title: wildtype_592_mRNA_seq_rep1

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

description: A plasmid with a 12-kb genomic fragment containing the human SOD1 gene (1) was modified by replacing a restriction fragment comprising upstream intron sequence, exon V, and 3'-untranslated sequence with a DNA fragment containing the intron sequence, exon V up to the stop codon, a 24-bp linker encoding the amino acid sequence LQLQASAV, the entire eYFP gene (Clontech), and the 3'-untranslated sequence (Fig. S1). This fragment was produced by PCR amplification in segments with oligonucleotides containing appropriate restriction sites for joining and was sequenced in its entirety. The G85R mutation was introduced into exon IV by replacing a genomic fragment spanning this exon with one containing the mutation, produced by oligonucleotide-directed PCR mutagenesis. The fragment was sequenced to verify that only the desired nucleotide change was present. The final constructs were digested with EcoRI and BamHI to produce DNA sequences that were injected into mouse embryos (C57BL/6J x SJL/J F2). Transgenic founder mice were identified by PCR amplification of DNA extracted from tail biopsies. Lines were maintained by periodic crossing with nontransgenic C57BL/6J x SJL/J F1 mice (Jackson Laboratories).

data_processing:
Align reads to genome bowtie (0.12.3) -m 1 -B 1 --solexa1.3-quals --sam --sam-nohead
Convert to Multiple Read Format (MRF) RSEQtools (0.6) bowtie2mrf
Calculate composite gene model gene expression RSEQtools (0.6) mrfQuantifier
Generate normalized signal plots RSEQtools (0.6) mrf2wig
Convert to bigWig wigToBigWig -clip
Genome_build: mm9
Supplementary_files_format_and_content: RSEQtools (0.6) gene expression format Columns: ucsc_cluster_id ucsc_transcript_id mgi_gene_symbol entrezgene_id #mapped_reads rpkm rpkm_plus

source_name: motor neuron cell bodies

extract_protocol: Total RNA extracted from laser microdissected motor neuron bodies.  Libraries prepared using standard Illumina paired-end protocol.

treatment_protocol: Wild type (strain 592) and mutant (strain 737) transgenic mice were sacrificed with a lethal dose of ketamine, followed by cardiac perfusion with PBS for 2 min.  Spinal cords were dissected within 5 min, divided transversely into 9 to 10 pieces, embedded in OCT, then frozen in 2-methybutane cooled with liquid nitrogen.  They were stored at -80°C until used for RNA preparation.  Twenty micron frozen tissue slices, each containing 9-10 individual sections, were produced using a Leica CM3050S cryostat at -20°C and mounted on RNase-free PEN-membrane 2 μm slides (Leica); they were kept at -20°C until used.  Individual slides were thawed and dried for 30-40 sec, followed by washing for 30-45 sec in RNase-free 70% ethanol for OCT removal.  The following steps were then performed in order: 30-45 sec incubation in 1% Azure B (MP Biomedicals) in 70% ethanol, two 30-40 sec washes in 70% ethanol, and 40 sec air-drying.  Azure B stained motor neuron cell bodies from the ventral horn from each section on the slide were laser dissected (Leica LMD6000, 20X objective) and collected in 30 μl guanidine thiocyanate buffer + DTT (RLT buffer; RNeasy Micro kit, Qiagen) in the 0.6 ml microfuge tube cap.  Recovery of all identifiable motor neurons from the 9-10 sections on each slide (~150 total) required <30 min.  Individual collection tubes were stored at -20°C until a sufficient number had been collected.  Samples were thawed and pooled, and total RNA was extracted from 3000 to 4000 motor neuron cell bodies from each animal using the RNeasy Micro kit (Qiagen) according to the protocol provided for LMD tissue.  The quality of the RNA was determined on an Agilent 2100 BioAnalyzer using an RNA Pico chip.  Total RNA preparations with an RNA Integrity Number (RIN) above 8 (usually 9-10) were used for RNA-Seq and qRT-PCR.

value: C57BL/6J x SJL/J

tag: age

value: 3 months

value: spinal cord sections

tag: genotype/variation

value: SOD1 YFP (wildtype 592)


title: Tumor sample 9T

status: Public on Dec 05 2012

type: SRA

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

country: USA

institute: University of Notre Dame

description: rRNA-depleted RNA

library_source: transcriptomic

data_processing: High-throughput sequencing reads were mapped against human genome assembly (NCBI Build GRCh37). The reads with at most 2 mismatches and a maximum of 10 mappable locations were retained for calculation of gene expression. The gene expression level is measured by RPKM (number of exon reads mapped per kilobase per million mapped reads). The gene differential expression was evaluated using the t-test and Baggerley's test.

molecule: total RNA

organism: Homo sapiens

source_name: esophageal cell type

growth_protocol: Esophageal squamous cell carcinoma and adjacent non-tumorous tissues were obtained from patients immediately following resection, snapped-frozen in liquid nitrogen and stored in -80C freezer prior to RNA extraction.

extract_protocol: The total RNA samples were treated with DNA-free Kit (Ambion, Inc. TX, USA) to digest the DNA. Large 18S and 28S rRNAs were removed from 1ug total RNA with the RiboMinusTM Transcriptome Isolation kit (Human/Mouse) (Invitrogen, Carlsbad, CA, USA). The rRNA-depleted RNA was precipitated with Pellet Paint (Novagen Inc., Madison, Wis.), quality checked on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). The rRNA-depleted RNA from 1 ug of total RNA was fragmented by incubation for 5 min at 94°C in 5 x Array Fragmentation Buffer (Ambion, Inc. TX, USA). The reaction was stop by chilling the tube on ice and precipitated with Pellet Paint. Double strand cDNA was synthesized with the SuperScript Double Stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) using random hexamers according to the manufacturer's instructions. The reaction was cleaned up on a QiaQuick PCR column (Qiagen, Valencia, CA, USA). Ds cDNA fragments were repaired with DNA Terminator End Repair Kit End (Lucigen, Middleton, WI, USA) by incubation for 30 min at 30°C and then were cleaned up on a QiaQuick PCR column. The Klenow 3' to 5' exo- (NEB, Ipswich, MA) was used to add a single 'A' base to the 3'end of blunt phosphorylated DNA fragments by incubation for 30 min at 30°C. After clean-up on a QiaQuick PCR column, Illumina PE Adapter was ligated to the end of DNA fragments with the Quick Ligation Kit (NEB, Ipswich, MA) by incubation for 15 min at room temperature. The reaction was cleaned up on a QiaQuick PCR column. 180-200 bp fragments were excised from a 2% low range agarose gel. Fragments were enriched by 10 cycles using AccuPrime Pfx DNA Polymerase (Invitrogen, Carlsbad, CA, USA). PCR product was run on Novex 8% TBE polyacrylamide gel (Invitrogen, Carlsbad, CA, USA) and stained with SYBR Gold (Invitrogen, Carlsbad, CA, USA). The gel slice was cut off and cleaned up by QiaQuick Gel Extraction Kit (Qiagen, Valencia, CA, USA). The concentration of gel purified DNA fragments was measured by using a ND-1000 UV/Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA)

tag: tissue

value: tumor


title: G85R_737_mRNA_seq_rep1

status: Public on Dec 04 2012

molecule: polyA RNA

organism: Mus musculus

tag: strain

value: SOD1 G85R YFP (737) transgenic mice


title: KAP1 ChIP: KAP1 KO IP

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

country: Switzerland

institute: EPFL

library_source: genomic

data_processing:
Raw reads were mapped to the mouse genome and transcriptome using Bowtie
Peaks were called using MACS
For histone modifications, enriched regions were defined using the ChIP-part suite
Genome_build: mm9

molecule: genomic DNA

source_name: KAP1 ChIP: KAP1 KO IP

growth_protocol: ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma: G5154) with sodium pyruvate (used at 1mM, Sigma: S8636), MEM non-essential amino acids (used at 1x, Gibco: 11140-035), L-glutamine (used at 2mM, Gibco: 25030-024), 2-mercaptoethanol (used at 0.1mM, Sigma), ES cell tested FBS (Gibco: 16141-079) and leukaemia inhibitory factor (LIF, used at 1,000 units/ml, Chemicon: ESG1107). Cells were grown on 0.2% gelatin (Sigma: 48723-500G-F)-coated plates and split every two days.

extract_protocol: ES cell samples were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x24mm tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 30 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment. Immunoprecipitations were performed in duplicates or triplicates with Dynabeads (100.03D) using 1-2x10e6 cells, 80ul pre-blocked beads and 5ug antibody (or no antibody as a control) per sample in IP buffer (167mM NaCl, 16.7mM Tris pH 8.1, 1.2mM EDTA, 0.5mM EGTA, 1.1%TritonX100 and protease inhibitors) overnight. After washing and reverse cross-linking (also overnight) and DNA extraction, results were quantified by SYBR green qPCR.

tag: cell type

value: Embryonic stem cells (ES3)

tag: time-point

value: KO:4 days post 4-OHT inducible CRE

tag: chip antibody

value: Tronolab, rabbit polyclonal SY 3267-68


title: KAP1 ChIP: KAP1 WT IP

description: The file "rbcc_wt_vs_ti_peaks.bed" was used in this paper:  586 of the 3099 peaks mapped here are included in our other Kap1 ChIP-seq (GSM773067_kap1.bed) that was performed in E14 cells.

source_name: KAP1 ChIP: KAP1 WT IP

value: WT cells cultured for 4 days


title: wildtype_592_mRNA_seq_rep2


title: rat_ts_3seq_rep1

city: Boulder

first: Edward

last: Chuong

address: 596 UCB

department: BioFrontiers

institute: University of Colorado Boulder

description: mRNA

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using Bowtie 0.12.7 with the settings --best --strata -k 10 -S --chunkmbs 190
Using Unipeak v1.0, Bowtie alignments were filtered by posterior probability (sam_map.pl from Unipeak), and transcription peaks were called using default settings.
Peaks (chromosomal coordinates) were associated with Ensembl (e67) gene database for mouse and rat, and multiple peaks for each gene were pooled.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain pooled gene x raw tag count

organism: Rattus norvegicus

source_name: Trophoblast stem cells

growth_protocol: Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004). Rat TSCs were cultured as previously (Asanoma et al, Developmental Biology 2011)

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

value: HSD

value: Trophoblast stem cells


title: KAP1 ChIP: KAP1 WT TI

source_name: KAP1 ChIP: KAP1 WT TI

extract_protocol: ES cell samples were washed 2x (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x24mm tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 30 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment.

value: None (Total Input)


title: mRNA-seq: ES KAP1 WT (ES3 cells)

description: See also Rowe et al., 2010 for analysis of this data for ERV expression

source_name: mRNA-seq: ES KAP1 WT (ES3 cells)

extract_protocol: After pooling duplicates, total RNA was extracted with TRizol (Invitrogen: 15596-018), purified using a PureLink RNA kit (Ambion: 12183018A) and treated with DNase (Ambion: AM1907) before checking the quality on a bioanalyzer and using 10ug for mRNA-seq library preparation.


