title: RNA-Seq CTRL2

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). Differential expression test between different groups was performed with Cuffdiff module, and genes with q-value < 0.05 were selected as differentially expressed genes. The GTF annotation files for UCSC mm9 was used for gene annotation.
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were marked and removed by PICARD tool. Bedgraph trace files were generated using HOMER software. Peak callings were also performed using HOMER. To call differential H2A-occupying peaks induced by NMDA or Etoposide treatment compared to control condition, findPeaks command of HOMER software was employed with option “-region” specified to handle enriched histone-occupying regions of variable length. Tag directories for NMDA and control H2A data were used as positive and input, respectively. Two other parameters for region finding “-size” and “-minDist” were set to the default values (150bp and 370bp, respectively). For peak filtering, “-F” option was set to 2.5, and the other parameters were default. Adjacent called peaks (700bp edge-to-edge distance) were combined and the regions not less than 1kb long were selected as broad differential H2A regions. Then those broad regions were further extended based on surrounding H2A normalized signals (bedgraph trace files). Bins with normalized signals > 1.5 and edge-to-edge distance < 1kb were merged with those broad differential H2A regions to generate expanded H2A foci.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq, FPKM table format for RNA-Seq and differentially expressed genes

source_name: Cultured primary neurons

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice were plated at a density of 12.5 million cells/plate for 10cm plates and 1.5 million cells/plate for 6 cm plates. The plates were coated beforehand by incubation with poly-D-lysine (0.5mg/ml) and laminin (0.005mg/ml) for 1 hour at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (Gibco), supplemented with L-glutamine, penicillin/streptomycin, and B27. For most experiments, cultured primary neurons were treated with 50μM NMDA for 10 minutes followed by recovery in NMDA-free conditional media for an additional 10 minutes. Etoposide (Sigma) was at 5μM.

extract_protocol:
Chromatin immunoprecipitation was performed using a ChIP assay kit (Millipore) as described by the manufacturer. Briefly, cultured primary neurons (1 x 10^7 cells) were crosslinked by treatment with formaldehyde (1% final) for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in lysis buffer containing 50mM Tris pH 8, 10mM EDTA, and 1% SDS. Cells were sonicated using a bioruptor (medium power, 30 seconds on/30 seconds off – 20 cycles).  Sheared chromatin was immunoprecipitated variously with antibodies against either γH2AX (Abcam – ab2893), or Topo IIβ (Abcam – ab58442), and using salmon sperm DNA-protein A-agarose beads. Crosslinked proteins were then eluted from the beads in a solution containing 100mM NaHCO3 and 1% SDS. Crosslinks were reversed by incubation at 65°C overnight, following which DNA was extracted using phenol/chloroform/isoamyl alcohol. For RNA-seq, total RNA was extracted from cultured primary neurons using the Qiagen RNeasy Plus Universal Kit (Qiagen) and by following the manufacturer’s recommended protocol.
Sequencing libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Ernst et al., 2011). Gel electrophoresis was used to retain library fragments between 300 and 600 bp.  Prior to sequencing, libraries were quantified using Quibit (Invitrogen) and quality-controlled using Agilent’s Bioanalyzer.  36bp single-end sequencing was performed using the Illumina HiSeq 2000 platform according to standard operating procedures. Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). For RNA-seq, Illumina TruSeq Total RNA Sample Prep Kits (Illmina) was used for library preparation. The bar-coded libraries were quantified before equal mixing for sequencing on the Illumina Hi-Seq 2000 system. The raw fastq data files of paired-end reads were collected for analysis.

treatment_protocol: 10 million cells were crosslinked by treatment with 1% formaldehyde for 10 minutes at 37°C.

tag: cell type

value: Cultured primary neurons from E16 cortex

value: Swiss-Webster


title: RNA-Seq NMDA

status: Public on Jun 04 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: CA528

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Non-protein coding and mitochondrial genes were filtered out.
Samples were selected for further analysis by using these criteria: unpaired reads examined/FASQ total read >0.75 and median CV coverage <1. Samples that had total counts less than one million were excluded.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) mexico_processed_data_for_GEO.csv: comma-separated matrix – first 6 columns contain Ensembl gene ID, Ensembl transcript ID, HGNC symbol, location information and chromosome name, remaining columns include read counts assigned for each library; data represents all processing steps up to and including "sample QC and filtering" but not downstream processing/normalization for analysis. (2) mexico_combined_metrics.csv: comma-separated matrix – the first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

molecule: polyA RNA

organism: Homo sapiens

source_name: children with diarrhea_EPEC

extract_protocol:
Total RNA was isolated using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion, TX) and RNA sample was globin reduced wit GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the Illumina TrueSeq RNA Sample Preparation kit according to manufacturer's instructions.

tag: age

value: 2 year-old or older

tag: group

value: Diarrhea

tag: organisms

value: EPEC

tag: severity

value: mild

tag: tissue

value: Whole blood

tag: flowcell

value: A

tag: lane


title: CA535

value: moderate


title: CA370

value: <2 year-old


title: CA450


title: CA356


title: CA464


title: CA352


title: ChIP-Seq ETOPOSIDE INPUT_TOP2B

library_source: genomic

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). Differential expression test between different groups was performed with Cuffdiff module, and genes with q-value < 0.05 were selected as differentially expressed genes. The GTF annotation files for UCSC mm9 was used for gene annotation.
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were marked and removed by PICARD tool. Bedgraph trace files were generated using HOMER software. Peak callings were also performed using HOMER. To call differential H2A-occupying peaks induced by NMDA or Etoposide treatment compared to control condition, findPeaks command of HOMER software was employed with option "-region" specified to handle enriched histone-occupying regions of variable length. Tag directories for NMDA and control H2A data were used as positive and input, respectively. Two other parameters for region finding "-size" and "-minDist" were set to the default values (150bp and 370bp, respectively). For peak filtering, "-F" option was set to 2.5, and the other parameters were default. Adjacent called peaks (700bp edge-to-edge distance) were combined and the regions not less than 1kb long were selected as broad differential H2A regions. Then those broad regions were further extended based on surrounding H2A normalized signals (bedgraph trace files). Bins with normalized signals > 1.5 and edge-to-edge distance < 1kb were merged with those broad differential H2A regions to generate expanded H2A foci.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq, FPKM table format for RNA-Seq and differentially expressed genes

molecule: genomic DNA

source_name: ChIP-Seq ETOPOSIDE INPUT_TOP2B

extract_protocol:
Chromatin immunoprecipitation was performed using a ChIP assay kit (Millipore) as described by the manufacturer. Briefly, cultured primary neurons (1 x 107 cells) were crosslinked by treatment with formaldehyde (1% final) for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in lysis buffer containing 50mM Tris pH 8, 10mM EDTA, and 1% SDS. Cells were sonicated using a bioruptor (medium power, 30 seconds on/30 seconds off – 20 cycles).  Sheared chromatin was immunoprecipitated variously with antibodies against either γH2AX (Abcam – ab2893), or Topo IIβ (Abcam – ab58442), and using salmon sperm DNA-protein A-agarose beads. Crosslinked proteins were then eluted from the beads in a solution containing 100mM NaHCO3 and 1% SDS. Crosslinks were reversed by incubation at 65°C overnight, following which DNA was extracted using phenol/chloroform/isoamyl alcohol. For RNA-seq, total RNA was extracted from cultured primary neurons using the Qiagen RNeasy Plus Universal Kit (Qiagen) and by following the manufacturer’s recommended protocol.
Sequencing libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Ernst et al., 2011). Gel electrophoresis was used to retain library fragments between 300 and 600 bp.  Prior to sequencing, libraries were quantified using Quibit (Invitrogen) and quality-controlled using Agilent’s Bioanalyzer.  36bp single-end sequencing was performed using the Illumina HiSeq 2000 platform according to standard operating procedures. Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). For RNA-seq, Illumina TruSeq Total RNA Sample Prep Kits (Illmina) was used for library preparation. The bar-coded libraries were quantified before equal mixing for sequencing on the Illumina Hi-Seq 2000 system. The raw fastq data files of paired-end reads were collected for analysis.


title: ChIP-Seq ETOPOSIDE INPUT_γH2AX

source_name: ChIP-Seq ETOPOSIDE INPUT_γH2AX


title: ChIP-Seq ETOPOSIDE TOP2B

source_name: ChIP-Seq ETOPOSIDE TOP2B

tag: antibody

value: Topo IIb Abcam-ab58442


title: CA287


title: CA644

source_name: children with diarrhea_Rotavirus

value: Rotavirus


title: CA117


title: CA056


title: CA940

source_name: children with diarrhea_EAEC

value: EAEC

value: B


title: CA253

source_name: children with diarrhea_Shigella

value: Shigella


title: CA714


title: CA711

value: severe


title: CA708


title: ChIP-Seq CTRL INPUT_TOP2B

source_name: ChIP-Seq CTRL INPUT_TOP2B


title: ChIP-Seq NMDA γH2AX

source_name: ChIP-Seq NMDA γH2AX

value: γH2AX Abcam-ab2893


title: CA388


title: CA345


title: CA319


title: CA329


title: CA282


title: CA251


title: CA169


title: CA155


title: ChIP-Seq CTRL INPUT_γH2AX

source_name: ChIP-Seq CTRL INPUT_γH2AX

value: Cultured primary neurons from E16 cortex


title: CA067


title: CA149


title: CA179


title: CA133


title: CA041


title: ChIP-Seq NMDA INPUT_TOP2B

source_name: ChIP-Seq NMDA INPUT_TOP2B

value: Swiss-Webster


title: ChIP-Seq NMDA TOP2B

source_name: ChIP-Seq NMDA TOP2B


title: RNA-Seq Etoposide

source_name: RNA-Seq Etoposide


title: CA926

source_name: children with diarrhea_DAEC

value: 2 year-old or older

value: DAEC


title: CA909

value: Diarrhea


title: CA101

value: mild


title: CA753

value: Whole blood


title: CA894

value: A


title: CA689


title: CA674


title: CA625


title: ChIP-Seq NMDA INPUT_γH2AX

source_name: ChIP-Seq NMDA INPUT_γH2AX


title: CA302


title: RNA-Seq CTRL

source_name: RNA-Seq CTRL


title: CA234


title: CA382


title: CT184

source_name: healthy children with bacterial colonization

value: Control

value: Salmonella


title: CT174


title: CA063


title: CA772

value: <2 year-old

value: moderate


title: CA437


title: CA273


title: CA036

value: EAEC


title: CA386


title: CA215


title: CA709


title: CA332


title: CA419


title: CT055


title: CT040


title: CT062

source_name: healthy children without bacterial colonization

value: Negative


title: CA209


title: CT063


title: CT061


title: CA110


title: CT171


title: CT047


title: CA130


title: CT057


title: CT046


title: CT044


title: CT032

value: B


title: CA061


title: CT013


title: CT020


title: CT114

value: EPEC


title: CT016


title: CT030


title: CT022


title: CT026


title: CT024


title: CT170


title: CT056


title: CT052


title: NS2

city: Tianjin

first: Wang

last: Xiaowei

address: Business park of Tianjin airport economic zone

country: China

institute: BGI-Tianjin Techonology Co., Ltd.

data_processing:
Basecalls performed using CASAVA version 1.4
After trimming the low quality sequences and removing the adapters, the remaining reads were aligned to rat genome sequence (Rattus norvegucus assembly, rn5) using SOAP2. BLAST was adopted to identify known miRNAs (miRBase 20) and other type RNAs (rRNA, tRNA, snRNA, snoRNA; GenBank&Rfam).
We normalized all miRNA reads as transcripts per million clean tags (TPM).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample replicates.

organism: Rattus norvegicus

source_name: hepatic normal tissue

extract_protocol:
Total RNA was extracted from liver tissues with TRIZOL (Invitrogen, Carlsbad, CA, US). The concentration and quality of the puriﬁed RNAs were evaluated on a Bioanalyzer 2100 (Agilent Technologies,PaloAlto,CA). Libraries were constructed using the Illumina Small RNA Sample Prep Kit V1.0.
RNA libraries were prepared for sequencing using standard Illumina protocol

treatment_protocol: Liver tissues were ﬁxed in 10% formaldehyde in NaCl⁄Pi buffer, dehydrated in alcohol, and embedded in parafﬁn. Sections were prepared and stained with hematoxylin-eosin (HE) and Masson trichrome (MT) stain.

