title: RNA-seq: Adar2


title: RNA-seq: Adar8

status: Public on Jan 01 2016

type: SRA

city: Bethesda

first: Allissa

middle: A

last: Dillman

state: MD

address: Center for Cancer Research National Cancer Institute Building 41, Room B626

department: Center for Cancer Research

country: USA

institute: NCI

library_source: transcriptomic

data_processing:
Tophat (v2.0.6)/Bowtie (2.02.0)
HT-SEQ
DESeq
DEXSeq
Samtools mpileup (samtools-01.19.0)
Genome_build: mm9
Supplementary_files_format_and_content: CSV DESEQ and DEXSEQ output, and A-to-I edit sites

molecule: total RNA

organism: Mus musculus

source_name: Frontal Cortex

extract_protocol:
Trizol
TruSeq stranded total RNA sample preparation kit, ribo-Zero gold rRNA removal beads

tag: strain

tag: genotype

tag: gender

value: male


title: D2 MN clone #2

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

data_processing:
Sequenced reads were mapped to mm9 genome using TopHat. FPKM values were calculated using the Cufflinks package.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.

molecule: polyA RNA

source_name: Day 2 mouse motor neuron cultures (D2 MN)

growth_protocol: HB9 mESCs were grown in aggregate culture in the presence of RA and SAG.

extract_protocol:
Total RNA was collected with the Trizol reagent. Poly-A RNA was selected for using oligo-dT beads.
Libraries were constructed with the Illumina TruSeq stranded kit.
The libraries were subjected to 50bp single-end sequencing (Illumina HiSeq2000).

treatment_protocol: I6 +/- clones were treated with transiently transfected with Cas9 and guide RNA sequences to generate heterozygous deletions at the Pbx1 intron 6 locus.

tag: cell type

value: HB9-GFP mESC

tag: genotype/variation

value: Wildtype Control

tag: protocol

value: mESC clones were harvested after Day 2 of differentiation in MN media


title: PrdmRescue_F10R_HA_ChIPseq

city: Stanford

first: Natalie

last: Nady

address: 265 Campus Dr.

department: Chemical and Systems Biology

institute: Stanford

library_source: genomic

data_processing:
Reads aligned to mm9 using default settings with Bowtie2.2.4
Wig files were generated with QuEST2.4
RNA-seq were aligned to mm9 and quantified against mouse ENSEMBL 78 (GRCm38) gene models using htseq-count. Variance-stabilizing transformation (VST) was applied across samples for processed data.
Genome_build: Alignments done using mm9 as reference
Supplementary_files_format_and_content: wig and tab delimited text

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: For maintenance all mouse ESC lines were grown in so-called “2i+LIF” medium that is serum  free N2B27-based medium supplemented with MEK inhibitor PD0325901 (0.8 μM) and GSK3β  inhibitor CHIR99021 (3.3 μM) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine  (Sigma) and 5 μg/ml laminine (BD) (Hayashi and Saitou, 2013; Hayashi et al., 2011). For ChIP-seq,  RNA-seq and immunoprecipitation experiments Stella:GFP mESC lines and FH-Prdm14 derivatives  were cultured for 5 days in feeder-free conditions in DMEM-high glucose medium (DMEM/high  glucose; HyClone) containing 15% (v/v) FBS, 1 mM glutamine, penicillin/streptomycin, 0.1mM  nonessential amino acids, 0.1 mM 2-mercaptoethanol and supplemented with LIF (serum+LIF  conditions).

extract_protocol:
ChIPs were performed using approximately 1-2 x 10^7 mESCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol.
Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).

value: Prdm14-/- + FLAG-HA-Prdm14

tag: antibody


title: MtgrRescue_A3R_RNAseq

value: Mtgr1-/- + FLAG-HA-Mtgr1


title: RNA-seq: Adar5

value: Adar2+/+ Gria2R/R


title: Mtgr1null_C1_Mtgr1_ChIPseq


title: PrdmRescue_G6R_Mtgr1_ChIPseq


title: Niche cells, rep3

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
PolyA RNA
The LPA1-GFP mice on a FVB/N-Swiss Webster background (STOCK Tg(Lpar1-EGFP)GX193Gsat/Mmucd) were rederived for our colony via IVF into C57BL/6.
Processed data file: Lpar_processed_counts.txt

data_processing:
Sequenced reads were mapped to the mm10 whole genome using RNAStar version 2.4.0.
Fragments/Reads Per Kilobase of Expressed exons per Megabase of library size (FPKEM) were calculated using the FPKEM algorithm (https://pypi.python.org/pypi/fpkem).
Log-normalised (log2(fpkem +1)).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file contains log2-normalised FPKEM values. Samples in columns, genes in rows.

source_name: Dentate gyrus cells

extract_protocol:
Cells were isolated from fresh dentate gyrus tissue with an Aria III FACS machine using the markers EGFR (Egfr), LPA1 (Lpar1) and Prominin1 (Prom1). RNA was extracted using the Qiagen RNeasy micro kit. RNA from 1000 cells was amplified using the Advantage 2 DNA Polymerase.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 8 weeks

tag: tissue

value: dentate gyrus

value: niche cells

tag: markers


title: Niche cells, rep4


title: Prdm14null_F10_Mtgr1_ChIPseq


title: Mtgr1null_C3_Mtgr1_ChIPseq


title: Progenitor cells, rep2

source_name: Neural progenitor cells

value: neural progenitor cells

value: LPA1-GFP+EGFR+Prominin-1-, LPA1-GFP+EGF-Prominin-1+ and LPA1-GFP+EGFR-Prominin-1-


title: wt_Mtgr1_ChIPseq

value: wild type


title: Prdm14null_G6_Mtgr1_ChIPseq


title: Niche cells, rep2


title: Progenitor cells, rep3


title: Stem cells, rep4

source_name: Neural stem cells

value: neural stem cells


title: Stem cells, rep3


title: PrdmRescue_F10R_Mtgr1_ChIPseq


title: KO3

city: Chicago

first: Brian

last: Layden

address: 303 E Chicago

institute: Northwestern

data_processing:
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  FPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Pancreatic islets

extract_protocol:
Total cellular RNA was extracted from isolated islets that were selected from pooled islet isolations from two pancreata using an RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic islets

value: 10-14 weeks


title: Stem cells, rep2


title: Stem cells, rep1


title: KO2


title: WT2

value: wildtype


title: WT1


title: WT3


title: Progenitor cells, rep1


title: KO1


title: Niche cells, rep1


title: DKO recipient 2

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

description: DKO Wt exosome recipient BMDCs

data_processing:
Reads were aligned to mm10 genome plus extended splice junctions using novoalign (2.08.03). Novoalign was run with adapter sequence trimming on (-a), soft-clipping off (-o FullNW), large gap penalites (-x 60, -g 60), 18bp read minimum (-l) and a maximum alignment score of 90 (-t).
Splice junction alignments were converted back to genomic space using the USeq (8.8.1) SamTranscriptomeParser application.
Reads that aligned to mir155 or mir146a were extracted for further analysis. A read was considered aligned to the miRNA if the start of the aligned read matches the start of the mature miRNA sequence.
The sequence of each aligned read was compared to the reference sequence.  If a mismatch is found and the remainder of the aligned read is made up of the nucleotide at the mismatch, the read is classified as a nontemplated nucleotide addition (NTA).  If the first encountered mismatch is not the start of a NTA, the remainder of the aligned read is scanned for additional mismatches that could lead to NTAs.  Reads are classified as NTAs if the mismatch occurs at the last position in the aligned read.
If the aligned read doesn't contain a NTA, but does contain at least one mismatch, the read is classified as an Isoform.
Aligned reads with no mismatches are classified as Canonical.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files that contain the percentage of each read class (Canonical, Isoform, NTA_A, NTA_T, NTA_C, NTA_G) for each sample

source_name: BMDC + Wt exosomes

growth_protocol: Complete RPMI supplemented with GM-CSF differentiated for 7 days

extract_protocol:
miRNeasy
Illumina TrueSeq Small RNA Sample Prep

value: miR-155 and miR-146a double knockout (DKO)

value: bone marrow-derived dendritic cells

tag: exosome added

value: Yes


title: DKO recipient 1

description: DKO Wt exosome recipient BMDCs


title: Wt Donor 1

description: Wt BMDC donor cells

source_name: BMDC

value: Wt

value: No


title: DKO recipient 3

description: DKO Wt exosome recipient BMDCs


title: Wt Donor 3

description: Wt BMDC donor cells


title: WT rep1

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.1
Reads were counted against gene model using htseq-count v0.5.4p3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw counts

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted, and cells FACS-sorted then RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Wt Donor 2

description: Wt BMDC donor cells


title: NHD13 mutant rep2

value: NHD13 mutant


title: NHD13 mutant rep3


title: WT rep3


title: 0_M

city: Seoul

first: Hyunsoo

last: Kim

address: 103 Daehakro, Jongro-gu

country: South Korea

institute: Seoul  National University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads for each sample were aligned to the mouse genome (NCBI build 37/mm9) using TopHat v2.0.7 with default settings.
Cufflinks v2.0.2 was used to quantify FPKM (Fragments Per Kilobase of exon per Megabase of library size) values of genes defined from RefSeq transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: mouse embryonic stem cells (E14)_normal

extract_protocol:
Total RNAs from E14 was extracted with Qiazol (QIAGEN). The mRNA in total RNA converted into a library of template molecules suitable for subsequent cluster generation using the reagents provided in the Illumina ® TruSeq™ RNA Sample Preparation Kit v2.
The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using a Caliper Labchip GX (Caliper Life Sciences,USA).

