title: mouse_tgc_h3k27me3

status: Public on May 29 2014

first: Roberta

middle: L

last: Hannibal

address: 300 Pasteur Drive

institute: Stanford University

description: ChIP-Seq

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 using BWA 0.5.9 (-q 10 -I), and filtered using samtools view (-q 10) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.10 with default settings
genome build:  = mm9
supplementary files format and content: ChIP-Seq bed files contain peaks called by MACS v2.0.10

source_name: Trophoblast giant cells - cultured

growth_protocol: Mouse trophoblast stem cells (TSCs) were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).

extract_protocol:
Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' 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 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: TSCs were differentiated into trophoblast giant cells (TGCs) by using differentiation media, which consisted of TS media without FGF4, Activin, and Heparin, with the addition of retinoic acid dissolved in ethanol to the media to a final concentration of 5 μM. TSCs were differentiated for five days, replacing media every other day, before harvesting.

tag: strain

tag: cell type

value: cultured trophoblast giant cells


title: mouse_tgc_input

type: SRA

city: Stanford

state: CA

department: Genetics

country: USA

description: Input chromatin

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: chip antibody

tag: sample type

value: Input chromatin


title: mouse_tgc_h3k4me1 (paired-end)

description: ChIP-Seq


title: mouse_tgc_h3k9me3

description: ChIP-Seq


title: mouse_tgc_h3k4me1

description: ChIP-Seq


title: mouse_tgc_h3k27me3 (paired-end)

description: ChIP-Seq


title: M2G RNA-seq

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

description: RNA-seq

library_source: transcriptomic

data_processing:
Reads were subtracted of rRNA/tRNA using bowtie 0.12.8, then unmapped reads were mapped to the Caulobacter NA1000 genome (CP001340) using bowtie 0.12.8.
RNAseq: The position of each alignment is distributed into to the 5' most base for 5' end mapping (X_RNA_5prime_ME.txt) or to the entire read length for transcript mapping (X_RNA_ME.txt).
Abundance measurements were done using R.P.K.M. by calculating the reads per kb per million mapped reads in each sample.
Genome_build: NA1000: CP001340
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on CP001340, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file, Reads aligning to rRNA, tRNA and non-coding RNA are not included.

molecule: total RNA

organism: Caulobacter vibrioides NA1000

source_name: Whole cell lystate

growth_protocol: Caulobacter crescentus NA1000 were innoculated at OD600 0.05 and grown to OD600 0.5 at 28C at 200RPM.

extract_protocol:
Cells were lysed by mixer mill using 6 cycles of 3 min at 15Hz.  In between cycles, the chamber was resuspended in liquid nitrogen to keep frozen. Frozen lysate were phenol chloroform extracted at 65C, ethanol precipitated, and sheared by base hydrolysis at 95C.  Resulting mRNA fragments were size selected via gel purification.
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].

treatment_protocol: Cells were incubated with 100ug/mL Chloramphenicol for 2 min and rapidly collected by centrifugation.  Cells were resuspended in lysis buffer and dripped into liquid nitrogen.

tag: growth medium


title: mouse_tgc_h3k27ac

description: ChIP-Seq


title: mouse_tgc_h3k4me3 (paired-end)

description: ChIP-Seq


title: e9.5_TGC_female_3seq_rep2

description: Tissue 3' RNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.5
3' RNA-seq reads were aligned to mm9 or rn4 using Bowtie 0.12.7 with the settings --best --strata -k 10 -S --chunkmbs 190
Using Unipeak v1.0, Bowtie alignments were filtered by posterior probability (sam_map.pl from Unipeak), and transcription peaks were called using default settings.
Peaks (chromosomal coordinates) were associated with Ensembl (e67) gene database for mouse and multiple peaks for each gene were pooled.
Read counts were normalized across libraries using DESeq
genome build:  = mm9
supplementary files format and content: txt files contain pooled gene x normalized tag count

molecule: polyA RNA

source_name: Trophoblast giant cells - e9.5

growth_protocol: Pregnant C57BL/6 mice were obtained from Charles River.  Copulation was determined by the presence of a vaginal plug the morning after mating, and embryonic day 0.5 (e0.5) was defined as noon of that day.  TGCs and embryos were dissected in 1X PBS (1:10 10X PBS, pH=7.4; Gibco) and stored on ice until further processing.  TGCs were dissected away from the placental disk, decidua, and, if possible, Reichert’s membrane.  For gathering RNA, the entire embryo was collected.  All experimental procedures were carried out in accordance with the APLAC protocol and the institutional guidelines set by the Veterinary Service Center at Stanford University.

extract_protocol:
mRNA was extracted directly from cell lysates using Dynabeads Oligo (dT)25 (Invitrogen).
500 ng of mRNA was then used to prepare 3’ RNA-Seq libraries as previously described (Beck et al, PLOS One 2010). Briefly, mRNA was heat sheared for 7.5 minutes to produce an average fragment size range of 100-400 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Size-selection was performed using E-gel SizeSelect agarose gels (Invitrogen), products were PCR amplified for 15 cycles, and purified using Ampure XP beads. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.

value: e9.5 trophoblast giant cells


title: mouse_tgc_h3k27ac (paired-end)

description: ChIP-Seq


title: mouse_tgc_h3k9me3 (paired-end)

description: ChIP-Seq


title: e9.5_TGC_male_3seq_rep2

description: Tissue 3' RNA-Seq


title: e9.5_TGC_female_3seq_rep1

description: Tissue 3' RNA-Seq


title: mouse_tgc_3seq_rep2

description: Cell culture 3' RNA-Seq

growth_protocol: Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).

extract_protocol:
mRNA was extracted directly from cell lysates using Dynabeads Oligo (dT)25 (Invitrogen).
500 ng of mRNA was then used to prepare 3’ RNA-Seq libraries as previously described (Beck et al, PLOS One 2010). Briefly, mRNA was heat sheared for 7 minutes to produce an average fragment size range of 300-500 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Size-selection was performed using E-gel SizeSelect agarose gels (Invitrogen), products were PCR amplified for 15 cycles, and purified using Ampure XP beads. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.


title: mM5

status: Public on May 30 2014

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

description:
Sample 95
mRNA
Processed data file: 4_species_comparable_gene_RPKM.tsv

data_processing:
We built custom exon-junction library for mapping. Human and mouse libraries were based on Ensembl66 annotation, while chimpanzee and rhesus macaque libraries were based on liftovered human annotation.
We used Bowtie2 with a default parameter setting to align the reads to the respective genomes, human version hg19, chimp panTro3, rhesus rheMac2 and mouse version mm9 from the Ensembl66, as well as custom exon-junction libraries.
We kept reads with alignment score > 150, and among those that mapped to two locations, only those with a difference in alignment score >= 5. Among reads that mapped to an exon and exon junction, those with higher scores were kept.
To calculate three species comparable gene expression, only reads in CDS regions which could be recipical liftoverable between human chimpanzee/rhesus macaque were considered. To calculate four species comparable gene expression, which could be recipical liftoverable between human and all other three species were considered.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Gene expression was quantified as 1000*P*N/(L-99) where N is the number of reads aligned to liftoverable CDS regions and L is the total length of these regions, P is coefficient used to normalize read number, which equal to mean of read number of all samples divided by read number of current sample.

source_name: muscle

extract_protocol:
Total RNA was extracted by a Trizol (Invitrogen) procedure according to the manufacturer's instructions. All RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the TruSeq RNA-Seq Sample Prep Kit (Illumina) according to the manufacturer's instructions.
Polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3'-end adenylation of these products, Illumina Single-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were then PCR-amplified (15 cycles). The RNA-seq libraries were sequenced (100 cycles) on the Illumina Hiseq 2000 platform.

tag: strain/background

tag: tissue

value: muscle

tag: Sex

value: F

tag: age (days)


title: HBI1-Ox 1#

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

country: China

institute: Shandong University

data_processing:
The sequence reads were mapped to the Arabidopsis genome using Tophat software, and differential gene expression was analyzed using DeSeq software.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Wild type Arabidopsis, 35S::HBI1-YFP and Col were grown on half-strength MS medium for 5 days under constant light.

extract_protocol:
Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma)
Libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Ilumina)

tag: genotype/variation

tag: Stage

value: 5 days plants


title: PYE RNA-seq

description: RNA-seq

value: PYE


title: mouse_tgc_3seq_rep1

description: Cell culture 3' RNA-Seq


title: mouse_tgc_h3k4me3

description: ChIP-Seq


title: e9.5_TGC_male_3seq_rep1

description: Tissue 3' RNA-Seq


title: KAP1 ChIP: WT cells 2

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description: See also Turelli et al., 2014

data_processing:
Raw reads were mapped to the human genome (hg19), transcriptome (refseq) and repbase (human 1709) using Bowtie 0.12.5
Chip-seq: peaks were called using MACS
RNA-seq: RPKM computed for all genes and repeated elements. For repeated elements on Repbase, the total number of reads mapped on the transcriptome were used for the normalization
Genome_build: hg19, human repbase 1709
Supplementary_files_format_and_content: RefSeq_all.txt and Repbase_all.txt contain RPKM values for all genes and all repeated elements respectively for the different conditions
Supplementary_files_format_and_content: bedfiles contain the results of the peakcalled using MACS

organism: Homo sapiens

source_name: H1-embryonic stem cells (p69)

growth_protocol: H1 ESCs (WA01, WiCell) were maintained in mTesRI (StemCell Technologies) on hES-qualified Matrigel (BD Biosciences). For transduction, hES were detached using TryPLE Express (Invitrogen), split at 40,000 cells/cm2 and maintained at least 12 hrs with ROCK inhibitor (Y-27632) to increase viability

extract_protocol:
ES cell samples were washed 2x (in KO medium), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde at RT), quenched with glycine at 125mM, incubated 5' on ice, washed 3x (cold PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed according to Covaris protocol: pellets were resuspended in ice cold buffer 1 (50mM HEPES-KOH pH7.4, 140mM NaCl, 1mM EDTA, o.5mM EGTA, 10% glycerol, 0.5% NP40, 0.25% TX100, antiproteases), then in ice cold buffer 2 (10mM Tris pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, antiproteases) then washed 3 times and resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to TC12 glass tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 15, 30 or 60 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification and quality control on a Bioanalyzer (Agilent 2100). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment and the 60' sonicated samples were used for further chromatin immunoprecipitation
Libraries were prepared according to Illumina's instructions. 10ng ChIPed DNA was used