value: hepatic normal tissue


title: PS2

source_name: hepatic fibrosis tissue

value: hepatic fibrosis tissue


title: PS1


title: NS1


title: WT_mRNA_diamide_rep2

city: Münster

first: Danny

middle: D.

last: Nedialkova

address: Von-Esmarch-Str. 54

department: Max Planck Research Group for RNA Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: processed data file: Scer_mRNA_rawCounts.txt.gz

data_processing:
Basecalls were performed with Illumina Casava 1.8.
3' adapter sequences were removed with FastX-toolkit
Reads were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of CDS sequences containing 18 nt of genomic flanking regions. only reads with unique matches to the sense strand were retained for further analysis.
Raw read counts were determined using custom scripts. Yeast footprint reads mapping within the first 15 codons of coding sequences were omitted to avoid effects of growth conditions and translation inhibitor treatement on ribosome density in the beginning of ORFs.
Genome_build: sacCer3; ce6
Supplementary_files_format_and_content: Tab-delimited text files containing gene annotations and raw read count data.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown from OD600 of 0.02 to OD600=0.4, collected by rapid vacuum filtration, and immediately frozen in liquid nitrogen.

extract_protocol:
Frozen cells were were resuspended in 50 mM NaOAc (pH=5.5), 10 mM EDTA, 1% SDS to 1% and homogenized in a Precellys 24 bead beater. Clarified ysates were treated with Proteinase Kand total RNA was extracted with acid phenol. Following DNase treatment,d poly(A) RNA was purified by two rounds of selection with Poly(A)Purist MAG Kit. Purified RNA was fragmented by alkaline hydrolysis and fragments of 50-80 nt were used for library preparation.
Fragmented poly(A) RNA was dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.

treatment_protocol: YPD medium; 1.5 mM diamide for 30 min; cycloheximide (1 min)

tag: strain background

tag: genotype/variation

value: wild-type

tag: tissue/cell type

value: Whole cells

tag: replicate


title: ncs2Δ_ribo_diamide_rep2

description: processed data file: Scer_ribo_rawCounts.txt.gz

extract_protocol:
Frozen cells were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.5 mM DTT, 100 µg/ml CHX. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction. Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.


title: WT_mRNA_diamide_rep1


title: ncs2Δ_mRNA_diamide_rep1


title: WT_mRNA_diamide_rep3


title: N2_adult_mRNA_rep2

description: processed data file: Celeg_mRNA_rawCounts.txt.gz

organism: Caenorhabditis elegans

growth_protocol: Animals were age-synchronized by bleaching, grown on plates seeded with E.coli OP50, and collected at day 1 of adulthood.

extract_protocol: Total RNA was isolated using Tri Reagent and poly(A) RNA sequencing libraries were generated with the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: Animals were washed off plates, washed 3 times in M9 medium, harvested by rapid filtration, and frozen in liquid nitrogen.

value: wild-type (N2)

value: Whole animals


title: N2_adult_mRNA_rep1


title: tut-1_elpc-1_adult_mRNA_rep1


title: WT_ribo_diamide_rep3


title: tut-1_L4_ribo_rep2

description: processed data file: Celeg_ribo_rawCounts.txt

growth_protocol: Animals were age-synchronized by bleaching, grown on plates seeded with E.coli OP50, and collected at L4 stage.

extract_protocol:
Frozen animals were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.5 mM DTT, 100 µg/ml CHX. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.


title: tut-1_elpc-1_adult_mRNA_rep2


title: WT_ribo_diamide_rep1


title: WT_ribo_diamide_rep2


title: tut-1_L4_ribo_rep1


title: ncs2Δelp6Δ_mRNA_YPD_rep3

treatment_protocol: YPD medium; cycloheximide (1 min)

value: ncs2-delta elp6-delta


title: elp6Δ_mRNA_YPD_rep3


title: elp6Δ_mRNA_YPD_rep1


title: N2_L4_ribo_rep2


title: ncs2Δelp6Δ_mRNA_YPD_rep2


title: N2_L4_ribo_rep1

treatment_protocol: Animals were washed off plates, washed 3 times in M9 medium, harvested by rapid filtration, and immediately frozen in liquid nitrogen.


title: elp6Δ_mRNA_YPD_rep2


title: ncs2Δ_ribo_diamide_rep3


title: ncs2Δ_ribo_diamide_rep1


title: ncs2Δ_mRNA_YPD_rep1


title: WT_mRNA_YPD_rep1


title: ncs2Δ_mRNA_YPD_rep3


title: ncs2Δelp6Δ_ribo_YPD_rep3


title: WT_mRNA_YPD_rep3


title: ncs2Δ_mRNA_YPD_rep2


title: WT_mRNA_YPD_rep2


title: ncs2Δelp6Δ_ribo_YPD_rep2


title: ncs2Δelp6Δ_mRNA_YPD_rep1


title: ncs2Δelp6Δ_ribo_paromomycin_rep3

treatment_protocol: YPD medium; 1 mg/ml paromomycin for 30 min; cycloheximide (1 min)


title: elp6Δ_ribo_YPD_rep1


title: WT_ribo_YPD_rep3


title: WT_ribo_YPD_rep1

extract_protocol:
Frozen cells were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.5 mM DTT, 100 µg/ml CHX. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.


title: ncs2Δelp6Δ_ribo_YPD_rep1


title: ncs2Δ_ribo_YPD_rep1


title: ncs2Δ_ribo_YPD_rep3


title: ncs2Δ_ribo_YPD_rep2


title: elp6Δ_ribo_YPD_rep3


title: elp6Δ_ribo_YPD_rep2


title: WT_ribo_YPD_rep2


title: ncs2Δ_ribo_YPD_noCHX_rep3

extract_protocol:
Frozen cells were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.5 mM DTT. Extracts were treated with RNAse I and resolved on sucrose gradients. RNA from monosome fractions was extracted by hot phenol and ribosome footprints of 28-32 nt were purified by size selection and gel extraction. Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.

treatment_protocol: YPD medium; no translation inhibitors


title: hbs1Δ_ribo_YPD_rep3


title: hbs1Δncs2Δelp6Δ_ribo_YPD_rep3

value: hbs1-delta ncs2-delta elp6-delta


title: dom34Δncs2Δelp6Δ_ribo_YPD_rep1

value: dom34-delta ncs2-delta elp6-delta


title: dom34Δncs2Δelp6Δ_ribo_YPD_rep2


title: hbs1Δ_ribo_YPD_rep1


title: ncs2Δelp6Δ_ribo_paromomycin_rep1


title: ncs2Δ_ribo_YPD_noCHX_rep2


title: hbs1Δncs2Δelp6Δ_ribo_YPD_rep2


title: WT_ribo_paromomycin_rep2


title: ncs2Δ_ribo_YPD_noCHX_rep1


title: hbs1Δncs2Δelp6Δ_ribo_YPD_rep1


title: WT_ribo_paromomycin_rep3


title: hbs1Δ_ribo_YPD_rep2


title: dom34Δncs2Δelp6Δ_ribo_YPD_rep3


title: ncs2Δelp6Δ_ribo_paromomycin_rep2


title: WT_ribo_YPD_noCHX_rep3


title: WT_ribo_YPD_noCHX_rep2


title: WT_ribo_YPD_noCHX_rep1


title: elp6Δ_ribo_tEKQ_rep3

description: processed data file: Scer_ribo_tKQE_rawCounts.txt.gz

treatment_protocol: SC-Leu medium; cycloheximide (1 min)


title: ncs2Δ_ribo_tEKQ_rep3


title: ncs2Δ_ribo_tEKQ_rep1


title: WT_ribo_tEKQ_rep3


title: elp6Δ_ribo_tEKQ_rep1


title: ncs2Δ_ribo_tEKQ_rep2


title: elp6Δ_ribo_tEKQ_rep2


title: WT_ribo_tEKQ_rep2


title: WT_ribo_tEKQ_rep1


title: WT_ribo_paromomycin_rep1


title: elp6Δ_ribo_empty_plasmid_rep2


title: WT_ribo_empty_plasmid_rep2


title: elp6Δ_ribo_empty_plasmid_rep1


title: ncs2Δ_mRNA_rapamycin_rep2

treatment_protocol: YPD medium; 12.5 nM rapamycin for 30 min; cycloheximide (1 min)


title: ncs2Δ_ribo_empty_plasmid_rep2


title: elp6Δ_ribo_empty_plasmid_rep3


title: WT_mRNA_rapamycin_rep3


title: WT_ribo_empty_plasmid_rep1


title: ncs2Δ_ribo_empty_plasmid_rep1


title: elp6Δ_ribo_rapamycin_rep3


title: WT_mRNA_rapamycin_rep1


title: ncs2Δ_mRNA_rapamycin_rep3


title: ncs2Δ_mRNA_rapamycin_rep1


title: elp6Δ_ribo_rapamycin_rep1


title: ncs2Δ_ribo_empty_plasmid_rep3


title: elp6Δ_ribo_rapamycin_rep2


title: ncs2Δ_ribo_rapamycin_rep3


title: ncs2Δ_ribo_rapamycin_rep2


title: ncs2Δ_ribo_rapamycin_rep1


title: WT_ribo_rapamycin_rep1


title: ncs2Δ_mRNA_diamide_rep3


title: WT_ribo_rapamycin_rep3


title: WT_ribo_empty_plasmid_rep3


title: WT_ribo_rapamycin_rep2


title: WT_mRNA_rapamycin_rep2


title: dksA 8hr Rep 2

city: Indianapolis

first: Concerta

middle: L

last: Holley

state: IN

address: 635 Barnhill Drive

department: Microbiology and Immunology

institute: Indiana University School of Medicine

description:
Sample 22
22-vdksA-2-8hr

data_processing:
Image analysis and base calling were performed with the HiSeq Control software and the Real Time Analysis software.
Demultiplexing was performed with the Illumina CASAVA software.
Sequenced reads were mapped with the Burrows-Wheeler Alignment tool
The total number of reads corresponding to the coding region of each gene was determined with the NGSUtils suite
Gene List was generated using an FDR cutoff of  0.1 and a fold change cutoff of 2 fold
Genome_build: ASM794v1 [AE017143]
Supplementary_files_format_and_content: Excel Sheets include CPM values for each sample as well as calculated fold change, p-value, and FDR.

organism: [Haemophilus] ducreyi 35000HP

source_name: bacteria

growth_protocol: Bacteria were grown in gonococcal broth supplemented with 5% fetal bovine serum, 1% IsoVitalex and 50 μg/ml hemin (Aldrich Chemical Co.) in a 33°C waterbath.