title: mRNA-seq: MEF KAP1 WT

source_name: mRNA-seq: MEF KAP1 WT

value: Mouse embryonic fibroblasts

value: WT cells cultured for 5 days


title: mRNA-seq: ES KAP1 KO (ES3 cells)

source_name: mRNA-seq: ES KAP1 KO (ES3 cells)


title: mRNA-seq: MEF KAP1 KO

source_name: mRNA-seq: MEF KAP1 KO

value: KO:5 days post 4-OHT inducible CRE (due to slower cell division time of MEFs)


title: GRIP1-ChIP  + 1uM Dex + LPS replicate

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the mouse genome (July 2007; mm9, NCBI Build 37) using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).

source_name: primary bone marrow-derived macrophages

growth_protocol: Bone marrow was purified and differentiated in DMEM containing 20% fetal bovine serum, 30% L929 conditioned media, and antibiotics for 5 days, then re-plated in macrophage serum free media (Invitrogen) overnight.

extract_protocol:
Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.
Standard Illumina DNA library construction

value: primary bone marrow-derived macrophages

tag: treatment

value: Dexamethasone treated, LPS-stimulated macrophages


title: GRIP1-ChIP + LPS

value: LPS-stimulated macrophages


title: IRF3-ChIP  + 1uM Dex + LPS

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline 1.7 and mapped to the mouse genome (July 2007; mm9, NCBI Build 37) using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: mm9
Supplementary_files_format_and_content: bowtie files are alignments made from fastq files with the Bowtie aligner; bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak files were generated using Homer.

extract_protocol: Standard Illumina DNA library construction

treatment_protocol: Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.


title: IRF3-ChIP + LPS


title: cJun-ChIP + LPS

value: cJun

value: LPS-stimulated


title: cJun-ChIP + 1uM Dex + LPS

source_name: cJun-ChIP_1uM Dex_LPS

value: Dexamethasone treated, LPS-stimulated


title: NF-kB/p65-ChIP + 1uM Dex +LPS

source_name: NF-kB/p65-ChIP_1uM Dex_LPS


title: GR-ChIP + 1uM Dex

source_name: GR-ChIP_1uM Dex

value: Glucocorticoid Receptor

value: Dexamethasone treated, unstimulated


title: GR-ChIP + 1uM Dex + LPS

source_name: GR-ChIP_1uM Dex_LPS


title: mouse_ts_h3k27ac

description: ChIP DNA

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using BWA 0.9.6 (-q 10 -I), and filtered using samtools view (-q 1) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.9 with default settings, using --broad setting for histone marks.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq bed files contain peaks called by MACS v2.0.9

extract_protocol:
Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or HiSeq following the manufacturer's protocols.


title: G85R_737_mRNA_seq_rep2

value: C57BL/6J x SJL/J

value: 3 months

value: spinal cord sections

value: SOD1 G85R YFP (737) transgenic mice


title: mouse_ts_input (paired-end)

description: Input chromatin

value: Trophoblast stem cells


title: mouse_ts_cdx2

description: ChIP DNA


title: SNPKI_DiMeK4

city: Cambridge

first: Judith

last: Schütte

address: Hills Road

country: United Kingdom

institute: Cambridge Institue for Medical Research

description: Chromatin IP against dimethyl-Histone H3 (Lys4)

data_processing: Processed alignment files include either .sam or .bw files. The .sam files were created using Bowtie 0.12.7. The .bw files were created by converting .sam files to .bed files, then to .wig files, then to .bw files using in house scripts. All alignments were made to the mm9 mouse genome.

source_name: Lin-Sca1-cKit+ cells

extract_protocol:
Chromatin imunoprecipitation assay cells were incubated in 1% formaldehyde for 10 minutes at room temperature. To quench the reaction 0.125M glycine was added and the cells were incubated at room temperature for 5 minutes. Cells were immediately harvested and washed in cold 1x PBS. Cells were harvested and resuspended in 1.5 x pellet volume of cell lysis buffer (10mM Tris pH 8.0, 10mM NaCl and 0.2% NP40) containing protease inhibitors (leupeptin, NaBu and PMSF), the cells were homogenised and incubated on ice for 10 minutes. The nuclei were harvested at 600 x g for 5 minutes at 4oC and resuspended in nuclei lysis buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) (same volume as cell lysis buffer) containing protease inhibitors (leupeptin, NaBu and PMSF), the cells were homogensised and incubated on ice for 10 minutes. An equal volume of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) containing protease inhibitors (leupeptin, NaBu and PMSF) was added. Cells were sonicated on ice-water (Biorupter, Diagenode) for 5 cycles (30s on, 30s off). The chromatin solution was centrifuged for 10 minutes at 3220 x g. After transferring the chromatin solution to a clean falcon tube, IP buffer was added to make 1:4 ratio final, nuclei lysis:IP dilution buffers. The chromatin solution was pre-cleared by the addition of 50μl of rabbit IgG (2 μg/μl) and incubated at 4oC for 1 hour, then Protein G sepharose beads (1:1 slurry in IP dilution buffer) were added to the chromatin solution and further incubated at 4oC for 2 hours. The beads/IgG were collected by centrifugation at 1791 x g for 2 minutes. The chromatin was transferred to 1.5 ml tubes, an input sample was removed and antibodies were added then incubated overnight at 4oC with rotation. Protein G agarose beads (1:1 slurry in IP dilution buffer) were added and incubated with the samples for 2 hours. The beads were harvested at 5400 x g for 2 minutes and washed twice with low salt buffer (20mM Tris pH 8.0, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), then once with LiCl buffer (10mM Tris pH 8.0, 1mM EDTA, 0.25M LiCl, 1% NP40, 1% Sodium deoxycholate monohydrate) and twice with 1x TE pH 8.0. The complexes were eluted twice from the beads by adding elution buffer (100mM NaHCO3, 1% SDS). To reverse the cross-linking 0.3M NaCl was added to all the IP samples and input, RNase was added and the samples were incubated at 65oC overnight. The samples were then treated with Proteinase K for 2 hours at 45oC. DNA was purified using Qiagen PCR clean up columns.
Chromatin was fixed in 1% formaldehyde, sheared to 150-400bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

tag: fusion protein/snp

value: Gfi1 36N

value: Compromises GMPs (Granulocytic-monocytic-progenitors), CMPs (Common-myeloid-progenitors) and MEPs (Megakaryocytic-erythroid progenitors)

tag: antibody

value: dimethyl-Histone H3 (Lys4)

tag: antibody vendor

value: Upstate

tag: antibody cat#

tag: antibody lot#

tag: background strain


title: MLL-ENL_Gfi1

description: Chromatin IP against Gfi1

source_name: MLL-ENL immortalized bone marrow progenitor cells

value: MLL-ENL

value: Factor-dependent cells capable of sustained growth in liquid medium containing RPMI/10%FCS/1%PenStrep, supplemented with 6ng/ml of recombinant interleukin 3

value: abcam


title: mouse_ts_elf5 (paired-end)

description:
ChIP DNA
processed data available on GSM1035390

value: Elf5 (Santa Cruz, sc-9645x, lot D2109)


title: mouse_ts_elf5

description: ChIP DNA


title: mouse_ts_h3k9me3 (paired-end)

description:
ChIP DNA
processed data available on GSM1035383


title: mouse_ts_eomes

description: ChIP DNA


title: mouse_ts_h3k27ac (paired-end)

description:
ChIP DNA
processed data available on GSM1035380


title: mouse_ts_h3k27me3 (paired-end)

description:
ChIP DNA
processed data available on GSM1035386


title: mouse_ts_h3k9me3

description: ChIP DNA


title: H3K27ac ChIP: KAP1 KD IP

description: no processed data

source_name: H3K27ac ChIP: KAP1 KD IP

value: Embryonic stem cells (ES3)

value: 4 days post puromycin selection of KAP1 shRNA vector (a time-point with similar expression to 4 days post KO)

value: H3K27ac (Abcam:ab4729)


title: H3K27ac ChIP: KAP1 WT IP

description: no processed data

source_name: H3K27ac ChIP: KAP1 WT IP

value: 4 days post puromycin selection of empty shRNA vector


title: mouse_ts_h3k27me3

description: ChIP DNA


title: H3K27ac ChIP: KAP1 WT TI

source_name: H3K27ac ChIP: KAP1 WT TI

value: None (Total Input)


title: H3K27ac ChIP: KAP1 KD TI

source_name: H3K27ac ChIP: KAP1 KD TI

value: 4 days post puromycin selection of KAP1 shRNA vector


title: H3K9me3 ChIP: KAP1 WT IP

description: The file "chip_part_es_h3k9_wt_only.bed" (KAP1-dependent H3K9me3 peaks) was used in this paper

source_name: H3K9me3 ChIP: KAP1 WT IP

value: WT cells cultured for 4 days

value: H3K9me3 (Abcam:ab8898)


title: H3K9me3 ChIP: KAP1 KO TI

source_name: H3K9me3 ChIP: KAP1 KO TI

value: KO:4 days post 4-OHT inducible CRE


title: H3K9me3 ChIP: KAP1 WT TI

source_name: H3K9me3 ChIP: KAP1 WT TI


title: mRNA-seq: ES KAP1 KD (Rex1GFP ES cells)

source_name: mRNA-seq: ES KAP1 KD (Rex1GFP ES cells)

value: Embryonic stem cells (Rex1GFP, Wray et al., Nat Cell Biol. 2011)


title: H3K9me3 ChIP: KAP1 KO IP

source_name: H3K9me3 ChIP: KAP1 KO IP

value: KO:4 days post 4-OHT inducible CRE (to parallel the mRNA-seq time-point, although H3K9me3 is decreased but not lost at this stage)


title: rat_ts_input

description: Input chromatin

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using BWA 0.9.6 (-q 10 -I), and filtered using samtools view (-q 1) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.9 with default settings, using --broad setting for histone marks.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-Seq bed files contain peaks called by MACS v2.0.9

source_name: Trophoblast stem cells

value: HSD

value: Trophoblast stem cells


title: mRNA-seq: ES KAP1 WT (Rex1GFP ES cells)

source_name: mRNA-seq: ES KAP1 WT (Rex1GFP ES cells)


title: rat_ts_h3k27me3 (paired-end)

description:
ChIP DNA
processed data available on GSM1035400


title: rat_ts_h3k27me3

description: ChIP DNA


title: WthKI_DiMeK4

value: Gfi1 36S

value: Compromises GMPs (Granulocytic-monocytic-progenitors), CMPs (Common-myeloid-progenitors) and MEPs (Megakaryocytic-erythroid progenitors)

value: dimethyl-Histone H3 (Lys4)

value: Upstate


title: HudsonAlpha_MethylRrbs_HepG2

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylRrbs

tag: datatype description

value: DNA Methyl Reduced Rep Bisulfite Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: hepatocellular carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: obtainedby

tag: obtainedby description

tag: replicate


title: rat_ts_h3k4me1

description: ChIP DNA

tag: strain

tag: chip antibody

tag: cell type


title: mouse_ts_eomes (paired-end)

description:
ChIP DNA
processed data available on GSM1035388


title: HudsonAlpha_MethylRrbs_PANC-1

tag: lab

tag: lab description

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

tag: treatment

value: UW

value: Stamatoyannopoulous - University of Washington


title: rat_ts_h3k9me3

description: ChIP DNA

value: HSD

value: Trophoblast stem cells


title: rat_ts_h3k27ac

description: ChIP DNA


title: rat_ts_h3k4me3

description: ChIP DNA


title: germ cell tumor A11

status: Public on Dec 03 2012

city: hsinchu

first: wei-chung

last: cheng

address: adqwerqr ew

country: Taiwan

institute: NTHU

data_processing:
3’ adaptors of the FASTQ raw data were trimmed, and trimmed data were collapsed by the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit).
For all datasets, reads that shorter than 17 nt or longer than 30 nt were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM value of mature miRNA across 34 samples

source_name: Brain

extract_protocol: TruSeq Small RNA Sample Prep Kit (Cat# RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Study cases were retrieved from the surgical pathology file of the Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taiwan. Patients in this study had provided informed consent, and all procedures were approved by the Institutional Review Board of Taipei Veterans General Hospital. Fresh tumor tissues removed during surgery were snap frozen and kept in liquid nitrogen for RNA extraction.