value: H1-embryonic stem cells

tag: chip antibody vendor

value: AbCam, ab10483, 5μl per IP


title: H3K4me1 ChIP: LV sh-non-specific transduced ES cells

description: See also Turelli et al., 2014

source_name: H1-embryonic stem cells

extract_protocol:
ES cell samples were washed 2x (in KO medium), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde at RT), quenched with glycine at 125mM, incubated 5' on ice, washed 3x (cold PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed according to Covaris protocol: pellets were resuspended in ice cold buffer 1 (50mM HEPES-KOH pH7.4, 140mM NaCl, 1mM EDTA, o.5mM EGTA, 10% glycerol, 0.5% NP40, 0.25% TX100, antiproteases), then in ice cold buffer 2 (10mM Tris pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, antiproteases) then washed 3 times and resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to TC12 glass tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 40 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification and quality control on a Bioanalyzer (Agilent 2100). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment and the sonicated samples were used for further chromatin immunoprecipitation
Libraries were prepared according to Illumina's instructions. 10ng ChIPed DNA was used

tag: transduction

value: LV sh-non-specific

tag: time point

value: 10 days post LV-sh transduction

value: Diagenode, pAb-037-050, 5mg per IP


title: mouse_tgc_input (paired-end)

description: ChIP-Seq


title: Col 2#


title: H3K4me1 ChIP: LV sh-TRIM28 transduced ES cells

description: See also Turelli et al., 2014

value: LV sh-TRIM28


title: H3K9me3 ChIP: WT cells

description: See also Turelli et al., 2014

source_name: H1-embryonic stem cells (p75)

value: Diagenode, pAb-056-050, 1 mg/uL, 10ul per IP


title: Total input of ChIP: LV sh-non-specific transduced ES cells

description: See also Turelli et al., 2014


title: KAP1 ChIP: WT cells 1

description: See also Turelli et al., 2014

value: Custom rabbit antibody, 60μl per IP


title: Total input of ChIP Ti-1

description: See also Turelli et al., 2014


title: RNA-seq: LV sh-empty transduced ES cells

description: See also Turelli et al., 2014

source_name: H1-embryonic stem cells (p59)

extract_protocol:
cytoplasmic RNA was extracted (with Qiagen RNeasy kit and on column DNAse treatment). The quality was assessed on a bioanalyzer, analysed by RT-qPCR with positive and negative controls, selected for polyA+ RNA and  sequenced.
Libraries were prepared according to Illumina's instructions. 10ng ChIPed DNA was used

value: LV sh-empty

value: 15 days post LV-sh transduction


title: M2G Ribosome profiling

description:
Ribosome profiling
treatment: Ribosome-protected mRNA by Ribosome footprint sample digested by micrococcal nuclease.

data_processing:
Reads were subtracted of rRNA/tRNA using bowtie 0.12.8, then unmapped reads were mapped to the Caulobacter NA1000 genome (CP001340) using bowtie 0.12.8.
Ribosome profiling: The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)][Li et al,. Nature 484, 538 (2012)].
Abundance measurements were done using R.P.K.M. by calculating the reads per kb per million mapped reads in each sample.
Genome_build: NA1000: CP001340
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on CP001340, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file, Reads aligning to rRNA, tRNA and non-coding RNA are not included.

extract_protocol:
Cells were lysed by mixer mill using 6 cycles of 3 min at 15Hz.  In between cycles, the chamber was resuspended in liquid nitrogen to keep frozen.  Ribosome protected mRNA fragments were size selected via gel purification.
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].


title: PYE Ribosome profiling


title: Total input of ChIP: WT cells

description: See also Turelli et al., 2014


title: wt_yesleu_total

status: Public on May 28 2014

city: Seattle

first: Arvind

middle: R

last: Subramaniam

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

description: extracted at OD600 = 0.6

data_processing:
PolyA tails were trimmed by identifying a continuous run of 10 or more As
Reads aligning to genome were trimmed by 8nt on either side, weighted by the inverse length of the fragment and assigned to the genomic coordinate
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on NC_000913.3.fna, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: whole cell lysate_total mRNA profiling

growth_protocol: 30C, 200rpm shaking

extract_protocol:
Rapid filtration followed by flash freezing of intact cells, cell lysis by glass bead beating, Micrococcal nuclease digestion of polysomes, purification of monosomes/disomes by sucrose-gradient centrifugation. Total mRNA was purified from the cell lysate by phenol-chloroform method, rRNA-subtracted (MicrobeExpress, Ambion) and heat fragmented for use in  sequencing library preparation.
A modified small RNA protocol (Subramaniam et al., in preparation) was used for both the construction of both ribosome-protected and total mRNA sequencing libraries.

treatment_protocol: Either amino acid rich medium (control) or 30 minutes of starvation for leucine or serine

tag: stress condition

value: none (rich medium control)

value: whole cell lysate

tag: molecule subtype

value: total mRNA


title: wt_yesleu_mono

description: extracted at OD600 = 0.6

source_name: whole cell lysate_ribosome profiling

value: Monosome protected mRNA


title: wt_yesleu_di

description: extracted at OD600 = 0.6

value: Disome protected mRNA


title: ssra_noleu_mono

description: extracted at OD600 = 0.6, after 30 min of leucine starvation

value: leuB::kan, tmRNA/ssrA::cat

value: leucine starvation


title: wt_noleu_di


title: wt_noleu_total


title: Total input of ChIP: LV sh-TRIM28 transduced ES cells

description: See also Turelli et al., 2014

value: H1-embryonic stem cells


title: 1μMOP449-12hr

city: Portland

first: Rosalie

last: Sears

state: OR

address: 3181 S.W. Sam Jackson Park Rd

department: MMG

institute: OHSU

data_processing:
Samples were sequenced on an Illumina HiSeq 2000 and assembled into fastq files using the CASAVA software at the OHSU Massively Parallel Sequencing Shared Resource.
Sequences were aligned to the human hg19 genome using Bowtie version 1.0.0 and seting requiring unique alignments with no more than 3 mismatches.
Trim settings for Bowtie were selected to discard the first 4 bases, align to the next 44, and discard remaining bases from each sequence.
Aligned sequences that fell in exonic regions of RefSeq gene models were counted and normalized for sequencing depth.
Genes that showed low normalized sequence counts for all samples were discarded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file containing normalized sequence counts for gene models before filtering out low expression genes.

source_name: MDA-MB-231 breast cancer cell line

extract_protocol:
RNA was extracted from cells by Trozol reagent.
Total RNA was purified and reverse transcribed with oligo dT. Second strand DNA was synthesized and ligated to proprietary indexed adapters. Ligated material was amplified using Illumina genomic primers and sequenced on an Illumina GAII sequencer.

treatment_protocol: SET or CIP2A were knocked out by siRNA for 48hours. For OP449 treatment, cells were treated for 12 hours with 1μMOP449.

tag: cell line

value: MDA-MB-231 breast cancer cell line

tag: treatment


title: Total input of ChIP Ti-2

description: See also Turelli et al., 2014

tag: cell type


title: Infected Leghorn

city: Davis

first: Huaijun

last: Zhou

address: 2247 Meyer hall, One shield AVE

department: Animal Science

institute: University of California Davis

data_processing:
CLC genomics workbench 4.0
Genome_build: Galgal4 (GCA_000002315.2)
Supplementary_files_format_and_content: tab-delimited text files include unique gene reads for each Sample ...

organism: Gallus gallus

source_name: Lung

growth_protocol: Thirty-five birds, 7 Leghorn and 28 Fayoumi birds, were housed in negative pressure Horsfall-Bauer, temperature-controlled isolation units and provided ad libitum access to water and commercial feed.

extract_protocol:
A total of eight chickens (two birds per line per treatment) were randomly selected from infected and non-infected Leghorn and Fayoumi birds, euthanized and lungs and trachea collected for RNA isolation. Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At three weeks of age, 5 Leghorn and 20 Fayoumi birds were inoculated by the intra-choanal cleft route with 107 EID50 of low-path H5N3 AIV, and the other 2 Leghorn and 8 Fayoumi birds were kept as controls and inoculated with PBS. All chickens were euthanized at four days post-inoculation (dpi), and lungs and trachea were harvested

value: lung

tag: breed

value: Leghorn

tag: infection

value: H5N3 AIV


title: cont-12hr

value: PBS control-12hr


title: T 80 NU2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
To the reads generated with TruSeq unstranded protocol library starting with 100ng of total RNA where spiked in  the reads (extracted from 80 million reads generated with NuGENv2 using 2ng total RNA as input) for the following UCSC mm9 transcripts:uc009txr.2, uc009ghp.2, uc007jtu.1, uc007jtv.2, uc008mib.2, uc009eup.1, uc008egx.1, uc012hbj.1, uc009oda.1, uc007mki.1, uc007mkf.1, uc007aui.1, uc012ffj.1, uc007hwe.1, uc009rfh.2, uc009nfj.1, uc007ris.1, uc009mpg.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008duz.1, uc007bxi.1, uc007irk.1, uc009kkq.2, uc009dns.1, uc008lly.1, uc008sht.2, uc007cyw.2,  uc007bcj.2, uc007wuw.1, uc008ovt.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007upl.2, uc007det.1, uc012cbp.1, uc007ijq.1, uc007ijp.1, uc008glh.1, uc008gli.1, uc009ktc.1, uc008ovv.1, uc007lnl.1, uc007jop.1, uc012ccj.1, uc007pdt.2 , uc007yrp.1, uc007ypv.1

data_processing:
C1-C5 and T1-T5 fastq files were mapped with STAR software. Cuffdiff 1 and Cuffdiff 2 were used for detection of alternative spliced isoforms between C1-C5 and T1-T5 groups using mm9 UCSC annotation.
Isoforms were considered differentially expressed if characterized by a q-value <= 0.05. For exon-level analysis DEXSeq was used. Isoforms were considered differentially expressed if at least one isoform-specific
exon was detected as differentially expressed between C1-C5 and T1-T5 group with a Benjamini & Hochberg adjusted p-value <= 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file containing exon-level FPKM for each spiked-in gene available in the dataset