tag: developmental stage

value: normal E14 cell

tag: lif(leukemia inhibitory factor) status

value: cultured with LIF


title: 24_M

value: cultured without LIF 24 hours and added LIF


title: WT rep2


title: PG_MEF__Aff3_shRNA-rep2

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

description:
RNAseq after Aff3-RNAi
Ribosomal RNA-depleted total RNA

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
ChIP-seq reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
RNA-seq and Nascent RNA-seq alignments were done using TopHat v2.0.9 with bowtie1 v0.12.9, using -g 1 option and allowing up to two mismatches.
[ChIP-seq] Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
[nascent-Seq and RNA-seq] Reads were aligned using Ensembl 67 GTF mouse annotations using TopHat v2.0.9 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

source_name: MEF cell culture

growth_protocol: The mouse ES cell lines used in the current study were grown on irradiated primary mouse embryonic fibroblast (MEF) feeder layers in 0.1% gelatin-coated tissue culture vessel. Mouse ES cells were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 15% ES-certified fetal bovine serum (Hyclone), recombinant LIF (Millipore), 2 mM L-glutamine, 0.1 mM nonessential amino acids and 0.1 mM β-mercaptoethanol. For experimental analyses, ES cells were grown for one passage without MEF feeder cells in tissue culture vessel for 30 minutes. The uniparental MEF cell lines were cultured in DMEM supplemented with 10% FBS (Sigma).

extract_protocol:
For ChIP-Seq, 5×107 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's kit or KAPA kit. For RNA-seq, cells were infected with lentivirus carrying either Non-targeting shRNA, Aff3 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, cells were selected with 2 ug/ml of puromycin for additional 48 hours and then ES were grown one passage off feeders for 30 min before harvesting. Total RNA was isolated with the RNeasy (74106 Qiagen) kit, treated with DNase I (M0303L NEB), and re-purified with RNeasy. For total RNA-seq analyses, total RNA was depleted of ribosomal RNA using Ribozero (Illumina) before library preparation performing Tru-seq sample prep (Illumina). For Nascent RNA-seq, about 1×108 fresh ES cells were washed twice in ice-cold PBS. The cells were then resuspended in Buffer A (10 mM HEPES, pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.5 mM DTT and proteinase inhibitors (Roche)) and incubated on ice for 15 min. Cell suspension was transferred to a pre-cold Dounce tissue grinder and homogenized 10 times by using a tight pestle on ice. After centrifugation the pellet containing enriched nuclei was washed twice in S1 buffer (0.25 M Sucrose, 10 mM MgCl2, 10 mM HEPES, pH 7.9, 1 mM DTT and proteinase inhibitors). To obtain the chromatin pellet, the nuclei pellet was then washed in ice-cold NUN buffer (20mM HEPES pH7.9, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP-40, 1 mM DTT, 20U/ml RNase Inhibitor (Ambion), and proteinase inhibitors) for 5 times. Chromatin bound RNA was isolated with RNeasy kit. The RNA was poly-A depleted by using Oligo(dT) magnetic beads (Invitrogen) and treated RNase free DNase I, and re-purified with the RNeasy column. 500 ng RNA was used for ribosomal RNA depletion with Ribo-zero Gold (Epicentre) and library preparation was performed with TruSeq Stranded Total RNA-seq Sample prep kit.
ChIP-seq, total RNA-seq and nascent RNA-seq libraries were prepared for sequencing using standard Illumina or KAPA protocols

value: PG MEF

value: mouse embryonic fibroblast

tag: shRNA


title: PG_MEF__Aff3_shRNA-rep1


title: PG_MEF_NonT_shRNA-rep2

description:
RNAseq after non-targeting-RNAi
Ribosomal RNA-depleted total RNA

value: non-targeting


title: 24_HP

source_name: mouse embryonic stem cells (E14)_Hk2/Pkm2 overexpression

value: Hk2 & Pkm2 overexpressed E14 cell


title: AG_MEF__Aff3_shRNA-rep2

value: AG MEF


title: AG_MEF__Aff3_shRNA-rep1


title: AG_MEF_NonT_shRNA-rep2


title: PG_MEF_NonT_shRNA-rep1


title: AG_MEF_NonT_shRNA-rep1


title: V6.5_Aff3_shRNA-rep2

source_name: ES cell culture

value: mouse embryonic stem cell


title: V6.5_Aff3_shRNA-rep1


title: V6.5_NonT_shRNA-rep2


title: Progenitor cells, rep4

value: 8 weeks

value: dentate gyrus

value: neural progenitor cells

value: LPA1-GFP+EGFR+Prominin-1-, LPA1-GFP+EGF-Prominin-1+ and LPA1-GFP+EGFR-Prominin-1-


title: V6.5_Aff3_shRNA-rep1 (nascent RNA)

description:
Nascent RNAseq after Aff3-RNAi
Ribosomal RNA-depleted nascent RNA


title: NHD13 mutant rep1


title: V6.5_NonT_shRNA-rep1


title: D40_HP

value: cultured without LIF 40 days


title: V6.5_Aff3_shRNA-rep2 (nascent RNA)


title: V6.5_NonT_shRNA-rep2 (nascent RNA)

description:
Nascent RNAseq after non-targeting-RNAi
Ribosomal RNA-depleted nascent RNA


title: V6.5_NonT_shRNA-rep1 (nascent RNA)


title: PG_MEF-WCE-rep2

description: whole cell extraction


title: PG_MEF-WCE-rep1

description: whole cell extraction


title: 0_HP


title: Zfp57_KO_WCE

description: whole cell extraction


title: TC1-WCE

description: whole cell extraction


title: KH2-WCE

description: whole cell extraction


title: v6.5-WCE-rep1

description: whole cell extraction


title: Pol_II_in_v6.5_NonT-shRNA

description: Chromatin IP of Pol II

value: Pol II (Santa Cruz N20)


title: Pol_II_in_v6.5_Aff3-shRNA

description: Chromatin IP of Pol II


title: H2K27ac_in_Zfp57_KO-rep1

description: Chromatin IP of H3K27ac

value: H3K27ac (Abcam Ab4729)


title: H2K27ac_in_Zfp57_KO-rep2

description: Chromatin IP of H3K27ac


title: H3K27ac_in_v6.5_Aff3-shRNA-rep2

description: Chromatin IP of H3K27ac


title: H2K27ac_in_Zfp57_WT-rep2

description: Chromatin IP of H3K27ac


title: H3K27ac_in_v6.5_NonT-shRNA-rep1

description: Chromatin IP of H3K27ac


title: H3K27ac_in_v6.5_NonT-shRNA-rep2

description: Chromatin IP of H3K27ac


title: AG_MEF-WCE-rep2

description: whole cell extraction


title: H3K9me3_in_PG_MEF_NonT_shRNA

description: Chromatin IP of H3K9me3

value: H3K9me3 (Abcam Ab8898)


title: H3K9me3_in_PG_MEF_Aff3_shRNA-1

description: Chromatin IP of H3K9me3


title: H3K9me3_in_AG_MEF_Aff3_shRNA-2

description: Chromatin IP of H3K9me3


title: AG_MEF-WCE-rep1

description: whole cell extraction


title: wt1_2i_RNAseq

value: wild type


title: H3K9me3_in_PG_MEF_Aff3_shRNA-2

description: Chromatin IP of H3K9me3


title: THP-1, input

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

data_processing:
Alignment to hg19 using Bowtie v1.0 with the following parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 with parameters: -m 5 50 –bw 150
Visualization as tdf in Integrative Genomics Viewer via conversion from sam to sorted bam (using samtools) and then to tdf (using igvtools)
Genome_build: hg19
Supplementary_files_format_and_content: TDF generated by IGVtools

organism: Homo sapiens

source_name: human monocytic cell line THP-1

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
proteins were crosslinked with formaldehyde to DNA, then VDR-bound fragments were pulled down by chromatin immunoprecipitation
Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany

treatment_protocol: cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or unstimulated


title: THP-1, CTCF ChIP-seq, 24 h 1,25(OH)2D3

description: Chromatin IP against VDR

tag: treatment

tag: treatment time

value: CTCF (Millipore 07-729)


title: THP-1, CTCF ChIP-seq, 24 h EtOH

description: Chromatin IP against VDR

value: EtOH


title: FAIRE-seq at 48 h, mix of replicates A, B, C

description: reverse-crosslinked before phenol-chloroform extraction

source_name: monocytic cell line

extract_protocol:
proteins were crosslinked with formaldehyde to DNA, then open chromatin fragments were isolated by phenol-chloroform extraction
Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany

tag: cell line


title: H3K9me3_in_AG_MEF_NonT_shRNA

description: Chromatin IP of H3K9me3

tag: strain


title: FAIRE-seq at 0 h, mix of replicates A, B, C

value: untreated

value: 0 h


title: v6.5-WCE-rep2

description: whole cell extraction


title: FAIRE-seq at 48 h, replicate C

description: crosslinked before phenol-chloroform extraction


title: FAIRE-seq at 24 h, replicate C


title: H3K9me3_in_AG_MEF_Aff3_shRNA-1

description: Chromatin IP of H3K9me3

value: mouse embryonic fibroblast


title: FAIRE-seq at 2 h, replicate C

value: 2 h


title: Pol_II_in_AG_MEF

description: Chromatin IP of Pol II

value: AG MEF


title: H2K27ac_in_Zfp57_WT-rep1

description: Chromatin IP of H3K27ac

value: mouse embryonic stem cell


title: Pol_II_in_PG_MEF

description: Chromatin IP of Pol II

value: PG MEF


title: Aff3_Ab1_in_PG_MEF

description: Chromatin IP of Aff3

value: Aff3 (Homemade#182)