tag: source tissue

value: Brain

tag: tissue

value: germ cell tumor


title: embryonal tumor A04

value: embryonal tumor


title: germ cell tumor A09


title: germ cell tumor A10


title: germ cell tumor A12


title: embryonal tumor A06


title: embryonal tumor A13


title: embryonal tumor A07


title: rat_ts_input (paired-end)

description: Input chromatin


title: glioma A01

value: glioma


title: glioma A02


title: embryonal tumor A15


title: embryonal tumor A17


title: embryonal tumor A14


title: germ cell tumor A18


title: H3K4me3_2x10e4_R3

city: Oslo

first: Gregor

middle: Duncan

last: Gilfillan

address: Medisinsk Genetikk

department: Medical Genetics

country: Norway

institute: Oslo Universitetssykehus

description: H3K4me3 ChIP, lowest cell number, replicate 3

data_processing:
Illumina GAIIx image analysis and base calling was performed using Illumina’s RTA software version 1.4 and experiments performed on the Illumina HiSeq 2000 were analysed using RTA version 1.12.
Reads were filtered to remove those with low base call quality using Illumina’s default chastity criteria.
Reads were mapped to the human reference genome using BWA version 0.5.9 with default settings
Filtering of alignment files to identify uniquely mapping, non-duplicate reads, was performed using samtools version 0.1.15.
Manipulation of alignments for display was performed using bedtools version 2.11.2 software, with visualisation in the IGV genome browser.
Peak calling was performed by MACS version 1.4 [25] using shift size determined by the size of sequencing library inserts, and switching off local background estimation.
Genome_build: hg18
Supplementary_files_format_and_content: bed files of peaks called in experiments scaling down ChIP with H3K4me3 in a benchmark technique, and in new technique from 2 x 10e7 cells / IP to 2 x 10e4 cells / IP

source_name: Primary (live-frozen) CD4+ cells

growth_protocol: Both cultured and primary CD4+ and CD8+ lymphocytes used. CD8+ and CD4+ cells were sequentially isolated using an AutoMACS Pro separator (Miltenyi Biotec, Köln, Germany) by positive and negative isolation, respectively. Cultured cells were activated using Human T-Expander CD3/CD28 (Invitrogen, Carlsbad, CA) according to manufacturers instructions and cells were cultured in X-VIVO media (Lonza) supplemented with Interleukin II (10 ng/ul) for a period of two weeks at 37oC in a humidified incubator under 5% CO2.

extract_protocol:
Native chromatin was prepared by lysing CD4+ cells in low salt buffer and digesting with Micrococcal nuclease. Lysates were then sonicated to assist in recovery of oligonucleosomes and adjusted to RIPA immunoprecipitation buffer conditions. Extracts were then incubated overnight with specific antisera prior to immunoprecipitation with protein A & G beads, and recovery of bound DNA using silica column purification.
Twenty five microliters of immunoprecipitated or input DNA (ranging from <1 ng – 4 ng DNA) was used for library preparation using Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation reagents, with ligation of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range.

tag: cell number

value: H3K4me3 (Diagenode, Cat# pAb-003-050)


title: embryonal tumor A16


title: H3K4me3_2x10e4_R2

description: H3K4me3 ChIP, lowest cell number, replicate 2


title: H3K4me3_2x10e4_R1

description: H3K4me3 ChIP, lowest cell number, replicate 1


title: H3K4me3_1x10e5_R1

description: H3K4me3 ChIP, low cell number, replicate 1


title: H3K4me3_1x10e5_R2

description: H3K4me3 ChIP, low cell number, replicate 2


title: H3K27me3_2x10e4_R2

description: H3K27me3 ChIP, lowest cell number, replicate 2

value: H3K27me3 (Upstate Biotech, Cat# 07-449)


title: H3K27me3_2x10e4_R1

description: H3K27me3 ChIP, lowest cell number, replicate 1


title: glioma A08


title: H3K27me3_2x10e4_R3

description: H3K27me3 ChIP, lowest cell number, replicate 3


title: embryonal tumor A05


title: glioma A03


title: New_input_2x10e4

description: Input, Lowest cell number , new protocol

source_name: Cultured CD4+ cells

value: Input Mnase digested DNA


title: H3K27me3_1x10e5_R1

description: H3K27me3 ChIP, low cell number, replicate 1


title: New_input_0.5x10e6

description: Input, Decreasing cell number , new protocol


title: New_input_1x10e5


title: New_input_2x10e7

description: Input, High cell number , new protocol


title: H3K27me3_1x10e5_R3

description: H3K27me3 ChIP, low cell number, replicate 3


title: New_input_2.5x10e6


title: Benchmark_input_2x10e7

description: Input, High cell number , published protocol


title: H3K27me3_1x10e5_R2

description: H3K27me3 ChIP, low cell number, replicate 2


title: glioma A55


title: glioma A52


title: glioma A50


title: glioma A51


title: glioma A58


title: glioma A60


title: glioma A53


title: glioma A61


title: M-P2

city: wuhan

first: shaopeng

last: zhang

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huangzhong agricultural university

description: Sample 6

data_processing:
We used Vmatch (www.vmatch.de) large-scale sequence analysis software to map the collapsed reads to the maize reference genome.the unique DpnII and NlaIII tags were queried for complete matches to all possible 20- and 21-mer sequences, respectively, using the Vmatch algorithm.
Tags that mapped uniquely up to three places in the maize genome were used to extract gene information using the Ensembl Application Perl Interface (http://uswest.ensembl.org/info/docs/api).
A working gene set was used (gene build 4a.53; maizesequence.org), and tags that mapped uniquely up to three places in the maize genome were selected to extract gene information using the Ensembl Application Perl Interface (http://uswest.ensembl.org/info/docs/api). In order to maximize the capture of complete UTRs, each gene model and the gene space was then computationally extended by 300 nucleotides at both 5' - and 3'-ends
In this study, genes that were differentially expressed between CK and P1, CK and P2, P1 and P2 stage were identified using a free open-source “DEseq” package based on R software, which allowed analysis of experiments with no biological replicates (http://www-huber.embl.de/users/anders/DESeq/)
Genome_build: B73 RefGen_v1
Supplementary_files_format_and_content: tab-delimited text files include P-values and log2 fold changse for each Sample

organism: Zea mays

growth_protocol: the seedlings were incubated in a culture chamber for further infection by S. reilianum at 23°C: 20°C (light : dark, 14:10 h) and 20% relative humidity

extract_protocol:
Radicle roots were selected based on PCR results, and corresponding RNAs were harvested using Trizol reagent.
Digital gene expression (DGE): 500 to 2,000 ng of DNaseI-treated total RNA was used in library construction:double-stranded cDNAs were synthesized using oligo(dT) beads (Invitrogen). The cDNAs were then digested with an anchoring restriction enzyme (NlaIII or DpnII) and ligated to an Illumina-specific adapter, Adapter A, containing a recognition site or the type IIS restriction enzyme MmeI (New England Biolabs). Following MmeI digestion and dephosphorylation with shrimp alkaline phosphatase (USB Corp.), cDNAs were purified and a second Illumina adapter, Adapter B, containing a 2-bp degenerate 3# overhang, was ligated. Tags flanked by both adapters were enriched by PCR using Phusion DNA polymerase (Finnzymes) and Gex PCR primers 1 and 2 (Illumina) following the manufacturer’s instructions.PCR products were visualized on a 12% PAGE gel. The 85-bp DNA band was excised and purified using a Spin-X filter column (Costar). DNA quantification and quality analysis was performed using an Agilent DNA 1000 series II assay, and the DNA sample was diluted to 10 nM. Cluster generation and sequencing were run on the Illumina cluster station and Genome Analyzer (Illumina). Raw sequences were extracted from the resulting image files using the open source Firecrest and Bustard applications (Illumina).

treatment_protocol: Mock-inoculated roots with water were set as the Control group (CK), After inoculation, there were two different phenotypes based on the PCR results: set negative PCR result as Post-inoculation stage 1 (P1) and positive PCR result as post-inoculation stage 2 (P2), which were considered as two different infection statuses in the root after inoculation

tag: line

tag: disease-resistance

value: resistant

value: radicle roots

tag: inoculated with

value: teliospores of Sporisorium reilianum f. sp. Zeae

tag: infection status

value: post-inoculation stage2 (P2)

tag: develpmental stage

value: 6 days post inoculation after seed germination


title: glioma A57


title: H3K4me3_1x10e5_R3

description: H3K4me3 ChIP, low cell number, replicate 3


title: M-P1

description: Sample 5

value: post-inoculation stage1 (P1)


title: germ cell tumor A22


title: M-CK

description: Sample 4

value: water (mock)

value: control stage (ck)


title: H-P1

description: Sample 2

value: susceptible


title: germ cell tumor A20


title: H-P2

description: Sample 3


title: New_H3K4me3_2x10e4

description: Lowest cell number ChIP, new protocol


title: glioma A54


title: DP input control

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court Suite 300

institute: TSRI

description: Chip-Seq input control

data_processing:
Data filtering by duplicate read removal.
Mapping with bowtie. Settings -q -y -a -v 2 -p 8 -m 3 --best --strata
Filtering for uniquely mapped reads as well as reads mapped to multiple locations within the IgH, TCR, and LINE repeats.
Binning of reads in 25 bp windows.
Significant bins determined by dynamic windows utilizing Poisson distribution where the null distribution is based upon the the greater of the entire genome, 1kb, 5kb, and 10kb windows as baseline.
Genome_build: mm9
Supplementary_files_format_and_content: dp-ctcf.wig - CTCF reads with input control reads subtracted. dp-ctcf.peaks.txt - significant peaks at 1e-5 threshold of significance.

