryza sativa spp indica cv NIL5 (near-isogenic line 5 of Zhu1s in the 93-11 background)

value: ~10cm panicles


title: NIL8 RNA-seq at 30°C

description: Sample 6

source_name: NIL8 RNA-seq at 30°C

value: Oryza sativa spp indica cv NIL8


title: 93-11 RNA-seq at 30°C

description: Sample 4

source_name: 93-11 RNA-seq at 30°C

value: Oryza sativa spp indica cv 93-11


title: NIL5 RNA-seq at 22°C

description: Sample 2

source_name: NIL5 RNA-seq at 22°C


title: NIL8 RNA-seq at 22°C

description: Sample 3

source_name: NIL8 RNA-seq at 22°C


title: 93-11 RNA-seq at 22°C

description: Sample 1

source_name: 93-11 RNA-seq at 22°C


title: MalePN_WT_3

data_processing:
Base calling is performed by CASAVA_v1.8.2
Alignment is performed by Bismark v0.7.6
Convert alignment results to information of each base of reference sequence, using SAMTools mpileup v0.1.18 (r982:295)
Identification of individual demethylated CpG site using the threshold: demethylation level >= 0.3, one-tail Fisher exact test with P < 0.05, Benjamini-Hochberg false discovery rate (FDR) < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: SingleCmet format files which records each covered cytosine's information like genomic coordinates, base read in reference genome, strand assignment, total depth, methylated and unmethylated reads occurrence, methylation level, cytosine context in reference and cytosine type (i.e., CpG, CHG or CHH).

source_name: WT male pronuclei

tag: genotype/variation

value: wild type

value: male

tag: tissue/cell type


title: MalePN_WT_2


title: Sperm

source_name: sperm

value: sperm


title: MalePN_Tet3KO_1

source_name: maternally Tet3 KO male pronuclei

value: Tet3 KO


title: MalePN_APH_1

source_name: Aphidicolin treated male pronuclei


title: FemalePN_Tet3KO_1


title: OTI-TRM+OVApep_6h_sample3

description:
datarun 2151_6
Sample 42

source_name: full-thickness skin

tag: tissue

value: skin

tag: genotype


title: OTI-TRM+OVApep_6h_sample2

description:
datarun 2151_5
Sample 41


title: FemalePN_WT_1


title: OTI-TRM+OVApep_9h_sample2

description:
datarun 2151_8
Sample 44


title: OTI-TRM+OVApep_9h_sample1

description:
datarun 2151_7
Sample 43


title: MalePN_APH_2


title: OTI-TRM+OVApep_3h_sample3

description:
datarun 2151_3
Sample 39


title: OTI-TRM+OVApep_6h_sample1

description:
datarun 2151_4
Sample 40


title: OTI-TRM+OVApep_3h_sample2

description:
datarun 2151_2
Sample 38


title: OTI-TRM+OVApep_9h_sample3

description:
datarun 2151_9
Sample 45


title: OTI-TRM+OVApep_3h_sample1

description:
datarun 2151_1
Sample 37


title: gBT-TRM+PBS_rep2_sample2

description:
datarun 149_8
Sample 36


title: gBT-TRM+PBS_rep2_sample1

description:
datarun 149_7
Sample 35


title: gBT-TRM+PBS_rep1_sample1

description:
datarun 149_5
Sample 31


title: gBT-TRM+HSV-1_rep2_sample1

description:
datarun 149_19
Sample 33


title: gBT-TRM+PBS_rep1_sample2

description:
datarun 149_6
Sample 32


title: gBT-TRM+HSV-1_rep1_sample1

description:
datarun 149_17
Sample 29


title: gBT-TRM+HSV-1_rep1_sample2

description:
datarun 149_18
Sample 30


title: OTI-TRM+OVApep_sample2

description:
datarun 2026_3
Sample 28


title: OTI-TRM+OVApep_sample1

description:
datarun 2026_2
Sample 27


title: OTI-TRM+OVApep_sample1 (Ifngr-/- recipients)

description:
datarun 2026_4
Sample 25

value: Ifngr-/- recipients


title: MalePN_Tet3KO_3


title: OTI-TRM+OVApep_sample2 (Ifngr-/- recipients)