extract_protocol:
Bacteria was collected and RNA was harvested using Trizol reagent. The Ribo-Zero Magnetic kit was used to remove rRNA and the Illumina TruSeq Stranded mRNA sample preparation kit (Cat# RS-122-2101) was used with 10 to 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: growth phase

value: Transition

tag: time point

value: 8 hours

value: deltadksA


title: WT 16hr Rep 3

description:
Sample 27
27-35000HP-3-16hr

value: Stationary

value: 16 hours

value: wild type


title: relAspoT 16hr Rep 3

description:
Sample 31
31-vrelAspoT-3-16hr

value: deltarelAspoT


title: dksA 16hr Rep 2

description:
Sample 34
34-vdksA-2-16hr


title: dksA 16hr Rep 3

description:
Sample 35
35-vdksA-3-16hr


title: relAspoT 16hr Rep 2

description:
Sample 30
30-vrelAspoT-2-16hr


title: dksA 16hr Rep 4

description:
Sample 36
36-vdksA-4-16hr


title: dksA 16hr Rep 1

description:
Sample 33
33-vdksA-1-16hr


title: WT 16hr Rep 4

description:
Sample 28
28-35000HP-4-16hr


title: relAspoT 8hr Rep 3

description:
Sample 19
19-vrelAvspoT-3-8hr


title: dksA 8hr Rep 3

description:
Sample 23
23-vdksA-3-8hr


title: relAspoT 8hr Rep 4

description:
Sample 20
20-vrelAvspoT-4-8hr


title: relAspoT 16hr Rep 1

description:
Sample 29
29-vrelAspoT-1-16hr


title: WT 16hr Rep 2

description:
Sample 26
26-35000HP-2-16hr


title: dksA 8hr Rep 1

description:
Sample 21
21-vdksA-1-8hr


title: relAspoT 16hr Rep 4

description:
Sample 32
32-vrelAspoT-4-16hr


title: relAspoT 8hr Rep 2

description:
Sample 18
18-vrelAvspoT-2-8hr


title: relAspoT 8hr Rep 1

description:
Sample 17
17-vrelAvspoT-1-8hr


title: WT 8hr Rep 3

description:
Sample 15
15-35000HP-3-8hr


title: WT 8hr Rep 4

description:
Sample 16
16-35000HP-4-8hr


title: ncs2Δ_mRNA_diamide_rep2


title: WT 8hr Rep 2

description:
Sample 14
14-35000HP-2-8hr


title: WT 8hr Rep 1

description:
Sample 13
13-35000HP-1-8hr


title: dksA 4hr Rep 3

description:
Sample 11
11-vdksA-3-4hr

value: Mid-log

value: 4 hours


title: dksA 4hr Rep 4

description:
Sample 12
12-vdksA-4-4hr


title: WT 16hr Rep 1

description:
Sample 25
25-35000HP-1-16hr


title: dksA 8hr Rep 4

description:
Sample 24
24-vdksA-4-8hr


title: dksA 4hr Rep 2

description:
Sample 10
10-vdksA-2-4hr


title: relAspoT 4hr Rep 2

description:
Sample 6
6-vrelAvspoT-2-4hr


title: relAspoT 4hr Rep 4

description:
Sample 8
8-vrelAvspoT-4-4hr


title: WT 4hr Rep 3

description:
Sample 3
3-35000HP-3-4hr


title: WT 4hr Rep 1

description:
Sample 1
1-35000HP-1-4hr


title: relAspoT 4hr Rep 3

description:
Sample 7
7-vrelAvspoT-3-4hr


title: WT 4hr Rep 4

description:
Sample 4
4-35000HP-4-4hr


title: dksA 4hr Rep 1

description:
Sample 9
9-vdksA-1-4hr


title: relAspoT 4hr Rep 1

description:
Sample 5
5-vrelAvspoT-1-4hr


title: WT 4hr Rep 2

description:
Sample 2
2-35000HP-2-4hr


title: akuB_S.4c

status: Public on Jun 03 2015

city: Berlin

first: Robert

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

institute: Max-Delbrück-centrum

description: Strain CEA17 (deletion of the gene Afu2g02620 in the CEA10 background)

data_processing:
FASTQ files were receiven from GATC, Konstanz, Germany
Mapping of read pairs using TopHat (v1.4.1; --GTF GTF from CADRE; -maxintronlength 4000, -g 1)
Read counting using R-package easyRNASeq, annotation from BioMart (fungi_mart_19)
Normalisation using R-package DESeq
Genome_build: Aspergillus fumigatusa1163 A1163 (CADRE)
Supplementary_files_format_and_content: comma seperated values (csv) with the normalised read counts

organism: Aspergillus fumigatus

source_name: fungal cells

growth_protocol: 10^6 spores / ml were inoculated in AMM media supplemented with Glucose (1% w/v), MgSO4 (1% w/v), and Hunter’s trace elements

extract_protocol:
Total RNA was prepared using the RNeasy Plant Mini kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols; 50 bp single end

treatment_protocol: After 16 hours incubation (37 °C, 200 rpm shaking), 0,1 mg / L Caspofungin and / or 1 mg / L Siamycin was added to the media and samples collected 4 hours after induction

value: strain CEA17

tag: mutant

value: akuB knock-out mutant

tag: treatment

value: siamycin


title: akuB.4b

tag: strain

value: CAS


title: akuB.4a


title: akuB_SC.4c

value: CAS + siamycin


title: akuB_S.4b


title: akuB.0c


title: akuB.0a


title: akuB.4c


title: akuB_SC.4a


title: DC Mutant (SRy93) Sample

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

description:
protocol: Hi-C
Two replicates were performed and merged in the analysis. Biological replicate 1 is represented by a library that was sequenced twice in two separate lanes (SRR1665092 and SRR1665093) and Biological replicate 2  is also represented by a library that was sequenced twice in two separate lanes (SRR1665094 and SRR1665095). More information on the replicates, SRR ID, and md5 checksums are available in the file "HiC_libraries_Info.xls" available on the series record.

data_processing:
Iterative mapping and error correction of the chromatin interaction data were performed as previously described (Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999-1003, doi:10.1038/nmeth.2148 (2012))
We obtained around 70 million valid pairs that represent chromatin interactions per replicate. The frequency of redundant read pairs, due to PCR amplification, were found to be below ~5%. Redundant read pairs were removed. The number of Hi-C interactions mapped to sequences belonging to homologous chromosomes (both intra-chromosomal [cis] and inter-homolog [trans] interactions) was much higher than the interactions mapped to non-homologous chromosomes (inter-chromosomal [trans] interactions). Assuming that inter-homolog interactions (trans) are as frequent as non-homologous inter-chromosomal interactions (trans), we estimate that 80-90% of interactions mapped to the same chromosomes are intra-chromosomal (cis) interactions, with DC mutant (90%) higher than wild-type (> 85%).
The data were binned at both 10 kb and 50 kb non-overlapping genomic intervals. Binned data were normalized for intrinsic biases such as differences in number of restriction fragments within bins using the previously developed ICE method41. To normalize for differences in read depth of different datasets we summed the entire genome-wide binned ICE-corrected interaction matrix, excluding the diagonal (x = y) bins. We then transformed each interaction into a fraction of the matrix sum (minus diagonal x = y bins). Each fraction was then multiplied by 106. Biological replicates were highly correlated (Pearson’s correlation coefficients > 0.98 for 50 kb binned data excluding short-range interactions up to 50 kb). The correlations between biological replicates were higher than those between wild-type and DC mutant. Overall these numbers indicate that the modified Hi-C procedure was reproducible and performed as expected. For most analyses sequence reads obtained for biological replicates were pooled and ICE-corrected as described above to create a combined replicate dataset.
To calculate the ‘insulation’ score of each bin in the 10 kb binned Hi-C data, we calculated the average number of interactions that occurred across each bin. This can be visualized by sliding a 500 kb x 500 kb (50 bins x 50 bins) (Extended Data Fig. 4) square along the matrix diagonal, and aggregating all signal within the square. The mean signal within the square was then assigned to the 10 kb diagonal bin and this procedure was then repeated for all 10 kb diagonal bins. For any bins within 500 kb of the matrix start/end, an insulation score was not assigned, as the 500 kb x 500 kb insulation square would extend beyond the matrix bounds. The insulation score was then normalized relative to all of the insulation scores across each chromosome by calculating the log2 ratio of each bin’s insulation score and the mean of all insulation scores. Valleys/Minima along the normalized insulation score vector represent loci of reduced Hi-C interactions that occur across the bin. These valleys/minima are interpreted as TAD boundaries or areas of high local insulation
We modeled the overall chromatin interaction decay with distance using a modified LOWESS method (alpha = 0.5%, ignore zeros, IQR filter), as described previously42. LOWESS calculates the weighted-average and weighted-standard deviation for every genomic distance by pooling all data genome-wide. We transformed interaction data into a Z-score by calculating: [(observed signal – lowess-average) / lowess-stdev]. By expressing interaction data as Z-scores, we correct for minor differences in the overall decay with genomic distance that can vary slightly between samples.
Genome_build: ce10
Supplementary_files_format_and_content: tar ball archive of all relevant HiC data (binned at 50kb/10kb).  Iced, zScore, zScore-difference, insulation, boundaries

source_name: mixed stage embryos

growth_protocol: Wild-type N2 worms were grown at 20°C on NG agar plates with concentrated HB101 bacteria. For DC-mutant embryos, 10 ml of packed synchronous sdc-2(y93) L1 worms were placed onto 10 cm RNAi plates (NG agar with 1 mM IPTG and 100 mg/ml Carbenicillin) seeded with 2-3 ml of concentrated HT115 (DE3) bacteria carrying the Ahringer feeding library plasmid expressing the coding region of sdc-2. The RNAi plates were incubated at 25°C overnight before L1s were added.  Mixed-stage embryos were harvested from gravid hermaphrodites.

extract_protocol:
To obtain nuclear extract, embryos were dounced 10 times using the large pestle, and then 10 times using the small pestle. All douncing steps were performed on ice. The dounced extract was spun for 5 min at 100xg at 4°C, and the supernatant was saved. The pellet was resuspended in 750 ml of supplemented lysis buffer and dounced again. This procedure was repeated 7-10 times. All supernatants containing only nuclei, and not broken carcasses, were combined. An aliquot of the combined supernatant was stained with DAPI and the nuclei were counted using a hemocytometer, and then spun down for 5 min at 2000xg at 4°C. The nuclei were resuspended in the appropriate volume of 1.25X DpnII buffer (NEB B0543S) to create a Hi-C library.
The 3C libraries were created based on the published protocols (Sexton, et al, 2012, van Berkum et al, 2013, Belton et al, 2012), with some modifications. Approximately 1.5 x 108 C. elegans nuclei were pipetted into 5-10 1.7 ml tubes and resuspended in 300 ml of 1.25X DpnII buffer. 38 ml of 1% (w/v) SDS was added per tube and the tubes were incubated at 65°C for 10 min. After the addition of 34 ml of 20% (v/v) Triton X-100, the tubes were incubated at 37°C for 1 hr, shaking at 1000 rpm. 30 ml (1500 U) of DpnII (NEB R0543M) were added to each tube, and they were incubated overnight at 37°C while rocking. 26 ml of 20% (w/v) SDS was added to each tube and they were incubated at 65°C for 20 min, 1000 rpm. The reaction was then added to 7.6 ml of ligation master mix (745 ml of 10% Triton X-100, 745 ml of 10X T4 ligation buffer (500 mM Tris-HCl, pH 7.5, 100 mM MgCl2, 100 mM DTT), 80 ml of 10 mg/ml BSA, 80 ml of 100 mM ATP, and 5.96 ml water). 100 ml (100 U) T4 DNA ligase (Invitrogen 15224-025) was added and the reactions were incubated for 4 hrs at 16°C. After incubation 50 ml of 10 mg/ml Proteinase K was added and the tubes were further incubated at 65°C overnight. The next day 50 ml of 10 mg/ml Proteinase K was added to the reactions and they were incubated at 65°C for an additional 2 hrs. 2 ml of RNaseA (1 mg/ml) was added to each sample and incubated for 30 min at 37°C. The ligated DNA was then phenol-chloroform extracted and ethanol precipitated overnight. DNA was pelleted at 14,000xg for 30 min at 4°C, and then washed twice with 70% ethanol and air-dried. The DNA pellets from all Hi-C reactions were combined and dissolved in a total of 500 ml of 1X TE buffer, pH 8.0. Excess salt was removed from the samples via centrifugation using a filter unit (AMICON® Ultra Centrifugal Filter Unit – 0.5 ml 30 KDa) following the manufacture’s instruction. The concentration of DNA was determined and 10 mg of the Hi-C library was resuspended in 100 ml of water. AMPure beads, supplied as a suspension of magnetic beads in a PEG solution (Beckman Coulter cat # A63880), were used to remove large DNA fragments (> 10 kb), following the protocol provided by the manufacturer. The eluted DNA was then adjusted to 125 µl with 1X TE, pH 8.0 and sheared to 500-1000 bp using a Covaris S2 (Covaris, 520045) in micro tubes with the following settings: duty cycle, 5%; intensity, 3; cycles/burst, 200; time, 65 sec. The sheared DNA was then size selected for fragments larger than ~100 bp using AMPure beads and eluted in 34 ml of water. The DNA was quantified and 500 ng was used to make a paired-end Illumina sequencing library following the standard protocol (PE-930-1001), with the exception that we size selected 500-600 bp at the gel excision step prior to adding adapters for sequencing.  The library was sequenced using 100 bp paired end reads.