source_name: Rag1 -/- with TCRb transgene, thymocytes

growth_protocol: Thymocytes were obtained from 4- to 8-wk-old Rag1−/− mice carying a rearranged TCRb transgene

extract_protocol:
B6 Rag1−/− thymocytes were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the lysates were sonicated using a Diagenode Biorupter. The chromatin solution was precleared with salmon sperm DNA-protein A agarose beads. The lysate was immunoprecipitated with antibodies against CTCF (Millipore 07-729). Immune complexes were isolated with protein A agarose beads.  Following elution, chromatin-antibody complexes and input DNA were reverse crosslinked by heating at 65°C overnight.  The DNA was purified using the Qiagen DNA purification kit.
The sequencing libraries were prepared using 10 ng double-stranded cDNA prepared by ChIP (pull-down and input). ChIP DNA samples ends were repaired using recommended Illumina protocol including T4 DNA polymerase, Klenow Large Fragment, and T4 polynucleotide kinase. DNA products were purified using DNA Clean&Concentrator™-5 Kit (Zymo Research). Next, DNA ends were A-tailed with Klenow (3’→5’ exo-) at 37C for 30 min. DNA products were again purified using the DNA Clean&Concentrator™-5 Kit. Next, Illumina Paired End-adapter oligonucleotides, at 0.33 μM concentration, were ligated to the A-tailed cDNA ends with T4 DNA ligase. DNA products were purified using DNA Clean&Concentrator™-5 Kit. The DNA library products were then separated on a 2% agarose gel and products corresponding to a size of approximately 200-250 bases were removed from the gel and cleaned using the Agencourt SPRI system (Beckman). The DNA material was PCR amplified with Phusion™ Polymerase (Finnzymes) with 0.6 μM PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles. The amplified DNA products were further purified on 2% agarose gel, excised, and isolated again using Zymoclean™Gel DNA recovery kit. The purified DNA library was quantitated using the Qubit quantitation platform (Invitrogen) and sized using the 2100 Bioanalyzer (Agilent). DNA products were then denatured in 0.1N NaOH and diluted to a final concentration of 10 pM before being loaded onto the Illumina paired-end flow-cell for massively parallel sequencing by synthesis on the Illumina GAIIx.

tag: genotype/variation

value: Rag1 -/- with TCRbeta transgene

tag: age

value: 4- to 8-wk-old

value: CD4+CD8+ (DP) thymocytes


title: pro-B input control

data_processing:
Data filtering by duplicate read removal.
Mapping with bowtie. Settings -q -y -a -v 2 -p 8 -m 3 --best --strata
Filtering for uniquely mapped reads as well as reads mapped to multiple locations within the IgH, TCR, and LINE repeats.
Binning of reads in 25 bp windows.
Significant bins determined by dynamic windows utilizing Poisson distribution where the null distribution is based upon the the greater of the entire genome, 1kb, 5kb, and 10kb windows as baseline.
Genome_build: mm9
Supplementary_files_format_and_content: prob-ctcf.wig - CTCF reads with input control reads subtracted. prob-ctcf.peaks.txt - significant peaks at 1e-5 threshold of significance.

source_name: Rag1 -/- pro-B cells

growth_protocol: Bone marrow cells were isolated from 5- to 8-wk-old Rag1−/− mice and were enriched for CD19+ cells with MACS microbeads.

extract_protocol:
B6 Rag1−/− pro-B cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the lysates were sonicated using a Diagenode Biorupter. The chromatin solution was precleared with salmon sperm DNA-protein A agarose beads. The lysate was immunoprecipitated with antibodies against CTCF (Millipore 07-729) . Immune complexes were isolated with protein A agarose beads.  Following elution, chromatin-antibody complexes and input DNA were reverse crosslinked by heating at 65°C overnight.  The DNA was purified using the Qiagen DNA purification kit.
The sequencing libraries were prepared using 10 ng double-stranded cDNA prepared by ChIP (pull-down and input). ChIP DNA samples ends were repaired using recommended Illumina protocol including T4 DNA polymerase, Klenow Large Fragment, and T4 polynucleotide kinase. DNA products were purified using DNA Clean&Concentrator™-5 Kit (Zymo Research). Next, DNA ends were A-tailed with Klenow (3’→5’ exo-) at 37C for 30 min. DNA products were again purified using the DNA Clean&Concentrator™-5 Kit. Next, Illumina Paired End-adapter oligonucleotides, at 0.33 μM concentration, were ligated to the A-tailed cDNA ends with T4 DNA ligase. DNA products were purified using DNA Clean&Concentrator™-5 Kit. The DNA library products were then separated on a 2% agarose gel and products corresponding to a size of approximately 200-250 bases were removed from the gel and cleaned using the Agencourt SPRI system (Beckman). The DNA material was PCR amplified with Phusion™ Polymerase (Finnzymes) with 0.6 μM PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles. The amplified DNA products were further purified on 2% agarose gel, excised, and isolated again using Zymoclean™Gel DNA recovery kit. The purified DNA library was quantitated using the Qubit quantitation platform (Invitrogen) and sized using the 2100 Bioanalyzer (Agilent). DNA products were then denatured in 0.1N NaOH and diluted to a final concentration of 7    s pM before being loaded onto the Illumina paired-end flow-cell for massively parallel sequencing by synthesis on the Illumina HiSeq2000.

value: 5- to 8-wk-old

value: pro-B cells


title: germ cell tumor A19

value: Brain

value: germ cell tumor


title: germ cell tumor A21


title: CTCF_DP ChIP_seq

description: CTCF_DP ChIP_seq

value: Anti-CTCF Antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: New_H3K4me3_1x10e5

description: Decreasing cell number ChIP, new protocol

tag: chip antibody

value: H3K4me3 (Diagenode, Cat# pAb-003-050)


title: New_H3K4me3_0.5x10e6


title: glioma A59

value: glioma


title: Benchmark_H3K4me3_2x10e7

description: High cell number ChIP, published protocol


title: New_H3K4me3_2.5x10e6


title: CTCF_DN ChIP_seq

description: CTCF_DN ChIP_seq

data_processing:
Data filtering by duplicate read removal.
Mapping with bowtie. Settings -q -y -a -v 2 -p 8 -m 3 --best --strata
Filtering for uniquely mapped reads as well as reads mapped to multiple locations within the IgH, TCR, and LINE repeats.
Binning of reads in 25 bp windows.
Significant bins determined by dynamic windows utilizing Poisson distribution where the null distribution is based upon the the greater of the entire genome, 1kb, 5kb, and 10kb windows as baseline.
Genome_build: mm9
Supplementary_files_format_and_content: dn-ctcf.wig - CTCF reads with input control reads subtracted. dn-ctcf.peaks.txt - significant peaks at 1e-5 threshold of significance.

source_name: Rag1 -/- CD4-CD8- (DN) thymocytes

growth_protocol: Thymocytes were obtained from 4- to 8-wk-old Rag1−/− mice

tag: strain

value: Rag -/-

value: CD4-CD8- (DN) thymocytes


title: glioma A56


title: DN input control

description: Chip-Seq input control


title: New_H3K4me3_2x10e7

description: High cell number ChIP, new protocol


title: CD3_547

status: Public on Dec 01 2012

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

country: Sweden

institute: Uppsala University

data_processing:
Image analysis and base calling were performed with Illumina pipeline v1.4.
The processed data file (DGE_RawTagExp_Normalized.txt) contains the trimmed, quality filtered, unique 17bp reads (column 1) and the frequency of each tag in transcripts per million (TPM) for each sample. Custom perl scripts were used to generate the processed data file.
The processed data file (DGE_Sense_GeneExpression_TPM.txt) contains the gene-level summary expression values in TPM. The HGNC and ENSEMBL gene identifiers are given in the first column.
The processed data file (DGE_Antisense_GeneExpression_TPM.txt) contains the summary gene-level expression values in TPM of tags annotated to the antisense (non-coding) strand of each gene.  The HGNC and ENSEMBL gene identifiers are given in the first column.
Genome_build: Hg19

source_name: Peripheral Blood

extract_protocol:
Qiagen ALLprep DNA/RNA
DGE-Tag Profiling NlaIII sample prep kit from Illumina

tag: cell type

value: Fractionated CD3+ T-cells

tag: disease state

value: healthy donor


title: CD3_546


title: CD3_549


title: CD19_465

value: Fractionated CD19+ B-cells


title: CD3_539


title: CTCF_pro-B


title: H-CK

description: Sample 1

value: susceptible

value: radicle roots

value: water (mock)

value: control stage (ck)

value: 6 days post inoculation after seed germination


title: CD19_196


title: CD19_377


title: RRBS HL60 rep2

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

description: Reduced Representation Bisulfite Sequencing of HL60

data_processing: Alignment: Sequencing reads were mapped to the reference genome hg19 using RRBSmap allowing 2 mismatches.

source_name: HL60 Cell lines

growth_protocol: HL-60 were grown in DMEM supplemented with 10%FBS, at 37 Â°C in a humidified atmosphere with 5% CO2

extract_protocol: DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C'CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5'-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected before subjecting to sequencing.

treatment_protocol: Genomic DNA was isolated from the myeloid cell lines HL-60. DNA was digested with MspI (NEB), a methylation-insensitive enzyme that cuts C'CGG. Digested DNA was size selected on a 4% NuSieve 3:1 Agarose gel (Lonza). For each sample, two slices containing DNA fragments of 40-120 bp and 120-220 bp, respectively, were excised from the unstained preparative portion of the gel. These two size fractions were kept apart throughout the procedure including the final sequencing. Pre-annealed Illumina adaptors containing 5'-methyl-cytosine instead of cytosine were ligated to size-selected MspI fragments. Adapter-ligated fragments were bisulfite-treated using the EZ DNA Methylation kit (Zymo Research, Orange, CA). The products were PCR amplified, size selected, and sequenced on the Illumina GA IIxat a reading length of 36 bp.

tag: cell line

tag: digestion

value: MspI

tag: treatment

value: bisulfite


title: IgG RIPSeq HL60

description: RNA IP against Igg

data_processing:
Alignment:  Paired-End reads were trimmed to 50bp and then aligned to the reference genome hg19 using BWA with the following parameters:  bwa aln -o 1 -l 25 -k 2; bwa sampe -o 200.
The wig files were generated using MACS 1.3.7.1 with a resolution of 100bp.