description:
datarun 2026_5
Sample 26


title: OTI-TRM+OVApep_sex matched_sample2

description:
datarun 2068_2
Sample 22


title: OTI-TRM+OVApep_sex matched_sample1

description:
datarun 2068_1
Sample 21


title: OTI-IFNgko-TRM+OVApep_sample1

description:
datarun 2068_3
Sample 23

value: Ifng-/- TRM


title: OTI-TRM+OVApep_sex mismatched_sample2

description:
datarun 2068_6
Sample 20


title: gBT-TRM+HSV-1_rep2_sample2

description:
datarun 149_20
Sample 34


title: OTI-TRM+OVApep_sex mismatched_sample1

description:
datarun 2068_5
Sample 19


title: OTI-TRM+gBpep_rep1_sample1

description:
datarun 2026_8
Sample 13


title: OTI-TRM+OVApep_rep1_sample2

description:
datarun 2026_7
Sample 12


title: gBT-TRM+gBpep_rep2_sample2

description:
datarun 149_11
Sample 8


title: gBT-TRM+OVApep_rep2_sample1

description:
datarun 149_13
Sample 9


title: OTI-TRM+gBpep_rep1_sample2

description:
datarun 2026_9
Sample 14


title: gBT-TRM+OVApep_rep2_sample2

description:
datarun 149_15
Sample 10


title: gBT-TRM+OVApep_rep1_sample3

description:
datarun 123_8
Sample 6


title: gBT-TRM+OVApep_rep1_sample2

description:
datarun 123_6
Sample 5


title: gBT-TRM+OVApep_rep1_sample1

description:
datarun 123_1
Sample 4


title: gBT-TRM+gBpep_rep1_sample2

description:
datarun 123_5
Sample 2


title: gBT-TRM+gBpep_rep1_sample1

description:
datarun 123_2
Sample 1


title: gBT-TRM+gBpep_rep1_sample3

description:
datarun 123_7
Sample 3


title: PTBP1-iCLIP_ plus nSR100

description: iCLIP barcode: NNGACCNNN. Antibody: anti-PTBP1

source_name: 293T, dox-inducible

treatment_protocol: A stable cell line was established by transducing cells with dox-inducible lentiviruses expressing Flag-nSR100 and selection with 2 ug/mL puromycin. For iCLIP experiments, cells were treated with 2 ug/mL dox and crosslinked (0.15 J/cm2) at 254 nm in a Stratalinker 1800


title: Lib64PseudoUHek293_CMC_treatment


title: OTI-IFNgko-TRM+OVApep_sample2

description:
datarun 2068_4
Sample 24


title: Lib72PUc11_input

value: fibroblast

value: input


title: Lib64PseudoUHek293_input


title: Lib64PseudoUHek293FT_input


title: Lib64PseudoUHek293FT_CMC_treatment


title: Lib72PUc11_CMC_treatment


title: Lib72PUc7_input


title: Lib72PUc7_CMC_treatment


title: OTI-TRM+OVApep_rep1_sample1

description:
datarun 2026_6
Sample 11


title: Lib72PUp11_input


title: Lib72PUp11_CMC_treatment


title: gBT-TRM+gBpep_rep2_sample1

description:
datarun 149_9
Sample 7


title: Lib72PUp7_input


title: Lib72PUp7_CMC_treatment


title: Lib72PUcontrolrep2_input


title: PTBP1-iCLIP_no nSR100

description: iCLIP barcode: NNGCCANNN. Antibody: anti-PTBP1

value: dox-inducible lentiviruses expressing Flag-nSR100


title: Lib72PUcontrolrep2_CMC_treatment


title: Lib72PUcontrolrep1_input


title: Lib72PUdkc1rep2_input


title: nSR100-iCLIP-hs

description: iCLIP barcode: NNTTAANNN. Antibody: anti-FLAG

value: FLAG


title: Lib72PUdkc1rep2_CMC_treatment


title: Lib72PUcontrolrep1_CMC_treatment


title: Lib72PUdkc1rep1_input


title: nSR100 PAR-iCLIP rep1

description:
PAR-iCLIP barcode: NNGGCGNNN.  Antibody: anti-FLAG
293TnSR100_PariCLIP_pool2.bedgraph

treatment_protocol: A stable cell line was established by transducing cells with dox-inducible lentiviruses expressing Flag-nSR100 and selection with 2 ug/mL puromycin. For PAR-iCLIP experiments, cells were  treated with 2 ug/mL dox, 100 uM 4-thiouridine, and crosslinked (0.15 J/cm2) at 365 nm in a Stratalinker 1800


title: Young (Enriched Environment) Replicate 2

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

description:
5hmC chemical-labelling and sequencing
YE2

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Supplementary_files_format_and_content: processed peak files

source_name: Young_Enriched Environment

growth_protocol: All of the mice that we used were on the C57BL/6 genetic background. All animal procedures were performed according to protocols approved by Emory University Institutional Animal Care and Use Committee.

extract_protocol:
Genomic DNA was purified from tissue using Wizard genomic DNA purification kit (Promega) with additional Proteinase K treatment and rehydrated in 10 mM Tris (pH 7.9). Genomic DNA samples were sonicated to 100-500 bp by Misonix sonicator 3000 (using microtip, 3 pulses of 30 seconds each with 2 min of rest and a power output level of two) or Bioruptor UCD-200 sonicator (Diagenode, Sparta). Output selector switch was set on High (H), and sonication interval was 30 seconds with 30 cycles of sonication performed. 5-hmC labelling reactions were performed in a 100-µL solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 300 ng/L sonicated genomic DNA (100-500 bp), 250 M UDP-6-N3-Glu or UDP-Glu, and 2.25 M wild-type BGT. The reactions were incubated for 1 hr at 37 °C. After the reaction, the DNA substrates were purified by Qiagen DNA purification kit or by phenol-chloroform precipitation and reconstituted in H2O. Biotin addition by click chemistry was performed by adding 150 M dibenzocyclooctyne modified biotin into the DNA solution, and the reaction mixture was incubated for 2 hr at 37 Â°C. The DNA samples were then purified by Qiagen DNA purification kit. Biotin Labeled 5-hmC DNAs were purified/enriched by Streptavidin-coupled Dynabeads (Dynabeads® MyOne™ Streptavidin T1, Life Technologies) following manufacturer's recommendations. After elution, the biotin-5-N3-gmC containing DNA was concentrated by 10 K Amicon Ultra-0.5 mL Centrifugal Filters (Millipore) and purified by Qiagen DNA purification kit. 25 ng genomic DNA, 5-hmC-captured DNA, or control captured DNA (in the absence of biotin) were used to initiate library preparation following the Illumina protocol for Preparing Samples for ChIP Sequencing of DNA (Part# 111257047 Rev. A). DNA fragments ~150-300 bp were gel purified after the adapter ligation step and amplified by 18 cycles PCR.
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 Genome Analyzer following the manufacturer's protocols.
5hmC containing DNA were chemically modified by Biotin and purified by Streptavidin-coupled Dynabeads