title: FAIRE-seq at 48 h, replicate B


title: H3K27ac_in_v6.5_Aff3-shRNA-rep1

description: Chromatin IP of H3K27ac


title: FAIRE-seq at 0 h, replicate C


title: Aff3_Ab1_in_AG_MEF

description: Chromatin IP of Aff3


title: FAIRE-seq at 24 h, replicate B


title: Aff3_Ab1_in_Zfp57_KO-rep2

description: Chromatin IP of Aff3


title: FAIRE-seq at 2 h, replicate B


title: Aff3_Ab1_in_Zfp57_KO-rep1

description: Chromatin IP of Aff3


title: FAIRE-seq at 0 h, replicate B


title: Aff3_Ab1_in_TC1_Zfp57_WT-rep2

description: Chromatin IP of Aff3


title: FAIRE-seq at 48 h, replicate A


title: Aff3_Ab1_in_TC1_Zfp57_WT-rep1

description: Chromatin IP of Aff3


title: FAIRE-seq at 0 h, replicate A


title: FAIRE-seq at 24 h, replicate A


title: FAIRE-seq at 2 h, replicate A


title: Aff3_Ab1_in_KH2

description: Chromatin IP of Aff3


title: RNA-seq at 24 h 1,25(OH)2D3, replicate C

data_processing:
Alignment to hg19 using Bowtie v1.0 with the following parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Visualization as tdf in Integrative Genomics Viewer via conversion from sam to sorted bam (using samtools) and then to tdf (using igvtools)
Differential gene expression using Cuffdiff with FDR < 0.05, and three replicates for each time

extract_protocol:
total RNA was extracted from the cells
Standard protocol as suggested by the manufacturer for RNA-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany

treatment_protocol: cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or with the solvent Ethanol


title: Aff3_Ab1_in_v6.5-rep1

description: Chromatin IP of Aff3


title: Aff3_Ab1_in_v6.5-rep2

description: Chromatin IP of Aff3


title: RNA-seq at 4 h 1,25(OH)2D3, replicate C

value: 4 h


title: RNA-seq at 4 h EtOH, replicate C

value: Ethanol


title: Aff3_Ab2_in_v6.5

description: Chromatin IP of Aff3

value: Aff3 (Homemade#13)


title: RNA-seq at 24 h EtOH, replicate C


title: RNA-seq at 24 h 1,25(OH)2D3, replicate B


title: RNA-seq at 2.5 h EtOH, replicate C


title: PE-4CSeq from MEF line 129S5E118, viewpoint 153.9 (10), allele 129S5

city: Cold Spring Harbor

first: Cinthya

middle: J

last: Zepeda-Mendoza

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_10._singlecores.txt
153.9_WT118_129S5

data_processing:
library strategy: 4C-seq
Obtained reads were separated using custom perl scripts based on the sample and genotyping SNP on PE1 reads. PE2 reads were trimmed to 30bp to have the highest quality bases for captures mapping. Alignments were performed using bowtie against a reduced database of sequences bordering HindIII restriction sites in the NCBI37/mm9 assembly. Up to 3 mismatches were accepted per read to account for SNPs in the 129S5/SvEvBrd sequence, and only uniquely mapped reads were taken into account for the 4C data analysis.
Polymer physic analysis as described on Zepeda-Mendoza et al, 2014 for the quantitative identification of differential interaction signals between viewpoints and the rest of chromosome 4
Genome_build: mm9
Supplementary_files_format_and_content: Files with the extension .bowtie_sum_sorted.hindiii_hits.txt contain the end of each HindIII restriction fragment on chromosome 4 in column 1 together with the number of mapped reads as detected by bowtie in column 2. Files with extension .singlecores contain fragments which differentially contact the specified viewpoints. Column 1 is the name of the fragment, column 2 is mouse chromosome, column 3 is fragment start, column 4 is fragment end.

growth_protocol: Embryos of Df/Dp male chimeras X C57BL6/J crosses were dissected at 13.5 days after plug observation. Heads were removed for DNA extraction and genotyping, and the bodies minced by passing through syringes with 18G1 ½ and 20G 1 ½ needles and plated on 10cm dishes previously coated with 0.1% gelatin and using for culture Dulbecco's Modified Eagle Medium (DMEM) High Glucose (4.5g/L) supplemented with 10% Fetal Bovine Serum (FBS) (v/v), 50U/ml Penicillin G, and 100µg/ml Streptomycin sulfate. Cells were incubated on 5% CO2 at 37°C, and passaged every 2-3 days depending on confluency and growth rate. All experiments were subsequently performed on MEF plates 10 hours after reaching confluency at passage 4.

extract_protocol:
4C templates for Df/+Bl6 (MEF lines 129S5E71 and 129S5E98) and +129/+Bl6 (MEF lines 129S5E117 and 129S5E118) were prepared as described in Splinter et al, 2012. Briefly, 1x107 MEFs were cross-linked for 10 min at RT using 2% formaldehyde (Calbiochem) and 10%FCS in PBS (pH 7.4). 10 ml reactions were transferred to ice and added 1.425ml of 1M glycine, followed by centrifugation for 8 min at 225g at 4°C. Supernatant was subsequently removed and the resulting cell pellet resuspended in 500 μl of ice cold nuclei buffer (10mM Tris pH 7.6, 10mM NaCl, 2mM MgCl2, dH2O) containing protease inhibitors (Roche) for 10 min on ice. An equal volume of nuclei buffer/0.5% NP-40 was added to the tube and incubated for 5 min on ice. Samples were vortexed for 10 s and centrifuged for 1 min at 1,000g and 4°C. Cells were washed once in nuclei buffer/0.5% NP-40 containing protease inhibitors and centrifuged for 1 min at 1,000g and 4°C. Pellets were resuspended in 450µl dH2O and 60µl 10X restriction buffer (buffer 2 supplied with HindIII enzyme, New England BioLabs), incubated 1 hr with 15µl 10% SDS shaking at 900RPM at 37°C, and followed by an additional 1 hr incubation with 75µl 20% Triton X-100. 5 µl aliquots were taken as undigested controls and stored at 4°C. Samples were subsequently digested by adding 800U of HindIII (New England BioLabs) and incubating overnight at 37°C while shaking. 5 µl aliquots were taken as digested controls and de-crosslinked by incubation with 10 μl Proteinase K (10mg/ml, Roche) in 90 μl of 10 mM Tris (pH 7.5) at 65 °C for 1 h. Digestion efficiencies were estimated based on the pattern of smear of the undigested and digested controls by running 20 μl of decrosslinked sample on a 0.6% agarose gel. If digestion was sufficient, HindIII was inactivated by incubating the sample for 20 min at 65°C (shaking gently). The digested nuclei were transferred to a 50 ml falcon tube and mixed with 5.7ml dH2O, 700 μl 10X Ligase Buffer, and 50U T4 Ligase (Roche), and incubated overnight at 16°C. Ligation efficiency was determined by taking 100 μl of ligation reaction and incubating 1 hr at 65°C with 5 μl Proteinase K (10 mg/ml). When run in a 0.6% agarose gel, ligated DNA should appear as a single upper band similar to the undigested control. If ligation occurred, DNA crosslinks were reversed by adding 30 μl of 10 mg/ml Proteinase K and incubation at 65 °C overnight. Subsequently, 15 μl of 20 mg/ml PureLink RNase A (Invitrogen) was added and the reactions incubated for 45 min at 37 °C, followed by phenol extraction and DNA purification as described in Splinter et al, 2012. The DNA pellet was dissolved in 150 μl of 10 mM Tris (pH 7.5), and digested overnight with 50U DpnII (New England BioLabs) at 37°C while shaking. An aliquot of 5 μl was taken from the DpnII reaction and mixed with 95 μl of 10 mM Tris (pH 7.5), and 20 μl loaded into a 0.6% agarose gel to assess digestion efficiency. If sufficient digestion was achieved, DpnII was heat inactivated by incubating 20 minutes at 65°C, and DNA was ligated at low concentrations (12.1ml dH2O, 1.3ml 10X ligation buffer, 100U T4 DNA Ligase) overnight at 16°C. DNA was phenol extracted and ethanol precipitated with glycogen (Roche) as a carrier. The resulting 4C templates were purified using QIAquick PCR purification kit columns (Qiagen), dissolved in 10 mM Tris (pH 7.5), and stored at -20°C.
Inverse 4C amplification primers were designed per viewpoint following standard rules for PCR primer design, and checking alignment uniqueness to the desired fragment as compared to the rest of the genome. Primers used in this study are listed in Supplementary Table 1c. Additionally, amplification primers for all viewpoints were added the PE1 and PE2 Illumina paired-end primers plus a 1-2 nucleotide barcode in their 5' ends for HiSeq PEx100 sequencing. Each of the 14 viewpoints was amplified from the available Df/+Bl6 and +129/+Bl6 4C templates in reactions using 3.2µg 4C template, 16µl dNTP (10mM, New England BioLabs), 24µl reading primer PE1 of a 1µg/µl primer stock, 24µl reading primer PE2 of a 1µg/µl primer stock, 11.2 µl Expand Long Template polymerase (Roche), 80µl 10X PCR buffer 1 (supplied with polymerase), and dH2O until completing 800µl total. This volume is then mixed and separated into 16x50µl PCR reactions, and run using the following program: 94 °C for 2 min, followed by 30 cycles of 15 s at 94 °C, 1 min at 55 °C and 3 min at 68 °C, and one final step of 5min at 68 °C. PCR reactions were subsequently collected and pooled together, and purified using the High Pure PCR Product Purification Kit (Roche) for viewpoints amplified on 129S5E71 and 129S5E117 4C templates, or using AMPure beads (Beckman Coulter) with a 0.9X volume ratio for viewpoints amplified from 129S5E98 and 129S5E118 4C templates. Equimolar amounts of isolated captured viewpoints were pooled together using the KK4824 kit to correct for insert size lengths (Kapa Biosystems). Pooled libraries were sequenced using two lanes of HiSeq 2000 PE100.