growth_protocol: HL-60 were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol: DNMT1 interacting RNA was immunoprecipitated by DNMT1 antibody. RNA was reverse transcribed into ds-cDNA before sequencing library preparation using Illumina ChIP-Seq sample preparation kit (cat# IP-102-1001) following manufacturer's instruction. DNA at the length of 150-200 bp was recovered by gel size selection before sequencing.

treatment_protocol: RNA immunoprecipitated with DNMT1 antibody (Abcam cat# ab87656) and IgG (Sigma Aldrich) was processed for sequencing as described with some modifications. Double stranded cDNA was synthesized using the Just cDNA Double-Stranded cDNA Synthesis Kit (Agilent Technology, Santa Clara, CA) according to the manufacturer's instructions. Illumina sequencing libraries were constructed from these cDNA using ChIP-Seq sample preparation kit (cat# IP-102-1001, Illumina, San Diego, CA) with some modifications. Illumina paired-end adaptor and PCR primers were used to replace the single read adaptor and primers in the kit. Constructed libraries were subjected to a final size-selection step on a 10% Novex TBE Gels (Invitrogen, Carlsbad). DNA fragments of 175-200 bp were excised from SYBR-green-stained gel. DNA was recovered from the gel and quantified following Illumina's qPCR quantification protocol. A paired end sequencing of these libraries was then performed on Illumina GA IIx to achieve 2-76 bp reads.

tag: rip antibody

value: IgG

tag: vendor

value: Sigma Aldrich


title: DNMT1 RIPSeq HL60

description: RNA IP against DNMT1

value: Abcam

tag: catalog#


title: RRBS HL60 rep1


title: MLL3WT_INPUT

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: Input DNA for MLL3(+/+) MEFs

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned to the fly genome (UCSC dm3), or mouse genome (UCSC mm9), using Bowtie v0.12.7, allowing unique reads only and up to three mismatches of the 50bp read length.
Enrichment for some ChIP-seq samples was determined by MACS v1.4.1 using default settings, the dm genome, and the associated input sample.  The publication utilized a subset of peaks meeting the criteria (p < 1e-5 and fold change > 5, or FDR < 5%) but all peaks with p < 1e-5 are included in this submission.
Genome_build: UCSC dm3; UCSC mm9
Supplementary_files_format_and_content: txt.bam.bed file represents UCSC BED format for alignments.
Supplementary_files_format_and_content: peaks.tab file represents MACS v1.4.1 tab-delimited format for all enriched regions at p < 1e-5.

source_name: MEF MLL3(+/+)

growth_protocol: S2 cells were grown in SFX medium (Thermo/HyClone #SH30278.02) with 1% Penicillin/Streptomycin (Invitrogen #15140) at room temperature.  Mouse embryonic fibroblasts were grown in DMEM with 10% FBS supplemented with glutamine.

extract_protocol:
S2 cells (one T75 flask per histone antibody and two T75 flasks for other antibodies) were cross-linked in 1% formaldehyde (by adding 37% formaldehyde to medium) on a nutator for 15 min at room temperature (RT). Samples were quenched by adding 2.5 M glycine to a final glycine concentration of 225 mM and incubated on a nutator for 5 min at RT. Following centrifugation for 5 min at 2000 g at 4°C the supernatant was aspirated. The cell pellet was resuspended in 5 ml Orlando/Paro buffer (10 mM Tris HCl pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, 0.5 mM DTT, protease inhibitors [Roche, complete, EDTA-free, Cat No. 05056489]) and centrifuged for 5 min at 2000 g at 4°C. The supernatant was aspirated and the wash step with Orlando/Paro buffer repeated for another two times. The cell pellet (~100 µl for one T75 flask) was resuspended in 1.5 ml RIPA buffer (25 mM Tris pH 7.5, 140 mM NaCl, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.5% of N-lauroylsarcosine, 0.5 mM DTT, protease inhibitors [Roche, complete, EDTA-free, Cat No. 05056489]) per 100 µl of cell pellet and 1.5 ml samples sonicated for 15 min (50% on/off cycle, high) (Bioruptor, Diagenode) in 15 ml hard plastic tubes (Corning, 430055). Sonicated chromatin was centrifuged for 20 min at 14,000 rpm at 4° and the supernatant kept. 10 μl of the sonicated chromatin was kept for gel analysis (to check sizing pattern) and 50 μl was used as an Input control. Sizing samples were reverse cross-linked over night at 65ºC by adding 90 μl RIPA and 3 μl proteinase K (30 mg/μl) and input samples by adding 50 μl RIPA and 5 μl proteinase K and processed/purified in the same way as the ChIP samples (see below). The remaining chromatin was diluted two-fold with RIPA buffer (without N-lauroylsarcosine) and incubated over night with the respective antibody on a nutator at 4ºC. 60 μl of protein A agarose (Invitrogen, 15918-014) was washed in 5 ml RIPA buffer, centrifuged for 2 min at 1,000 rpm at 4ºC. The supernatant was aspirated, the chromatin sample added and incubated for 2 h on a nutator at 4ºC. After centrifugation for 2 min at 1,000 rpm at 4ºC the protein A agarose was transferred into a 1.5 ml tube, washed with 1 ml RIPA buffer, incubated for 5 min on a nutator at room temperature and centrifuged for 2 min at 2,500 rpm at 4ºC. The supernatant was aspirated and the previous washing steps repeated another five times. Elution was performed on a nutator at room temperature for 20 min with 300 μl elution buffer (0.1 M NaHCO3, 1% SDS) containing proteinase K (1 ml elution buffer and 5 μl proteinase K [30 mg/μl]) and the sample centrifuged for 2 min at 2,500 rpm at room temperature. The supernatant was kept and the elution step repeated. Elution fractions were pooled and reverse cross-linked over night at 65ºC. 1 µl of RNase A (R4642, Sigma) was added to reverse cross-linked samples followed by incubation for 1 h at 37°C. DNA was isolated with the Qiagen PCR purification kit (#28106) and eluted in 50 μl H2O and DNA concentration determined by Pico Green Assay (Invitrogen #P7581).  Mouse embryonic fibroblasts (MEFs) ChIP was performed according to a previously described protocol (Wang et al. 2009). Briefly, approximately 10^7 MEFs for each assay were cross-linked with 1% formaldehyde and sonicated. 10 µg of antibody and 50 µl protein A agarose were used in the ChIP assays.
Libraries were prepared with the Illumina TruSeq RNA Sample Preparation Kit (#RS-122-2001,RS-122-2002) according to Illumina's instructions, adapted for multiplexing ChIP-seq samples by starting at the end repair step using 1/3 of the adapters.  Libraries were sequenced on the Illumina Hi-Seq 2000 following the manufacturer's protocols.

treatment_protocol: We used 10 µg of dsRNA per 1.5 x 106 cells per 60 mm well (6 well plate) or 80 µg of dsRNA per 12 x 106 cells per T75 flask with 2.5 ml SFX medium(Thermo/HyClone #SH30278.02) and 1% Penicillin/Streptomycin (Invitrogen #15140) per 60 mm well and 20 ml SFX medium (1% Penicillin/Streptomycin) per T75 flask. dsRNA was mixed with the corresponding volume of S2 cells (0.6 x 106 S2 cells/ml) and distributed in either 60 mm wells or T75 flasks. RNAi-mediated knockdown was performed for 5 days.  MEFs are homozygous wild-type or homozygous knock-outs of MLL1 or MLL3 as described in (Wang et al. Mol Cell Biol. 2009 November; 29(22): 6074–6085)

value: Mouse Embryonic Fibroblasts (MEF)

value: MLL3 WT


title: MLL3WT_H3K4MONO

description: Chromatin Immunoprecipitation of H3K4me1 in MLL3(+/+) MEFs

value: (rb) α-H3K4me1 (39297;Active Motif)


title: MLL3KO_INPUT

description: Input DNA for MLL3(-/-) MEFs

source_name: MEF MLL3(-/-)

value: MLL3 KO


title: MLL3KO_H3K27TRI

description: Chromatin Immunoprecipitation of H3K27me3 in MLL3(-/-) MEFs

value: (rb) α-H3K27me3 (39155; Active Motif)


title: MLL3KO_H3K4MONO

description: Chromatin Immunoprecipitation of H3K4me1 in MLL3(-/-) MEFs


title: MLL1WT_INPUT

description: Input DNA for MLL1(+/+) MEFs

source_name: MEF MLL1(+/+)

value: MLL1 WT


title: MLL3WT_H3K27TRI

description: Chromatin Immunoprecipitation of H3K27me3 in MLL3(+/+) MEFs


title: MLL1WT_H3K27TRI

description: Chromatin Immunoprecipitation of H3K27me3 in MLL1(+/+) MEFs


title: MLL1KO_INPUT

description: Input DNA for MLL1(-/-) MEFs

source_name: MEF MLL1(-/-)

value: MLL1 KO


title: MLL1KO_H3K27TRI

description: Chromatin Immunoprecipitation of H3K27me3 in MLL1(-/-) MEFs


title: MLL1KO_H3K4MONO

description: Chromatin Immunoprecipitation of H3K4me1 in MLL1(-/-) MEFs


title: Input_DNA_Rep2

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

data_processing:
Basecalls were performed by CASAVA version 1.7 (Replicate1) and CASAVA version 1.8.2 (Replicate2).
For Replicate 1 reads were converted to Sanger phred scores and filtered with fastq_quality_filter, excluding reads with more than 6 bases calls with a phred quality score less than 20.
For Replicate 2 reads were filtered to exclude those failing the CASAVA chastity filter.
Reads were aligned with Bowtie version 0.12.8 with nondefault parameters --best -l 20 -n 3 -m1 (Replicate 1) or --best -l 28 -n 3 -m1 (Replicate 2).
Peaks were called with MACS version 1.4.2 with default parameters and genome size set to -g mm.
Genome_build: mm9
Supplementary_files_format_and_content: Bed and Wig files were produced by MACS, except for top_pitx1_peaks.bed that was generated using BedTools 2.16.2 and in R.

source_name: embryonic hindlimb

extract_protocol: After cross-linking in 1% formaldehyde in PBS for 30 minutes, hindlimb buds were rinsed and treated with trypsin for 5 minutes to generate a single cell suspension. Samples were then sheared with a Branson 450 Sonifier to generate a chromatin size range of 200–600 bp. PureProteome Protein G Magnetic Beads (Millipore) were pre-incubated with Pitx1 antibody before incubating overnight with 400 μg of chromatin. After washing, immune complexes were eluted from the beads, and protein-DNA crosslinks were reversed by incubating at 65˚C overnight. After treatment with RNase followed by proteinase K, samples were purified with the GeneJET PCR Purification Kit (Fermentas). Material from three independent ChIP’s was used to generate Illumina ChIP-Seq libraries. ChIP and input chromatin control libraries were produced using the Illumina ChIP-Seq DNA Sample Prep Kit (IP-102-1001) as directed by the manufacturer. Libraries were sequenced on an Illumina GA IIx at the HudsonAlpha Institute for Biotechnology.