treatment_protocol: Worms were harvested and bleached to release the embryos and remove the carcasses. Following bleaching, embryos were centrifuged for ~45 sec at 1500-1800 rpm and washed 3 times in 1X M9 buffer to remove bleach solution. An equal volume of 1X M9 was added to the embryos and they were frozen in 1 ml aliquots and stored at -80°C. The frozen embryos were thawed on ice and supplemented with 1 mM PMSF and 5 mM DTT. The embryos were then washed once in 50 ml formaldehyde solution (1X M9 solution with 2% (v/v) formaldehyde, Polysciences 18814-20). Embryos were cross-linked in 50 ml of formaldehyde solution for 30 min at room temperature while shaking. Following crosslinking embryos were washed once with 50 ml of 100 mM Tris-HCl, pH 7.5, followed by two 50 ml washes of 1X M9. The embryos were then washed once in lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl and 0.2% (v/v) Igepal CA-630 (Sigma I8896)) supplemented with 5 mM DTT, 1 mM PMSF, 0.1% (v/v) protease inhibitors (EMD 539134) and 0.5 mM EGTA.

value: sdc-2(y93) with RNAi against sdc-2

tag: genotype

value: sdc-2 mutant


title: Wild-Type (N2) Sample

description:
protocol: Hi-C
Two replicates were performed and merged in the analysis. Biological replicate 1 is represented by three technical replicates (SRR1665087, SRR1665088, SRR1665089) while Biological replicate 2 is represented by two technical replicates (SRR1665090 and SRR1665091). More information on the replicates, SRR ID, and md5 checksums are available in the file "HiC_libraries_Info.xls" available on the series record.


title: WES_LC-MBT-15_Pt_blood

city: Seoul

first: Kyu-Tae

last: Kim

address: Irwon-Ro 81

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

description: bulk whole exome sequencing

data_processing:
RNA-Seq reads were aligned to the human genome reference (hg19) together with splice junction information of each sample using the 2-pass mode of STAR_2.4.0d.
Transcripts Per Million (TPM) was quantified by implementing RSEM v1.2.18 in default mode with Genecode v.19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Each row of the tab-delimited text file includes ENSEMBL gene ID, corresponding gene name and gene type for samples.

source_name: blood, LC-MBT-15

growth_protocol: Animal experiments were conducted in accordance with the Institute for Laboratory Animal Research Guide for the Care and Use of Laboratory Animals and within the protocols approved by the appropriate IRB at the Samsung Medical Center. Xenograft tumor specimens were dissociated into single cells. Dissociated cells were cultured in neurobasal media-A supplemented with N2 (×1/2), B27 (×1/2) (GIBCO, Carlsbad, CA), bFGF/EGF (25ng/ml each), neuregulin 1 (hNRG1, 10ng/ml), and long-insulin growth factor 1 (IGF1, 100ng/ml) (R&D Systems, Minneapolis, MN). As spheres appeared in suspension culture conditions, they were dissociated with accutase (PAA Laboratories GmbH, Cölbe, Germany) and expanded by reseeding.

extract_protocol:
In order to isolate single-cells and amplify initial RNA content enough to transcriptome sequencing, we adopted the C1TM Single-Cell Auto Prep System (Fluidigm, CA, USA) with the SMARTer kit (Clontech, CA, USA). Cells were captured on the C1 chip (17-25 μm) and determined as a live single cell by fluorescence microscopic observation. Quantity and quality of amplified cDNAs from individual single cells were checked by Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) and 2100 Bioanalyzer (Agilent Inc., CA, USA). RNAs from bulk cell samples were also amplified using a SMARTer kit with 10 ng of starting material. For WES, gDNAs were prepared using QIAamp® DNA Mini kit (QIAGEN, CA, USA). Exome sequencing was carried using the SureSelect XT Human All Exon V5 kit (Agilent Inc., CA, USA), according to the manufacturer’s standard protocol.
Libraries were prepared using the Nextera XT DNA Sample Prep Kit (Illumina, CA, USA) following the manufacturer’s instruction, assayed the quantity and quality, pooled, and then sequenced on the HiSeq 2500 (Illumina) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea).  Sequencing of the exome library was carried out on the HiSeq 2500 (Illumina, CA, USA) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea).

treatment_protocol: For drug screening, PDX cells in the serum free sphere culture condition were seeded in 384-well plates (500 cells/well). Two hours after plating, cells were treated with a drug library (Selleck, Houston, TX) in 3 folds and 10 points serial dilution (n=3 for each condition). After 6 days incubation at 37°C in a 5% CO2 humidified incubator, cell viability was analyzed using an ATP monitoring system based on firefly luciferase (ATPliteTM 1step, PerkinElmer, Waltham, CA). Test concentrations for each drug have been derived empirically to produce a clinically relevant spectrum of drug activity. Dose response curves and corresponding half maximal (50%) inhibitory concentration values (IC50) were calculated using the S+ Chip Analyzer (Samsung Electro-Mechanics, Suwon, Korea).