source_name: TruSeq 100ng NuGENv2 80M reads spike-in

extract_protocol:
Total RNA was extracted from D1 mouse cell line with Trizol Reagent (Invitrogen) followed by Rneasy micro clean-up procedure (Qiagen) as per manufacturer's instructions. Total RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent)
TruSeq: D1 total RNA was mixed with ERCC RNA Spike in Control Mix 1 (Ambion) and subjected to library preparation using Illumina TruSeq RNA Sample Preparation kit version 1 (Low Sample Protocol) with slight modifications. Briefly, polyA-containing RNA molecules were purified from the D1 RNA samples using polyT oligo-attached magnetic beads. Thermal fragmentation followed after two rounds of enrichment for polyA+ mRNA. cDNA was synthesized from the RNA fragments using reverse transcriptase (Superscript II) and random primers. This was followed by second strand cDNA synthesis and the resulting dsDNA went through an end repair process, the addition of a single A base, and ligation of the adapters. The products were purified and enriched with 12 cycles of PCR to create the cDNA library. Two additional rounds of purification of the cDNA libraries were done using Agencourt Ampure XP SPRI beads (Beckamn Courter) to remove >600 bp double stranded cDNA. The length distribution of cDNA libraries was monitored using DNA 1000 kits on the Agilent Bioanalyzer


title: siCIP2A

value: CIP2A siRNA


title: wt_noleu_mono

tag: strain

tag: sample type


title: Non-infected Fayoumi

tag: tissue

value: Fayoumi


title: T 40 TS

description:
To the reads generated with TruSeq unstranded protocol library starting with 100ng of total RNA where spiked in  the reads (extracted from 40 million reads generated with TruSeq unstranded using 100ng total RNA as input) for the following UCSC mm9 transcripts:uc009txr.2, uc009ghp.2, uc007jtu.1, uc007jtv.2, uc008mib.2, uc009eup.1, uc008egx.1, uc012hbj.1, uc009oda.1, uc007mki.1, uc007mkf.1, uc007aui.1, uc012ffj.1, uc007hwe.1, uc009rfh.2, uc009nfj.1, uc007ris.1, uc009mpg.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008duz.1, uc007bxi.1, uc007irk.1, uc009kkq.2, uc009dns.1, uc008lly.1, uc008sht.2, uc007cyw.2,  uc007bcj.2, uc007wuw.1, uc008ovt.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007upl.2, uc007det.1, uc012cbp.1, uc007ijq.1, uc007ijp.1, uc008glh.1, uc008gli.1, uc009ktc.1, uc008ovv.1, uc007lnl.1, uc007jop.1, uc012ccj.1, uc007pdt.2 , uc007yrp.1, uc007ypv.1

source_name: TruSeq 100ng TruSeq 40M reads spike-in


title: T 80 TS

description:
To the reads generated with TruSeq unstranded protocol library starting with 100ng of total RNA where spiked in  the reads (extracted from 80 million reads generated with TruSeq unstranded using 100ng total RNA as input) for the following UCSC mm9 transcripts:uc009txr.2, uc009ghp.2, uc007jtu.1, uc007jtv.2, uc008mib.2, uc009eup.1, uc008egx.1, uc012hbj.1, uc009oda.1, uc007mki.1, uc007mkf.1, uc007aui.1, uc012ffj.1, uc007hwe.1, uc009rfh.2, uc009nfj.1, uc007ris.1, uc009mpg.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008duz.1, uc007bxi.1, uc007irk.1, uc009kkq.2, uc009dns.1, uc008lly.1, uc008sht.2, uc007cyw.2,  uc007bcj.2, uc007wuw.1, uc008ovt.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007upl.2, uc007det.1, uc012cbp.1, uc007ijq.1, uc007ijp.1, uc008glh.1, uc008gli.1, uc009ktc.1, uc008ovv.1, uc007lnl.1, uc007jop.1, uc012ccj.1, uc007pdt.2 , uc007yrp.1, uc007ypv.1

source_name: TruSeq 100ng TruSeq 80M reads spike-in


title: RNA-seq: LV sh-non specific transduced ES cells

description: See also Turelli et al., 2014

value: LV sh-non specific


title: T 40 NU2

description:
To the reads generated with TruSeq unstranded protocol library starting with 100ng of total RNA where spiked in  the reads (extracted from 40 million reads generated with NuGENv2 using 2ng total RNA as input) for the following UCSC mm9 transcripts:uc009txr.2, uc009ghp.2, uc007jtu.1, uc007jtv.2, uc008mib.2, uc009eup.1, uc008egx.1, uc012hbj.1, uc009oda.1, uc007mki.1, uc007mkf.1, uc007aui.1, uc012ffj.1, uc007hwe.1, uc009rfh.2, uc009nfj.1, uc007ris.1, uc009mpg.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008duz.1, uc007bxi.1, uc007irk.1, uc009kkq.2, uc009dns.1, uc008lly.1, uc008sht.2, uc007cyw.2,  uc007bcj.2, uc007wuw.1, uc008ovt.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007upl.2, uc007det.1, uc012cbp.1, uc007ijq.1, uc007ijp.1, uc008glh.1, uc008gli.1, uc009ktc.1, uc008ovv.1, uc007lnl.1, uc007jop.1, uc012ccj.1, uc007pdt.2 , uc007yrp.1, uc007ypv.1

source_name: TruSeq 100ng NuGENv2 40M reads spike-in


title: MycPlusPin1

description: RNA-seq

data_processing: Illumina reads were mapped to UCSC hg19 assembly (GRCh37) using the Bowtie binary (http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/).  The MycPlusGFP sample was sequenced to 101 bases and bar coded.  Only sequces matching the 5 base bar code are reported.  Only the first 41 bases of this sample (after bar code) were mapped and the rest were discarded.  Up to three mis-matches were alowed during mapping.  The MycPlusPin1 sample was sequence to 36 bases and was not bar coded.  All 36 bases were mapped and only 2 mis-matches were alowed.   Custom scripts were used to parse and annotate mapped reads.

source_name: MCF10A-Myc cells

growth_protocol: Stable expression of Doxycycline-inducible c-Myc by lentiviral infection.  Cells were grown to sub-confluence in DMEM/F12.

extract_protocol: Total RNA was purified and reverse transcribed with oligo dT. Second strand DNA was synthesized and ligated to proprietary indexed adapters. Ligated material was amplified using Illumina genomic primers and sequenced on an Illumina GAII sequencer.

treatment_protocol: Cells were infected with AdGFP (control) or AdPin1 for 18 hrs and Myc was turned on in both with Doxycycline for 4 hrs before RNA extraction.

value: normal breast epithlial

tag: phenotype


title: Infected Fayoumi


title: RNA-seq: LV sh-TRIM28 transduced ES cells

description: See also Turelli et al., 2014

value: LV sh-TRIM28

value: 15 days post LV-sh transduction


title: MycPlusGFP

description: RNA-seq

value: GFP-expressing


title: siNT

value: control siRNA-48hr


title: Non-infected leghorn


title: C 80 TS

description:
To the reads generated with TruSeq unstranded protocol library starting with 1000ng of total RNA where spiked in  the reads (extracted from 80 million reads generated with TruSeq unstranded using 100ng total RNA as input) for the following UCSC mm9 transcripts: uc009gho.2, uc007gin.1, uc009eup.1, uc007wps.1,uc012baj.1, uc007dpl.2,uc009fyx.1, uc009gyv.2, uc009rfi.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008dvb.1, uc007jjq.1, uc008lmc.1, uc008eog.1, uc008vpi.1, uc011zhz.1, uc007avh.1, uc009dnu.1, uc012gwx.1, uc008eoh.1, uc007jjs.1, uc007irn.1, uc009mhp.1, uc008ind.1, uc007bxm.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007cky.1, uc012gpo.1, uc007ijo.1, uc008glj.1, uc009kta.1, uc008xda.1, uc011yuy.1, uc007pdu.2, uc007yro.1, uc007yrn.1, uc007ypx.1, uc007ypw.1, uc008gob.1

source_name: TruSeq 1000ng TruSeq 80M reads spike-in


title: C 80 NU2

description:
To the reads generated with TruSeq unstranded protocol library starting with 1000ng of total RNA where spiked in  the reads (extracted from 80 million reads generated with NUGENv2 using 2ng total RNA as input) for the following UCSC mm9 transcripts: uc009gho.2, uc007gin.1, uc009eup.1, uc007wps.1,uc012baj.1, uc007dpl.2,uc009fyx.1, uc009gyv.2, uc009rfi.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008dvb.1, uc007jjq.1, uc008lmc.1, uc008eog.1, uc008vpi.1, uc011zhz.1, uc007avh.1, uc009dnu.1, uc012gwx.1, uc008eoh.1, uc007jjs.1, uc007irn.1, uc009mhp.1, uc008ind.1, uc007bxm.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007cky.1, uc012gpo.1, uc007ijo.1, uc008glj.1, uc009kta.1, uc008xda.1, uc011yuy.1, uc007pdu.2, uc007yro.1, uc007yrn.1, uc007ypx.1, uc007ypw.1, uc008gob.1

source_name: TruSeq 1000ng NuGENv2 80M reads spike-in


title: T 20 NU2

description:
To the reads generated with TruSeq unstranded protocol library starting with 100ng of total RNA where spiked in  the reads (extracted from 20 million reads generated with NuGENv2 using 2ng total RNA as input) for the following UCSC mm9 transcripts:uc009txr.2, uc009ghp.2, uc007jtu.1, uc007jtv.2, uc008mib.2, uc009eup.1, uc008egx.1, uc012hbj.1, uc009oda.1, uc007mki.1, uc007mkf.1, uc007aui.1, uc012ffj.1, uc007hwe.1, uc009rfh.2, uc009nfj.1, uc007ris.1, uc009mpg.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008duz.1, uc007bxi.1, uc007irk.1, uc009kkq.2, uc009dns.1, uc008lly.1, uc008sht.2, uc007cyw.2,  uc007bcj.2, uc007wuw.1, uc008ovt.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007upl.2, uc007det.1, uc012cbp.1, uc007ijq.1, uc007ijp.1, uc008glh.1, uc008gli.1, uc009ktc.1, uc008ovv.1, uc007lnl.1, uc007jop.1, uc012ccj.1, uc007pdt.2 , uc007yrp.1, uc007ypv.1