value: ICR

tag: tissue

value: embryonic hindlimb bud

tag: genotype

value: wild type


title: wt macrophages #3

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

country: Germany

institute: Institute of Immunology

data_processing:
Read Alignment : pBWA version 0.5.9-r32-MPI-patch2 against mm9
Counts per feature: Reads per exon were computed using bedtools version 2.16.2, summarized per gene based on Ensembl Gene 61 annotation.
Normalization of reads per gene: The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.6.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
genome build: mm9 (UCSC)
processed data files format and content: tab delimited file with sample size normalized counts per gene (rows) and sample (columns)

source_name: mouse peritoneal macrophages

extract_protocol: Cells were lysed immediately in μMACS  mRNA Isolation Kit lysis buffer and cleaned with with LysateClear Columns (Miltenyi Biotec). mRNA was enriched using Oligo(dT) beads. Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596

value: WT

value: 10 weeks

tag: Sex

value: male and female


title: ko macrophages #2

tag: genotype/variation

value: SAMHD1 KO

value: 15 weeks

value: male


title: ko macrophages #3

tag: age

value: 13 weeks


title: wt macrophages #2

value: 21 weeks


title: Pitx1_ChipSeq_Rep2

value: Pitx1 (Santa Cruz, sc-18922, lot # G0105 )


title: ko macrophages #1

value: 22 weeks


title: CD19_573

value: Fractionated CD19+ B-cells

value: healthy donor


title: del hns, ydgT; replicate 2

city: Hinxton

first: Aswin Sai Narain

last: Seshasayee

address: Wellcome Trust Genome Campus

institute: EMBL-EBI

data_processing:
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to mRNA and stable sRNA (but not rRNA and tRNA) were obtained based on gene annotations in the Ecocyc database. The number of reads falling within each read was computed using custom scripts. For further analysis these  counts were fed into the EdgeR package in Bioconductor to estimate differential expression between the mutants and the wildtype. For within-sample gene expression comparisons, the  read counts for each gene was divided by the length of the gene.
Supplementary_files_format_and_content: fastq.sam.hits.expression.txt.txt files; column 1: gene name; column 2: number of reads in the gene

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

source_name: del hns, ydgT; replicate 2

extract_protocol:
Overnight grown culture of E. Coli K-12 MG1655 wildtype and the mutant strains (Appendix 1) were subcultured in 100mL of Fresh LB and incubated at 37°C. Two biological replicates were performed for each sample. Cells were harvested during the mid exponential phase (OD600 at 0.5 and 0.9 for MG1655 ΔHns ΔStpA and other strains respectively). Media was removed by spinning the cells at 8000 rpm for 10 minutes at 4°C and the collected cells were washed with autoclaved DEPC water and total RNA was extracted by using Ambion TRIzol reagent (Cat.No 15596-026). Cells were frozen in liquid nitrogen and lysed using sterile pestle followed by TRIzol treatment. Lysed cells were incubated at 4°C for 5 minutes and chloroform was added to achieve phase separation and centrifuged at 12000 rpm for 15 minutes. Following centrifugation the mixture separates into lower phenol chloroform phase, an upper aqueous phase and an interphase. RNA remains in the aqueous phase. Aqueous phase was transferred to the fresh eppendorf and the RNA was precipitated by using Isopropanol and mixed well to promote RNA precipitation from the aqueous phase. Precipitated RNA was washed with Ice cold 70% ethanol and spun at 12000 rpm to pellet down the RNA. Ethanol was removed and the residual ethanol was removed by air-drying at room temperature. RNA was dissolved in RNAse free water and stored at -80°C until required.
DNA contamination in the total RNA was removed by treating 10μg of the RNA with DNAse according to the manufacturer’s protocol (Invitrogen Cat.No.18068-015)1. Concentration and the purity of the RNA was determined using Nanodrop machine and by visualizing on the Agarose gel.
mRNA was enriched by Ambion MICROBExpress Bacterial mRNA purification kit (Cat.No AM1905) according to manufacturer’s protocol 2. Concentration and quality of the enriched mRNA was determined using Nanodrop.
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer.

value: del hns, ydgT

tag: growth stage

value: mid-exponential phase


title: del hns, ydgT; replicate 1

source_name: del hns, ydgT; replicate 1


title: wildtype; replicate 1

source_name: wildtype; replicate 1

value: wildtype


title: MLL1WT_H3K4MONO

description: Chromatin Immunoprecipitation of H3K4me1 in MLL1(+/+) MEFs

value: Mouse Embryonic Fibroblasts (MEF)

value: MLL1 WT

value: (rb) α-H3K4me1 (39297;Active Motif)


title: del hns, hha; replicate 2

source_name: del hns, hha; replicate 2

value: del hns, hha


title: del hns, stpA; replicate 2

source_name: del hns, stpA; replicate 2

value: del hns, stpA


title: del ydgT; replicate 2

source_name: del ydgT; replicate 2

value: del ydgT


title: del hns, hha; replicate 1

source_name: del hns, hha; replicate 1


title: wildtype; replicate 2

source_name: wildtype; replicate 2


title: del ydgT; replicate1

source_name: del ydgT; replicate1


title: del hha; replicate 2

source_name: del hha; replicate 2

value: del hha


title: del hns, stpA; replicate 1

source_name: del hns, stpA; replicate 1


title: del hha; replicate 1

source_name: del hha; replicate 1


title: del stpA; replicate 2

source_name: del stpA; replicate 2

value: del stpA


title: wt macrophages #1

value: WT

value: 25 weeks

value: male


title: del stpA; replicate 1

source_name: del stpA; replicate 1


title: Total RNA polyA(-)

data_processing:
Bases were called using Casava 1.8.4 with default settings.
76-bp paired-end reads were aligned to human genome (hg19) using tophat 2.0.2 with default settings and without a reference assembly.
Assemblies were generated using Cufflinks 2.0.2 again, without reference assembly
Overlap with DNMT1-RIP-Seq was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Whole-transcriptome .gtf assemblies of Total and polyA(-) RNA samples, including FPKM values.

source_name: Myeloid Leukemia

extract_protocol:
Total RNA was extracted with TRI REAGENT® (MRC). Total RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase inhibitor). Non-polyadenylated RNA fractions were selected with the MicroPoly (A) PuristTM purification kit (Ambion). Total and not-polyadenylated RNA were depleted of ribosomal RNA with Ribo-ZeroTM  Magnetic Gold Kit (cat. # MRZG126 Epicentre).
Double stranded cDNA libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (cat. # SSV21106 Epicentre) followed by Duplex Specific Nuclease (DSN) normalization (Evrogen, EA001). DSN treated libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced (1/lane) on a HiSeq 2000 Illumina instrument.

tag: rna fraction

value: Non-polyadenylated RNA


title: Input_DNA_Rep1

source_name: embryonic hindlimb

value: ICR

value: embryonic hindlimb bud

value: wild type

tag: chip antibody


title: DGE_MLL-11q23_1

source_name: Bone marrow

value: leukemic cells

tag: cytogenetic background

value: acute lymphoblastic leukemia (ALL)

tag: all lineage

value: BCP ALL


title: Total RNA

value: Total RNA


title: DGE_HeH_10

tag: cell type

value: High Hyperploidy

tag: disease state


title: DGE_t12-21_4


title: DGE_t1-19_1


title: DGE_HeH_9


title: Pitx1_ChipSeq_Rep1

tag: strain

value: Pitx1 (Santa Cruz, sc-18922, lot # G0105 )


title: del hns; replicate 2

source_name: del hns; replicate 2

value: del hns

value: mid-exponential phase


title: del hns; replicate 1

source_name: del hns; replicate 1


title: PR-R360_ChIPSeq

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

description: processed data file: PRbs_datasets.txt

data_processing:
Basecalls performed using Illumina pipeline version 1.4.0
PR ChIP-Seq reads were aligned to the reference genome (hg19) using GEM (http://www.ncbi.nlm.nih.gov/pubmed/22276185) keeping only uniquely mapped reads with up to 2 mismatches
We used Pyicos (http://regulatorygenomics.upf.edu/pyicos/) to call significant peaks with the following parameters: maximum of 4 duplicates, read extension of 130bp, control T0 subtraction, removed artificats, splitted the peaks where the read coverage goes below 5% of the peak summit and a Poisson analysis using peak-height with a p-value cutoff of <=0.001.
Genome_build: hg19
Supplementary_files_format_and_content: File containing PR binding-sites locations (PRbs_datasets.txt) and Excel file containing nucleosome occupancy and H3K4 me1 and me3 enrichment in PRbs (PRbs_properties.txt).

source_name: T47D-MTVL breast cancer cell line

growth_protocol: Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation
It was performed using the NEBNext DNA sample prep Reagents set 1

treatment_protocol: For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were incubated with R5020 (10 nM) for different times between 0 and 360 minutes

tag: treatment

value: R5020 360 minutes

value: anti-PR (H190, Santa Cruz, #sc 7208, D2705 lot)

tag: cell line


title: PR-R30_ChIPSeq

description: processed data file: PRbs_datasets.txt

value: R5020 30 minutes


title: PR-R5_ChIPSeq

description: processed data file: PRbs_datasets.txt

value: R5020 5 minutes


title: PR-T0_ChIPSeq

description: processed data file: PRbs_datasets.txt

value: unstimulated cells


title: PR-R60_ChIPSeq

description: processed data file: PRbs_datasets.txt, PRbs_properties.txt

value: R5020 60 minutes


title: Human Brain

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA

data_processing: The sequence reads were aligned to human (hg18) and mouse (mm8) genomic sequence using Bowtie (Langmead et al., Genome Biol. 2009 10).

source_name: Wildtype human brain

extract_protocol: Illumina FastTrack mRNA-Seq library construction

value: wildtype

value: brain


title: Human Liver

description: RNA-Seq performed on polyadenylated RNA

source_name: Wildtype human liver


title: cmc_rpmi_donor_5

city: Nijmegen

first: Eugene

middle: Thomas Pieter

last: Verwiel

state: Gelderland

address: Geert Grooteplein zuid 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Centre

description: Human_peripheral blood mononuclear cells_cmc_rpmi_donor_5

data_processing:
XSQ conversion to csfasta and qual using xsqconvert version 1.4
Reads alignment using tophat v1.4.1, insert size set 110 bp
Abundances were calculated using cufflinks v2.0.0
Log2 transformation (with an offset of 1.0) of FPKM expression values using Partek 6.6
A multifactoral ANOVA was performed with factors; GROUP, TREATMENT and INDIVIDUAL using Partek 6.6.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample as created by cufflinks 2.0.0

source_name: peripheral blood mononuclear cells

growth_protocol: Cells were isolated and resuspended in RPMI 1640 culture medium Dutch modifications (Sigma-Aldrich) supplemented with 1% gentamicin, 1% L-glutamine and 1% pyruvate (Life Technologies)

extract_protocol:
RNA was extracted in 800 μl of TRIzol reagent (Invitrogen), according to the protocol of the manufacturer
Libraries were prepared using the instructions for the whole transcriptome library preparation: low input of the SOLiD® Total RNA-Seq kit (part no 4445374) Poly(A) RNA was selected by the ambion® MircoPoly(A) purist kit (part no AM1919).

