title: P1219

city: Beijing

first: zemin

last: zhang

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

description: Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001002430

data_processing:
Sequencing data from Illumina Hiseq2500 or Hiseq4000 sequencer were first processed to filter out low quality reads which were defined as: 1) “N” bases account for 10% reads’ length; 2) bases with quality < 5 account for 50% reads’ length; 3) contain adapter sequence.
Reads were then aligned to ribosomal RNA sequences download from RFam using the GSNAP alignment tool.
Next the unmapped reads were mapped with GSNAP to reference sequences, containing human genome reference sequence version 19 (hg19) downloaded from UCSC and 92 ERCC spike-in RNA sequences obtained from the datasheet of the External RNA Controls Consortium kit. In addition, a gene model file named knownGene.txt was downloaded from UCSC and used to define known exon-exon junctions with the adjustable parameters “--novelsplicing 1 -n 10 -i 1 -M 2” except other default parameters.
After retrieving reads overlapping with genes defined in the gene model file with R function findOverlaps, the read counts of each gene were obtained (NSCLC.TCell.S8760.count.txt.gz).
Low-quality cells were filtered if cell library sizes (column sum of the count table) or the numbers of expressed genes (counts > 0) were smaller than the median of all cells minus 3×MAD (Median Absolute Deviation), or if the mitochondrial gene count proportion of a cell was larger than 10%. We also filtered out cells following these steps: 1) to discard cells with transcripts per million (TPM) of CD3D less than 3; 2) to discard FACS sorted CD8+ T cells with TPM of CD8A < 3 or with TPM of CD4 > 30; 3) to discard FACS sorted CD4+ T cells with TPM of CD4 < 3 or with TPM of CD8A > 30.
The count table of cells passing the above filtration was processed to keep only genes with the average count > 1,  than The counts were normalized by scran method (L. Lun et al., 2016) and centered by patient (NSCLC.TCell.S7205.norm.centered.txt.gz).
genome build: hg19 downloaded from UCSC
Supplementary_files_format_and_content: NSCLC.TCell.S12346.TPM.txt: Tab-delimited text file includes gene expression measured in TPM.

source_name: T cells

extract_protocol:
Based on FACS analysis, single cells of different subtypes, including CD8+ T cells (CD3+ and CD8+), T helper cells (CD3+, CD4+ and CD25-), and regulatory T cells (CD3+, CD4+ and CD25high), were sorted into wells of 96-well plates (Axygen) with lysis buffer, which contained 1 µl 10 mM dNTP mix (Fermentas), 1 µl 10 µM Oligo dT primer, 1.9 µl 1% Triton X-100 (Sigma) plus 0.1 µl 40 U/µl RNase Inhibitor (Takara). The sealed plates were stored frozen at −80 ℃. Single cell transcriptome amplifications were performed following the Smart-Seq2 protocol. The amplified cDNA products were purified with 1x Agencourt XP DNA beads (Beckman). Following the first round of beads purification, the cDNA of each single cell was quantified with qPCR of CD3D, and fragment analysis (using fragment analyzer AATI).
For those single cell samples with high quality, the DNA products were further cleaned with 0.5x Agencourt XP DNA beads (Beckman) to eliminate short fragments (less than 500 bp). At this step, the concentration of each sample was quantified with Qubit HsDNA kits (Invitrogen), and libraries were then constructed with the TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme).

tag: patient

value: T cells from NSCLC patient


title: P1208

status: Public on Jun 25 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: P0706


title: P1120


title: mouse_OPC_ATAC-seq_Chd8cKO

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 whole genome by Tophat with default options
RNA-seq: Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
ChIP-seq: Sequenced reads were trimmed for adaptor sequence.
ChIP-seq: Reads mapped to rn5(mm10) whole genome by Bowtie2 with default options
ChIP-seq: Use samtools to delete the duplicate reads
ChIP-seq: Peak calling was performed using MACS1.4 with a default p value cut off.
ATAC-seq: Adaptor sequence were trimmed by cutadapt.
ATAC-seq: Reads mapped to mm10 whole genome by Bowtie2 with default options
ATAC-seq: Use Picard to delete the duplicate reads
ATAC-seq: Convert bam to wig by bam2wig
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: wig

molecule: genomic DNA

organism: Mus musculus

source_name: mouse OPC

growth_protocol: Chip-seq: Briefly, mixed glial cells were initially cultured in DMEM-F12 medium supplied with 15% FBS, then switched to B104 conditioned medium for 2 days before isolating OPCs by mechanical detachment in an orbital shaker. Isolated rat OPCs were grown in Sato growth medium supplemented with mitogens 10 ng/ml PDGF-AA and 10 ng/ml bFGF, and differentiated in OL Differentiation Medium (Sato medium supplemented with 15 nM T3 and 10 ng/ml ciliary neurotrophic factor).