treatment_protocol: Exposure of mice to EE was achieved by keeping a group of mice in the EE chamber, which is larger than the standard cage, includes novel objects, such as toys of varied color and texture, tunnels, an exercise wheel for voluntary exercise, and extra bedding material, along with free access to food and water. Daily exposure to EE was kept at 5 hours during the daylight cycle for 4 consecutive weeks. Control animals were kept in their small cages that are used as standard housing cages (CE) containing bedding, food and access to water.

value: 6 weeks

tag: exposed to

value: enriched environment (EE)

value: Hippocampus


title: PTBP1-PAR-iCLIP

description: PAR-iCLIP barcode: NNTGGCNNN. Antibody: anti-PTBP1

treatment_protocol: For PAR-iCLIP experiments, cells were treated with 100 uM 4-thiouridine, and crosslinked (0.15 J/cm2) at 365 nm in a Stratalinker 1800


title: nSR100 PAR-iCLIP rep3

description:
PAR-iCLIP barcode: NNTTAANNN. Antibody: anti-FLAG
293TnSR100_PariCLIP_pool2.bedgraph


title: nSR100 PAR-iCLIP rep2

description:
PAR-iCLIP barcode: NNAATANNN. Antibody: anti-FLAG
293TnSR100_PariCLIP_pool2.bedgraph


title: Lib72PUdkc1rep1_CMC_treatment


title: Young (Controlled Environment) Replicate 2

description:
5hmC chemical-labelling and sequencing
YC2

source_name: Young_Controlled Environment

value: standard controlled environment (CE)


title: small polysome extensive footprint

city: Brighton

first: Juan Pablo

last: Couso

address: Falmer

institute: University of Sussex

description: Libraries were sequenced on Illumina HiSeq2000 and MiSeq machines with 50bp SingleEnd read protocol.

data_processing:
Sequencing reads were clipped, trimmed and aligned to an rRNA & tRNA reference using Bowtie, discarding the rRNA and tRNA alignments and collecting unaligned reads (Ingolia et al 2012).
Unaligned reads were mapped to FlyBase (Release 5.50) using TopHat. We only retained reads that mapped uniquely, but allowed up to two mismatches
Genome_build: dmel3(r5.50)
Supplementary_files_format_and_content: Summary of ribosome density (expressed as RPKM) and ribosome coverage for flybase annotation protein coding genes, no-coding RNA ORFs and upstream ORFs.

source_name: S2 cell

growth_protocol: S2 cells were grown under standard conditions in Schneiders medium with 10% FBS

extract_protocol:
We purified mRNAs in small polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S) and large polysomes. Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
28-34 nt ribosome footprints and 50-80 nt mRNA fragments were gel purified and prepared as previously described (Ingolia et al, 2012; Ingolia et al, 2009; Ingolia et al, 2011) for Next Generation Sequencing

treatment_protocol: Cells were pelleted, washed (1 X PBS, 100 mg/ml cycloheximide) and resuspended in lysis buffer; 50 mM Tris-HCl pH8, 150 mM NaCl, 10 mM MgCl2, 1 mM DTT, 1% NP40, 100 µg/ml cycloheximide, Turbo DNase (Invitrogen), RNasin® Plus RNase Inhibitor (Promega), cOmplete protease inhibitor (Roche). Nuclei were removed and cytoplasmic lysates were loaded onto sucrose gradients and subjected to ultracentrifugation.