tag: cell type

value: blood


title: WES_LC-PT-45_Pt_tumor

description: bulk whole exome sequencing

source_name: primary tumor, LC-PT-45

value: primary tumor


title: WES_LC-PT-45_Pt_blood

description: bulk whole exome sequencing

source_name: blood, LC-PT-45


title: akuB_SC.4b


title: akuB_S.4a


title: akuB.0b


title: WES_H358

description: bulk whole exome sequencing

source_name: human lung cancer cell line

tag: cell line


title: LC-MBT-15_SC95

description: scRNA-Seq

source_name: PDX, LC-MBT-15

value: PDX


title: LC-PT-45-Selumetinib_R7

description: bulk RNA-Seq

source_name: PDX, LC-PT-45


title: LC-PT-45-Selumetinib_R0

description: bulk RNA-Seq


title: LC-PT-45-Selumetinib_R3

description: bulk RNA-Seq


title: LC-PT-45-mock

description: bulk RNA-Seq


title: WES_LC-MBT-15_Pooled

description: bulk whole exome sequencing


title: LC-MBT-15_SC79

description: scRNA-Seq


title: LC-MBT-15_SC72

description: scRNA-Seq


title: LC-MBT-15_SC73

description: scRNA-Seq


title: LC-MBT-15_SC67

description: scRNA-Seq


title: LC-MBT-15_SC87

description: scRNA-Seq


title: LC-MBT-15_SC65

description: scRNA-Seq


title: LC-MBT-15_SC94

description: scRNA-Seq


title: LC-MBT-15_SC92

description: scRNA-Seq


title: LC-MBT-15_SC89

description: scRNA-Seq


title: LC-MBT-15_SC80

description: scRNA-Seq


title: WES_LC-MBT-15_Pt_tumor

description: bulk whole exome sequencing

source_name: primary tumor, LC-MBT-15


title: LC-MBT-15_SC78

description: scRNA-Seq


title: LC-MBT-15_SC62

description: scRNA-Seq


title: LC-MBT-15_SC75

description: scRNA-Seq


title: LC-MBT-15_SC71

description: scRNA-Seq


title: LC-MBT-15_SC60

description: scRNA-Seq


title: LC-MBT-15_SC64

description: scRNA-Seq


title: LC-MBT-15_SC55

description: scRNA-Seq


title: LC-MBT-15_SC96

description: scRNA-Seq


title: LC-MBT-15_SC74

description: scRNA-Seq


title: LC-MBT-15_SC52

description: scRNA-Seq


title: LC-MBT-15_SC84

description: scRNA-Seq


title: LC-MBT-15_SC85

description: scRNA-Seq


title: LC-MBT-15_SC59

description: scRNA-Seq


title: WES_LC-PT-45_Pooled

description: bulk whole exome sequencing


title: LC-MBT-15_SC63

description: scRNA-Seq


title: LC-MBT-15_SC76

description: scRNA-Seq


title: LC-MBT-15_SC51

description: scRNA-Seq


title: LC-MBT-15_SC57

description: scRNA-Seq


title: LC-MBT-15_SC56

description: scRNA-Seq


title: LC-MBT-15_SC34

description: scRNA-Seq


title: LC-MBT-15_SC54

description: scRNA-Seq


title: LC-MBT-15_SC25

description: scRNA-Seq


title: LC-MBT-15_SC50

description: scRNA-Seq


title: LC-MBT-15_SC41

description: scRNA-Seq


title: LC-MBT-15_SC45

description: scRNA-Seq


title: LC-MBT-15_SC24

description: scRNA-Seq


title: LC-MBT-15_SC15

description: scRNA-Seq


title: LC-MBT-15_SC42

description: scRNA-Seq


title: LC-MBT-15_SC22

description: scRNA-Seq


title: LC-MBT-15_SC20

description: scRNA-Seq


title: LC-MBT-15_SC16

description: scRNA-Seq


title: LC-MBT-15_Pooled

description: bulk RNA-Seq


title: LC-MBT-15_SC07

description: scRNA-Seq


title: LC-MBT-15_SC02

description: scRNA-Seq


title: LC-MBT-15_SC09

description: scRNA-Seq


title: LC-MBT-15_SC58

description: scRNA-Seq


title: LC-MBT-15_Tivantinib

description: bulk RNA-Seq


title: LC-MBT-15_SC10

description: scRNA-Seq


title: LC-PT-45-Re_SC92

description: scRNA-Seq

source_name: PDX, LC-PT-45-Re


title: LC-MBT-15_DAPT

description: bulk RNA-Seq


title: LC-PT-45-Re_SC89

description: scRNA-Seq


title: LC-MBT-15_Erlotinib

description: bulk RNA-Seq


title: LC-MBT-15_SC11

description: scRNA-Seq


title: LC-MBT-15_SC14

description: scRNA-Seq


title: LC-PT-45-Re_SC84

description: scRNA-Seq


title: LC-PT-45-Re_SC67

description: scRNA-Seq


title: LC-PT-45-Re_SC71

description: scRNA-Seq


title: LC-MBT-15_SC08

description: scRNA-Seq


title: LC-PT-45-Re_SC78

description: scRNA-Seq


title: LC-MBT-15_Carboplatin

description: bulk RNA-Seq


title: LC-MBT-15_Afatinib

description: bulk RNA-Seq


title: LC-PT-45-Re_SC87

description: scRNA-Seq


title: LC-PT-45-Re_SC90

description: scRNA-Seq


title: LC-PT-45-Re_SC91

description: scRNA-Seq


title: LC-MBT-15_Docetaxel

description: bulk RNA-Seq


title: LC-PT-45-Re_SC85

description: scRNA-Seq


title: LC-PT-45-Re_SC44

description: scRNA-Seq


title: LC-PT-45-Re_SC46

description: scRNA-Seq


title: LC-PT-45-Re_SC47

description: scRNA-Seq


title: LC-PT-45-Re_SC55

description: scRNA-Seq


title: LC-PT-45-Re_SC80

description: scRNA-Seq


title: LC-PT-45-Re_SC70

description: scRNA-Seq


title: LC-PT-45-Re_SC59

description: scRNA-Seq


title: LC-PT-45-Re_SC40

description: scRNA-Seq


title: LC-PT-45-Re_SC39

description: scRNA-Seq


title: LC-PT-45-Re_SC61

description: scRNA-Seq


title: LC-PT-45-Re_SC57

description: scRNA-Seq


title: LC-PT-45-Re_SC56

description: scRNA-Seq


title: LC-PT-45-Re_SC25

description: scRNA-Seq


title: LC-PT-45-Re_SC33

description: scRNA-Seq


title: LC-PT-45-Re_SC28

description: scRNA-Seq


title: LC-PT-45-Re_SC17

description: scRNA-Seq


title: LC-PT-45-Re_SC54

description: scRNA-Seq


title: LC-PT-45-Re_SC22

description: scRNA-Seq


title: LC-PT-45-Re_SC53

description: scRNA-Seq


title: LC-PT-45-Re_SC51

description: scRNA-Seq


title: LC-PT-45-Re_SC43

description: scRNA-Seq


title: LC-PT-45-Re_SC69

description: scRNA-Seq


title: LC-PT-45-Re_SC38

description: scRNA-Seq


title: LC-PT-45-Re_Docetaxel

description: bulk RNA-Seq


title: LC-PT-45-Re_SC01

description: scRNA-Seq


title: LC-PT-45-Re_SC26

description: scRNA-Seq


title: LC-PT-45-Re_SC72

description: scRNA-Seq


title: LC-PT-45-Re_SC31

description: scRNA-Seq


title: LC-PT-45-Re_SC13

description: scRNA-Seq


title: LC-PT-45-Re_Carboplatin

description: bulk RNA-Seq


title: LC-PT-45-Re_DAPT

description: bulk RNA-Seq


title: LC-PT-45-Re_BEZ235

description: bulk RNA-Seq


title: LC-PT-45-Re_SC09

description: scRNA-Seq


title: LC-PT-45-Re_SC11

description: scRNA-Seq


title: LC-PT-45_SC91

description: scRNA-Seq


title: LC-PT-45-Re_SC08

description: scRNA-Seq


title: LC-PT-45-Re_SC06

description: scRNA-Seq


title: LC-PT-45_SC76

description: scRNA-Seq


title: LC-PT-45-Re_Selumetinib

description: bulk RNA-Seq


title: LC-PT-45-Re_BKM120

description: bulk RNA-Seq


title: LC-PT-45_SC95

description: scRNA-Seq


title: LC-PT-45_SC94

description: scRNA-Seq


title: LC-PT-45_SC88

description: scRNA-Seq


title: LC-PT-45_SC53

description: scRNA-Seq


title: LC-PT-45_SC54

description: scRNA-Seq


title: LC-PT-45_SC93

description: scRNA-Seq


title: LC-PT-45_SC87

description: scRNA-Seq


title: LC-PT-45_SC35

description: scRNA-Seq


title: LC-PT-45_SC45

description: scRNA-Seq


title: LC-PT-45_SC23

description: scRNA-Seq


title: LC-PT-45_SC28

description: scRNA-Seq


title: LC-PT-45_SC79

description: scRNA-Seq


title: LC-PT-45-Re_Pooled

description: bulk RNA-Seq


title: LC-PT-45_SC77

description: scRNA-Seq


title: LC-PT-45_SC13

description: scRNA-Seq


title: LC-PT-45_SC10

description: scRNA-Seq


title: LC-PT-45-Re_SC36

description: scRNA-Seq


title: LC-PT-45_SC72

description: scRNA-Seq


title: LC-PT-45_SC04

description: scRNA-Seq


title: LC-PT-45_SC49

description: scRNA-Seq


title: LC-PT-45_SC34

description: scRNA-Seq


title: LC-PT-45_SC67

description: scRNA-Seq


title: LC-PT-45_SC65

description: scRNA-Seq


title: LC-PT-45_Carboplatin

description: bulk RNA-Seq


title: LC-PT-45_DAPT

description: bulk RNA-Seq


title: LC-PT-45_Pooled

description: bulk RNA-Seq


title: LC-PT-45_SC01

description: scRNA-Seq


title: LC-PT-45_Pt_tumor

description: bulk RNA-Seq


title: H358_SC91

description: scRNA-Seq


title: H358_SC93

description: scRNA-Seq


title: H358_SC90

description: scRNA-Seq


title: H358_SC89

description: scRNA-Seq


title: H358_SC87

description: scRNA-Seq


title: LC-PT-45_SC15

description: scRNA-Seq


title: LC-PT-45_SC14

description: scRNA-Seq


title: LC-PT-45_SC50

description: scRNA-Seq


title: LC-PT-45_SC30

description: scRNA-Seq


title: LC-PT-45_SC61

description: scRNA-Seq


title: H358_SC80

description: scRNA-Seq


title: LC-PT-45_SC09

description: scRNA-Seq


title: LC-PT-45_SC06

description: scRNA-Seq


title: H358_SC79

description: scRNA-Seq


title: LC-PT-45_SC58

description: scRNA-Seq


title: H358_SC76

description: scRNA-Seq


title: H358_SC74

description: scRNA-Seq


title: H358_SC73

description: scRNA-Seq


title: LC-PT-45_SC05

description: scRNA-Seq


title: LC-PT-45_SC02

description: scRNA-Seq


title: H358_SC69

description: scRNA-Seq


title: LC-PT-45_Docetaxel

description: bulk RNA-Seq


title: H358_SC96

description: scRNA-Seq


title: H358_SC68

description: scRNA-Seq


title: H358_SC95

description: scRNA-Seq


title: H358_SC67

description: scRNA-Seq


title: LC-PT-45_BKM120

description: bulk RNA-Seq


title: H358_SC63

description: scRNA-Seq


title: H358_SC94

description: scRNA-Seq


title: H358_SC55

description: scRNA-Seq


title: H358_SC57

description: scRNA-Seq


title: H358_SC53

description: scRNA-Seq


title: H358_SC52

description: scRNA-Seq


title: H358_SC42

description: scRNA-Seq


title: H358_SC86

description: scRNA-Seq


title: H358_SC39

description: scRNA-Seq


title: H358_SC84

description: scRNA-Seq


title: H358_SC85

description: scRNA-Seq


title: H358_SC34

description: scRNA-Seq


title: H358_SC83

description: scRNA-Seq


title: H358_SC75

description: scRNA-Seq


title: H358_SC71

description: scRNA-Seq


title: H358_SC70

description: scRNA-Seq


title: H358_SC29

description: scRNA-Seq


title: H358_SC32

description: scRNA-Seq


title: H358_SC18

description: scRNA-Seq


title: H358_SC65

description: scRNA-Seq


title: H358_SC59

description: scRNA-Seq


title: H358_SC17

description: scRNA-Seq


title: H358_SC14

description: scRNA-Seq


title: H358_SC62

description: scRNA-Seq


title: H358_SC16

description: scRNA-Seq


title: H358_SC38

description: scRNA-Seq


title: H358_SC24

description: scRNA-Seq


title: H358_SC05

description: scRNA-Seq


title: H358_SC44

description: scRNA-Seq


title: H358_SC25

description: scRNA-Seq


title: PGC_17W_embryo1_F_HiSeq2500

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

description:
bisulfite treated  genomic DNA
PGC_17W_embryo1_F_methylation_calling.bed

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
For RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings (Trapnell et al., 2009). And for WGBS, bisulfite-converted reads were aligned to the human refference genome (hg19) using Bismark software (v0.7.6).
For RNA-seq, Cufflinks (v2.2.1) with default parameters was further used to assemble the transcripts and quantify transcription levels (FPKM, fragments per kilobase of transcript per million mapped reads) of annotated genes (Trapnell et al., 2010). And for WGBS, CpG methylation level of covered cytosines was estimated using comstomized Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the FPKM values of RefSeq genes, and the bed files which include the methylation level of cytosines in CpG, CHH and CHG context.

source_name: Primordial Germ Cells

extract_protocol:
For single cell transcriptome analysis, the protocol for single-cell RNA-Seq has been published previously (Tang et al., 2010; Tang et al., 2009). Briefly, after a MACS or FACS procedure, a single PGC or somatic cell was randomly picked by using a mouth pipette and transferred into lysate buffer. And for DNA methylome analysis, the KIT-positive PGCs that were obtained by FACS were further washed with DPBS, and then DNA was isolated from the cell pellets using DNeasy Blood & Tissue Kits (Qiagen).
For single cell RNA-seq library construction, a total of 20–100 ng of cDNA was sheared into 150 bp to 350 bp by Covaris S2 after the generation of cDNA from a single cell, and the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, Inc.) was used to prepare the sequencing library following the manufacturer’s protocol. Briefly, the fragmented cDNA was end-repaired, dA tailed, adapter ligated and then subjected to 10–12 cycles of PCR amplification. Libraries were pooled and sequenced on Illumina HiSeq2500 sequencers for 100-bp paired-end sequencing. And for whole genome bisulfite sequencing (WGBS) library construction, samples of 5–100 ng of genomic DNA were used to construct the PBAT library, as previously described with minor modifications (Miura et al., 2012; Smallwood et al., 2014). Briefly, the isolated genomic DNAs, together with 1% unmethylated lambda DNA (Thermo Scientific), were subjected to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions. The bisulfite-converted templates were then annealed using random nonamer primers with a 5’ biotin tag and a truncated Illumina P5 adapter (5’-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) supplemented with 50 units of klenow polymerase (3’ to 5’ exo-, NEB). The excess primers were removed using 40 U exonuclease I (NEB) before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter). Then, the newly synthesized DNA strands were immobilized using the Dynabeads M280 Streptavidin (Invitrogen) and the original bisulfite-treated DNA templates were removed via two rounds of 0.1 N NaOH washes. The second strands were synthesized using 50 units klenow polymerase (3’ to 5’ exo-, NEB) with random nonamer primers containing a truncated P7 Illumina adapter (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads were further collected and were washed several times, and the library was finally amplified with 4–6 cycles of PCR using 1 U Kapa HiFi HS DNA Polymerase (Kapa Biosystems) together with 0.4 µM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 µM pre-indexed Illumina Reversed primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates index sequences). Amplified libraries were purified with 0.8× Agencourt Ampure XP beads twice and were assessed on the Agilent Bioanalyzer 2100 platform and quantified with a standard curve-based qPCR assay (Kapa Biosystems). The final quality-ensured libraries were pooled and sequenced on the Illumina HiSeq2000/2500 sequencer for 100 bp or 150 bp paired-end sequencing.

tag: developmental stage

value: 17 week gestation

tag: gender

value: female


title: PGC_10W_embryo1_F_rep1_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_10W_embryo1_F_rep1_methylation_calling.bed

value: 10 week gestation


title: H358_SC12

description: scRNA-Seq


title: Soma_19W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
Soma_19W_embryo1_M_methylation_calling.bed

source_name: Gonadal Somatic Cells

value: 19 week gestation

value: male


title: Soma_11W_embryo1_M_HiSeq2500_deeper

description:
bisulfite treated  genomic DNA
Soma_11W_embryo1_M_methylation_calling.bed

value: 11 week gestation


title: H358_SC23

description: scRNA-Seq


title: H358_SC11

description: scRNA-Seq


title: Soma_11W_embryo1_M_HiSeq2500


title: H358_SC10

description: scRNA-Seq


title: H358_Pooled

description: bulk RNA-Seq


title: H358_SC09

description: scRNA-Seq


title: PGC_10W_embryo2_M_PBAT_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_10W_embryo2_M_PBAT_methylation_calling.bed


title: PGC_10W_embryo2_M_TA-PBAT_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_10W_embryo2_M_TA-PBAT_methylation_calling.bed


title: Soma_7W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
Soma_7W_embryo1_M_methylation_calling.bed

value: 7 week gestation


title: Soma_17W_embryo1_F_HiSeq2500

description:
bisulfite treated  genomic DNA
Soma_17W_embryo1_F_methylation_calling.bed


title: PGC_11W_embryo1_F_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_11W_embryo1_F_methylation_calling.bed


title: PGC_11W_embryo1_M_rep2_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_11W_embryo1_M_rep2_methylation_calling.bed


title: PGC_10W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_10W_embryo1_M_methylation_calling.bed


title: PGC_7W_embryo2_M_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_7W_embryo2_M_methylation_calling.bed


title: Soma_7W_embryo2_M_HiSeq2500

description:
bisulfite treated  genomic DNA
Soma_7W_embryo2_M_methylation_calling.bed


title: Heart_5W_embryo1_HiSeq2500_deeper

description:
bisulfite treated  genomic DNA
Heart_5W_embryo1_methylation_calling.bed

source_name: Heart

value: 5 week gestation


title: Soma_10W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
Soma_10W_embryo1_M_methylation_calling.bed


title: PGC_11W_embryo1_M_rep1_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_11W_embryo1_M_rep1_methylation_calling.bed