value: C57BL/6J & 129S5SvEvBrd

value: Mouse Embryonic Fibroblasts (MEFs)

tag: passages

value: confluent passage 4


title: PE-4CSeq from MEF line 129S5E118, viewpoint 154.9 (11), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
154.9_WT118_129S5


title: PE-4CSeq from MEF line 129S5E118, viewpoint 155.5 (12), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
155.5_WT118_129S5


title: PE-4CSeq from MEF line 129S5E118, viewpoint 153.9 (10), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_10._singlecores.txt
153.9_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 154.9 (11), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
154.9_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 155.5 (12), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
155.5_WT118_C57Bl6


title: RNA-seq at 24 h EtOH, replicate B


title: RNA-seq at 4 h EtOH, replicate B


title: RNA-seq at 2.5 h 1,25(OH)2D3, replicate C


title: PE-4CSeq from MEF line 129S5E118, viewpoint 153.4 (9), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_9._singlecores.txt
153.4_WT118_129S5


title: RNA-seq at 2.5 h 1,25(OH)2D3, replicate B


title: PE-4CSeq from MEF line 129S5E118, viewpoint 153.4 (9), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_9._singlecores.txt
153.4_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 152.9 (8), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_8._singlecores.txt
152.9_WT118_129S5


title: RNA-seq at 24 h 1,25(OH)2D3, replicate A


title: RNA-seq at 24 h EtOH, replicate A


title: PE-4CSeq from MEF line 129S5E118, viewpoint 152.4 (7), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_7._singlecores.txt
152.4_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 152.1 (6), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_6._singlecores.txt
152.1_WT118_129S5


title: PE-4CSeq from MEF line 129S5E118, viewpoint 152.4 (7), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_7._singlecores.txt
152.4_WT118_129S5


title: PE-4CSeq from MEF line 129S5E118, viewpoint 151.6 (5), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_5._singlecores.txt
151.6_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 151.6 (5), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_5._singlecores.txt
151.6_WT118_129S5


title: RNA-seq at 4 h 1,25(OH)2D3, replicate B


title: PE-4CSeq from MEF line 129S5E118, viewpoint 150.9 (4), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_4._singlecores.txt
150.9_WT118_C57Bl6


title: RNA-seq at 4 h 1,25(OH)2D3, replicate A


title: RNA-seq at 4 h EtOH, replicate A


title: RNA-seq at 2.5 h 1,25(OH)2D3, replicate A


title: RNA-seq at 2.5 h EtOH, replicate A


title: PE-4CSeq from MEF line 129S5E118, viewpoint 150.4 (3), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_3._singlecores.txt
150.4_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 150.4 (3), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_3._singlecores.txt
150.4_WT118_129S5


title: PE-4CSeq from MEF line 129S5E118, viewpoint 152.9 (8), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_8._singlecores.txt
152.9_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 148.9 (2), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_2._singlecores.txt
148.9_WT118_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 155.5 (12), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
155.5_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 147.9 (1), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_1._singlecores.txt
147.9_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 148.9 (2), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_2._singlecores.txt
148.9_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 147.9 (1), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_1._singlecores.txt
147.9_WT118_129S5


title: RNA-seq at 2.5 h EtOH, replicate B


title: PE-4CSeq from MEF line 129S5E117, viewpoint 155.5 (12), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
155.5_WT117_129S5


title: PE-4CSeq from MEF line 129S5E118, viewpoint 152.1 (6), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_6._singlecores.txt
152.1_WT118_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 154.9 (11), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
154.9_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 153.9 (10), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_10._singlecores.txt
153.9_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 153.9 (10), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_10._singlecores.txt
153.9_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 153.4 (9), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_9._singlecores.txt
153.4_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 153.4 (9), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_9._singlecores.txt
153.4_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 152.9 (8), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_8._singlecores.txt
152.9_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 152.9 (8), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_8._singlecores.txt
152.9_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 152.4 (7), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_7._singlecores.txt
152.4_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E118, viewpoint 150.9 (4), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_4._singlecores.txt
150.9_WT118_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 151.6 (5), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_5._singlecores.txt
151.6_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 152.1 (6), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_6._singlecores.txt
152.1_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 152.1 (6), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_6._singlecores.txt
152.1_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 152.4 (7), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_7._singlecores.txt
152.4_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 148.9 (2), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_2._singlecores.txt
148.9_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 150.9 (4), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_4._singlecores.txt
150.9_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 150.4 (3), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_3._singlecores.txt
150.4_WT117_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 150.4 (3), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_3._singlecores.txt
150.4_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 154.9 (11), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
154.9_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E117, viewpoint 148.9 (2), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_2._singlecores.txt
148.9_WT117_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 155.5 (12), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_12.singlecores.txt
155.5_Df98_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 147.9 (1), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_1._singlecores.txt
147.9_WT117_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 153.9 (10), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
153.9_Df98_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 154.9 (11), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_11.singlecores.txt
154.9_Df98_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 153.9 (10), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_10._singlecores.txt
153.9_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 153.4 (9), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_9._singlecores.txt
153.4_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 153.4 (9), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
153.4_Df98_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 152.9 (8), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
152.9_Df98_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 152.9 (8), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_8._singlecores.txt
152.9_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 152.4 (7), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_7._singlecores.txt
152.4_Df98_C57Bl6


title: H1299_ShMETTL3_1

city: Boston

first: Peng

last: Du

state: MA

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

data_processing:
For RNA-seq data, Bowtie is used to map reads to mRNA with two mismatches permitted, and self-developed perl scripts were used to coculate the reads of each genes
For Methylated RNA IP seq, the adaptor sequences were removed firstly, and then reads (>=13) were alignmented to human genomic sequence using Tophat. MAC14 was then used to call the peak based on the .bam generated before.
Genome_build: hg19
Supplementary_files_format_and_content: A549_RNAseq.txt and H1299_RNAseq.txt provided a matrix table, which contained four columns including the gene's name, reads numbers in different samples; .bed files provided the information of m6A peaks in A549 and H1299 cell lines identified, which were generated by comparing IP samples with input samples.

source_name: Lung cancer

growth_protocol: cells were cultured with DMEM supplemented with 10% FBS and antibiotics.

extract_protocol:
mRNA was first purified from total RNA using PolyATtract® mRNA Isolation Systems (Promega). Then 5 g mRNA was fragmented and immunoprecipated with anti-m6A antibody (Synaptic Systems, 202003), the immunoprecipated RNA was washed and eluted by competition with N6-Methyladenosine (Sigma-Aldrich, M2780). The purified RNA fragments from m6A meRIP were used for library construction using TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101)
Library was constructed using TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101) according to the manufacturer’s instructions.

value: Lung cancer cells

tag: type

value: RNA-seq

value: No


title: H1299_ShGFP

tag: cell type


title: PE-4CSeq from MEF line 129S5E117, viewpoint 151.6 (5), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_5._singlecores.txt
151.6_WT117_129S5

tag: genotype/variation


title: PE-4CSeq from MEF line 129S5E98, viewpoint 152.4 (7), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
152.4_Df98_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 152.1 (6), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_6._singlecores.txt
152.1_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 152.1 (6), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
152.1_Df98_129S5


title: PE-4CSeq from MEF line 129S5E117, viewpoint 150.9 (4), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_4._singlecores.txt
150.9_WT117_129S5


title: H1299_input


title: H1299_m6A_IP

value: Methylated RNA IP seq


title: A549_ShMETTL3_2


title: PE-4CSeq from MEF line 129S5E98, viewpoint 151.6 (5), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_5._singlecores.txt
151.6_Df98_C57Bl6


title: A549_ShMETTL3_1


title: PE-4CSeq from MEF line 129S5E117, viewpoint 147.9 (1), allele 129

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_1._singlecores.txt
147.9_WT117_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 150.9 (4), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_4._singlecores.txt
150.9_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 151.6 (5), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
151.6_Df98_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 154.9 (11), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
154.9_Df98_C57Bl6


title: A549_m6A_IP1


title: A549_ShGFP


title: H1299_ShMETTL3-2


title: PE-4CSeq from MEF line 129S5E98, viewpoint 150.4 (3), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
150.4_Df98_129S5


title: A549_input

description: M6A_1_A549_peaks.bed; M6A_1_A549_peaks.bed


title: PE-4CSeq from MEF line 129S5E98, viewpoint 155.5 (12), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_12._singlecores.txt
155.5_Df98_C57Bl6


title: A549_m6A_IP2


title: PE-4CSeq from MEF line 129S5E98, viewpoint 150.4 (3), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_3._singlecores.txt
150.4_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 148.9 (2), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_2._singlecores.txt
148.9_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 147.9 (1), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_1._singlecores.txt
147.9_Df98_C57Bl6


title: PE-4CSeq from MEF line 129S5E98, viewpoint 147.9 (1), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_1.singlecores.txt
147.9_Df98_129S5


title: Lesion II

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Demyelinated brain lesion

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.
Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Read alignment was performed using Bowtie2 v2.1.0 to the h19 human reference genome.
SAMfiles were converted and sorted by samtools 0.1.19
reads per gene were counted via htseq version 0.5.4.p3.
Differential expression analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages. Candidate genes were filtered to a minimum of 2 x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: hg19
Supplementary_files_format_and_content: Original fastq files and gene counts

source_name: Brain

extract_protocol:
total RNA from homogenized brain tissue was extracted using RNeasy Micro (QIAGEN, Hilden, Germany) following manufacturer’s instructions.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA with Ribo-Zero Gold removing both cytoplasmic and mitochondrial rRNA (Illumina, Cat N° RS-122-2201). 200 ng of total RNA were used as start material . Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp;5- 6 GB ca. 30-35 million reads per sample).