value: S2 cell

tag: sample type

value: small polysome extensive ribosome footprint


title: Aged (Enriched Environment) Replicate 2

description:
5hmC chemical-labelling and sequencing
AE2

source_name: Aged_Enriched Environment

value: 18 months


title: Aged (Enriched Environment) Replicate 1

description:
5hmC chemical-labelling and sequencing
AE1


title: Young (Enriched Environment) Replicate 1

description:
5hmC chemical-labelling and sequencing
YE1


title: Aged (Controlled Environment) Replicate 1

description:
5hmC chemical-labelling and sequencing
AC1

source_name: Aged_Controlled Environment


title: total cytoplasmic mRNA

value: total cytoplasmic mRNA


title: small polysome footprint

value: small polysome ribosome footprint


title: Young (Controlled Environment) Replicate 1

description:
5hmC chemical-labelling and sequencing
YC1


title: large polysome footprint

value: large polysome ribosome footprint


title: Lib66PUSacCerLogPhaseR3_CMC_treatment

source_name: Saccharomyces cerevisiae_CMC_treatment

tag: growth condition

value: log growth phase


title: Lib66PUSacCerLogPhaseR2_input

source_name: Saccharomyces cerevisiae_input

tag: knockdown


title: Aged (Controlled Environment) Replicate 2

description:
5hmC chemical-labelling and sequencing
AC2


title: Lib66PUSacCerLogPhaseR2_CMC_treatment

tag: knockout


title: Lib66PUSacCerHeatShock_CMC_treatment

value: Heat shock


title: Lib66PUSacCerSat_input

value: Saturation


title: Lib75PUpus7HSrep3_CMC_treatment

value: 45 deg


title: Lib66PUSacCerLogPhaseR3_input

value: input


title: all polysome footprint

value: all polysome ribosome footprint


title: Lib75PUpus7HSrep2_input


title: Lib66PUSacCerLogPhaseR1_CMC_treatment


title: Lib66PUSacCerHeatShock_input


title: Lib66PUSacCerColdShock_input

value: Cold shock


title: Lib66PUSacCerSat_CMC_treatment


title: Lib75PUpus7HSrep1_input


title: Lib75PUpus7HSrep1_CMC_treatment


title: Lib66PUSacCerLogPhaseR1_input


title: Lib75PUpus7rep2_input

value: 30 deg


title: Lib75PUpus7rep3_input


title: Lib75PUpus7rep3_CMC_treatment


title: Lib75PUpus7rep2_CMC_treatment


title: Lib75PUcontrolHSrep2_input


title: Lib75PUpus7rep1_CMC_treatment


title: Lib75PUcontrolHSrep3_CMC_treatment


title: Lib75PUcontrolHSrep2_CMC_treatment


title: Lib75PUpus7rep1_input


title: Lib75PUpus7HSrep3_input


title: Lib66PUSacCerColdShock_CMC_treatment


title: Lib75PUcontrolrep3_CMC_treatment


title: Lib75PUcontrolHSrep1_CMC_treatment


title: Lib75PUcontrolrep3_input


title: Lib75PUpus7HSrep2_CMC_treatment


title: Lib75PUcontrolrep1_CMC_treatment


title: Lib75PUcontrolrep2_CMC_treatment


title: Lib75PUcontrolrep1_input


title: Lib75PUcontrolrep2_input


title: Lib65PUPus6_CMC_treatment


title: Lib65PUPus5_CMC_treatment


title: Lib75PUcontrolHSrep3_input


title: Lib65PUPus1_CMC_treatment


title: Lib65PUPus9_CMC_treatment


title: Lib65PUsnR3_CMC_treatment


title: Lib65PUsnR49_CMC_treatment


title: Lib65PUPus7_CMC_treatment


title: Lib65PUPus4_CMC_treatment


title: NEB 15 cycles rep2

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Data were mapped to the Arabidopsis thaliana reference genome version 10 (TAIR10)
MethylC-Seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers

organism: Arabidopsis thaliana

source_name: NEB 15 cycles rep2

growth_protocol: Arabidopsis thaliana were grown in long days (16 hours of light) at 24C

extract_protocol: Genomic DNA (gDNA) was purified from Arabidopsis thalina leaf tissue using a Qiagen DNease Plant Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Schmitz, R.J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369-73 (2011) with slight variations to either enzyme used or PCR cycle as described in the manuscript.