title: PGC_10W_embryo1_F_rep2_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_10W_embryo1_F_rep2_methylation_calling.bed


title: PGC_13W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_13W_embryo1_M_methylation_calling.bed

value: 13 week gestation


title: PGC_7W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_7W_embryo1_M_methylation_calling.bed


title: Brain_5W_embryo1_HiSeq2500_deeper

description:
bisulfite treated  genomic DNA
Brain_5W_embryo1_methylation_calling.bed

source_name: Brain


title: Heart_5W_embryo1_HiSeq2500


title: Brain_5W_embryo1_HiSeq2500


title: F_PGC_8W_embryo1_ps9

description: polyA RNA

value: 8 week gestation


title: F_PGC_8W_embryo1_ps8

description: polyA RNA


title: F_PGC_8W_embryo1_ps5

description: polyA RNA


title: F_PGC_8W_embryo1_ps6

description: polyA RNA


title: F_PGC_8W_embryo1_ps3

description: polyA RNA


title: F_PGC_8W_embryo1_ps7

description: polyA RNA


title: F_PGC_8W_embryo1_ps4

description: polyA RNA


title: F_PGC_8W_embryo1_ps2

description: polyA RNA


title: F_PGC_8W_embryo1_ps1

description: polyA RNA


title: PGC_19W_embryo1_M_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_19W_embryo1_M_methylation_calling.bed


title: F_Soma_17W_embryo1_sc9

description: polyA RNA

source_name: Somatic Cells


title: F_Soma_17W_embryo1_sc8

description: polyA RNA


title: F_Soma_17W_embryo1_sc7

description: polyA RNA


title: F_Soma_17W_embryo1_sc3

description: polyA RNA


title: F_Soma_17W_embryo1_sc6

description: polyA RNA


title: F_Soma_17W_embryo1_sc4

description: polyA RNA


title: F_Soma_17W_embryo1_sc5

description: polyA RNA


title: PGC_19W_embryo2_M_HiSeq2500

description:
bisulfite treated  genomic DNA
PGC_19W_embryo2_M_methylation_calling.bed


title: F_Soma_17W_embryo1_sc1

description: polyA RNA


title: F_Soma_11W_embryo3_sc10

description: polyA RNA


title: F_Soma_11W_embryo3_sc9

description: polyA RNA


title: F_Soma_11W_embryo3_sc8

description: polyA RNA


title: F_Soma_11W_embryo3_sc3

description: polyA RNA


title: F_Soma_11W_embryo3_sc7

description: polyA RNA


title: F_Soma_11W_embryo3_sc5

description: polyA RNA


title: F_Soma_11W_embryo3_sc6

description: polyA RNA


title: F_Soma_11W_embryo3_sc4

description: polyA RNA


title: F_Soma_11W_embryo3_sc2

description: polyA RNA


title: F_Soma_11W_embryo3_sc1

description: polyA RNA


title: F_Soma_10W_embryo2_sc3

description: polyA RNA


title: F_Soma_8W_embryo1_sc8

description: polyA RNA


title: F_Soma_8W_embryo1_sc7

description: polyA RNA


title: F_Soma_8W_embryo1_sc5

description: polyA RNA


title: F_Soma_10W_embryo2_sc1

description: polyA RNA


title: F_Soma_8W_embryo1_sc10

description: polyA RNA


title: F_Soma_10W_embryo2_sc2

description: polyA RNA


title: F_Soma_17W_embryo1_sc2

description: polyA RNA


title: F_Soma_8W_embryo1_sc4

description: polyA RNA


title: F_Soma_8W_embryo1_sc3

description: polyA RNA


title: F_Soma_8W_embryo1_sc9

description: polyA RNA


title: F_Soma_8W_embryo1_sc2

description: polyA RNA


title: F_Soma_4W_embryo2_sc5

description: polyA RNA

value: 4 week gestation


title: F_Soma_4W_embryo2_sc4

description: polyA RNA


title: F_Soma_4W_embryo2_sc6

description: polyA RNA


title: F_Soma_8W_embryo1_sc6

description: polyA RNA


title: F_Soma_8W_embryo1_sc1

description: polyA RNA


title: F_Soma_4W_embryo2_sc3

description: polyA RNA


title: F_Soma_4W_embryo2_sc2

description: polyA RNA


title: F_Soma_4W_embryo2_sc1

description: polyA RNA


title: M_Soma_19W_embryo2_sc1

description: polyA RNA


title: M_Soma_11W_embryo2_sc3

description: polyA RNA


title: M_Soma_11W_embryo2_sc1

description: polyA RNA


title: M_Soma_11W_embryo1_sc2

description: polyA RNA


title: M_Soma_10W_embryo1_sc10

description: polyA RNA


title: M_Soma_19W_embryo1_sc1

description: polyA RNA


title: M_Soma_11W_embryo2_sc6

description: polyA RNA


title: M_Soma_11W_embryo2_sc4

description: polyA RNA


title: M_Soma_11W_embryo2_sc5

description: polyA RNA


title: M_Soma_10W_embryo1_sc6

description: polyA RNA


title: M_Soma_10W_embryo1_sc11

description: polyA RNA


title: M_Soma_10W_embryo1_sc8

description: polyA RNA


title: M_Soma_7W_embryo3_sc6

description: polyA RNA


title: M_Soma_10W_embryo1_sc4

description: polyA RNA


title: M_Soma_11W_embryo1_sc1

description: polyA RNA


title: M_Soma_10W_embryo1_sc2

description: polyA RNA


title: M_Soma_7W_embryo3_sc5

description: polyA RNA


title: M_Soma_7W_embryo3_sc3

description: polyA RNA


title: M_Soma_19W_embryo1_sc2

description: polyA RNA


title: M_Soma_10W_embryo1_sc5

description: polyA RNA


title: M_Soma_7W_embryo3_sc1

description: polyA RNA


title: M_Soma_10W_embryo1_sc9

description: polyA RNA


title: M_Soma_11W_embryo2_sc2

description: polyA RNA


title: M_Soma_7W_embryo2_sc7

description: polyA RNA


title: M_Soma_10W_embryo1_sc3

description: polyA RNA


title: M_Soma_7W_embryo2_sc6

description: polyA RNA


title: M_Soma_7W_embryo2_sc5

description: polyA RNA


title: M_Soma_7W_embryo1_sc13

description: polyA RNA


title: M_Soma_10W_embryo1_sc1

description: polyA RNA


title: M_Soma_7W_embryo1_sc9

description: polyA RNA


title: M_Soma_7W_embryo3_sc2

description: polyA RNA


title: F_PGC_17W_embryo1_sc31

description: polyA RNA


title: M_Soma_7W_embryo1_sc5

description: polyA RNA


title: M_Soma_7W_embryo3_sc4

description: polyA RNA


title: Flag-Barx1_Input

city: New York

first: Chenura

last: Jayewickreme

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

data_processing:
Basecalls performed using CASSAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.2.1 with default settings. Only uniquely aligned tags were retained and PCR duplicates were removed
Peaks were called using MACS2 with the following settings: Q value <=0.01, bandwith = 220.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files and Peak Bed file generated with MACS2

source_name: Immortalized E13.5 stomach mesenchymal cells

growth_protocol: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 20% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Cells were fixed in 1.1% formaldehyde in phosphate-buffered saline for 10 min at room temperature. Nuclei were extracted in a hypotonic buffer and chromatin was sheared by sonication. Immunoprecipitation was done using 10 ug of Flag M2 antibody (Sigma) and Protein G dynabeads (Invitrogen).
DNA was amplified using ThruPLEX kit (Rubicon Genomics)

treatment_protocol: Infected with 3xFLAG-BARX1-P2A-EGFP lentivirus generated from 293FT cells, cultured for 7 days