extract_protocol:
RNA-seq: Total RNA was extracted per the Trizol (Life Technologies) protocol and cleanup using Rneasy kit (Qiagen).
Chip-seq: In brief, chromatin was cross-linked and sheared with a Covaris S220 sonicator from primary oligodendrocyte cultures of newborn rat or mouse cortex. Immunoprecipitation was overnight at 4°C using antibodies directed against or control immunoglobulins in the presence of protein A/G Sepharose CL-4B beads (Life Technologies) pretreated with BSA. Rabbit anti-CHD8 (ab114126) antibodies were used for immunoprecipitation. After reverse crosslink, proteinase K treatment, the precipitated chromatin DNA was purified.
RNA-seq: RNA-seq libraries from control and mutant OPC cells were prepared using Illumina RNA-Seq Preparation Kit and sequenced using a HiSeq 2500 sequencer.
Chip-seq: libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB cat # E6240L), and then to sequence on the Illumina sequencer HS2500.
ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 30,000 sorted cells from the mouse cortex in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.

treatment_protocol:
RNA-seq: For mouse OPC sorting, single cell suspension was prepared from control and Chd8 cKO mouse cortices with papain dissociation and cells were re-suspended in PBS with 2 mM EDTA and 0.5% BSA and incubated with rat anti- CD140a/PDGFRa and O4+ primary monoclonal antibody.
ATAC-seq: For mouse OPC sorting, single cell suspension was prepared from control and Chd8 cKO mouse cortices with papain dissociation and cells were re-suspended in PBS with 2 mM EDTA and 0.5% BSA and incubated with rat anti- CD140a/PDGFRa and O4+ primary monoclonal antibody.

tag: strain background

value: mixed

tag: genotype/variation

tag: cell type

value: FACS sorted PDGFRa+/O4+


title: E6.5_P0_embryo2_cell8_RNAseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw bisulfite sequence reads had the first 6 base pairs clipped off the 5' end to remove 6N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 6, Cutadapt v1.8.1). Remaining sequences were then aligned to the mouse genome (build GRCm38) with Bismark (v0.19.0) in single-end mode (parameters: --non_directional). Methylation calls were extracted after duplicate sequences had been excluded.
RNA-seq sequences were trimmed using trim_galore (v0.4.2, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default settings. Trimmed data was separately mapped to the mouse GRCm38 genome assemblies using HISAT2 (v2.1.0) with options --sp 1000,1000 --no-mixed --no-discordant.
Genome_build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
RNA-Seq count table: A tab-deliminated text file in which rows are genes and columns are samples. Data is gene expression counts generated using Rsubread::featureCounts (R v3.4.3) with transcript annotation (gtf format) downloaded from Ensembl version 87.

source_name: Embryo

extract_protocol:
Cells were sorted into 2.5ul RLT plus lysis buffer (QIAGEN) containing SUPERase-In (Ambion).
Single-cell methylome and transcriptome libraries were prepared from embryos as previously described (Angermueller et al., 2016).
Single cell Bisulfite-Seq (scBS-Seq) and Single cell RNA-Seq (Smart-seq2)