value: ~3 week old plants

tag: ecotype

value: leaf


title: Lib65PUPus9_input


title: Lib75PUcontrolHSrep1_input


title: Lib65PUsnR32_input


title: NEB 15 cycles rep1

source_name: NEB 15 cycles rep1


title: NEB 8 cycles rep2

source_name: NEB 8 cycles rep2


title: Lib65PUsnR34_input


title: NEB 8 cycles rep1

source_name: NEB 8 cycles rep1


title: Kapa 8 cycles rep1

source_name: Kapa 8 cycles rep1


title: NEB 4 cycles rep2

source_name: NEB 4 cycles rep2


title: Kapa 4 cycles rep2

source_name: Kapa 4 cycles rep2


title: Lib65PUsnR35_CMC_treatment


title: Kapa 15 cycles rep2

source_name: Kapa 15 cycles rep2


title: Lib73PUcbf5controlrep1_input


title: Cfx 8 cycles rep1

source_name: Cfx 8 cycles rep1


title: Lib65PUsnR189_CMC_treatment


title: Cfx 4 cycles rep2

source_name: Cfx 4 cycles rep2


title: NEB 4 cycles rep1

source_name: NEB 4 cycles rep1


title: Lib65PUPus1_input


title: Kapa 4 cycles rep1

source_name: Kapa 4 cycles rep1


title: Lib65PUDeg1_CMC_treatment


title: Lib65PUsnR34_CMC_treatment


title: Lib65PUPus2_CMC_treatment


title: Cfx 4 cycles rep1

source_name: Cfx 4 cycles rep1


title: Lib73PUcbf5rep1_input


title: Lib73PUcbf5controlrep2_input


title: Cfx 15 cycles rep2

source_name: Cfx 15 cycles rep2


title: Kapa 15 cycles rep1

source_name: Kapa 15 cycles rep1


title: Lib73PUcbf5controlrep2_CMC_treatment

source_name: Saccharomyces cerevisiae_CMC_treatment


title: Cfx 8 cycles rep2

source_name: Cfx 8 cycles rep2


title: Lib65PUsnR32_CMC_treatment


title: Lib73PUcbf5controlrep1_CMC_treatment


title: Lib73PUcbf5rep2_CMC_treatment


title: Kapa 8 cycles rep2

source_name: Kapa 8 cycles rep2


title: Lib66PUCanAlbYPD2hr_input

organism: Candida albicans

source_name: Candida albicans_input


title: Lib66PUCanAlbYPD2hr_CMC_treatment

source_name: Candida albicans_CMC_treatment


title: Lib73PUcbf5rep1_CMC_treatment


title: Cfx 15 cycles rep1

source_name: Cfx 15 cycles rep1


title: ORGL2

status: Public on Sep 10 2014

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
Post processing was done using Illumina Casava 1.82
Reads were aligned to the Drosophila melanogaster reference genome release 5.45 using Bowtie 2.1.
Count tables were generated in R  using UCSC Refseq Genes
Transcripts with a combined count less than 27 in the 9 samples were filtered out.
Count data was normalized and converted to Count Per Million (cpm) using the Voom package.
RPKM values were calculated for each transcript and averages of different isoforms were taken for each gene for downstream analysis.
Genome_build: Dm3 R5.45
Supplementary_files_format_and_content: Text files with gene RPKM values

source_name: Whole gut from adult female

extract_protocol:
Guts were dissected and put in Trizol on ice. RNA was harvested using Trizol reagent.
Illumina TruSeq Stranded mRNA LT kit (cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: diet

value: 10% glucose

tag: repeat

value: Oregon R

value: gut


title: ORSM1

value: Standard medium


title: HITS CLIP replicate 1

city: Cleveland

last: Sundermeier

state: OHIO

address: 2109 Adelbert Road/W317

department: Pharmacology

institute: Case Western Reserve University

description: retinal mRNA (co-purifying with Argonaute Proteins

data_processing:
Base-calling was performed using the Illumina pipeline software Casava 1.8.1
reads were mapped to bovine genome release bosTau7 using GSNAP with 2 mismatches allowed
enrichment in HITS-CLIP target mRNAs was analyzed using MACS program by considering corresponding bovine retina transcriptome samples as the control. High confidence miRNA target sites were defined as peaks with a P-value for enrichment less than 1 * 10-20 present in all three biological replicates (defined as having a summit within 100bp). The genes wherein the identified miRNA target sites are found were annotated by hand using the UCSC genome browser.
Genome_build: bostau7
Supplementary_files_format_and_content: xlsx file showing regions of the bovine genome with highly statistically significant enrichment in HITS-CLIP reads vs. transcriptome reads and their annotation

organism: Bos taurus

source_name: bovine retina HITS CLIP replicate 1

extract_protocol:
Eyes were enucleated and retinas were dissected, triturated to clusters of cells, and subjected to in vivo protein-RNA crosslinking (3X 400mJ/cm2)
Argonaute HITS-CLIP library preparation was performed according to Chi et. al (2)

value: Mixed

value: Retina


title: ORGL3


title: Transcriptome replicate 3

description: retinal mRNA

data_processing:
Base-calling was performed using the Illumina pipeline software Casava 1.8.1
Data were processed and aligned with the University of California-Santa Cruz (UCSC) bovine genome assembly and transcript annotation (bostau7) using Genomic Short-read Nucleotide Alignment Program (GSNAP),.
The raw read counts for bovine RefSeq genes were extracted using HTSeq-count program and used for calculations of fragments per kilobase per million mapped reads (FPKM) values
Genome_build: bostau7
Supplementary_files_format_and_content: xlsx files include FPKM values for each sample

source_name: bovine retina replicate 3

extract_protocol:
Eyes were enucleated and retinas were dissected and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity.
Retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer’s directions to further homogenize the  tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer’s directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer’s instructions. Pooled total RNA was used for each retina library preparation.  For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.   The Illumina library was prepared according to the manufacturer’s instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3’ to 5’ exo minus) and incubated at 37°C for 30 min to add an ‘A’ base to the 3’ end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip. Each library was sequenced as one lane on an Illumina HiScan instrument.


title: Transcriptome replicate 2

description: retinal mRNA

source_name: bovine retina replicate 2


title: pad4 rep2

city: Vienna

first: Jiradet

last: Gloggnitzer

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute of Molecular Plant Biology

data_processing:
FASTQC for quality control
Tophat v2.0.8b for mapping to TAIR10
custom R-scripts for counting reads per gene (RPKM, Reads Per Kilobase of exon per Megabase of library size)
differential gene expression per gene computed with DESeq (v1.10.1)
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab separated file (tsv), quantification of raw and normalized RNA-seq reads mapping to gene body or exons only annotated in the Arabidopsis Genome version TAIR 10, including statistics

source_name: leaves

growth_protocol: Plants were germinated on soil and grown for 3 weeks at 21°C, 16 h