source_name: TruSeq 100ng NuGENv2 20M reads spike-in


title: C 40 TS

description:
To the reads generated with TruSeq unstranded protocol library starting with 1000ng of total RNA where spiked in  the reads (extracted from 40 million reads generated with TruSeq unstranded using 100ng total RNA as input) for the following UCSC mm9 transcripts: uc009gho.2, uc007gin.1, uc009eup.1, uc007wps.1,uc012baj.1, uc007dpl.2,uc009fyx.1, uc009gyv.2, uc009rfi.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008dvb.1, uc007jjq.1, uc008lmc.1, uc008eog.1, uc008vpi.1, uc011zhz.1, uc007avh.1, uc009dnu.1, uc012gwx.1, uc008eoh.1, uc007jjs.1, uc007irn.1, uc009mhp.1, uc008ind.1, uc007bxm.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007cky.1, uc012gpo.1, uc007ijo.1, uc008glj.1, uc009kta.1, uc008xda.1, uc011yuy.1, uc007pdu.2, uc007yro.1, uc007yrn.1, uc007ypx.1, uc007ypw.1, uc008gob.1

source_name: TruSeq 1000ng TruSeq 40M reads spike-in


title: hiPS2

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

description: Sample 9

data_processing:
Each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000.
Reads were prefiltered by trimming away adapter sequences and selecting reads that contain 5' MspI site
Reads were mapped to the hg18 genome via BS-Seeker
wiggle files contain the ratio of methylated cytosines to total cytosines covered at single base position
only cytosines with at least 5 or more covered reads were considered
Genome_build: hg18
Supplementary_files_format_and_content: wiggle files containing the ratio of methylated cytosines to total cytosines covered at single base position

source_name: induced pluripotent stem cells

growth_protocol: Pluripotent stem cells (hESC and iPSCs) were plated onto gamma-rays irradiation mouse embryonic feeder cells with DMEM/F12 culture medium containing 20% Knock-Out Serum Replacement, 0.1 mM nonessential amino acids, 0.1 mM b-mercaptoethanol and 100 ng/ml zebrafish basic fibroblast growth factor (zfbFGF) on a 6-well plate. RPE medium were changed to support pigment cluster expansion [containing α-MEM, 1×N2 supplement(Gibco), 1×Non-essential amino acid solution, 250 mg/ml taurine, 13 ng/ml Triiodo thyronin (Sigma-Aldrich, Gillingham, UK), 20 ng/ml Hydrocortisone (Sigma), 2 mM L-glutamine (Invitrogen, Paisley, UK), 1×Penicillin-streptomycin and 10% Hyclone heat-inactivat-ed foetal bovine serum (Thermo Scientific, Northumberland, UK)], which was replaced daily.

extract_protocol:
Genomic DNA was isolated from all samples by traditional phenol/chloroform method.
One µg genomic DNA was digested with the methylation insensitive restriction enzyme MspI (NEB). Ends of each restriction fragment were filled in and a 3′ adenosine was added with Klenow Fragment (3′→5′ exo-minus; NEB). Methylated paired-end Illumina adapters were ligated to the ends of the DNA fragments using T4 DNA Ligase (NEB). Fragments between 100 bp and 400 bp were purified by agarose gel extraction. The purified fragments were treated with sodium bisulfite and then amplified by PCR.

treatment_protocol: Cells were cultured at 37℃ in 5% CO2 for 6-10 days after which zfbFGF was omitted to facilitate spontaneous cell differentiation.

value: induced pluripotent stem cells


title: HDF RPE

description: Sample 8

source_name: retinal pigmented epithelium

value: iPS-derived RPE


title: UCLA4 RPE

description: Sample 12

value: ES-derived RPE


title: UCLA4 ESC

description: Sample 11

source_name: embryonic stem cells

value: embryonic stem cells


title: siSET

value: MDA-MB-231 breast cancer cell line

value: SET siRNA-48hr


title: HDF iPS

description: Sample 7


title: C 20 TS

description:
To the reads generated with TruSeq unstranded protocol library starting with 1000ng of total RNA where spiked in  the reads (extracted from 20 million reads generated with TruSeq unstranded using 100ng total RNA as input) for the following UCSC mm9 transcripts: uc009gho.2, uc007gin.1, uc009eup.1, uc007wps.1,uc012baj.1, uc007dpl.2,uc009fyx.1, uc009gyv.2, uc009rfi.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008dvb.1, uc007jjq.1, uc008lmc.1, uc008eog.1, uc008vpi.1, uc011zhz.1, uc007avh.1, uc009dnu.1, uc012gwx.1, uc008eoh.1, uc007jjs.1, uc007irn.1, uc009mhp.1, uc008ind.1, uc007bxm.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007cky.1, uc012gpo.1, uc007ijo.1, uc008glj.1, uc009kta.1, uc008xda.1, uc011yuy.1, uc007pdu.2, uc007yro.1, uc007yrn.1, uc007ypx.1, uc007ypw.1, uc008gob.1

source_name: TruSeq 1000ng TruSeq 20M reads spike-in


title: H9 RPE

description: Sample 6


title: C 20 NU2

description:
To the reads generated with TruSeq unstranded protocol library starting with 1000ng of total RNA where spiked in  the reads (extracted from 20 million reads generated with NuGENv2 using 2ng total RNA as input) for the following UCSC mm9 transcripts: uc009gho.2, uc007gin.1, uc009eup.1, uc007wps.1,uc012baj.1, uc007dpl.2,uc009fyx.1, uc009gyv.2, uc009rfi.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008dvb.1, uc007jjq.1, uc008lmc.1, uc008eog.1, uc008vpi.1, uc011zhz.1, uc007avh.1, uc009dnu.1, uc012gwx.1, uc008eoh.1, uc007jjs.1, uc007irn.1, uc009mhp.1, uc008ind.1, uc007bxm.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007cky.1, uc012gpo.1, uc007ijo.1, uc008glj.1, uc009kta.1, uc008xda.1, uc011yuy.1, uc007pdu.2, uc007yro.1, uc007yrn.1, uc007ypx.1, uc007ypw.1, uc008gob.1

source_name: TruSeq 1000ng NuGENv2 20M reads spike-in


title: C 40 NU2

description:
To the reads generated with TruSeq unstranded protocol library starting with 1000ng of total RNA where spiked in  the reads (extracted from 40 million reads generated with NuGENv2 using 2ng total RNA as input) for the following UCSC mm9 transcripts: uc009gho.2, uc007gin.1, uc009eup.1, uc007wps.1,uc012baj.1, uc007dpl.2,uc009fyx.1, uc009gyv.2, uc009rfi.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008dvb.1, uc007jjq.1, uc008lmc.1, uc008eog.1, uc008vpi.1, uc011zhz.1, uc007avh.1, uc009dnu.1, uc012gwx.1, uc008eoh.1, uc007jjs.1, uc007irn.1, uc009mhp.1, uc008ind.1, uc007bxm.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007cky.1, uc012gpo.1, uc007ijo.1, uc008glj.1, uc009kta.1, uc008xda.1, uc011yuy.1, uc007pdu.2, uc007yro.1, uc007yrn.1, uc007ypx.1, uc007ypw.1, uc008gob.1

source_name: TruSeq 1000ng NuGENv2 40M reads spike-in


title: hiPS2 RPE

description: Sample 10


title: H9 PD

description: Sample 5

source_name: partially differentiated ESCs

value: partially differentiated ESCs


title: 4-Months old WT

city: Birmingham

first: David

last: Crossman

state: AL

address: 720 20th Street South

institute: University of Alabama at Birmingham

data_processing:
raw data was converted to fastq using illumina's CASAVA version 1..8.1
TopHat version 1.2.0 was used to align the raw RNA- Seq
Cufflinks version 1.0.3 was used to align the reads from TopHat to assemble transcripts, estimate their abundances and test for differential expression and regulation
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample calculated by Cufflinks/Cuffdiff

source_name: Lens

extract_protocol:
Total RNA was isolated from 2 & 4-months old lenses by Trizol method
TruSeq library generation kit instructions

tag: mouse model

value: RNA was isolated from lenses of 4- months old CRYAAWT transgenic mice expressing WT alpha A crystallin

tag: genotype

value: lens


title: H9 ESC

description: Sample 3


title: 4-Months old CRYAAN101D

value: RNA was isolated from lenses of 4- months old CRYAAN101D transgenic mice expressing deamidated alpha A crystallin (N101D)


title: 2-Months old WT

value: RNA was isolated from lenses of 2- months old CRYAAWT transgenic mice expressing WT alpha A crystallin


title: wt_yesser_mono

description: extracted at OD600 = 0.6

organism: Escherichia coli BW25113

source_name: whole cell lysate_ribosome profiling

value: none (rich medium control)

value: whole cell lysate

value: Monosome protected mRNA


title: wt_yesser_total

description: extracted at OD600 = 0.6

source_name: whole cell lysate_total mRNA profiling

value: total mRNA


title: fetal RPE 2

description: Sample 2

value: primary RPE


title: H9 PC

description: Sample 4

source_name: pigmented cluster

value: ES-derived pigmented cluster


title: 2-Months old CRYAAN101D

value: RNA was isolated from lenses of 2- months old CRYAAN101D transgenic mice expressing deamidated alpha A crystallin (N101D)


title: wt_noser_total

description: extracted at OD600 = 0.6, after 30 min of serine starvation

value: serine starvation


title: fetal RPE 1

description: Sample 1


title: wt_noser_mono


title: RING1A/B_cKO_H3K27me3_treated_rep2

status: Public on May 27 2014

city: London

first: Hamish

middle: W

last: King

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: RING1AB_cKO_H3K27me3_treated_merged.bigwig

data_processing:
Single-end 51bp reads from ChIP-seq experiments were mapped to mm9 using bowtie v1.1.2. Reads which could be aligned to more than one site in the genome were supressed (-m 1).
Duplicate reads were removed. Biological replicates were down-sampled using Picard (v1.97) to the same total read count (of mapped reads).
MACS(v1.4) was used to call peaks for each biological replicate with the control input sample. Peaks from different biological replicates were merged using Bedops (v2.2.0) and intervals not represented in all independent replicates were eliminated.
Genome_build: mm9
Supplementary_files_format_and_content: Wig/BigWig files were created from merged BAM files.