tag: tissue

value: Stomach

tag: passage

tag: chip antibody


title: M_Soma_7W_embryo1_sc12

description: polyA RNA


title: M_Soma_10W_embryo1_sc7

description: polyA RNA


title: F_PGC_17W_embryo1_sc28

description: polyA RNA


title: M_Soma_7W_embryo2_sc4

description: polyA RNA


title: M_Soma_7W_embryo2_sc3

description: polyA RNA


title: M_Soma_7W_embryo2_sc2

description: polyA RNA


title: F_PGC_17W_embryo1_sc23

description: polyA RNA


title: M_Soma_7W_embryo2_sc1

description: polyA RNA


title: M_Soma_7W_embryo1_sc10

description: polyA RNA


title: F_PGC_17W_embryo1_sc21

description: polyA RNA


title: M_Soma_7W_embryo1_sc11

description: polyA RNA


title: M_Soma_7W_embryo1_sc7

description: polyA RNA


title: F_PGC_17W_embryo1_sc26

description: polyA RNA


title: M_Soma_7W_embryo1_sc8

description: polyA RNA


title: M_Soma_7W_embryo1_sc2

description: polyA RNA


title: F_PGC_17W_embryo1_sc15

description: polyA RNA


title: M_Soma_7W_embryo1_sc4

description: polyA RNA


title: M_Soma_7W_embryo1_sc1

description: polyA RNA


title: F_PGC_17W_embryo1_sc14

description: polyA RNA


title: F_PGC_17W_embryo1_sc30

description: polyA RNA


title: F_PGC_17W_embryo1_sc11

description: polyA RNA


title: F_PGC_17W_embryo1_sc12

description: polyA RNA


title: F_PGC_17W_embryo1_sc27

description: polyA RNA


title: M_Soma_7W_embryo1_sc6

description: polyA RNA


title: F_PGC_17W_embryo1_sc22

description: polyA RNA


title: M_Soma_7W_embryo1_sc3

description: polyA RNA


title: F_PGC_17W_embryo1_sc24

description: polyA RNA


title: F_PGC_17W_embryo1_sc25

description: polyA RNA


title: F_PGC_17W_embryo1_sc8

description: polyA RNA


title: F_PGC_17W_embryo1_sc20

description: polyA RNA


title: F_PGC_17W_embryo1_sc5

description: polyA RNA


title: F_PGC_17W_embryo1_sc29

description: polyA RNA


title: F_PGC_17W_embryo1_sc18

description: polyA RNA


title: F_PGC_17W_embryo1_sc4

description: polyA RNA


title: F_PGC_17W_embryo1_sc19

description: polyA RNA


title: F_PGC_11W_embryo3_sc10

description: polyA RNA


title: Flag-Barx1_ChIP

value: Flag M2 Antibody Sigma


title: F_PGC_17W_embryo1_sc2

description: polyA RNA


title: F_PGC_17W_embryo1_sc17

description: polyA RNA


title: F_PGC_11W_embryo3_sc9

description: polyA RNA


title: F_PGC_11W_embryo3_sc8

description: polyA RNA


title: F_PGC_17W_embryo1_sc1

description: polyA RNA


title: F_PGC_11W_embryo3_sc7

description: polyA RNA


title: F_PGC_17W_embryo1_sc16

description: polyA RNA


title: F_PGC_17W_embryo1_sc13

description: polyA RNA


title: F_PGC_11W_embryo3_sc4

description: polyA RNA


title: F_PGC_11W_embryo3_sc3

description: polyA RNA


title: F_PGC_17W_embryo1_sc9

description: polyA RNA


title: F_PGC_10W_embryo2_sc7

description: polyA RNA


title: F_PGC_17W_embryo1_sc7

description: polyA RNA


title: F_PGC_10W_embryo2_sc5

description: polyA RNA


title: F_PGC_10W_embryo2_sc6

description: polyA RNA


title: F_PGC_17W_embryo1_sc6

description: polyA RNA


title: F_PGC_10W_embryo2_sc3

description: polyA RNA


title: F_PGC_8W_embryo1_sc15

description: polyA RNA


title: F_PGC_10W_embryo2_sc2

description: polyA RNA


title: F_PGC_8W_embryo1_sc16

description: polyA RNA


title: F_PGC_17W_embryo1_sc10

description: polyA RNA


title: F_PGC_11W_embryo3_sc6

description: polyA RNA


title: F_PGC_8W_embryo1_sc18

description: polyA RNA


title: F_PGC_10W_embryo2_sc13

description: polyA RNA


title: F_PGC_11W_embryo3_sc2

description: polyA RNA


title: F_PGC_11W_embryo3_sc1

description: polyA RNA


title: F_PGC_17W_embryo1_sc3

description: polyA RNA


title: F_PGC_8W_embryo1_sc14

description: polyA RNA


title: F_PGC_10W_embryo2_sc12

description: polyA RNA


title: F_PGC_10W_embryo2_sc9

description: polyA RNA


title: F_PGC_10W_embryo2_sc10

description: polyA RNA


title: F_PGC_10W_embryo2_sc8

description: polyA RNA


title: F_PGC_10W_embryo2_sc1

description: polyA RNA


title: F_PGC_8W_embryo1_sc17

description: polyA RNA


title: F_PGC_8W_embryo1_sc12

description: polyA RNA


title: F_PGC_8W_embryo1_sc11

description: polyA RNA


title: F_PGC_8W_embryo1_sc8

description: polyA RNA


title: F_PGC_8W_embryo1_sc7

description: polyA RNA


title: F_PGC_8W_embryo1_sc5

description: polyA RNA


title: F_PGC_11W_embryo3_sc5

description: polyA RNA


title: F_PGC_8W_embryo1_sc13

description: polyA RNA


title: F_PGC_8W_embryo1_sc3

description: polyA RNA


title: F_PGC_8W_embryo1_sc4

description: polyA RNA


title: F_PGC_8W_embryo1_sc6

description: polyA RNA


title: F_PGC_8W_embryo1_sc10

description: polyA RNA


title: F_PGC_10W_embryo2_sc4

description: polyA RNA


title: F_PGC_8W_embryo1_sc2

description: polyA RNA


title: F_PGC_4W_embryo2_sc7

description: polyA RNA


title: F_PGC_4W_embryo2_sc5

description: polyA RNA


title: F_PGC_4W_embryo2_sc4

description: polyA RNA


title: F_PGC_4W_embryo2_sc10

description: polyA RNA


title: F_PGC_4W_embryo2_sc6

description: polyA RNA


title: F_PGC_8W_embryo1_sc1

description: polyA RNA


title: F_PGC_4W_embryo2_sc9

description: polyA RNA


title: F_PGC_4W_embryo2_sc2

description: polyA RNA


title: F_PGC_4W_embryo1_sc2

description: polyA RNA


title: F_PGC_4W_embryo2_sc3

description: polyA RNA


title: F_PGC_4W_embryo2_sc1

description: polyA RNA


title: F_PGC_8W_embryo1_sc9

description: polyA RNA


title: F_PGC_4W_embryo1_sc1

description: polyA RNA


title: M_PGC_19W_embryo2_sc25

description: polyA RNA


title: M_PGC_19W_embryo2_sc26

description: polyA RNA


title: M_PGC_19W_embryo2_sc24

description: polyA RNA


title: M_PGC_19W_embryo2_sc23

description: polyA RNA


title: M_PGC_19W_embryo2_sc21

description: polyA RNA


title: F_PGC_4W_embryo2_sc8

description: polyA RNA


title: M_PGC_19W_embryo2_sc22

description: polyA RNA


title: M_PGC_19W_embryo2_sc19

description: polyA RNA


title: M_PGC_19W_embryo2_sc17

description: polyA RNA


title: M_PGC_19W_embryo2_sc16

description: polyA RNA


title: M_PGC_19W_embryo2_sc18

description: polyA RNA


title: M_PGC_19W_embryo2_sc15

description: polyA RNA


title: M_PGC_19W_embryo2_sc13

description: polyA RNA


title: F_PGC_10W_embryo2_sc11

description: polyA RNA


title: M_PGC_19W_embryo2_sc14

description: polyA RNA


title: M_PGC_19W_embryo2_sc11

description: polyA RNA


title: M_PGC_19W_embryo2_sc10

description: polyA RNA


title: M_PGC_19W_embryo2_sc2

description: polyA RNA


title: M_PGC_19W_embryo2_sc12

description: polyA RNA


title: M_PGC_19W_embryo2_sc5

description: polyA RNA


title: M_PGC_19W_embryo2_sc3

description: polyA RNA


title: M_PGC_19W_embryo2_sc9

description: polyA RNA


title: M_PGC_19W_embryo2_sc8

description: polyA RNA


title: M_PGC_19W_embryo2_sc6

description: polyA RNA


title: M_PGC_19W_embryo2_sc4

description: polyA RNA


title: M_PGC_19W_embryo1_sc30

description: polyA RNA


title: M_PGC_19W_embryo1_sc31

description: polyA RNA


title: M_PGC_19W_embryo2_sc20

description: polyA RNA


title: M_PGC_19W_embryo1_sc29

description: polyA RNA


title: M_PGC_19W_embryo1_sc26

description: polyA RNA


title: Soma_11W_embryo1_M_HiSeq2000

description:
bisulfite treated  genomic DNA
Soma_11W_embryo1_M_methylation_calling.bed


title: M_PGC_19W_embryo1_sc27

description: polyA RNA


title: M_PGC_19W_embryo1_sc24

description: polyA RNA


title: M_PGC_19W_embryo1_sc23

description: polyA RNA


title: M_PGC_19W_embryo1_sc25

description: polyA RNA


title: Soma_7W_embryo2_M_HiSeq2000


title: Soma_10W_embryo1_M_HiSeq2000


title: M_PGC_19W_embryo1_sc21

description: polyA RNA


title: Soma_7W_embryo1_M_HiSeq2000

description:
bisulfite treated  genomic DNA
Soma_7W_embryo1_M_methylation_calling.bed


title: M_PGC_19W_embryo1_sc22

description: polyA RNA


title: M_PGC_19W_embryo1_sc20

description: polyA RNA


title: M_PGC_19W_embryo2_sc7

description: polyA RNA


title: PGC_11W_embryo1_M_rep2_HiSeq2000


title: M_PGC_19W_embryo2_sc1

description: polyA RNA


title: PGC_11W_embryo1_M_rep1_HiSeq2000


title: M_PGC_19W_embryo1_sc28

description: polyA RNA


title: PGC_7W_embryo1_M_HiSeq2000


title: M_PGC_19W_embryo1_sc16

description: polyA RNA


title: M_PGC_19W_embryo1_sc18

description: polyA RNA


title: Heart_5W_embryo1_HiSeq2000


title: PGC_7W_embryo2_M_HiSeq2000


title: M_PGC_19W_embryo1_sc15

description: polyA RNA


title: M_PGC_19W_embryo1_sc14

description: polyA RNA


title: M_PGC_19W_embryo1_sc13

description: polyA RNA


title: M_PGC_19W_embryo1_sc12

description: polyA RNA


title: M_PGC_19W_embryo1_sc11

description: polyA RNA


title: Brain_5W_embryo1_HiSeq2000


title: M_PGC_19W_embryo1_sc10

description: polyA RNA


title: PRDM12 wildtype female (control to D31Y)

city: Vienna

first: Vanja

last: Nagy

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using Tophat v2.0.10 and bowtie v0.12.9.
aligned reads were counted with HTSeq
FPKM estimation was performed with Cufflinks (v2.1.1) and differential expression analysis with DESeq2 (v1.2.10)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample (standard output cufflinks)

source_name: PRDM12 wildtype fibroblasts

extract_protocol:
Total RNA was purified using RNAeasy mini Kit (Qiagen). poly-T selected RNA was isolated and dUTP-containing cDNA was generated.
Illumina TruSeq protocol

value: skin

value: fibroblasts


title: PRDM12 mutant female D31Y

source_name: PRDM12 mutant fibroblasts


title: PRDM12 mutant male E172D


title: M_PGC_19W_embryo1_sc9

description: polyA RNA


title: PRDM12 wildtype male (control to E172D)


title: Celrr_RNA-seq_JR863

first: Abbie

last: Groff

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
processed data files format and content: the DiffTable output from cummeRbund, or essentially a tab-delimited file with all of the expression values and differential expression test statistics as called by cuffdiff for each gene in the transcriptome for each wt-v-ko comparison.

extract_protocol:
E14.5 whole brains were harvested and homogenized in TRIzol. Adult brains were harvested immediately after euthanasia, snap frozen in liquid nitrogen, and stored at -80C. These brains were pulverized in liquid nitrogen and homogenized in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

value: lincRNA knockout (KO)

tag: lncrna previous name

tag: Sex

tag: timepoint

tag: litter

value: whole brain


title: M_PGC_19W_embryo1_sc8

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR862

source_name: Trp53cor1 _RNA-seq_KO_E14.5

tag: genotype/variation


title: M_PGC_19W_embryo1_sc7

description: polyA RNA


title: M_PGC_19W_embryo1_sc19

description: polyA RNA


title: Tug1_RNA-seq_JR861


title: M_PGC_19W_embryo1_sc6

description: polyA RNA


title: PGC_10W_embryo1_M_HiSeq2000


title: M_PGC_19W_embryo1_sc17

description: polyA RNA


title: M_PGC_19W_embryo1_sc5

description: polyA RNA


title: M_PGC_19W_embryo1_sc4

description: polyA RNA


title: Pantr1_RNA-seq_JR859


title: Pantr1_RNA-seq_JR858


title: M_PGC_19W_embryo1_sc3

description: polyA RNA


title: Tug1_RNA-seq_JR857


title: Control 29

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Control Placenta_6 CB_1029

data_processing:
Basecalls performed using CASAVA version 1.8.2
Clean Adapter performed using custom script in perl.
Aligmnent perfomed using smalt version 0.7.5
Coverage of sequence alignments performed using coverageBed function from   BEDTools version 2.16.2
Data were filtered removing miRNA's without at least 1 read per million in 3 of the samples, using a custom R script
Normalization and differential expression process were performed with edgeR v.3.4.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values and gene expresion for each Sample, performed with edgeR v.3.4.2. Please note that colums 6 to 19 correspond to raw counts and from columns 20 to 33 correspond to normalized counts.

extract_protocol:
The placental biopsies were subjected to mechanical homogenization, and the enriched small RNA fraction was isolated using a mirVanaTM miRNA Isolation Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer's specifications.
Libraries were constructed according to the TruSeq Small RNA Sample Prep Kit Set A protocol (Illumina) using a total of 50 ng of small RNA in the 5’ and 3’ RNA adapters ligation step. cDNA synthesis was performed using the SuperScript ® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by 15 PCR cycles to enrich the sample. The first quality control step for the libraries was performed using a High Sensitivity DNA Analysis kit on the 2100 Bioanalyzer System (both Agilent Technologies). Libraries were selected (fraction of ~145-160 bp) by non-denaturing polyacrylamide gel electrophoresis using 6% of acrylamide gels followed by a concentration step with a standard ethanol/sodium acetate/glycoblue protocol. A second quality control step for the libraries was performed using a High Sensitivity DNA Analysis Kit/2100 Bioanalyzer system. The libraries were quantified using the dsDNA HS Assay Kit (Invitrogen) on a Qubit fluorometer and were each adjusted to a concentration of 20 pM. In the clonal amplification of the libraries, bridge PCR was performed using the TruSeq SR Cluster v5 kit on a Cluster Station (Illumina). The sequencing was performed on the Illumina GAIIx platform with a configuration of 36 cycles for single-end reads. Each sample was sequenced on 1/3 lanes of a flow cell, resulting in a range of 7 to 13 million reads.