tag: condition

value: Multiple sclerosis

value: brain

tag: gender

value: female

value: 36 years-old


title: PE-4CSeq from MEF line 129S5E98, viewpoint 148.9 (2), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_2.singlecores.txt
148.9_Df98_129S5


title: Lesion III

description: Demyelinated brain lesion

tag: age


title: Lesion I

description: Demyelinated brain lesion

tag: tissue


title: Immunoprecipitation with IGG antibody from cells treated with DFO

city: New York

first: Augustine

middle: MK

last: Choi

address: 525 East 68th Street, Room M-522, Box 130

department: Department of Medicine

institute: Weill Cornell Medical College

data_processing:
Sequenced readswere aligned to the human hg19 known transcriptome using bowtie2-2.0.6 and tophat-2.0.7.Linux_x84_64. Any unmapped reads were then allowed to map to the hg19 genome.
Aligned reads from replicates were combined using the 'merge' function in samtools-0.1.18, creating one bam file each for CONTROL, CONTROL IGG, DFO and DFO IGG
the 'findPeaks' function in homer v4.4 (style=factor) was used to to call peaks with a two-fold tag enrichment in a given 'samples' relative to a given 'control' and a Poisson p-value less than 0.1
Peaks common between multiple comparisons were identified with the 'mergePeaks' function in homer v4.4
Peaks were mapped to hg19 genes using the 'annotatePeaks' function in homer v4.4.
Peaks with a homer "peak-score" greater than 5 were retained for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: txt (homer findPeaks output) includes the locations of peaks called by HOMER and statistical scores associated with these peaks
Supplementary_files_format_and_content: txt (homer annotatePeaks output) includes information included in the "homer findPeaks output" as well as additional information about the genomic features related to the peak regions
Supplementary_files_format_and_content: SC1_CONTROL_12_Peaks_LowFilter.txt: peak calls comparing CONTROL to CONTROL-IGG
Supplementary_files_format_and_content: SC2_DFO_12_Peaks_LowFilter.txt: peak calls comparing DFO to DFO-IGG
Supplementary_files_format_and_content: CTRL12vsDFO12_Peaks_LowFilter.txt: peak calls comparing CONTROL to DFO
Supplementary_files_format_and_content: DFO12vsCTRL12_Peaks_LowFilter.txt: peak calls comparing DFO to CONTROL
Supplementary_files_format_and_content: CTRL__Both.txt_Annotated.txt: annotated peaks common to CONTROL/CONTROL-IGG and CONTROL/DFO peaks calls
Supplementary_files_format_and_content: DFO__Both.txt_Annotated.txt: annotated peaks common to DFO/DFO-IGG and DFO/CONTROL peaks calls
Supplementary_files_format_and_content: IREB__Both.txt_Annotated.txt: annotated peaks common to CONTROL/CONTROL-IGG and DFO/DFO-IGG peaks calls

source_name: human bronchial epithelial cells (Beas2B cells)

growth_protocol: Beas2B cells were seeded into 15cm2 dishes and left overnight.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Samples were prepared for RNA-Seq using the TruSeq RNA-Seq Lib Prep Reagent (Illumina)

treatment_protocol: Beas2B cells were treated with 10 μM DFO (16 h) (15 cm2 dishes) and were washed with ice cold PBS and collected into 2 ml eppendorfs by scraping.

tag: antibody

value: IgG (sc-2749, Santa Cruz)

value: DFO


title: IRP2 immunoprecipitation from cells treated with DFO, replicate 2

description:
DFO12vsCTRL12_Peaks_LowFilter.txt (peak calls comparing IRP2 immunoprecipitation in DFO versus CTL treatments)
SC2_DFO_12_Peaks_LowFilter.txt (peak calls comparing IRP2 and IGG immunoprecipitation)

value: Irp2 (7H6:sc-33682, Santa Cruz)


title: PE-4CSeq from MEF line 129S5E71, viewpoint 155.5 (12), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_12._singlecores.txt
155.5_Df71_C57Bl6


title: IRP2 immunoprecipitation from cells treated with DFO, replicate 1


title: Immunoprecipitation with IGG antibody from untreated cells


title: PE-4CSeq from MEF line 129S5E71, viewpoint 155.5 (12), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_12.singlecores.txt
155.5_Df71_129S5


title: IRP2 immunoprecipitation from untreated cells, replicate 2

description:
CTRL12vsDFO12_Peaks_LowFilter.txt (peak calls comparing IRP2 immunoprecipitation in DFO versus CTL treatments)
SC1_CONTROL_12_Peaks_LowFilter.txt (peak calls comparing IRP2 and IGG immunoprecipitation)


title: IRP2 immunoprecipitation from untreated cells, replicate 1


title: PE-4CSeq from MEF line 129S5E71, viewpoint 154.9 (11), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_11.singlecores.txt
154.9_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 153.9 (10), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_10._singlecores.txt
153.9_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 154.9 (11), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_11._singlecores.txt
154.9_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 153.9 (10), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
153.9_Df71_129S5


title: PE-4CSeq from MEF line 129S5E98, viewpoint 150.9 (4), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
150.9_Df98_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 153.4 (9), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_9._singlecores.txt
153.4_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 153.4 (9), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
153.4_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 152.9 (8), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_8._singlecores.txt
152.9_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 152.9 (8), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
152.9_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 152.4 (7), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_7._singlecores.txt
152.4_Df71_C57Bl6


title: HRT1_RNF2_ChIPSeq

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: HMEL-BRAF-RNF2 overexpressing tumor cells

data_processing:
Basecalling performed using CASAVA.
RNF2 ChIP-Seq reads were aligned using Bowtie (version 0.12.2) (PMID: 19261174) to human genome assembly NCBI Build 37 (UCSC hg19).
Enriched regions were detected by MACS version 1.4.0 (PMID: 18798982) with a p-value cut-off of 10^-8.
Genome_build: GRCh37
Supplementary_files_format_and_content: Wig files were generated using MACS 1.4.0; Scores represent normalized tag counts for 10 million reads.

source_name: Hmel human melanocytes, RNF2 ChIP

growth_protocol: Cells were maintained in standard tissue culture conditions (5% CO2 , 37oC).

extract_protocol:
Cells (5 million per antibody) were crosslinked using 1% paraformaldehyde for 10mins at 37 degrees. Reaction was quenched by 0.125M glycine for 5mins, cells washed with PBS and stored at -80oC. Next day cells were thawed on ice and lysed with RIPA buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 140mM NaCl, 1% Triton x-100, 0.2%SDS, 0.1% DOC) for 10min on ice. Sonication was performed using Branson Sonifier 250 to achieve shear length of 200-500bp. Antibodies [Rabbit IgG, V5 (Abcam)] were bound to Dynabeads for 1 hr at 4oC. Extracts were then incubated overnight with antibody-Dynabead mixture. Immune complexes were then washed 5 times with RIPA buffer, once with RIPA-500 (RIPA with 500mM NaCl) and once with LiCl wash buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and decrosslinking was performed in direct elution buffer (10mM Tris-Cl pH 8.0, 5mM EDTA, 300mM NaCl, 0.5% SDS) by incubating immune complexes at 65oC for 4-16hrs. Proteinase K (20mg/ml) and RNaseA treatment was performed and DNA cleaned up using SPRI beads (Beckman-Coulter).
Libraries were prepared using NEB reagents as described (Garber et al. 2012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300-500 bp (insert plus adaptor and PCR primer sequences) were size selected by SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: Cells were infected with pLenti6.3-RNF2WT or pLenti6.3-GFP lentiviruses, selected with blasticidine (5mg/ml) till control uninfected cells were dead.

value: immortalized melanocytes

tag: chip antibody


title: PE-4CSeq from MEF line 129S5E71, viewpoint 152.4 (7), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
152.4_Df71_129S5


title: LR_InputDNA

description: HMEL-BRAF-RNF2 overexpressing cells

source_name: Hmel human melanocytes, input

value: rabbit IgG


title: HRT1_InputDNA


title: LR_RNF2_ChIPSeq

description: HMEL-BRAF-RNF2 overexpressing cells


title: PE-4CSeq from MEF line 129S5E71, viewpoint 151.6 (5), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_5._singlecores.txt
151.6_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 152.1 (6), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
152.1_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 150.9 (4), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_4._singlecores.txt
150.9_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 151.6 (5), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
151.6_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 150.9 (4), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
150.9_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 148.9 (2), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_2._singlecores.txt
148.9_Df71_C57Bl6


title: PE-4CSeq from MEF line 129S5E71, viewpoint 150.4 (3), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
150.4_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 147.9 (1), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_1.singlecores.txt
147.9_Df71_129S5


title: PE-4CSeq from MEF line 129S5E71, viewpoint 148.9 (2), allele 129S5

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-129DiffPositions_st__whole_chrm__vp_2.singlecores.txt
148.9_Df71_129S5


title: 18NNK_LPS_I3C6

city: Minneapolis

first: Fekadu

last: Kassie

state: MN

address: 425 East River Road, 560E MCRB

department: Veterinary Clinical Sciences

institute: University of Minnesota

description: Replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using CLC Bio Genomics Workbench 6.5 with default settings: read alignment mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distances, strand specific = both, and maximum number of hits for a read = 10.
Total exon reads for each gene was recorded and used as expression value.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes total exon read values for each gene in all samples (not normalized).