treatment_protocol: Freshly isolated cells were incubated for 4 hours with heat-killed Candida albicans (1x10^6/mL) or left untreated. After 4 hours, supernatants were removed and trizol was added to cells. Samples were stored at -80C until RNA extraction

tag: group

value: cmc

value: rpmi

tag: individual


title: cmc_rpmi_donor_4

description: Human_peripheral blood mononuclear cells_cmc_rpmi_donor_4


title: DGE_undefined_1

value: leukemic cells

value: undefined

value: acute lymphoblastic leukemia (ALL)


title: rat_ts_h3k4me1 (paired-end)

first: Edward

last: Chuong

address: 596 UCB

institute: University of Colorado Boulder

description:
ChIP DNA
processed data available on GSM1035398

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using BWA 0.9.6 (-q 10 -I), and filtered using samtools view (-q 1) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.9 with default settings, using --broad setting for histone marks.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-Seq bed files contain peaks called by MACS v2.0.9

source_name: Trophoblast stem cells

extract_protocol:
Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or HiSeq following the manufacturer's protocols.

value: HSD

value: Trophoblast stem cells


title: control_rpmi_donor_3

description: Human_peripheral blood mononuclear cells_control_rpmi_donor_3

value: control


title: control_candida_donor_3

description: Human_peripheral blood mononuclear cells_control_candida_donor_3

value: candida


title: cmc_candida_donor_4

description: Human_peripheral blood mononuclear cells_cmc_candida_donor_4


title: infected M28

city: Harbin

first: Fangkun

last: Wang

address: 427 Maduan Street

department: Harbin Veterinary Research Institute

institute: Chinese Academy of Agricultural Sciences

description: M28 INFECTED CELLS

data_processing:
Raw sequences were transformed into Clean Tags by the Illumina pipeline. All clean tags were mapped to the reference sequences mouse genome (mm9 version from UCSC site) and mouse transcriptome (all refseq, mRNA and ESTs found in GenBank), and only one mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered
To compare the DE of gene across samples (M28/Mc, M90/Mc, and M90/M28), the number of raw clean tags in each library was normalized to Tags Per Million (TPM) to obtain normalized gene expression level. DE detection of gene or tag across samples was performed according to the previous description.Refer to Benjamini,FDR need no excess 0.01. We use "FDR≤0.001 and the absolute value of log2Ratio≥1" as the threshold to judge the significance of gene expression difference.

source_name: peritoneal macrophages

growth_protocol: 6–8-week-old BALB/c female mice were purchased from Vital River Laboratories (VRL). Peritoneal macrophages were recovered by peritoneal lavage with 5 ml of cold RPMI 1640 medium and isolated by centrifugation,according the method described by Kim JG with some modifications.For adherent cells, cells (2×106) were plated on 6-well tissue culture plates and cultured in RPMI 1640 medium  (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 0.2 mM L-glutamine, antibiotic-antimycotic (100 U/mL penicillin G, 100 µg/mL streptomycinfor 2hr in a humidified incubator at 37°C and 5% CO2. Nonadherent cells were removed by being washed once with RPMI 1640 containing 10% serum and then being washed twice with Hanks’ balanced salt solution. Adherent cells were cultured in RPMI 1640with 10% serum in an atmosphere containing 5% CO2.

extract_protocol: The main reagents and supplies are Illumina Gene Expression Sample Prep Kit and Illumina Sequencing Chip (flowcell), and the main instruments are Illumina Cluster Station and Illumina HiSeq™ 2000 System. Sequence tag preparation was done with Illumina's Digital Gene Expression Tag Profiling Kit according to the manufacturer's protocol. The DNA was purified and followed by Illumina sequencing.

treatment_protocol: Peritoneal macrophages from mice were pooled and plated at 2 x 106 cells/well 6-well tissue culture plates 12–24 hr prior to infection, in supplemented RPMI 1640 without antibiotics. Macrophages were infected with 1 mL of a stationary phase Brucella spp. culture (MOI 200:1). Control macrophages(Mc) and infected macrophages(M28 or M90) were incubated for 4 hr at 37°C with 5% CO2, washed once with PBS and then lysed for RNA collection (RNeasy, Qiagen, Germantown, MD)

value: peritoneal macrophages

tag: genetic background

value: BALB/c

tag: gender

value: female mice

tag: infection

value: B. melitensis M-28


title: cmc_candida_donor_5

description: Human_peripheral blood mononuclear cells_cmc_candida_donor_5


title: infected M90

description: M90 INFECTED CELLS

value: B. melitensis M-90


title: control Mc

description: blank control


title: control_candida_donor_1

description: Human_peripheral blood mononuclear cells_control_candida_donor_1


title: control_rpmi_donor_1

description: Human_peripheral blood mononuclear cells_control_rpmi_donor_1


title: control_candida_donor_2

description: Human_peripheral blood mononuclear cells_control_candida_donor_2


title: luxS deletion mutant, replicate 1

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

description: luxS deletion mutant, replicate 1

data_processing:
The 50 base unpaired SOLiD short reads were aligned in color space to the ATCC 33277 genome scaffold using BWA version 0.5.8 using default parameters [1].  This process began by combining the separate color space read and quality files from the sequencer into a single color space FASTQ file with the ‘solid2fastq.pl’ script distributed with BWA.  Next, the ATCC 33277 scaffold was indexed by BWA and the alignments were generated. Then, the SAMtools software was used to generate a ‘pileup’ file from the BWA output [2].  Finally, the pileup data were loaded in a MySQL database and the reads mapped per ORF statistics were generated by a standard SQL ‘SUM over GROUP BY’ operation. Differential abundance analyses were computed using R version 2.11.1 [3].  In order to normalize the samples prior to differential analysis, we applied ‘quantile normalization,’ after artificial base-lining zero read mapped ORFs, to assure the reads mapped per ORF distribution had the same empirical distribution across all replicates and experiments [4]. The quantile normalization was performed with the ‘normalizeBetweenArrays’ function of LIMMA [5].  In addition, we calculated RPKMs from the normalized reads mapped per ORF as follows: the quantile normalized number of reads mapped was divided by the size of each gene in kilo-bases and the count of the millions of reads mapped in the quantile normalized sample [6].
master_view.txt = genome build: ATCC_33277

organism: Porphyromonas gingivalis

source_name: luxS deletion mutant, replicate 1

growth_protocol: Bacteria were cultured in trypticase soy broth (TSB) supplemented with yeast extract (1 mg ml–1), hemin (5 µg ml–1), and menadione (1 µg ml–1), anaerobically, at 37°C.  Overnight cultures were diluted in TSB to OD600 0.25 and grown to OD600 0.5.

extract_protocol:
RNA was isolated by Trizol according to the manufacturer’s instructions (Invitrogen, CA).  RNA was treated by Turbo-DNA free (Ambion, TX) at 37C for 1hour, and then purified by a RNeasy mini kit (QIAGEN, CA).  16S and 23S rRNAs were removed by MICROBExpress Bacterial mRNA Enrichment Kit according to the manufacturer’s instructions (Ambion, TX).  Double-stranded cDNAs were synthesized by a SuperScript Double-stranded cDNA synthesis kit according to the manufacturer’s instructions (Invitrogen, CA).
A fragment DNA library was prepared according to SOLiD v3 plus procedure (Applied Biosystems, CA).  Briefly, cDNA was sheared to 100-110 bp fragments by using a Covaris S2 sonication system.  The fragmented DNA was subsequently blunted using end-polishing enzymes, and short oligonucleotide adaptors P1 and P2 were ligated to the ends of the end-repaired purified DNA.  The oligonucleotide adaptors provide priming sequence for both amplification and sequencing of sample-library DNA fragments.  Adaptor-ligated, purified and size selected 150-200 bp DNA fragments were nick translated and amplified by library PCR primers 1 and 2 using Platinum PCR amplification mix.  The sample library was quantitated by a NanoDrop spectrophotometer.  The quality of the libraries and fragment distribution was verified using Agilent Bioanalyzer.  The appropriate amount of dsDNA library was immobilized onto SOLiD P1 DNA beads.  The bead-bound library was then clonally amplified by emPCR according to the manufacturer’s protocol.

treatment_protocol: mutant construction: luxS, gppX and cdhR genes were inactivated by allelic replacement with the ermF gene or EM cassette introduced into the bacterial cells by electroporation. The mutants were selected on blood ager plate containing 5 micro g/ml Erythromycin.

value: mutant


title: cdhR mutant, replicate 2

description: cdhR mutant, replicate 2

source_name: cdhR mutant, replicate 2


title: cdhR mutant, replicate 1

description: cdhR mutant, replicate 1

source_name: cdhR mutant, replicate 1


title: GppX mutant, replicate 1

description: GppX mutant, replicate 1

source_name: GppX mutant, replicate 1


title: wild-type sample, replicate 2

description: wild-type sample, replicate 2

source_name: wild-type sample, replicate 2

value: wild-type


title: wild-type sample, replicate 1

description: wild-type sample, replicate 1

source_name: wild-type sample, replicate 1


title: wild-type sample, replicate 3

description: wild-type sample, replicate 3

source_name: wild-type sample, replicate 3


title: luxS deletion mutant, replicate 2

description: luxS deletion mutant, replicate 2

source_name: luxS deletion mutant, replicate 2


title: luxS deletion mutant, replicate 3

description: luxS deletion mutant, replicate 3

source_name: luxS deletion mutant, replicate 3


title: GppX mutant, replicate 2

description: GppX mutant, replicate 2

source_name: GppX mutant, replicate 2


title: LPT_H3K27me3_4

description: Chromatin Immunoprecipitation of H3K27me3 in LPT_4

organism: Drosophila melanogaster

source_name: Schneider's Drosophila Line 2; S2 cells

tag: genotype/variation

value: LPT knock-down

value: (rb) α-H3K27me3 (39155; Active Motif)


title: LPT_H3K4me1_4

value: (rb) α-H3K4me1 (39297;Active Motif)


title: LPT_Input_4

description: Input DNA for LPT knock-down samples named_4


title: trr_H3K4me3_6

description: Chromatin Immunoprecipitation of H3K4me3 in trr_6

value: Trr knock-down

value: (rb) α-H3K4me3 (#528; Ali Shilatifard)