extract_protocol:
RNA was extracted with peqgold RNA pure (peqlab), DNAse digested with TURBO DNA-free (Ambion)
Ribosomal rRNA depleted single end libraries were generated using Scriptseq Complete kit (Plant) (Epicentre)

tag: genetic accession

value: Columbia-0 (Col-0)

value: leaves

tag: age

value: 3 weeks


title: smg7 pad4 rep 2

value: smg7-1 pad4-1


title: HITS CLIP replicate 2

source_name: bovine retina HITS CLIP replicate 2

tag: strain


title: Transcriptome replicate 1

description: retinal mRNA

source_name: bovine retina replicate 1


title: Blastocyst_replicate2

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description: embryo

data_processing:
Sequencing adapters were trimmed using Cutadapt (https://code.google.com/p/cutadapt/) and sequencing reads of low quality were pre-filtered by FASTX-Toolkit before mapping (http://hannonlab.cshl.edu/fastx_toolkit/), using the options “fastq_quality_trimmer -Q 33 –v –t 20 -l 30 –I”.  The quality of reads after filtering was examined using ‘fastQC’ (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Filtered reads were mapped to the Btau_4.6.1 assembly using Tophat. Individual mapped reads were fed to Cufflinks to construct transcriptome models.  Any novel genes and transcripts that did not fit the supplied gene models (NCBI RefGene) were also assembled.  Cuffmerge was used to converge individual transcriptome to produce a master gene model.  Genes and transcripts mapped to uncertain chromosomes and contigs were eliminated.
The merged gene model and mapping result BAM files from each RNA-seq library were used to quantify the expression levels of all genes using the Python package, HTSeq.
Genome_build: UCSC Btau_4.6.1
Supplementary_files_format_and_content: tab-delimited text files include read counts for each gene of each Sample

source_name: Blastocyst

extract_protocol:
Total RNA were isolated from individual oocytes/embryos using TRIzol (Invitrogen, Grand Island, NY) and co-precipitated the RNA with linear acrylamide (Ambion). RNA was then amplified twice using the TargetAmp 2-round aminoallyl-aRNA amplification kit 1.0 (Epicentre, Madison, WI) according to the manufacturer’s instructions.
500 ng of amplified RNA (aRNA) from individual oocytes/embryos were used to construct the sequencing library following the manufacturer’s instructions by SOLiD™ Total RNA-Seq Kit (Life Technologies, Grand Island, NY).

tag: developmental stage

value: Blastocyst


title: Lib73PUcbf5rep2_input

source_name: Saccharomyces cerevisiae_input

tag: treatment

value: input


title: HITS CLIP replicate 3

source_name: bovine retina HITS CLIP replicate 3


title: Compact_morula_replicate2

description: embryo

source_name: Compact morula

value: Compact morula


title: Blastocyst_replicate1

description: embryo


title: smg7 pad4 rep 1


title: ORSM3


title: smg7 pad4 rep 3


title: pad4 rep3


title: pad4 rep1


title: ORSM2


title: Compact_morula_replicate1

description: embryo


title: Early_morula_replicate2

description: embryo

source_name: Early morula

value: Early morula


title: 16cell_replicate1

description: embryo

source_name: 16cell embryo

value: 16cell embryo


title: 8cell_replicate1

description: embryo

source_name: 8cell embryo

value: 8cell embryo


title: 4cell_replicate2

description: embryo

source_name: 4cell embryo

value: 4cell embryo


title: 16cell_replicate2

description: embryo


title: 8cell_replicate2

description: embryo


title: 4cell_replicate1

description: embryo


title: MII_Oocyte_replicate2

description: oocyte

source_name: MII oocyte

value: MII oocyte


title: 2cell_replicate1

description: embryo

source_name: 2cell embryo

value: 2cell embryo


title: 2cell_replicate2

description: embryo


title: MII_Oocyte_replicate1

description: oocyte


title: PF_drug_6hr_rep1

city: Madison

first: Elena

last: Sorokin

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: UW-Madison

data_processing:
Basecalls performed using CASAVA Illumina software 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ce10 whole genome and WS220 poly(A)+ transcriptome using tophat with options -m 2 -G 1 -g 1
Normalized gene and isoform counts per million were obtained from SAM files using scripts with the DESeq vignette (Anders and Huber, Genome Biology, 2010).
Genome_build: ce10
Supplementary_files_format_and_content: tab-delimited text files including CPM (counts per million) for each sample

organism: Caenorhabditis elegans

source_name: young adult hermaphrodites

growth_protocol: Synchronized L1 worms were grown to young adulthood on seeded NGM plates.

extract_protocol:
Worms were washed and pelleted, flash frozen with liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For DMSO or U0126 treatments, young adults were transferred to 1 mL of S media supplemented with OP50 bacteria and either DMSO vehicle alone or 100 uM U0126 (Sigma).

value: puf-8 fbf-1

tag: treatment type

tag: treatment length (hrs)

value: young adult hermaphrodites


title: WT

city: West Lafayette

first: Elizabeth

last: Tran

state: IN

address: 175 S. University Street

institute: Purdue University

description:
WT rep 1
WT rep 2
Genome wide RNA sequencing.