source_name: Lung tissue

extract_protocol:
Total RNA was extracted from pooled dissected mouse lung tumors from 3 mice/group (for groups treated with NNK) or normal lung tissue (for groups treated with vehicle or LPS alone) using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.
Samples were prepared, using a Illumina TruSeq RNA Sample Preparation Kit (version 2), according to the manufacturer's instructions for RNA-Seq sample preparation.

treatment_protocol: Mice were intraperitoneally treated with a single dose of NNK (100 mg/kg, in 0.1 ml physiological saline) or the vehicle alone. Beginning one week after NNK administration, groups of mice were intranasally instilled with LPS (5 µg/mouse in 50 μL of phosphate buffered saline), once a week, until the end of the study. I3C (20 μmol/g diet) and Sil (20 μmol/g diet) were administered in the diet, individually or in combination.

value: A/J

tag: Sex

value: Lung

tag: time point

value: 22 weeks post-treatment

value: NNK + LPS + indole-3-carbinol (I3C)


title: 21NNK_LPS_Sil_I3C10

description: Replicate 3

value: NNK + LPS + Sil + I3C


title: 17NNK_LPS_I3C3

description: Replicate 2


title: 14NNK_LPS_Sil2

description: Replicate 2

value: NNK + LPS + Silibinin (Sil)


title: 16NNK_LPS_I3C1

description: Replicate 1


title: 20NNK_LPS_Sil_I3C9

description: Replicate 2


title: 15NNK_LPS_Sil8

description: Replicate 3


title: 19NNK_LPS_Sil_I3C8

description: Replicate 1


title: PE-4CSeq from MEF line 129S5E71, viewpoint 152.1 (6), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_6._singlecores.txt
152.1_Df71_C57Bl6

value: C57BL/6J & 129S5SvEvBrd

value: Mouse Embryonic Fibroblasts (MEFs)

value: confluent passage 4


title: 11NNK_LPS6

description: Replicate 2

value: NNK + LPS


title: 10NNK_LPS4

description: Replicate 1

value: female


title: 13NNK_LPS_Sil1

description: Replicate 1


title: 9LPS3a

description: Replicate 3

value: LPS


title: 7LPS1a

description: Replicate 1


title: 12NNK_LPS8

description: Replicate 3


title: 6NNK6

description: Replicate 3

value: NNK


title: PE-4CSeq from MEF line 129S5E71, viewpoint 150.4 (3), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_3._singlecores.txt
150.4_Df71_C57Bl6


title: 4NNK1

description: Replicate 1


title: 5NNK5

description: Replicate 2


title: 2Con2

description: Replicate 2

value: Control


title: 1Con1

description: Replicate 1


title: PE-4CSeq from MEF line 129S5E71, viewpoint 147.9 (1), allele C57Bl/6J

description:
PCR amplified products of different sizes, sequenced in Illumina's HiSeq 2000
processed data file: Df-WT-Bl6DiffPositions_st__whole_chrm__vp_1._singlecores.txt
147.9_Df71_C57Bl6


title: 3Con3

description: Replicate 3


title: gfp(RNAi) glp-4(-) L3

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

data_processing:
To generate BAM files, more than 50 millions of reads (length of 73 bp) for sample were mapped against the C. elegans worm version WS236 following GEMTools pipeline (http://gemtools.github.io/).
These BAM files were analyzed using the SeqSolve software, which use Cufflinks/Cuffdiff for differential gene/transcript expression analyses (Trapnell et al. 2012)
Genome_build: WS236
Supplementary_files_format_and_content: xls format. Contain a list of genes up and down regulated for the 11 transcriptomes/samples analyzed

organism: Caenorhabditis elegans

growth_protocol: synchronized N2 and smg-1(r861) L1 larvae fed for 24 hours at 20 °C with the RNAi clones of prp-6, prp-8, prp-31 and gfp; and 5-day adult glp-4(bn2) worms grown at 25 °C and fed first, for 72 hours with OP50 and next, for 48 more hours with the RNAi clones of prp-8, prp-31 and gfp

extract_protocol:
RNA was isolated with TRI Reagent (MRC, Inc.), and purified by using the Purelink RNA Mini kit (Ambion) and Purelink DNAse (Ambion)
Poly(A) enriched samples were multiplexed in libraries through the CNAG (Centro Nacional de Análisis Genómico) sequencing facility
paired-end RNA-Sequencing on Illumina Hiseq 2000 platform. FASTQs are in standard format with Sanger qualities (Phred+33). read lenght of 73 bp. More than 50 millions of reads per sample

treatment_protocol: RNAi by feeding on plates

tag: developmental stage

value: Adult

tag: treated with

value: gfp (RNAi)


title: prp-31(RNAi) glp-4(-) L3

value: adult

value: prp-31 (RNAi)


title: prp-31(RNAi) smg-1(-) L3

value: Larva 3 (L3)


title: prp-8(RNAi) glp-4(-) L3

value: prp-8 (RNAi)


title: 8LPS2a

description: Replicate 2

value: A/J

value: Lung

value: 22 weeks post-treatment

tag: treatment


title: prp-31(RNAi) N2 L3

source_name: wild type N2

value: wild type


title: prp-8(RNAi) N2 L3


title: gfp(RNAi) smg-1(-) L3


title: prp-6(RNAi) N2 L3

value: prp-6 (RNAi)


title: H3K9m3_DP_KO

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalling was performed using standard system equipped with ABI SOLiD system.
Color-space fasta and quality files were combined using our in-house program.
Sequences were aligned on mouse genome (mm9) using bowtie (version 1.0.0)
Genome_build: mm9

source_name: thymus

extract_protocol:
Isolated cells were immediately cross-linked with 1% formaldehyde/PBS for 10 minutes at room temperature.  After washing, the cell pellet was lysed in the lysis buffer having the following final concentration: 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% sodium dodecyl sulfate (SDS), 1 mM phenylmethylsulfonyl fluoride (PMSF), 1x proteinase inhibitor complete cocktail (Roche).  The lysed solution was subjected to chromatin shearing by using Covaris S2 System (Covaris, Woburn, MA) to shear the chromatin into 100–300 bp fragments.
ChIP-seq libraries were prepared for sequencing using the SOLiD Fragment Library Construction Kit and multiplexed by using SOLiD™ Fragment Library Barcoding Kit Module 1-16 according to the manufacturer’s instructions.

tag: genotype

value: ESET-/-

value: H3K9m3 (Abcam, clone ab8898)


title: input_DP_KO

tag: strain


title: F1 TSC Dnase-Seq

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

data_processing:
DNase-Seq reads were trimmed prior to all analyses to include only the first 20 bases; the remainder were linker derived (see Song L, et al. Genome Res. 2011; PMID 21750106).
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/).
Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.
SNP-containing reads were extracted using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BED files were generated from mm9 alignments, and reported read ends reflect average fragment size of corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.

source_name: F1 BC.1 trophoblast stem cells

growth_protocol: TSCs were grown under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006; PMID: 16251740). To eliminate feeder cell contamination of TSC RNA and chromatin preparations, TSC cultures grown on sub-lethally irradiated feeders were trypsinized and pre-plated for 40 minutes before transferring to new plates. TSC cultures were then split an additional 2x before harvesting.

extract_protocol: DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106)

value: C57BL/6J mother X CAST/EiJ father


title: input_DP_WT


title: prp-6(RNAi) smg-1(-) L3


title: H3K9m3_DP_WT


title: F1 TSC CTCF ChIP-Seq

data_processing:
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/).
Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.
SNP-containing reads were extracted using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BED files were generated from mm9 alignments, and reported read ends reflect average fragment size of corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.

extract_protocol: ChIP-Seq libraries were prepared according to Illumina instructions.

value: CTCF (Pugacheva et. al. 2005 Hum Mol Genet 14, 953-965; PMID:15731119)


title: prp-8(RNAi) smg-1(-) L3


title: gfp(RNAi) N2 L3


title: Normal HepG2 cells-mRNA Sequencing

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequences and independently aligned using CLC Genomic Workbench 6.0 with default setting against Human genome assembly (GRCH 37. P13).
Differential expression, p-value and fold changes for each gene were determined using CLC Genomic Workbench 6.0 with default parameters.
Genome_build: NCBI, Human genome assembly (GRCH 37. P13).
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene of respective samples

source_name: HepG2 cells

growth_protocol: SLTRiP-KO, PB268-KO or PBANKA-WT sporozoites (2x106), isolated from the salivary glands of infected mosquitoes, were added to the monolayer HepG2 cells (1x106 cells /well. The plates were incubated at 37˚C and 5% CO2. The media was refreshed after 3hrs of sporozoites infection.

extract_protocol:
RNA was isolated from FACS sorted parasitized HepG2 cells using Trizol method and concentration of RNA determined by Qubit flourimeter (Invitrogen) using QubitTM RNA Assay Kit. The total RNA for each sample was analyzed on Agilent bioanalyzer using Agilent RNA 6000 Pico kit.
Libraries were prepared according to Illumina's instructions accompanying theTruseq standed RNA sample preparation kit (FC-122-1001). Briefly, the poly-A containing mRNA molecules were purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was fragmented into small pieces, using divalent cations under elevated temperature, and converted into first strand cDNA using reverse transcriptase and random primers. The second strand of cDNA was synthesized using DNA polymerase-I and RNAse-H enzymes. The synthesized cDNA have an additional ‘A’ base, which is required for adapter ligation. The products were purified and enriched with PCR to create the final cDNA library. The cDNA library for each sample was analyzed on Agilent 2100 Bioanalyzer using Agilent DNA 1000 kit.