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, H3K27me3 ChIP

growth_protocol: Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells were cultured on Mitomycin C inactivated mouse embryonic fibroblasts (MEFs) in DMEM (Gibco, Carlsbad, CA) supplemented with 15% FBS, 10 ng/mL leukemia-inhibiting factor (LIF), penicillin/streptomycin, beta-mercaptoethanol, l-glutamine and non-essential amino-acids on 0.1% gelatin-coated dishes. Prior to use in ChIPseq experiments, the cells were allowed to settle overnight without feeders and cultured in the absence or presence of 4-hydroxy tamoxifen (800 nM) for 48hr to delete RING1B.

extract_protocol:
To prepare material for ChIP-seq, immunoprecipitation was performed overnight at 4°C with approximately 3 µg of antibody and chromatin corresponding to 5 × 10^6 cells. Antibody bound chromatin was isolated on protein A magnetic Dynabeads (Invitrogen, Carlsbad, CA) and washes were performed with low salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP40, 1% Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and TE buffer (x2) (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To prepare ChIP-seq material, ChIP DNA was eluted, and cross-links reversed at 65°C, then samples were then sequentially treated with RNase and proteinase K before being purified on a PureLink PCR micro column (Invitrogen). ChIP sequencing libraries were generated as described previously (Blackledge et al., 2010) and sequenced on the Illumina HiSeq2000 platform with 51 bp reads. ChIP sequencing experiments were performed in biological duplicates with matched input controls.
Performed by the High-Throughput Sequencing  centre at the Wellcome Trust Centre for Human Genetics (Oxford, United Kingdom) according to standard Illumina library generation protocol.

treatment_protocol: Chromatin was prepared as described previously (Farcas et al 2012), with minor modifications. Briefly, the cells were fixed for 1 hr in 2 mM EGS, followed by 15 min in 1% formaldehyde. Formaldehyde was quenched by the addition of glycine to a final concentration of 125 μM. Sonication was performed using a BioRuptor sonicator (Diagenode, Liege, Belgium) to produce fragments of approximately 0.5–1 kb. For RNA-Seq, total RNA was extracted using the Qiagen RNeasy Mini kit. Approximately 10 μg RNA was treated with Turbo DNase (Ambion, Carlsbad, CA) at 37°C for 30 min, according to the manufacturer's instructions. Genomic DNA-free RNA samples were further purified using the RNeasy kit RNA cleanup protocol. Samples were run on a 1% agarose gel to check quality of RNA preparation and integrity of 18S and 28S rRNA bands.

tag: passage

tag: chip antibody


title: RING1A/B_cKO_H3K27me3_untreated_rep2

description: RING1AB_cKO_H3K27me3_untreated_merged.bigwig

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, H3K27me3 ChIP


title: T 20 TS

description:
To the reads generated with TruSeq unstranded protocol library starting with 100ng of total RNA where spiked in  the reads (extracted from 20 million reads generated with TruSeq unstranded using 100ng total RNA as input) for the following UCSC mm9 transcripts:uc009txr.2, uc009ghp.2, uc007jtu.1, uc007jtv.2, uc008mib.2, uc009eup.1, uc008egx.1, uc012hbj.1, uc009oda.1, uc007mki.1, uc007mkf.1, uc007aui.1, uc012ffj.1, uc007hwe.1, uc009rfh.2, uc009nfj.1, uc007ris.1, uc009mpg.1
 ### Synthetic spike-in characterized by unform transcript coverage and complex background of non-differentially expressed isoforms: uc008duz.1, uc007bxi.1, uc007irk.1, uc009kkq.2, uc009dns.1, uc008lly.1, uc008sht.2, uc007cyw.2,  uc007bcj.2, uc007wuw.1, uc008ovt.1
 ### Synthetic spike-in characterized by unform transcript coverage and endogenous background of non-differentially expressed isoforms: uc007upl.2, uc007det.1, uc012cbp.1, uc007ijq.1, uc007ijp.1, uc008glh.1, uc008gli.1, uc009ktc.1, uc008ovv.1, uc007lnl.1, uc007jop.1, uc012ccj.1, uc007pdt.2 , uc007yrp.1, uc007ypv.1

source_name: TruSeq 100ng TruSeq 20M reads spike-in


title: RING1A/B_cKO_H3K27me3_untreated_rep1


title: RING1A/B_cKO_H3K27me3_treated_rep1


title: RING1A/B_cKO_EZH2_treated_rep2

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, EZH2 ChIP

value: EZH2 Ab (Cell Signaling #5246S)


title: RING1A/B_cKO_SUZ12_treated_rep2

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, SUZ12 ChIP

value: SUZ12 Ab (Cell Signaling #3737S)


title: RING1A/B_cKO_EZH2_untreated_rep1

description: RING1AB_cKO_EZH2_untreated_merged.bigwig

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, EZH2 ChIP


title: RING1A/B_cKO_EZH2_treated_rep1


title: RING1A/B_cKO_SUZ12_treated_rep1


title: RING1A/B_cKO_SUZ12_untreated_rep2

description: RING1AB_cKO_SUZ12_untreated_merged.bigwig

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, SUZ12 ChIP


title: RING1A/B_cKO_Input_rep2

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, sonicated control


title: RING1A/B_cKO_RING1B_treated_rep1

description: RING1AB_cKO_RING1B_treated_merged.bigwig

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, RING1B ChIP

value: RING1B ab (Atsuta et al., 2001; PMID 11289226)


title: RING1A/B_cKO_RING1B_untreated_rep1

description: RING1AB_cKO_RING1B_untreated_merged.bigwig

source_name: RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, RING1B ChIP


title: RING1A/B_cKO_RING1B_treated_rep2


title: RING1A/B_cKO_RING1B_untreated_rep2


title: RING1A/B_cKO_SUZ12_untreated_rep1


title: RING1A/B_cKO_Input_rep1


title: KDM2Bfl/fl_RNAseq_treated_rep1

data_processing:
Single-end 51bp reads from ChIP-seq experiments were mapped to mm9 using bowtie v1.1.2. Reads which could be aligned to more than one site in the genome were supressed (-m 1).
Duplicate reads were removed. Biological replicates were down-sampled using Picard (v1.97) to the same total read count (of mapped reads).
MACS(v1.4) was used to call peaks for each biological replicate with the control input sample. Peaks from different biological replicates were merged using Bedops (v2.2.0) and intervals not represented in all independent replicates were eliminated.
Paired end 51-bp reads from RNA-seq experiments were aligned to the mm9 reference genome using Tophat2 (v0.5) with default parameters.
FPKM values were obtained from biological triplicates of the Kdm2bfl/fl and 72 hr tamoxifen treated cells using cufflinks(v2.1.1) and cuffdiff(v2.1.1) on a refGene set obtained from the UCSC table browser.
genome build: mm9
processed data files format and content: Wig/BigWig files were created from merged BAM files using MACS. Tab delimited text files containing FPKM values for refGene gene IDs were obtained from Cufflinks.

source_name: Embryonic stem cells, tamoxifen treated, RNA

growth_protocol: kdm2b fl/fl cell were cultured on Mitomycin C inactivated mouse embryonic fibroblasts (MEFs) in DMEM (Gibco, Carlsbad, CA) supplemented with 15% FBS, 10 ng/mL leukemia-inhibiting factor (LIF), penicillin/streptomycin, beta-mercaptoethanol, l-glutamine and non-essential amino-acids on 0.1% gelatin-coated dishes. Prior to use in ChIPseq and RNA-seq experiments, the cells were allowed to settle overnight without feeders and cultured in the absence or presence of 4-hydroxy tamoxifen (800 nM) for 72 hr to delete KDM2B ZF-CxxC domain.

extract_protocol:
To prepare material for ChIP-Seq, immunoprecipitation was performed overnight at 4°C with approximately 3 µg of antibody and chromatin corresponding to 5 × 106 cells. Antibody bound chromatin was isolated on protein A magnetic Dynabeads (Invitrogen, Carlsbad, CA) and washes were performed with low salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP40, 1% Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and TE buffer (x2) (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To prepare ChIP-seq material, ChIP DNA was eluted, and cross-links reversed at 65oC, then samples were then sequentially treated with RNase and proteinase K before being purified on a PureLink PCR micro column (Invitrogen). ChIP sequencing libraries were generated as described previously (Blackledge et al., 2010) and sequenced on the Illumina HiSeq2000 platform with 51 bp reads. ChIP sequencing experiments were performed in biological triplicates for KDM2B and RING1B and biological duplicates for SUZ12. For mRNA-seq analysis 1 μg of purified total RNA was used to first isolate polyA plus RNA and then a directional library was prepared using the NEBNext UltraTM Directional RNA library Prep Kit for Illumina (NEB, Ipswich, MA).
Performed by the High-Throughput Sequencing  centre at the Wellcome Trust Centre for Human Genetics (Oxford, United Kingdom) according to standard Illumina library generation protocol.

value: MS12 KDM2Bfl/fl ES cells


title: KDM2Bfl/fl_RNAseq_treated_rep2


title: KDM2Bfl/fl_RNAseq_treated_rep3


title: KDM2Bfl/fl_RNAseq_untreated_rep2

source_name: Embryonic stem cells, untreated control, RNA


title: KDM2Bfl/fl_SUZ12_treated_rep2

source_name: Embryonic stem cells, tamoxifen treated, SUZ12 ChIP


title: KDM2Bfl/fl_SUZ12_untreated_rep2

source_name: Embryonic stem cells, untreated control, SUZ12 ChIP


title: KDM2Bfl/fl_RNAseq_untreated_rep1


title: KDM2Bfl/fl_SUZ12_treated_rep1


title: KDM2Bfl/fl_SUZ12_untreated_rep1


title: KDM2Bfl/fl_RING1B_treated_rep2

source_name: Embryonic stem cells, tamoxifen treated, RING1B ChIP


title: KDM2Bfl/fl_RING1B_treated_rep3


title: KDM2Bfl/fl_RING1B_treated_rep1


title: KDM2Bfl/fl_RING1B_untreated_rep2

source_name: Embryonic stem cells, untreated control, RING1B ChIP


title: RING1A/B_cKO_EZH2_untreated_rep2


title: KDM2Bfl/fl_RING1B_untreated_rep1


title: KDM2Bfl/fl_RING1B_untreated_rep3


title: KDM2Bfl/fl_KDM2B_treated_rep2

source_name: Embryonic stem cells, tamoxifen treated, KDM2B ChIP

value: KDM2B ab (Farcas et al., 2012; PMID 23256043)