data_processing:
Colorspace reads were aligned to sacCer3 reference genome using LifeScope (v 2.5.1) with default conditions
Cufllinks (v 2.1.1) was used for transcript quantification in RPKM format and individual GTF files were merged.
Cuffdiff (v 2.1.1.) was used in conjuction with the LifeScope BAM files for differential expression analysis.
Genome_build: sacCer3 from UCSC
Supplementary_files_format_and_content: Tab-delimited .txt files report abundance measurements.

organism: Saccharomyces cerevisiae BY4741

source_name: wild type (reference) strain

growth_protocol: Cultures were grown at 30°C in YP+2% Glucose  (rich media) to mid-log phase. Cells were harvested by centrifugation and flash frozen in liquid nitrogen.

extract_protocol:
RNA was extracted using a standard hot acid phenol protocol. Total RNA was depleted for ribosomal RNA using the Ribominus Transcriptome Isolation Kit (yeast and bacteria) from Life Technologies.  Ribosomal RNA depeletion was conducted twice and resulting RNA integrity was verified using a bioanalyzer.
Libraries were prepared using Life Technologies SOLiD Total RNA-seq kit (4452437) according to manufacturer's instructions.

value: WT

tag: genotype/variation

value: MATa his3<delta>1 leu2<delta>0 met15<delta>0 ura3<delta>0


title: PF_vehicle_4hr_rep1

tag: genotype

value: DMSO vehicle control


title: dbp2Δ

description:
dbp2Δ rep 1
dbp2Δ rep 2
Genome wide RNA sequencing.

source_name: dbp2Δ strain

value: MATa dbp2::KanMx ura3<delta>0 leu2<delta>0 his3<delta>0 TRP1 met- lys<delta>


title: PF_vehicle_6hr_rep1


title: H9_Naive1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.3.3, default parameters).
Remaining sequences were mapped to the human GRCh37 genome using Bismark (Krueger and Andrews, 2011) (v0.9.0, parameters --bowtie2); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts. Global methylation comparison was calculated by averaging 1kb window methylation levels of CpGs covered by at least 30 reads.
Genome_build: GRCh37
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Embryonic Stem Cells

growth_protocol: Human embryo derived cells, H9 (WiCell Research Institute) (Thomson et al., 1998) were cultured on mouse embryonic fibroblast (MEF) cells. Conventional PSC cell medium (FGF/KSR) comprised DMEM/F12 (Sigma-Aldrich) with 10ng/ml bFGF (prepared in-house) and 20% KSR (Invitrogen) supplemented with 100 mM 2-mercaptoethanol (Sigma-Aldrich, cat. M7522), MEM nonessential amino acids (Invitrogen, cat. 11140050), 2 mM L-glutamine (Invitrogen, cat. 25030024). Conventional PSC were passaged every five to seven days as small clumps by dissociation with 0.025% Trypsin, 1mg/ml Collagenase IV (Invitrogen17104-019), KSR (final 20%), 1mM CaCl2. Throughout this study cells were maintained in incubators at 5% oxygen.

extract_protocol:
Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN)
Genomic DNA was fragmented by sonication (Covaris) and adaptor ligated using Illumina supplied methylated adaptors and NEBnext library preparation kit. Subsequently DNA was bisulfite-treated using the Sigma Imprint kit according to the manufacturer’s instructions (one step protocol). Final library amplification (11 cycles) was done using KAPA Uracil+ (KAPA Biosystems), after which the libraries were purified using Ampure beads (x1).

treatment_protocol: To induce resetting, transfected PSC expressing NANOG and KLF2 were dissociated with trypsin and replated as single cells in the presence of ROCK inhibitor. Doxycycline (DOX, 1μM) was added the next day and 24h later medium was changed to N2B27 medium (Ndiff227, StemCells Inc., SCS-SF- NB-02) with 1μM PD0325901 (PD03), human LIF (prepared in-house), DOX and either 3μM CHIR99021 (2iL+DOX) or 1μM CHIR99021 (t2iL+DOX). Medium was changed every day. Cells were split every five to seven days after dissociation to single cells with Accutase (Life Technologies) for 10 minutes. Around two weeks after DOX induction, cells were transferred to t2iL+5μM PKC inhibitor Gö6983 (Sigma-Aldrich) (t2iL+Gö). Reset cells cultured in t2iL+Gö were also passaged every five to seven days as single cells. Cells transferred to t2iL+Gö proliferate slowly for the initial couple of passages after withdrawal of DOX. Cells were maintained on MEF feeders throughout.

tag: cell line

tag: condition

value: Reset


title: H9_Naive3


title: PF_drug_2hr_rep1


title: H9_Primed1

value: Conventional


title: H9_Primed3


title: Early_morula_replicate1

description: embryo


title: PF_drug_4hr_rep1


title: H9_Primed2


title: PF_drug_1hr_rep1


title: PF_vehicle_1hr_rep1


title: PF_vehicle_2hr_rep1


title: PF_untreated_rep1

value: no treatment


title: PL_vehicle_1hr_rep3

value: puf-8; lip-1


title: PL_vehicle_18hr_rep1


title: PL_drug_18hr_rep2


title: PF_untreated_rep2


title: PL_drug_18hr_rep1


title: PL_drug_1hr_rep3


title: PL_vehicle_18hr_rep2


title: H9_Naive2


title: BF_kidney

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

institute: BGI-Shenzhen, Shenzhen 518083, China

description: Sequenced reads were generated from BF_kidney

data_processing:
use Fukomys damarensisgenome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.3.1 with default parameters except  -I 50000  --solexa1.3-quals, then we use our in-house pipeline to calculate the RPKM of each gene
Genome_build: Fukomys_damarensis_v1
Supplementary_files_format_and_content: bedGraph file, and the format is: scaffold or contig ID, start, end, transcrptome depth