treatment_protocol: After 22hrs of sporozoites infection, the cells were washed with 1XPBS and trypsinize with 250µl of Trypsin-EDTA (Gibco) per well of six well plate. Trypsinized cells were centrifuged at 800rpm for 5minutes to remove the trypsin and washed twice with 1XPBS with 10%FBS.  HepG2 cells were resuspended in 1XPBS with 2mM EDTA for fluorescence activated cell sorting (FACS).

value: Liver

tag: cell line

tag: plasmodium infection

value: Normal HepG2 cells


title: HepG2-PBSLTRiP-KO-mRNA Sequencing

tag: cell type

value: Plasmodium berghei SLTRiP-KO parasite

tag: infection time point

value: 22 hrs of post sporozoite infection of HepG2 cells


title: B

city: Guangzhou

first: Jingxin

last: Zhang

state: Guangdong

country: China

institute: Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P.R.China

description: mock-treated blast resistant rice line

data_processing: After eliminating adaptors and low quality tags,18-30 nt clean tags, clean tags were mapped to the rice genome downloaded from the TIGR FTP database (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/) by SOAP. Some tags were removed when matched to NCBI Genebank, Rfam database or known rice miRNA precursors and the small RNAs. These perfectly matching known miRNA hairpin were aligned in the processed data files, their format as follows: 1,hairpin name; 2,mature name; 3,tag name; 4,unique count of the dominant mature sequence; 5,total count of the dominant mature sequence; 6,arm this mature located; 7,dominant mature sequence; 8, miRBase mature sequence; 9, difference between the dominant mature sequence and miRBase mature sequence (D: different, S: same).  It provides large numbers of high-quality reads, expecially when low quality reads are filtered strictly.

organism: Oryza sativa Indica Group

source_name: seedling

growth_protocol: Resistant rice line H4 and susceptible rice line Zhonger-ruanzhan were grown on sterilized soil in growth chambers with 13 h light/day and 11 h dark/night, 28.5°C during the day and 25°C during the night, and 85% relative humidity.

extract_protocol: Eighteen- to 30-nt small RNAs from >20 µg of total RNA were gel extracted from a 15% denaturing acrylimide gel. After elution from the gel, sRNAs were precipitated. A 5',3' adapter was ligated to the sRNAs, and subsequently the 50-70nt fragments were gel extracted. Adapter-ligated sRNAs were subjected to reverse transcription using standard protocols.PCR products were gel extracted and sent to illumina high-seq for sequencing.

treatment_protocol: At trefoil stage, the plants were sprayed by rice blast isolate GD0193 suspension with 5×104 spores per ml and water control separately.

value: trefoil stage

value: leaf

value: Blast-resistant rice line

tag: line

tag: library

value: 12157795, mock-treated blast resistant rice line


title: D

address: Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences

description: blast-treated blast resistant rice line

tag: age

value: 11138187, blast-treated blast resistant rice line


title: C

description: blast-treated susceptible rice line

tag: tissue

value: Blast-susceptible rice line

value: Zhonger-Ruanzhan

value: 9937360, blast-treated susceptible rice line


title: ESC(R1)

city: Beijing

first: Junqing

last: Ye

address: Yi He Yuan Road #5

institute: Peking University

data_processing:
The transcriptome reads were aligned to the mouse genome using TopHat program
Aligned reads were assembled using Cufflinks program.
The gene expression level was calculated by using FPKM method.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking files including FPKM values for the analysis of gene expression

source_name: embryonic stem cells (R1)

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB).

treatment_protocol: Treatment protocol was described in Experimental Procedures section of the paper

value: ESCs


title: IEC_CiPSC_10

source_name: small intestinal epithelial cell-derived CiPS cell line 10

value: CiPSCs


title: IEC

source_name: primary small intestinal epithelial cells isolated from E13.5 embryos

value: small intestinal epithelial cells


title: A

description: mock-treated susceptible rice line

value: Blast-susceptible rice

value: 8749036, mock-treated susceptible rice line


title: HepG2- PBANKA-WT-mRNA Sequencing

value: Liver

value: Plasmodium berghei parasite


title: IEC_CiPSC_13

source_name: small intestinal epithelial cell-derived CiPS cell line 13


title: NSC_CiPSC_1

source_name: neural stem cell-derived CiPS cell line 1


title: NSC_CiPSC_3

source_name: neural stem cell-derived CiPS cell line 3


title: NSC_CiPSC_2

source_name: neural stem cell-derived CiPS cell line 2


title: HepG2-PB268-KO-mRNA Sequencing

value: Plasmodium berghei 268-KO parasite


title: CD133(high)CD71(low) cells

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

data_processing:
Reads per kilobase per million (RPKM) were calculated for RefSeq transcripts using an expectation-maximization algorithm in Partek Genomics Suite
Reads were aligned to the mouse genome (build mm10)
RPKM values were then further normalized via log2 transformation following the addition of a scaling factor of 0.1
P values were calculated by one-way ANOVA using the normalized RPKM values
Transcripts were defined as differentially expressed if they showed a fold-change value higher than 1.5 and FDR lower than 0.05
Genome_build: mm10
Supplementary_files_format_and_content: text files with normalized RPKM values.

source_name: pancreas

extract_protocol:
RNA was extracted from lysate of sorted cells using the Qiagen Rneasy Micro Kit (Cat. No. 74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly sorted cells

value: pancreas

tag: cell markers


title: CD133(high)CD71(low) cells-1


title: CD133(high)CD71(low) cells-2


title: CD133(positive)CD71(negative) cells-2


title: CD133(positive)CD71(negative) cells-1


title: NP1063

city: Tallahassee

first: Michelle

last: Arbeitman

state: FL

address: 1115 West Call Street

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
Sequences from Illumina adapters were trimmed using Trimmomatic ( version 0.32, minlen set to 50, 2 seed mismatches )
Unique reads were aligned to Mus musculus genome, release 75 (Ensembl) using Tophat ( version 2.0.8, --read-mismatches and --read-edit-dist set to 6 )
Expression was quantified for genes, to raw counts using easyRNASeq ( from Bioconductor version 3.0.2, geneModels summarization )
edgeR, Fisher's exact test for differential expression ( from Bioconductor version 3.0.2, tagwise dispersion, Benjamini-Hochberg FDR correction )
Cufflinks quantification to Fragments Per Kilobase Per Million Mapped Reads (FPKM) (Cufflinks version 2.1.1, -- no-effective-length-correction )
Genome_build: Ensembl release 75
Supplementary_files_format_and_content: Excel file containing raw count information
Supplementary_files_format_and_content: Excel file containing FPKM information

source_name: Adult Neocortex tissue

growth_protocol: After eight-week-old male and female C57BL/6J (B6) mice were purchased from the Jackson Laboratory (Bar Harbor, ME), nulliparous B6 females were trio bred to B6 males to generate timed pregnancies. The breeding condition is repeated in B99. Mice were fed standard chow diet (Purina 5001) and distilled water ad libitum.

extract_protocol:
The cerebellum, hippocampus, hypothalamus, and neocortex were dissected rapidly, flash-frozen in liquid nitrogen, and placed on dry ice until storage at -80°C. Frozen brain tissue was homogenized in 1ml TRIzol® solution (Life Technologies™ 15596-018), using a motorized homogenizer. Samples were than centrifuged at 4°C for ten minutes at 4,000 rpm to separate out debris and the resulting supernatant was processed for total RNA extraction procedure as manufacture suggested.
Total RNA was treated with TURBO™ DNase (Ambion® AM223) and purified with Zymo Research RNA Clean & Concentrator™-25kit (Zymo Research R1018). 5ug (cerebellum, neocortex, and hippocampus) or 1ug (hypothalamus) of total RNA was used for subsequent steps.  The External RNA Controls Consortium (ERCC) RNA Spike-in Controls (Ambion® 4456740) 1:10 and 1:100 were added to the total RNA 5ug and 1ug, respectively as suggested. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs® Inc. E7530L), 12 PCR cycles, quality was examined using Agilent High Sensitivity DNA Bioanalyzer Chips (Agilent Technologies 5067-4626) and quantified by KAPA Library Quantification Kits for Illumina sequencing platforms (KAPA Biosystems KK4824).

treatment_protocol: Nulliparous B6 females were trio bred to B6 males to generate timed pregnancies.  Post-conception (PC) day 1 is the day the vaginal plug was observed.  Postpartum samples are abbreviated PP. Randomly cycling, age-matched virgin females were used to establish the basal level of gene expression to compare to PC14, PC16, PP1, PP3 and PP10 dams.