title: KDM2Bfl/fl_KDM2B_untreated_rep2

source_name: Embryonic stem cells, untreated control, KDM2B ChIP


title: KDM2Bfl/fl_KDM2B_untreated_rep3


title: KDM2Bfl/fl_KDM2B_treated_rep1


title: KDM2Bfl/fl_KDM2B_untreated_rep1


title: KDM2Bfl/fl_Input

source_name: Embryonic stem cells, untreated control, sonicated control


title: PAT081

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

description:
processed data file: StrokeMethylome_Ziemann_etal2014_CountMatrix_1MbpIntervals.txt
processed data file: StrokeMethylome_Ziemann_etal2014_CountMatrix_1kbpIntervals.txt

data_processing:
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8)
36 bp reads were checked for quality using FastQC.
Reads were aligned to the Human genome (HG19) using BWA (aln algorithm v0.6) with default settings.
Bedtools makewindows was used to generate 1kbp intervals across the genome and these were annotated with GENCODE v14 genenames using Bedtools intersect.
The density of read mapping in these intervals for each patient was determined using Bedtools multicov to generate a count matrix.
Genome_build: HG19
Supplementary_files_format_and_content: Count matrix

source_name: ischemic stroke patient_female

extract_protocol:
Peripheral blood mononuclear cell (PBMC) genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit according to the manufacturer's protocol. After sonication of DNA with Diagenode bioruptor, enrichment of methyl-CpG containing DNA was performed with the Methylminer DNA Enrichment Kit (Life Technologies) according to the manufacturer's protocol with an elution buffer salt concentration of 600 mM.
Library preparation was undertaken using 5 ng of methyl-enriched DNA using the NEBNext DNA Library Preparation Kit for Illumina (New England Biolabs). Library DNA was quantified with MultiNA capillary electrophoresis instrument with DNA-500 kit. Cluster generation was done using library DNA at a concentration of 10 pM on Cluster Station (Illumina). Sequencing by synthesis was performed on Genome Analyzer IIx (Illumina) for 36 cycles using RTAv1.8 base calling software.

tag: ethnicity

value: Singaporean with Chinese ethnicity

tag: gender

value: Female

tag: age (yrs)

tag: hypertensive status

value: Normotensive

tag: plasma homocysteine (μmol/l)

value: Peripheral blood mononuclear cells


title: PAT125

source_name: ischemic stroke patient_male

value: Male

value: Hypertensive


title: PAT135


title: PAT137


title: PAT128


title: KDM2Bfl/fl_RNAseq_untreated_rep3

tag: cell line


title: PAT076


title: PAT147

description:
processed data file: StrokeMethylome_Ziemann_etal2014_CountMatrix_1MbpIntervals.txt
processed data file:  StrokeMethylome_Ziemann_etal2014_CountMatrix_1kbpIntervals.txt


title: KDM2Bfl/fl_KDM2B_treated_rep3


title: 131216_DRM2_WT_5

first: Christopher

middle: Joel

last: Hale

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description: genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

data_processing:
BS-seq reads for 130615 libraries were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. BS-seq reads for 131216 libraries were mapped with BSmap (Xi Y, Li W, 2009 BMC Bioinformatics) using identical parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).
Supplementary_files_format_and_content: Concatenated per-chromosome plain text UCSC Genome Browser wiggle files with UNIX-style line endings, compressed with GNU gzip, files are variable step with each value represented the %methylation of a single cytosine of a CG at a given position. Note: Positive values denote cytosines on a positive strand, negative values denote a cytosine on the negative strand.

source_name: 2-week old leaf_DRM2_WT_5

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013

value: drm2 mutant carrying a DRM2 wildtype transgene

tag: ecotype

value: Columbia

value: leaf

tag: age

value: 2-week old


title: PAT058


title: 131216_DRM2_WT_6

source_name: 2-week old leaf_DRM2_WT_6


title: 131216_DRM2_WT_1

source_name: 2-week old leaf_DRM2_WT_1


title: Bol-Stem

city: Shenzhen

first: Zhangyan

last: Wu

address: Yantian district, Shenzhen

institute: Beijing Genomics Institute

description: Sequenced reads were generated from stem tissue of 7-week old Brassica oleracea plant

data_processing:
Used Brassica oleracea genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat-1.0.13 with default parameters except -N 1, -r 20, -p 4, --coverage-search, --microexon-search
Supplementary_files_format_and_content: bedgraph and counts

organism: Brassica oleracea

source_name: Stem tissues of Brassica oleracea

growth_protocol: The flower, leaf, root, silique, stem, bud from the Brassica oleracea plants, which were grown in the greenhouse under condition of temperature,15-25℃ and sunlight. The tissue of callus were generated in the illumination box under the 25℃ using tissue culture. All the tissues were generated by Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,China in 2010.

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

value: stem

value: 7-week old


title: 131216_DRM2_M5_4

source_name: 2-week old leaf_DRM2_M5_4

value: drm2 mutant carrying a DRM2 transgene with 5 mutations in the putative dimerization domain


title: Bol-Bud

description: Sequenced reads were generated from bud tissue of the same size (length 0.8cm)

source_name: Bud tissues of Brassica oleracea

value: bud

value: same size (length 0.8cm)


title: Bol-Silique

description: Sequenced reads were generated from Silique tissue of 15-day after pollination

source_name: Silique tissues of Brassica oleracea

value: silique

value: 15-day after pollination


title: Bol-Flower

description: Sequenced reads were generated from flower tissue, blooming in the same day without floral shoot

source_name: Flower tissues of Brassica oleracea

value: flower

value: blooming in the same day


title: Bol-Callus

description: Sequenced reads were generated from callus tissue using tissue culture

source_name: Callus tissues of Brassica oleracea

value: callus


title: 130615_DRM2_WT

source_name: 2-week old leaf_DRM2_WT


title: Bol-Root

description: Sequenced reads were generated from root tissue of 7-week old Brassica oleracea plant

source_name: Root tissues of Brassica oleracea

value: root


title: 131216_DRM2_M5_10

source_name: 2-week old leaf_DRM2_M5_10


title: Bol-Leaf

description: Sequenced reads were generated from leaf tissue of 7-week old Brassica oleracea plant

source_name: Leaf tissues of Brassica oleracea


title: 130615_DRM2_uba

source_name: 2-week old leaf_DRM2_uba

value: drm2 mutant carrying a DRM2 transgene with a three point mutations within UBA domains


title: 130615_Col

source_name: 2-week old leaf_Wildtype_Columbia

value: Wild type


title: 130615_DRM2_cat

source_name: 2-week old leaf_DRM2_cat

value: drm2 mutant carrying a DRM2 transgene with a catalytic site mutation


title: IM012_13_IFN_3_mRNA

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

description: mRNA

data_processing:
Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2.
Zipped using gzip.
For mRNA-seq, reads were mapped against the mm9 transcriptome with SOAPaligner/soap2.
For Total RNA-seq, reads were mapped against mm9 using STAR.
HTSeq was used to generate gene counts.
Genome_build: MGSCv37 (mm9), Ensembl release 67.
Supplementary_files_format_and_content: Tab-delimited text file includes: [1] scaled gene counts for each sample of mRNA-seq and [2] scaled gene counts for each sample of Total RNA-seq.

source_name: lung, IFN, 12 hr

growth_protocol: Whole animal.

extract_protocol:
Qiagen miRNeasy Isolation Kit from Trizol homogenates.
Illumina TruSeq mRNA.

treatment_protocol: Intranasally dosed (10,000 U of recombinant interferon) or mock dosed (PBS).

tag: strain/background

value: 6 weeks

value: lung

tag: treatment

value: interferon (IFN)

tag: time post treatment

value: 12 hr


title: IM012_11_IFN_1_mRNA

description: mRNA

tag: tissue


title: IM012_14_IFN_4_mRNA

description: mRNA


title: IM012_11_IFN_1_WT

description: total RNA


title: IM012_13_IFN_3_WT

description: total RNA


title: IM012_8_PBS_1_WT

description: total RNA

source_name: lung, PBS, 12 hr

value: PBS


title: IM012_9_PBS_2_WT

description: total RNA


title: IM012_10_PBS_3_mRNA

description: mRNA


title: IM012_9_PBS_2_mRNA

description: mRNA


title: IM012_8_PBS_1_mRNA

description: mRNA


title: S1_RNA-Seq

first: Rekin's

last: Janky

address: Herestraat 49 box 602

department: Department of Human Genetics

institute: KU Leuven

description: Stimulated RNA-seq replicate 1 (S1)

data_processing:
An initial filtering was performed to remove reads containing residual adapter sequences (fastx_clipper, version 0.013, option –M15).
Next, a quality report was generated using the FastQC software (version 0.9) checking the reads for PHRED quality (> 20), read length (> 20) and primer- contamination.
Filtered reads were mapped to the human reference genome hg19 (UCSC) using TopHat (v1.3.3) with its default settings.
Gene expression was measured with HT-Seq (–str=no parameter, version 0.5.3p3) using the human RefSeq annotation, release 42.
DESeq was used to calculate differential expression between Nutlin3a-stimulated and non-stimulated samples. Only genes containing more then 1 read per million in at least two samples were measured. A final list of differentially expressed genes was obtained using cutoff values for both the adjusted p-value (< 0.05) and the log2 fold change (|log2FC| > 1).
Genome_build: hg19
Supplementary_files_format_and_content: raw abundance counts from htseq-counts compiled in a text file and normalized counts

source_name: MCF7_Nutlin stimulated

growth_protocol: Wild-Type (WT) MCF-7 cells were plated onto 24-well plates (60000 cells/well) in RPMI medium (+ L-glutamaat, Gibco) supplemented with 10% fetal bovine serum, 0.4mM sodium pyruvate (Gibco), 100μm/ml penicillin/streptomycin (Invitrogen), 1x non-essential aminoacids (Gibco) and 10μg/ml Insulin (Sigma).

extract_protocol:
After 24h, cells were washed in PBS (Gibco) and prepared for RNA extraction according to the RNeasy protocol (Qiagen), yielding around 2 μg of total RNA per sample.
Illumina TruSeqTM RNA Sample preparation guide using the appropriate indices

treatment_protocol: The next day, cells were either stimulated with 5μM Nutlin-3a (in case of p53-WT cells) or left untreated.