title: trr_H3K4me1_4

description: Chromatin Immunoprecipitation of H3K4me1 in trr_4


title: trr_H3K27me3_4

description: Chromatin Immunoprecipitation of H3K27me3 in trr_4


title: control_rpmi_donor_2

description: Human_peripheral blood mononuclear cells_control_rpmi_donor_2

value: rpmi


title: trr_H3K27ac_2

description: Chromatin Immunoprecipitation of H3K27ac in trr_2


title: trr_LPT470_3

description: Chromatin Immunoprecipitation of LPT in trr_3

value: (rb) α-LPT (#470, Ali Shilatifard)


title: trr_H3K4me1_1

description: Chromatin Immunoprecipitation of H3K4me1 in trr_1


title: trr_Input_3

description: Input DNA for trr knock-down samples named_3


title: trr_H3K27ac_1

description: Chromatin Immunoprecipitation of H3K27ac in trr_1


title: trr_Input_4

description: Input DNA for trr knock-down samples named_4


title: trr_dUTX663_3

description: Chromatin Immunoprecipitation of dUTX in trr_3

value: (rb) α-dUTX (#663, Ali Shilatifard)


title: trr_Input_1

description: Input DNA for trr knock-down samples named_1


title: trr_Input_2

description: Input DNA for trr knock-down samples named_2


title: WT_H3K4me3_6

description: Chromatin Immunoprecipitation of H3K4me3 in WT_6

value: WT


title: WT_H3K4me3_5

description: Chromatin Immunoprecipitation of H3K4me3 in WT_5


title: WT_H3K4me1_4

description: Chromatin Immunoprecipitation of H3K4me1 in WT_4


title: WT_H3K27me3_4

description: Chromatin Immunoprecipitation of H3K27me3 in WT_4


title: WT_H3K4me1_1

description: Chromatin Immunoprecipitation of H3K4me1 in WT_1


title: WT_H3K27ac_2

description: Chromatin Immunoprecipitation of H3K27ac in WT_2


title: WT_LPT470_3

description: Chromatin Immunoprecipitation of LPT in WT_3


title: WT_Input_5

description: Input DNA for WT samples named_5


title: WT_Input_6

description: Input DNA for WT samples named_6


title: WT_H3K27ac_1

description: Chromatin Immunoprecipitation of H3K27ac in WT_1


title: WT_Trr_6

description: Chromatin Immunoprecipitation of Trr in WT_6

value: (rb) α-Trr (#570, Ali Shilatifard)


title: WT_RNAPolII_5

description: Chromatin Immunoprecipitation of RNA PolII in WT_5

value: (rb) α-Rpb1 (#828+829, Ali Shilatifard)


title: WT_Input_4

description: Input DNA for WT samples named_4


title: WT_Input_3

description: Input DNA for WT samples named_3


title: WT_Input_2

description: Input DNA for WT samples named_2


title: WT_Input_1

description: Input DNA for WT samples named_1


title: trr_Input_6

description: Input DNA for trr knock-down samples named_6


title: Tx601 Treated Midgut Replicate C

city: University Park

first: Howard

middle: W

last: Fescemyer

address: 208 Mueller Lab

department: Biology

institute: The Pennsylvania State University

data_processing:
Filtering and Trimming: SOLiD sequence reads were filtered using NextGENe® version 2.0 (SoftGenetics, State College, PA).  Reads accepted had a median score threshold ≥12, contained ≥25 bases and contained one or more bases with a score ≥14.
Reference preparation: The 138911 Sanger ESTs in SPODOBASE (http://bioweb.ensam.inra.fr/spodobase) were assembled into a reference transcriptome using SeqMan Pro version 8.0.2 (DNASTAR Lasergene®, Madison, WI) and default parameters for Sanger sequences as recommended by the manufacturer.  Preassembly involved a medium end trim, a vector scan and contaminant sequence screen that used a minimum of 5 mismatches; vector and contaminant sequence catalogs were those provided by the software.  Assembly parameters were match size of 25, minimum match of 85%, match spacing of 150, minimum sequence length of 100, gap penalty of zero, gap length of 0.7 and maximum mismatch end bases of 15.  Consensus calling used primary trace evidence of 50%, a majority of 75%, and quality weights of nine before and 400 after.  Calling conflicts and single nucleotide polymorphisms (SNPs) used a minimum coverage of four, minimum inconsistency of 25% and two bases, and no pairing was specified.  The assembled reference contained 7869 contigs (7,049,947 nt) that more correctly should be considered gene models.
Mapping: The reads from each library representing a replicate within a maize inbred treatment were mapped separately to the reference transcriptome using the Bowtie-like algorithm in NextGENe® with the requirement that 85% of 12 or more nucleotides comprising a read must match the reference.  A read was allowed to map only once (i.e., no ambiguous mapping).  The number of mapped reads per gene in each library, representing a replicate within a maize inbred treatment, were summed by NextGENe® as read counts per gene.  These data representing transcript abundance were subsequently used in differential expression analyses.
Differential expression: The R software package (v2.15.0) was used to confirm the overall data quality (frequency distribution histogram plots, hexagonal binning plots with R hexbin package v1.26.0, MA plots with R edgeR package v2.6.7, complete linkage cluster dendrogram plots, frequency histograms of Fisher’s exact test P-values with R SAGEnhaft package v1.22.0), filter low expressing genes, and normalize the read counts.  Low expressing genes were filtered by summing raw read counts per gene across replicate libraries within a maize inbred treatment; a gene was deleted when this sum for either treatment was less than 20.  The filtered read count data were normalized using the trimmed mean of M values (TMM) method as follows; a scaling factor was computed for each replicate library within a maize inbred treatment via the normFact routine in edgeR using filtered read count data and the A-replicate of the Tx601 treatment as a reference.  Filtered counts for each gene within a mapped library were divided by the product of the scaling factor multiplied by the library size. Normalized read counts were used to perform two-tailed paired t-tests for each gene.  Estimated P-values from each t-test and log2 fold change values for each gene were used to create a volcano plot.  False discovery rate for differentially expressed genes was set at an experiment-wide rate of 5% using the Q-value method (R qvalue package v1.18.0).
Orthologous functional annotation: Functional annotation of contigs in the reference used an approach that first obtained a full-length lepidopteran ortholog (BLASTx) against predicted proteins from the whole genome sequence of Bombyx mori [SilkDB version 2.0).  These protein orthologs were in turn used to search (BLASTp) and obtain functional orthologs from Drosophila melanogaster (predicted proteins in Flybase release FB2012_04).  Functional annotations of genes with significant differential expression were compared to those of all midgut genes in the filtered read count dataset using GO analysis (DAVID v6.7).
Genome_build: Not applicable
Supplementary_files_format_and_content: A tab delimited text file (Filtrd&NormalizdReadCountsSeqsAnnot.txt) contains processed data used to form conclusions in the published manuscript.  This file contains information about the reference contigs to which sequence reads were mapped (e.g., contig assembly data, contig sequence, best-hit BLAST annotation results) is given in the data table in addition to the final processed mRNA-seq data (e.g., raw and normalized read counts, t-test P-values, fold differences).  The file only contains data for contigs that passed the low expressing gene filter.
Supplementary_files_format_and_content: The matched.csfasta contain processed reads consisting of filtered and trimmed sequence reads that mapped to the reference transcriptome.

organism: Spodoptera frugiperda

source_name: Midgut tissue from last instar larvae fed on susceptible Tx601 maize

growth_protocol: Beginning as neonates, fall armyworm larvae used in the mRNA-seq experiment were reared on yellow-green midwhorl foliage from resistant Mp708 maize or susceptible Tx601 maize.  Old foliage and frass were removed every other day and replaced with fresh foliage.

extract_protocol:
Isolation of total RNA was performed separately for each midgut from an individual larva.  Nearly all RNAlater® was removed after centrifugation.  Several 2.3 mm diameter stainless steel beads were added to the concial tube containing a midgut and everything was frozen in liquid nitrogen.  Tubes were transferred to adapter blocks prechilled at -20°C and tissue was first disrupted (20 Hz, 45 sec) and then homogenized in TRIzol® reagent (20 Hz, 3 min) on a mixer milll.  Isolation of RNA from the homogenate followed the TRIzol manufacturer’s protocol (Invitrogen), except for additional acid phenol:chloroform:isoamyl alcohol (25:24:1, v:v:v) and chloroform phase separation steps prior to RNA precipitation to reduce DNA contamination.  Agilent Bioanalysis (RNA Nano Chip) indicated that the isolated total RNA had no detectable DNA contamination and RNA integrity numbers ranged from 8.3 to 9.7.  Equal amounts (3 µg) of total RNA from an individual MG were randomly pooled into three replicates per treatment (i.e., Mp708 or Tx601) such that each treatment replicate derived from 12-13 MGs.  Each pool of total RNA was separately enriched for poly(A+) RNA using the MicroPoly(A)Purist™ Kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions.  Enrichment involved two rounds of oligo(dT) selection with a fresh spin column used in each round.  The resulting poly(A+) RNA showed little degradation of the mRNA with a broad peak ranging from 200 nt to 5000 nt centered at about 1880 nt (Agilent Bioanalyzer RNA Pico Chip).  Estimated rRNA contamination ranged from 3.2% to 6.1%.
The Penn State Genomics Core Facility (University Park, PA) prepared transcriptome libraries and performed sequencing.  Libraries were separately prepared from each of the six poly(A+) RNA samples using the strand-specific SOLiD™ Total RNA-Seq Kit (Applied Biosystems) according to the manufacturer’s protocol.  Briefly, samples were fragmented with RNAse III and purified.  Fragmented RNA (100 ng) was ligated overnight to adaptors and subsequently reverse transcribed.  Purified cDNA was size selected and then amplified using barcoded primers.  The resulting material was purified and assessed for proper amplification using an Agilent Bioanalyzer DNA 1000 chip (Agilent Technologies).
Barcoded libraries were combined in equimolar quantities and prepared for sequencing according to the “Applied Biosystems SOLiD 3 Plus System Templated Bead Preparation Guide.”  Barcode sequencing and fragment library sequencing (50 bp) was performed on a full plate run of the SOLiD 3 Plus System according to the “Applied Biosystems SOLiD 3 Plus System Instrument Operation Guide.”

treatment_protocol: Larvae were reared in an environmental chamber at 27°C, 14:10 (light:dark) photoperiod, and 70% relative humidity.  Midguts were dissected from feeding larvae 2 d after molting to the last instar with masses between 300 and 400 mg.  Dissections were done with cold anesthetized larvae submerged in Bombyx saline.  After removing Malpighian tubules, foregut anterior to the stomodial valve, hindgut and food bolus, the midgut was transferred from the body cavity, rinsed well with cold saline, and preserved in RNAlater®.

tag: insect strain

value: Corn Strain

tag: tissue

value: midgut

tag: Stage

value: last instar larvae

value: reared on susceptible Tx601 maize


title: Tx601 Treated Midgut Replicate B


title: Mp708 Treated Midgut Replicate D

source_name: Midgut tissue from last instar larvae fed on resistant Mp708 maize

value: reared on susceptible Mp708 maize