tag: brain region

value: Neocortex

tag: Stage

value: Female


title: NVirB

value: Virgin

tag: Sex


title: NVirO


title: NP353


title: NP1071


title: NP357


title: NP1052


title: NE1658


title: NP146


title: NP156


title: NE1464


title: NE1654


title: NP149


title: NE1467


title: NE1655


title: TVirM

source_name: Adult Hypothalamus tissue

value: Hypothalamus


title: TP1063


title: TVirB


title: TVirO


title: NSC

source_name: cultured neural stem cells(P2) isolated from E13.5 embryos

value: neural stem cells


title: NE1468


title: TP1052


title: TP357


title: NVirM


title: TP353


title: TP156


title: TP347


title: TP149


title: TP146


title: TE1655


title: TE1654


title: TE1464


title: TE1658


title: TE1467


title: TP1071


title: HP1052

source_name: Adult Hippocampus tissue

value: Hippocampus


title: HP1071


title: HP357


title: HP353


title: HVirO


title: HVirB


title: TE1468


title: HVirM


title: HP347


title: HP149


title: HP146


title: HE1658


title: NP347


title: HE1655


title: HE1654


title: HE1468


title: CVirO

source_name: Adult Cerebellum tissue

value: Cerebellum


title: HE1467


title: HE1464


title: CVirB


title: CvirM


title: HP1063


title: CP1071


title: HP156


title: CP1063


title: CP1052


title: CP156


title: CP357


title: CP347


title: CP149


title: CE1658


title: CE1655


title: CE1654


title: CP353


title: CP146


title: CE1467


title: CE1468


title: WT ER mRNA-seq, no Tg (rep2)

city: Durham

first: David

last: Reid

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

description:
NMR1mrna
Processed data file: mRNA_expression.xlsx

data_processing:
Cutadapt: Trim AAGATCGGAAGAGCACACGTCT: cutadapt -a AAGATCGGAAGAGCACACGTCT -m 20 DBA37-P.fastq -o trimDBA37-P.fastq: cutadapt 1.6 with Python 2.7.6.
Bowtie: bowtie -p 7 -v 0 --norc database/chosenTranscripts reads/trimDBA37-P.fastq mapped/DBA37-P.map: Bowtie 1.1.1.
Read counting (Python script): Count reads in coding sequence, output as RPKM.
Genome_build: MGSCv37 (NCBI v37)
Supplementary_files_format_and_content: XLSX; RPKM values for all genes within the coding sequence.

source_name: C57BL/6 mouse embryonic fibroblasts, ER, untreated

extract_protocol:
Cells fractionated between cytosol and ER using digitonin and DDM.
Ribosome profiling samples: digested with micrococcal nuclease, pellet ribosomes, end polish with PNK, gel purify ribosome footprint.
mRNA samples: Deplete rRNA using RiboZero, fragment RNA 20 min 95C in Mg-containing buffer, end polish with PNK.
NEB Directional Small RNA kit. Libraries purified by gel electrophoresis.

treatment_protocol: 1 uM Thapsigargin for a timecourse from 30 min to 4h.

value: mouse embryonic fibroblasts

tag: strain/background

tag: genotype/variation

value: WT

tag: subcellular compartment

value: endoplasmic reticulum

value: untreated

tag: method

value: mRNA


title: WT cytosol mRNA-seq, no Tg (rep2)

description:
NCR2mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, cytosol, untreated

value: cytosol

tag: treatment


title: WT ER mRNA-seq, 4 h Tg (rep2)

description:
4MR2mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, ER, 4 h Tg

value: 4 h Thapsigargin


title: WT ER mRNA-seq, 4 h Tg (rep1)

description:
4MR1mrna
Processed data file: mRNA_expression.xlsx


title: WT cytosol mRNA-seq, no Tg (rep1)

description:
NCR1mrna
Processed data file: mRNA_expression.xlsx


title: WT cytosol mRNA-seq, 4 h Tg (rep2)

description:
4CR2mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, cytosol, 4 h Tg


title: WT cytosol mRNA-seq, 4 h Tg (rep1)

description:
4CR1mrna
Processed data file: mRNA_expression.xlsx


title: WT ER mRNA-seq, 2 h Tg (rep2)

description:
2MR2mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, ER, 2 h Tg

value: 2 h Thapsigargin


title: WT ER mRNA-seq, 1 h Tg (rep1)

description:
1MR1mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, ER, 1 h Tg

value: 1 h Thapsigargin


title: WT ER mRNA-seq, 2 h Tg (rep1)

description:
2MR1mrna
Processed data file: mRNA_expression.xlsx


title: WT cytosol mRNA-seq, 2 h Tg (rep2)

description:
2CR2mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, cytosol, 2 h Tg


title: WT ER mRNA-seq, 1 h Tg (rep2)

description:
1MR2mrna
Processed data file: mRNA_expression.xlsx


title: WT cytosol mRNA-seq, 1 h Tg (rep1)

description:
1CR1mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, cytosol, 1 h Tg


title: WT cytosol mRNA-seq, 1 h Tg (rep2)

description:
1CR2mrna
Processed data file: mRNA_expression.xlsx


title: CE1464

tag: strain


title: WT cytosol mRNA-seq, 0.5 h Tg (rep2)

description:
05CR2mrna
Processed data file: mRNA_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, cytosol, 0.5 h Tg

value: 0.5 h Thapsigargin


title: WT ER ribosome profiling, no Tg (rep1)

description:
NM1fp
Processed data file: translation_expression.xlsx

data_processing:
Library strategy: Ribo-Seq
Cutadapt: Trim AAGATCGGAAGAGCACACGTCT: cutadapt -a AAGATCGGAAGAGCACACGTCT -m 20 DBA37-P.fastq -o trimDBA37-P.fastq: cutadapt 1.6 with Python 2.7.6.
Bowtie: bowtie -p 7 -v 0 --norc database/chosenTranscripts reads/trimDBA37-P.fastq mapped/DBA37-P.map: Bowtie 1.1.1.
Read counting (Python script): Count reads in coding sequence, output as RPKM.
Genome_build: MGSCv37 (NCBI v37)
Supplementary_files_format_and_content: XLSX; RPKM values for all genes within the coding sequence.

value: ribosome profiling


title: WT ER mRNA-seq, no Tg (rep3)

description:
NMR2mrna
Processed data file: mRNA_expression.xlsx


title: WT ER ribosome profiling, no Tg (rep2)

description:
NM2fp
Processed data file: translation_expression.xlsx


title: WT cytosol mRNA-seq, 0.5 h Tg (rep1)

description:
05CR1mrna
Processed data file: mRNA_expression.xlsx


title: WT cytosol ribosome profiling, no Tg (rep1)

description:
NC1fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, no Tg (rep2)

description:
NC2fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 4 h Tg (rep1)

description:
4M1fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 4 h Tg (rep2)

description:
4M2fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 2 h Tg (rep1)

description:
2M1fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, 4 h Tg (rep2)

description:
4C2fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, 4 h Tg (rep1)

description:
4C1fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, 2 h Tg (rep1)

description:
2C1fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 2 h Tg (rep2)

description:
2M2fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 1 h Tg (rep2)

description:
1M2fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 1 h Tg (rep1)

description:
1M1fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, 1 h Tg (rep2)

description:
1C2fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, 1 h Tg (rep1)

description:
1C1fp
Processed data file: translation_expression.xlsx


title: WT ER ribosome profiling, 0.5 h Tg (rep2)

description:
05M2fp
Processed data file: translation_expression.xlsx

source_name: C57BL/6 mouse embryonic fibroblasts, ER, 0.5 h Tg


title: WT cytosol mRNA-seq, 2 h Tg (rep1)

description:
2CR1mrna
Processed data file: mRNA_expression.xlsx


title: WT ER ribosome profiling, 0.5 h Tg (rep1)

description:
05M1fp
Processed data file: translation_expression.xlsx


title: WT cytosol ribosome profiling, 0.5 h Tg (rep2)

description:
05C2fp
Processed data file: translation_expression.xlsx


title: WT ER mRNA-seq, 0.5 h Tg (rep2)

description:
05MR2mrna
Processed data file: mRNA_expression.xlsx


title: WT cytosol ribosome profiling, 0.5 h Tg (rep1)

description:
05C1fp
Processed data file: translation_expression.xlsx


title: WT ER mRNA-seq, 0.5 h Tg (rep1)

description:
05MR1mrna
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A ER mrna, 4 h Tg (rep 2)

description:
T4Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 4 h Tg

value: eIF2a S51A


title: eIF2A S51A ER mrna, untreated (rep 2)

description:
TNMmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, untreated


title: eIF2A S51A cytosol mrna, untreated (rep 2)

description:
TNCmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, untreated


title: eIF2A S51A cytosol mrna, 4 h Tg (rep 2)

description:
T4Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 4 h Tg


title: eIF2A S51A ER mrna, 2 h Tg (rep 2)

description:
T2Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 2 h Tg


title: eIF2A S51A ER mrna, 1 h Tg (rep 2)

description:
T1Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 1 h Tg


title: eIF2A S51A cytosol mrna, 2 h Tg (rep 2)

description:
T2Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 2 h Tg


title: eIF2A S51A cytosol mrna, 1 h Tg (rep 2)

description:
T1Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 1 h Tg


title: WT cytosol ribosome profiling, 2 h Tg (rep2)

description:
2C2fp
Processed data file: translation_expression.xlsx


title: eIF2A S51A ER mrna, untreated (rep 1)

description:
SNMmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A cytosol mrna, 0.5 h Tg (rep 2)

description:
T05Cmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, cytosol, 0.5 h Tg


title: eIF2A S51A ER mrna, 2 h Tg (rep 1)

description:
S2Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A cytosol mrna, untreated (rep 1)

description:
SNCmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx


title: eIF2A S51A ER mrna, 0.5 h Tg (rep 2)

description:
T05Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx

source_name: eIF2a S51A mouse embryonic fibroblasts, ER, 0.5 h Tg


title: eIF2A S51A ER mrna, 4 h Tg (rep 1)

description:
S4Mmrna
eIF2a S51A MEFs: Scheuner et al. (PMID 11430820)
Processed data file: mRNA_expression.xlsx