tag: cell type

value: breast cancer cells

tag: stimulated with

value: 5μM Nutlin-3a for 24hr


title: 131216_DRM2_M5_1

source_name: 2-week old leaf_DRM2_M5_1

tag: genotype

value: drm2 mutant carrying a DRM2 transgene with 5 mutations in the putative dimerization domain

value: Columbia

value: leaf

value: 2-week old


title: NS1_RNA-Seq

description: Non stimulated RNA-seq replicate 1 (NS1)

value: none (unstimluated (NS) control)


title: S_input_ChIP-Seq

description: ChIP-seq with input DNA on Stimulated cells

data_processing:
An initial filtering was performed to remove reads containing residual adapter sequences (fastx_clipper, version 0.013, option –M15).
Next, a quality report was generated using the FastQC software (version 0.9) checking the reads for PHRED quality (> 20), read length (> 20) and primer- contamination.
Filtered reads were mapped to the human reference genome hg19 (UCSC) using bowtie (v2.0.0-beta3) with the addition of parameter –local, allowing for further soft clipping of the reads.
An extra filtering on the mapping score ensured that only reads with a minimum score of 4 were kept for further analysis.
Peak calling was performed using MACS (version 1.4.2) with a threshold for p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: output bed files from MACS and merged nutlin stimulated wig file

source_name: MCF7_Nutlin stimulated_input

growth_protocol: p53-WT MCF-7 cells were seeded at a density of 5 million cells per 15 cm dish and grown ON at 37°C to a confluency of 80-90%.

extract_protocol:
ChIP samples were prepared following the Magna ChIP-seqTM preparation kit
5-10 ng of precipitated DNA was used to perform library preparation according to the Illumina TruSeqTM DNA Sample preparation guide. In brief, the immunoprecipitated DNA was end-repaired, A-tailed, and ligated to diluted sequencing adapters (dilution of 1/100). After PCR amplification with 15-18 cycles and gel size selection of 200–300bp fragments, the libraries were sequenced using the HiSeq 2000 (Illumina).

treatment_protocol: Cells were either stimulated with 5μM Nutlin-3a (in case of p53-WT cells) for 24h or left untreated.


title: S2_RNA-Seq

description: Stimulated RNA-seq replicate 2 (S2)


title: NS2_RNA-Seq

description: Non stimulated RNA-seq replicate 2 (NS2)


title: S_p53_ChIP-Seq

description: ChIP-seq with p53 antibody on Stimulated cells, replicate 1

data_processing:
An initial filtering was performed to remove reads containing residual adapter sequences (fastx_clipper, version 0.013, option –M15).
Next, a quality report was generated using the FastQC software (version 0.9) checking the reads for PHRED quality (> 20), read length (> 20) and primer- contamination.
Filtered reads were mapped to the human reference genome hg19 (UCSC) using bowtie (v2.0.0-beta3) with the addition of parameter –local, allowing for further soft clipping of the reads.
An extra filtering on the mapping score ensured that only reads with a minimum score of 4 were kept for further analysis.
Peak calling was performed using MACS (version 1.4.2) with default threshold and a threshold for p-value < 0.05 (to run GSEA Preranked).
Genome_build: hg19
Supplementary_files_format_and_content: Nutlin stimulated wig

source_name: MCF7_Nutlin stimulated_ChIP

value: p53 Antibody (DO-1)

tag: chip antibody vendor

value: santa cruz biotechnology, inc.

tag: chip antibody cat. #

tag: chip antibody lot #


title: second_trimester_euploid_male1 [RNA-Seq]

city: Boston

first: Lillian

last: Zwemer

state: MA

address: 800 Washington St, Box 394

department: Mother Infant Research Institute

institute: Tufts Medical Center

description: gene expression data from normal second trimester fetus

data_processing:
Basepair calls performed using CASAVA-1.8.2
Reads were aligned to the Hg19 UCSC genome using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.3.0e). The STAR reference genome was created with a specific library of splice junctions (Gencode version 15 from the Ensembl 70 March 2012 freeze) and the sdjbOverhang 49 option. The following custom settings were used in STAR alignment scripts: sjdbScore, outFilterType BySSJout, outFilterIntronMotifs RemoveNoncanonicalUnannotated, outSAMstrandField intronMotif.  All other parameters were run according to default including multi-mapping of up to 10.
Cufflinks version 2.1.1 was used with the Hg19 goldenPath UCSC annotation GTF file (Feb 2009 assembly). All default Cufflinks parameters were employed, including multimapping.
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab delimited text files of Cufflinks FPKM tracking File output including FPKM values

source_name: cell-free RNA from second trimester amniotic fluid supernatant

extract_protocol:
RNA was extracted from 10 mL amniotic fluid supernatant (centrifugation at 350g, 4C, 10, min).All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation RNA-Seq System V2 and then purified with the MinElute Reaction Cleanup Kit.
Library preparation was undertaken on 500 ng cDNA according to standard practice with the alterations described: Fragmentation was not undertaken due to the already degraded and fragmented nature of cffRNA. In light of the small amount of starting material, a bead-based purification (AmPure XP Beads, Agencourt, Beckman Coulter, USA) was used in lieu of a gel-based size selection for the purpose of library clean up. Bioanalysis was performed to ensure the absence of primer-dimer peaks as well as determine the approximate insert size. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq 2000 following the manufacturer's protocols. One paired-end indexed library was sequenced per sample to a length of 50 nucleotides per mate.

tag: gender

value: male

tag: source


title: s41C_int_ret

status: Public on May 26 2014

city: Helsinki

first: Marco

last: Savarese

address: Topeliuksenkatu 20

department: Samfundet Folkhälsan i svenska Finland r.f.

country: Finland

institute: Folkhälsan Research Center

description:
For the Intron retention analysis, the read (single or pairs) that were fully mapped to the introns or exons of the U12 transcripts were taken into account.
u12_transcripts_Intron_retention.tsv

data_processing:
Mapping: Mapping of the sequence reads were done using SOLiD Bioscope V1.3
Extracting unique reads: PCR duplicates were removed.
Summarization: Reads that were mapped to introns or exons of transcripts with at least one U12 intron were counted. For the Intron retention analysis, the fragments that were fully mapped to the introns or exons of the transcripts were taken into account (see u12_transcripts_Intron_retention.tsv). Furthermore, reads mapped to the Intron-exon junctions (see u12_transcripts_Intron_exon_junction.tsv) of U12 transcripts and also intron retentions of the U2 introns from randomly picked transcripts that feature U2 type introns only (see u2Random_transcripts_Inron_retention.tsv) were estimated through separate analysis.
Normalization: FPKM values were calculated by normalizing the number of fragments to the length of the introns/exons and to the number of fragments that were mapped to the transcript in order to remove the bias of intron/exon length and transcript expression.
Differentiation analysis: Log-fold change of the FPKM values together with the edge-R Pvalues were calculated to estimate the significance of changes in intron retention across ctrl (i.e. sGN) and knock-downs (i.e. s41N and sD3N).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including annotatuion of Introns or exons of U12 transcripts,read counts and FPKM values for Nuclear (sGN) and Cytoplasmic ctrl (sGC) and samples in which the exosome was deactivated by knocking down Rrp41 (s41N for nuclear and s41C for cytoplasmic) and DIS3 (sD3N and sD3C) subunits.

source_name: Cytoplasm

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and antibiotics in humidified incubator with 5% CO2 with regular passaging.

extract_protocol:
Cells were trypsinized, washed once with cold PBS, resuspended in hypotonic buffer (10 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0,5 mM DTT, protease inhibitors) and incubated on ice 10 min. Then cells were spun down, resuspended in hypotonic buffer, and lysed with Kontes tight pestle (B) douncer. Lysis was monitored under the microsocpe with Trypan blue. Lysate was layered over 1 M sucrose in hypotonic buffer and spun 5000 rpm 30 min 4 °C, which pelleted the nuclei at the bottom of sucrose cushion. Nuclei were washed once with sucrose hypotonic buffer. Samples were sonicated 3 x 30 sec using Bioruptor sonicator, and cleared by 10 min 13 000 rpm centrifugation in an Eppendorf centrifuge.
Sequencing library was constructed from fractionation pools using SOLiD Total RNA-Seq Kit (Applied Biosystems). Briefly, library construction contained the following steps: ribosomal RNA removal, fragmentation using RNaseIII, reverse transcription, amplification (14 cycles), and size selection (70-150 bp).

treatment_protocol: 1.8E6 cells were seeded in T175 flasks 24 h prior to transfection. 750 pmol siRNA was transfected using Oligofectamine (Invitrogen) according to manufacturer's protocol.

value: HEp-2 cells

tag: analysis type

value: Intron retention

value: Rrp41 knockdown (Cytoplasm)


title: second_trimester_euploid_male2 [RNA-Seq]

value: second trimester amniotic fluid supernatant


title: second_trimester_euploid_female1 [RNA-Seq]

value: female


title: sD3C_int_ret

value: Dis3 knockdown (Cytoplasm)


title: second_trimester_euploid_male3 [RNA-Seq]


title: sGC_int_ret

value: Control (Cytoplasm)


title: sGN_int_ret

source_name: Nuclear

value: Control (Nuclear)


title: IM012_14_IFN_4_WT

description: total RNA

value: 6 weeks

value: lung

value: interferon (IFN)

value: 12 hr


title: sD3N_int_ret

value: Dis3 knockdown (Nuclear)


title: MucR1_ChIPseq

status: Public on May 25 2014

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

institute: University of Geneva

data_processing:
Base calling: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3, CASAVA-1.8.2
Alignment: Bowtie-0.12.9, samtools-0.1.18
Peak calling: SeqMonk software (Braham Bionformatics Institute)
Peak refinement and annotation: SeqMonK output were processed by Java and Perl programs (in house written, decribed in the paper) to refine the peaks annotation and eliminate background
ChIPseq comparisons: Peaks list after being proccessed were scanned for common target, then ratio of each peak abundance were computed and reported as the log2 fold variation
Genome_build: Caulobacter crescentus : NC_011916.1; Sinorhizobium fredii :  NC_012587.1,  NC_000914.2,  NC_012586.1
Supplementary_files_format_and_content: the xls files reporting peaks annotations and abundance were generated by Java and Perl programs (described in the paper) and consist of two sheet the ANNO and the NO-ANNO sheet. The ANNO probes sheets are organized in columns as follows:  column 1: gene name to which the peak is associated is reported in the reference genome used for the reads alignment  column 2 : probe start   column 3 : probe end  column 4 : COG categories to which the gene associated to the corresponding peak belongs to  column 5 : PubMed Identification number of the protein encoded by the gene associated to the peak  column 6 : Length of the protein  column 7 : The gene strand of the gene associated to the peak (0 plus strand, 1 reverse strand)  column 8 : Gene start  column 9 : Gene end  column10: Probe distance, the distance of the probe from ORF start  column 11 : It is reported here the abundance of reads per probe expressed as the percentage of total reads number  column 12: N possible association, it is reported here the number of possible association that the probe associated to the gene reported in the first column can have (i.e.: two genes that are divergent but shares the same peak)  column 13 : Name of the gene that can be associated to this probe and the distance of the probe from the gene start)  The NO-ANNO probes files contain all those probes that made the cut off, (are recognized as peaks) but they cannot be associated to any genes. File organization is the same as before except that only information about the probe location and reads abundance are reported.