organism: Fukomys damarensis

source_name: breeding female kidney

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: tissue

value: kidney


title: BF_ovary

description: Sequenced reads were generated from BF_ovary

source_name: breeding female ovary

value: ovary


title: 3F_ovary

description: Sequenced reads were generated from 3F_ovary

source_name: 3 years old non-breeding female ovary


title: PL_drug_6hr_rep1


title: BM_liver

description: Sequenced reads were generated from BM_liver

source_name: breeding male liver

value: liver


title: PL_vehicle_6hr_rep1


title: BM_testis

description: Sequenced reads were generated from BM_testis

source_name: breeding male testis

value: testis


title: PL_vehicle_6hr_rep2


title: 3F_kidney

description: Sequenced reads were generated from 3F_kidney

source_name: 3 years old non-breeding female kidney


title: 3F_brain_front

description: Sequenced reads were generated from 3F_brain_front

source_name: 3 years old non-breeding female frontal brain

value: frontal brain


title: PL_drug_4hr_rep2


title: M5y_kidney

description: Sequenced reads were generated from M5y_kidney

source_name: 5 years old non-breeding male kidney


title: PL_vehicle_4hr_rep2


title: BF_brain_front

description: Sequenced reads were generated from BF_brain_front

source_name: breeding female frontal brain


title: BM_brain_front

description: Sequenced reads were generated from BM_brain_front

source_name: breeding male frontal brain


title: PL_drug_4hr_rep1


title: 3F_liver

description: Sequenced reads were generated from 3F_liver

source_name: 3 years old non-breeding female liver


title: PL_vehicle_4hr_rep1


title: M5y_brain

description: Sequenced reads were generated from M5y_brain

source_name: 5 years old non-breeding male brain

value: brain


title: M5y_liver

description: Sequenced reads were generated from M5y_liver

source_name: 5 years old non-breeding male liver


title: PL_drug_2hr_rep2

source_name: young adult hermaphrodites


title: PL_drug_6hr_rep2


title: PL_vehicle_2hr_rep1


title: PL_vehicle_2hr_rep2


title: PL_drug_2hr_rep1


title: PL_drug_1hr_rep1


title: PL_drug_1hr_rep2


title: M5y_testis

description: Sequenced reads were generated from M5y_testis

source_name: 5 years old non-breeding male testis


title: PL_untreated_rep2


title: PL_untreated_rep1


title: PL_vehicle_1hr_rep1


title: PL_vehicle_1hr_rep2


title: BF_liver

description: Sequenced reads were generated from BF_liver

source_name: breeding female liver


title: N2_drug_18hr_rep1

value: Wild-type N2


title: N2_vehicle_18hr_rep1


title: N2_vehicle_18hr_rep2


title: N2_drug_6hr_rep2


title: N2_vehicle_6hr_rep2


title: N2_drug_2hr_rep2


title: N2_drug_6hr_rep1


title: BM_kidney

description: Sequenced reads were generated from BM_kidney

source_name: breeding male kidney


title: N2_vehicle_2hr_rep2


title: N2_vehicle_6hr_rep1


title: N2_drug_1hr_rep2


title: N2_drug_2hr_rep1


title: N2_drug_1hr_rep1


title: N2_vehicle_1hr_rep1


title: N2_untreated_rep2


title: C40280_FB

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

institute: University of Chicago

description: Sample 21

data_processing:
Mapping with TopHat2/Bowtie2
Removal of reads that do not map to highly orthologous regions between human and chimpanzee with featureCounts
Loess normalization on log2 CPM using voom
RPKM calculation
Genome_build: PanTro3
Supplementary_files_format_and_content: Processed data .txt file reports RPKMs

organism: Pan troglodytes

source_name: dermal fibroblast

growth_protocol: Standard iPSC and precursor cell line conditions as described in text

extract_protocol:
Qiagen Rneasy
TruSeq

tag: cell type (precursor used to generate ipscs)

value: dermal fibroblast

tag: passage

tag: gender

value: Female


title: N2_untreated_rep1

value: young adult hermaphrodites


title: N2_vehicle_1hr_rep2


title: C8861_FB

description: Sample 19

value: Male


title: C4955_FB

description: Sample 18


title: C3649_FB

description: Sample 16


title: C3651_FB

description: Sample 17


title: N2_drug_18hr_rep2


title: C40210_iPSC

description: Sample 6

source_name: induced pluripotent stem cell line

value: induced pluripotent stem cell line


title: C4955_iPSC

description: Sample 4


title: C8861_iPSC

description: Sample 5


title: C3649_iPSC

description: Sample 2


title: N2_vehicle_2hr_rep1

value: DMSO vehicle control


title: C3647_iPSC

description: Sample 1