tag: subject status

value: normotensive pregnant women

value: Placental biopsy

tag: molecule subtype

value: Enriched small RNA fraction


title: Control 32

description: Control Placenta_7 CB_1032


title: Control 27

description: Control Placenta_5 CB_1027


title: Control 25

description: Control Placenta_4 CB_1025


title: M_PGC_19W_embryo1_sc2

description: polyA RNA

value: 19 week gestation


title: M_PGC_19W_embryo1_sc1

description: polyA RNA

value: male


title: lincenc1_RNA-seq_JR839


title: Control 23

description: Control Placenta_3 CB_1023


title: Eldr_RNA-seq_JR838

value: linc-Egfr


title: Control 21

description: Control Placenta_2 CB_1021


title: Control 19

description: Control Placenta_1 CB_1019


title: M_PGC_11W_embryo2_sc15

description: polyA RNA

value: 11 week gestation


title: M_PGC_11W_embryo2_sc13

description: polyA RNA


title: Pantr2_RNA-seq_JR836

value: female

value: Adult


title: Pantr1_RNA-seq_JR837


title: M_PGC_11W_embryo2_sc14

description: polyA RNA


title: Case 30

description: Preeclamsia (PE) Placenta_7 CB_1030

source_name: preeclampsia case_placenta

value: preeclampsia patient


title: Pantr2_RNA-seq_JR835


title: Pantr1_RNA-seq_JR860


title: Crnde_RNA-seq_JR830


title: M_PGC_11W_embryo2_sc12

description: polyA RNA


title: Ptgs2os2_RNA-seq_JR829


title: M_PGC_11W_embryo2_sc11

description: polyA RNA


title: Case 12

description: Preeclamsia (PE) Placenta_5 CB_1012


title: Case 11

description: Preeclamsia (PE) Placenta_4 CB_1011


title: lincenc1_RNA-seq_JR827

value: WT


title: Case 10

description: Preeclamsia (PE) Placenta_3 CB_1010


title: Halr1_RNA-seq_JR826


title: M_PGC_11W_embryo2_sc10

description: polyA RNA


title: lincenc1_RNA-seq_JR825


title: M_PGC_11W_embryo2_sc9

description: polyA RNA


title: Kantr_RNA-seq_JR824


title: M_PGC_11W_embryo2_sc7

description: polyA RNA


title: M_PGC_11W_embryo2_sc8

description: polyA RNA


title: Kantr_RNA-seq_JR823


title: M_PGC_11W_embryo2_sc6

description: polyA RNA


title: M_PGC_11W_embryo2_sc5

description: polyA RNA


title: Case 18

description: Preeclamsia (PE) Placenta_6 CB_18


title: Kantr_RNA-seq_JR821


title: M_PGC_11W_embryo2_sc4

description: polyA RNA


title: M_PGC_11W_embryo2_sc3

description: polyA RNA


title: Peril_RNA-seq_JR822


title: Kantr_RNA-seq_JR820


title: M_PGC_11W_embryo2_sc2

description: polyA RNA


title: Kantr_RNA-seq_JR819


title: M_PGC_11W_embryo2_sc1

description: polyA RNA


title: Input_Intestine

city: Madison

first: Mark

middle: B

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: *.bed files contain the ChIP-seq peak locations, *.bedgraph files are for display in the UCSC genome browser

source_name: proxmial half site of small intestine

growth_protocol: Wildtype mice were fed a standard rodent chow diet (Harlan Teklad, #5008).

extract_protocol:
Intestinal epithelial cells were isolated using EDTA as reported previously (Sato, T. et al, (2009) Nature 459:262). In brief, collected proximal half site of small intestines were cleaned with cold PBS and sliced into small pieces. The tissues were then incubated in cold PBS containing 2 mM EDTA on ice for 30 minutes and washed with cold PBS. Epithelial cells were isolated by vortexing the tissues with cold PBS 5 times for 1.5 minutes with 30-seconds intervals on ice and then by passing the mixture through 70-micrometer cell strainer. The isolated cells were centrifuged at 2000 rpm for 5 minutes, washed with cold PBS and subjected to chromatin immunoprecipitation using either a control IgG antibody or anti-VDR antibody as described previously (Meyer, M. B. et al (2012) Mol Endocrinol 26:37).
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions. During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols. ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp. Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina GAIIx [for all samples sequenced before June, 2011] or the Illumina HiSeq2000 [after June, 2011] sequencers by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver. 3) on an Illumina cBot (Illumina) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver. 3).  Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  Each ChIP sample was repeated in biological replicate in the same manner (minimum of 2 replicates).  Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Mice at 8 weeks of age were treated with vehicle or 10 ng/g body weight of 1,25(OH)2D3 for 1 hours prior to tissue harvesting.

value: duodenum and jejunum

tag: treatment

tag: antibody


title: Case 6

description: Preeclamsia (PE) Placenta_1 CB_1006


title: Case 7

description: Preeclamsia (PE) Placenta_2 CB_1007


title: Intestine_Veh_1

value: vehicle control

value: anti-VDR (Santa Cruz Biotechnology; sc-1008)


title: Intestine_Veh_2


title: M_PGC_11W_embryo1_sc12

description: polyA RNA


title: Crnde_RNA-seq_JR815


title: Ptgs2os2_RNA-seq_JR816


title: Intestine_1,25_1


title: Intestine_Veh_3


title: M_PGC_11W_embryo1_sc11

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR814


title: Kantr_RNA-seq_JR812

value: linc-Jarid1c_L13-4 ***


title: M_PGC_11W_embryo1_sc10

description: polyA RNA


title: Intestine_1,25_3


title: M_PGC_11W_embryo1_sc9

description: polyA RNA


title: Duo_rescue diet_1,25_6

data_processing:
TopHat with default settings and sample type "fr-secondstrand" for directional libraries
ArrayStar (DNASTAR) with default RNA sequencing settings.  Imported BAM files from TopHat output.
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated text files include RPKM values for each sample

source_name: Duodenum

growth_protocol: Cyp27b1 null mice were fed on highly purified vitamin D-deficient diet containing 0.47% Ca, 0.3% P and vitamins A, E, and K (normal diet) or on the same diet containing 20% lactose, 2% Ca, 1.25% P (rescue diet) at weaning and until 8 weeks of age.

extract_protocol:
RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH). Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions
Directional RNA-seq libraries were prepared with the Epicentre (Madison, WI) ScriptSeq v2 RNA-seq Library Preparation Kit per manufacturer’s instructions.  Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Cyp27b1 null mice at 8 weeks of age were treated with vehicle or 2 ng/g body weight of 1,25(OH)2D3 for 6 hours prior to RNA harvesting.

tag: strain

value: Cyp27b1 null mice

tag: age

value: 8 weeks old

tag: diet

value: rescue

value: Duodenum

value: 1,25(OH)2D3 (2 ng/g body weight (bw))


title: Duo_rescue diet_1,25_5


title: Intestine_1,25_2


title: Duo_rescue diet_1,25_4


title: Halr1_RNA-seq_JR811

value: whole brain


title: M_PGC_11W_embryo1_sc8

description: polyA RNA

tag: developmental stage

value: male


title: M_PGC_11W_embryo1_sc7

description: polyA RNA

tag: gender


title: Duo_rescue diet_1,25_2

tag: tissue


title: Ptgs2os2_RNA-seq_JR809

value: lincRNA knockout (KO)


title: Duo_rescue diet_1,25_1


title: Pantr2_RNA-seq_JR808


title: M_PGC_11W_embryo1_sc6

description: polyA RNA

value: 11 week gestation


title: M_PGC_11W_embryo1_sc5

description: polyA RNA


title: Tug1_RNA-seq_JR807


title: Duo_rescue diet_Veh_6


title: Duo_rescue diet_Veh_5


title: M_PGC_11W_embryo1_sc3

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR805

source_name: Trp53cor1 _RNA-seq_KO_Adult


title: M_PGC_11W_embryo1_sc4

description: polyA RNA


title: M_PGC_11W_embryo1_sc2

description: polyA RNA


title: Peril_RNA-seq_JR806


title: Duo_rescue diet_Veh_4


title: M_PGC_11W_embryo1_sc1

description: polyA RNA


title: Duo_rescue diet_Veh_3


title: Celrr_RNA-seq_JR804


title: Halr1_RNA-seq_JR803


title: Duo_normal diet_1,25_6

value: normal


title: Duo_rescue diet_Veh_1


title: Mannr_RNA-seq_JR802

value: female

value: Adult


title: Eldr_RNA-seq_JR810

value: linc-Egfr


title: M_PGC_10W_embryo1_sc19

description: polyA RNA

value: 10 week gestation


title: Duo_rescue diet_Veh_2

value: vehicle control


title: M_PGC_10W_embryo1_sc20

description: polyA RNA


title: M_PGC_10W_embryo1_sc18

description: polyA RNA


title: Duo_rescue diet_1,25_3


title: Duo_normal diet_1,25_5


title: M_PGC_10W_embryo1_sc17

description: polyA RNA


title: Duo_normal diet_1,25_4


title: M_PGC_10W_embryo1_sc16

description: polyA RNA


title: lincenc1_RNA-seq_JR800

value: WT


title: Eldr_RNA-seq_JR799


title: M_PGC_10W_embryo1_sc15

description: polyA RNA


title: Ptgs2os2_RNA-seq_JR798


title: Duo_normal diet_1,25_2


title: Duo_normal diet_1,25_3


title: Pantr2_RNA-seq_JR797


title: M_PGC_10W_embryo1_sc14

description: polyA RNA


title: M_PGC_10W_embryo1_sc13

description: polyA RNA


title: Duo_normal diet_Veh_6


title: Pantr1_RNA-seq_JR796


title: Crnde_RNA-seq_JR793


title: M_PGC_10W_embryo1_sc12

description: polyA RNA


title: Mannr_RNA-seq_JR801


title: Duo_normal diet_Veh_5


title: M_PGC_10W_embryo1_sc11

description: polyA RNA


title: Crnde_RNA-seq_JR789


title: M_PGC_10W_embryo1_sc9

description: polyA RNA


title: Crnde_RNA-seq_JR790


title: Duo_normal diet_Veh_4


title: M_PGC_10W_embryo1_sc10

description: polyA RNA


title: Duo_normal diet_Veh_2


title: Mannr_RNA-seq_JR788


title: Duo_normal diet_Veh_1


title: Peril_RNA-seq_JR792


title: Eldr_RNA-seq_JR787


title: M_PGC_10W_embryo1_sc8

description: polyA RNA


title: M_PGC_10W_embryo1_sc7

description: polyA RNA


title: Trp53cor1 _RNA-seq_JR786


title: Duo_normal diet_1,25_1


title: Duo_normal diet_Veh_3


title: M_PGC_10W_embryo1_sc6

description: polyA RNA


title: Crnde_RNA-seq_JR785


title: M_PGC_10W_embryo1_sc5

description: polyA RNA


title: BSW007i5

data_processing:
100 base single end Illumina sequences were trimmed to remove reads that failed quality control, barcodes were trimmed off reads using cutadapt version 0.9.5
Reads were aligned to the transcriptome using GSNAP version 2012-01-11
Uniquely mapping reads were assigned to genes using HTSeq version 0.5.4p3 using the union mode
Changes in gene expression were determined by analysis with DESeq
Genome_build: WormBase WS220
Supplementary_files_format_and_content: csv file with averaged FPKM values for N2 and sdc-2(y93).

source_name: mixed stage embryos

extract_protocol:
RNA was extracted using a the protocol described in Baugh, Hunter Development 2002 except that 10 µL of a 20 mg/mL glycogen solution was used as a carrier.
Libraries were prepared from 10 µg of total RNA. PolyA RNA was purified using the Dynabeads mRNA purification kit (Ambion) and fragmented using Fragmentation Reagent (Ambion). First strand cDNA was synthesized from polyA RNA using the SuperScript III Reverse Transcriptase Kit with random primers (Invitrogen). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNAse H (Invitrogen). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina).

value: sdc-2(y93) with RNAi against sdc-2

tag: genotype

value: sdc-2 mutant

value: embryo


title: BSW0011i4

value: wild type


title: Crnde_RNA-seq_JR784


title: Celrr_RNA-seq_JR783


title: M_PGC_10W_embryo1_sc3

description: polyA RNA


title: BSW0012i4


title: Halr1_RNA-seq_JR782


title: M_PGC_10W_embryo1_sc2

description: polyA RNA


title: BSW008i4


title: M_PGC_10W_embryo1_sc1

description: polyA RNA

value: 7 week gestation


title: Mannr_RNA-seq_JR780


title: lincenc1_RNA-seq_JR779


title: BSW0012i5


title: M_PGC_7W_embryo3_sc13

description: polyA RNA