organism: Caulobacter vibrioides

source_name: Mid-log phase cells

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or M2G, while Sinorhizobium fredii NGR234 was grown at 30°C in TY (Triptone yeast extract).

extract_protocol:
Mid-log phase cells were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1%  formaldehyde at room temperature for 10 min and on ice for 30 min thereafter, washed  thrice in phosphate buffered saline (PBS) and lysed in a Ready-Lyse lysozyme solution  (Epicentre, Madison, WI) according to the manufacturer`s instructions. Lysates were  sonicated (Sonifier Cell Disruptor B-30; Branson Sonic Power. Co., Danbury, CT) on ice  using 10 bursts of 20 sec at output level 4.5 to shear DNA fragments to an average length  of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were  normalized by protein content, diluted to 1 mL using ChIP buffer (0.01% SDS, 1.1%  Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease  inhibitors (Roche) and pre-cleared with 80 μL of protein-A agarose (Roche, Switzerland)  and 100 uμg BSA. Ten % of the supernatant was removed and used as total chromatin  input DNA as described before (Radhakrishnan et al., 2008).  Two microliters of polyclonal antibodies to CtrA (Domian et al., 1997), SciP (Gora et al.,  2010; Tan et al., 2010) (note that for ChIP experiments reported in Table S6 we used  antibodies that we raised against His6-SUMO-SciP), FlbD (Davis and Viollier, 2011),  RpoC (Neoclone, Madison, WI), MucR1 or MucR2 were added to the remains of the  supernatant, incubated overnight at 4°C with 80 μL of protein-A agarose beads pre  saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2  mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1%  Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) and LiCl buffer  (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH  8.1) and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The  protein•DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS,  0.1 M NaHCO3), supplemented with NaCl to a final concentration of 300 mM and  incubated overnight at 65°C to reverse the crosslinks. The samples were treated with 2 μg  of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA  extracted using phenol:chloroform:453 isoamyl alcohol (25:24:1), ethanol-precipitated  using 20 ug glycogen as carrier and re-suspended in 100uL of water. For deep  sequencing (ChIP-seq) total chromatin input DNA was not saved.
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland

tag: strain

value: wild type

tag: antibody


title: FlbD_ChIPseq


title: CtrA_∆pleC_ChIPseq

value: ∆pleC


title: SciP_∆mucR12_ChIPseq

value: ∆mucR1 ∆mucR2


title: IM012_10_PBS_3_WT

description: total RNA

value: PBS


title: SciP_ChIPseq


title: Small-size group

city: WuHan

first: Yi

middle: Shao

last: Kui

state: HuBei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricultural University

description: small RNA-Seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads with poly A, reads shorter than 18nt and masked for low-quality sequence.The *clean files consist of reads ID, reads count and sequences.
Reads were mapped to Danio rerio whole genome using SOAP with parameters soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap. The *match_genome files shows small RNA sequences perfectly matching reference genome sequence  Format:1.small RNA sequence Id 2.chromosome 3.start position 4.end position 5.strand  6.small RNA sequence 7.count of this small RNA sequence
Align small RNA tags to the miRNA precursor/mature miRNA of all plants/animals in miRBase19 using -tag2miRNA. The sequence and abundance of these reads were counted. These txt file shows read ID,reads count and sequence.
Genome_build: Danio rerio Zv9
Supplementary_files_format_and_content: tab-delimited text files and fasta files;

organism: Megalobrama amblycephala

source_name: brain, pituitary, liver and muscle

extract_protocol:
Tissue samples including brain, pituitary, liver and muscle from the big-size and small-size groups were collected within the same population, respectively. Total RNA was isolated from each sample using Trizol reagent (TaKaRa, Dalian, China) according to the manufacturer’s protocol.
Small RNA libraries were constructed for brain, pituitary, liver and muscle tissues from the big-size and small-size groups. Briefly, Small small RNAs of 16–30 nt in length were first isolated from the total RNA by size fractionation, and these small RNAs were ligated to with 5´-RNA and 3´-RNA adapters and then reverse transcription PCR using the RT primer was used to create cDNA.

tag: growth performance

value: selective population; small size group

tag: developmental age

value: 3 month-18 month old

value: brain, pituitary, liver and muscle


title: Big-size group

description: small RNA-Seq

value: selective population; Big-size group


title: s41N_int_ret

tag: cell line

value: HEp-2 cells

value: Intron retention

value: Rrp41 knockdown (Nuclear)


title: CtrA_ChIPseq


title: second_trimester_euploid_female2 [RNA-Seq]

value: female

value: second trimester amniotic fluid supernatant


title: sfSciP_ChIPseq

organism: Sinorhizobium fredii


title: sfMucR2_ChIPseq


title: NS_input_ChIP-Seq

description: ChIP-seq with input DNA on Non stimulated cells

value: breast cancer cells

value: none (unstimluated (NS) control)

tag: chip antibody


title: human ES cell line UCLA6 (ucla6)

status: Public on May 24 2014

first: Julien

last: Duc

address: Station 19 CH-1015 Lausanne

description:
ucla6
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt

data_processing:
Illumina pipeline Casava 1.82
Sequenced reads were aligned to human hg19 using bowtie 0.12.7 with parameters -n 3 -l 79 --best --strata -a -M 1 and to the human repeats consensus sequence RepBase v17.09 using bowtie with parameters  -n 3 -l 79 --best --strata -a -M 1
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited RPKM values for each samples (columns) and each gene/Repeat family of interest (rows). Files separated if mapped on repbased or on refseq and based on their origin.

source_name: Human CD34+ cells from cord blood

growth_protocol: mTesR medium

extract_protocol:
Trizol RNA extraction
Illumina protocols TruSeq RNA

value: ES cell


title: sfCtrA_ChIPseq


title: human ES cell line UCLA5 (ucla5)

description:
ucla5
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt


title: human ES cell line UCLA4 (ucla4)

description:
ucla4
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt


title: sfMucR1_ChIPseq


title: human ES cell line UCLA2 (ucla2)

description:
ucla2
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt


title: human ES cell line UCLA1 (ucla1)

description:
ucla1
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt


title: human ES cell line H1 (es_nc)

description:
Replicate of es sample
es_nc
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: human ES cell line H1 (ucla_h1)

description:
ucla_h1
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt


title: human ES cell line H1 (es)

description:
es
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: iPS clone 45 (ips45)

description:
ips45
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: iPS clone


title: human ES cell line UCLA3 (ucla3)

description:
ucla3
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt


title: iPS clone 43 (ips43)

description:
ips43
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: MucR2_ChIPseq

value: wild type


title: iPS clone 14 (ips14)

description:
ips14
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: iPS clone 2 (ips2)

description:
ips2
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: iPS clone 9 (ips9)

description:
ips9
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: day 19 of reprogramming (d19)

description:
d19
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: reprogramming CD34+

tag: time

value: day 19


title: day 21 of reprogramming (d21)

description:
d21
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 21


title: day 14 of reprogramming (d14)

description:
d14
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 14


title: day 12 of reprogramming (d12)

description:
d12
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 12


title: day 16 of reprogramming (d16)

description:
d16
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 16


title: day 8 of reprogramming (d8)

description:
d8
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 8


title: day 6 of reprogramming (d6)

description:
d6
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 6


title: day 10 of reprogramming (d10)

description:
d10
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 10


title: day 4 of reprogramming (d4)

description:
d4
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: day 4


title: parental human CD34+ (d10_nt)

description:
CD34 no reprogramming
d10_nt
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt

value: parental CD34+


title: parental human CD34+ (d8_nt)

description:
CD34 no reprogramming
d8_nt
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: parental human CD34+ (d4_nt)

description:
CD34 no reprogramming
d4_nt
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: Soybean Early Maturation Seed Coat Palisade- biological replicate 4

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

description: Compartments collected from seeds ranging 6.0-7.0mm in length

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: Glycine max V1.1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.

organism: Glycine max

growth_protocol: Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days.  Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots.  Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg  C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with one microgram of double-stranded cDNA using Illumina TruSeq DNA Sample prep kit (Hayward, CA), according to manufacturer's instructions except for the PCR enrichment step where Agilent Pfu Turbo Cx hotstart DNA polymerase was used for 15 cycles of amplification.  Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: seed compartments/tissue


title: Soybean Early Maturation Seed Coat Parenchyma- biological replicate 2


title: Soybean Early Maturation Cotyledon Adaxial Parenchyma- biological replicate 4


title: Soybean Early Maturation Cotyledon Vasculature- biological replicate 3


title: Soybean Early Maturation Endosperm- biological replicate 2

source_name: Soybean Early Maturation Endosperm

value: Soybean Early Maturation Endosperm


title: Soybean Early Maturation Seed Coat Parenchyma- biological replicate 3


title: Soybean Early Maturation Endosperm- biological replicate 1


title: human ES cell line H9 (ucla_h9)

institute: EPFL

description:
ucla_h9
processed data file: all_hes_UCLA_rpkm.txt
processed data file: all_hes_UCLA_repbase.txt

tag: cell type


title: iPS clone 6 (ips6)

description:
ips6
processed data file: all_hes_rpkm.txt
processed data file: all_hes_repbase_rpkm.txt


title: Soybean Early Maturation Cotyledon Adaxial Parenchyma- biological replicate 1


title: Soybean Early Maturation Cotyledon Adaxial Parenchyma- biological replicate 3


title: Soybean Early Maturation Cotyledon Adaxial Epidermis- biological replicate 2


title: Soybean Early Maturation Cotyledon Adaxial Epidermis- biological replicate 1