tag: developmental stage

tag: strain


title: E6.5_P0_embryo2_cell9_RNAseq


title: E6.5_P0_embryo2_cell94_RNAseq


title: E6.5_P0_embryo2_cell90_RNAseq


title: E6.5_P0_embryo2_cell95_RNAseq


title: E6.5_P0_embryo2_cell93_RNAseq


title: E6.5_P0_embryo2_cell96_RNAseq


title: P0619


title: P0616P


title: P1010


title: P0616A


title: P1011


title: E6.5_P0_embryo2_cell91_RNAseq


title: P0913


title: E6.5_P0_embryo2_cell7_RNAseq


title: E6.5_P0_embryo2_cell84_RNAseq


title: E6.5_P0_embryo2_cell79_RNAseq


title: E6.5_P0_embryo2_cell80_RNAseq


title: E6.5_P0_embryo2_cell72_RNAseq


title: E6.5_P0_embryo2_cell70_RNAseq


title: E6.5_P0_embryo2_cell82_RNAseq


title: E6.5_P0_embryo2_cell6_RNAseq


title: E6.5_P0_embryo2_cell83_RNAseq


title: E6.5_P0_embryo2_cell81_RNAseq


title: E6.5_P0_embryo2_cell69_RNAseq


title: E6.5_P0_embryo2_cell78_RNAseq


title: E6.5_P0_embryo2_cell58_RNAseq


title: E6.5_P0_embryo2_cell68_RNAseq


title: E6.5_P0_embryo2_cell48_RNAseq


title: E6.5_P0_embryo2_cell47_RNAseq


title: E6.5_P0_embryo2_cell67_RNAseq


title: E6.5_P0_embryo2_cell59_RNAseq


title: E6.5_P0_embryo2_cell54_RNAseq


title: E6.5_P0_embryo2_cell57_RNAseq


title: E6.5_P0_embryo2_cell44_RNAseq


title: E6.5_P0_embryo2_cell43_RNAseq


title: E6.5_P0_embryo2_cell45_RNAseq


title: E6.5_P0_embryo2_cell35_RNAseq


title: E6.5_P0_embryo2_cell92_RNAseq


title: E6.5_P0_embryo2_cell42_RNAseq


title: E6.5_P0_embryo2_cell66_RNAseq


title: E6.5_P0_embryo2_cell56_RNAseq


title: E6.5_P0_embryo2_cell60_RNAseq


title: E6.5_P0_embryo2_cell71_RNAseq


title: E6.5_P0_embryo2_cell34_RNAseq


title: E6.5_P0_embryo2_cell46_RNAseq


title: E6.5_P0_embryo2_cell30_RNAseq


title: E6.5_P0_embryo2_cell21_RNAseq


title: E6.5_P0_embryo2_cell20_RNAseq


title: E6.5_P0_embryo2_cell23_RNAseq


title: E6.5_P0_embryo2_cell18_RNAseq


title: E6.5_P0_embryo2_cell55_RNAseq


title: E6.5_P0_embryo2_cell31_RNAseq


title: E6.5_P0_embryo2_cell11_RNAseq


title: E6.5_P0_embryo1_cell88_RNAseq


title: E6.5_P0_embryo1_cell87_RNAseq


title: E6.5_P0_embryo1_cell89_RNAseq


title: E6.5_P0_embryo2_cell33_RNAseq


title: E6.5_P0_embryo1_cell86_RNAseq


title: E6.5_P0_embryo2_cell32_RNAseq


title: E6.5_P0_embryo1_cell77_RNAseq


title: E6.5_P0_embryo1_cell85_RNAseq


title: E6.5_P0_embryo1_cell75_RNAseq


title: E6.5_P0_embryo1_cell76_RNAseq


title: E6.5_P0_embryo2_cell22_RNAseq


title: E6.5_P0_embryo2_cell10_RNAseq


title: E6.5_P0_embryo2_cell12_RNAseq


title: E6.5_P0_embryo2_cell36_RNAseq


title: E6.5_P0_embryo1_cell61_RNAseq


title: E6.5_P0_embryo1_cell65_RNAseq


title: E6.5_P0_embryo2_cell24_RNAseq


title: E6.5_P0_embryo1_cell73_RNAseq


title: E6.5_P0_embryo1_cell53_RNAseq


title: E6.5_P0_embryo2_cell19_RNAseq


title: E6.5_P0_embryo1_cell5_RNAseq


title: E6.5_P0_embryo1_cell63_RNAseq


title: E6.5_P0_embryo1_cell4_RNAseq


title: E6.5_P0_embryo1_cell40_RNAseq


title: E6.5_P0_embryo1_cell41_RNAseq


title: E6.5_P0_embryo1_cell3_RNAseq


title: E6.5_P0_embryo1_cell52_RNAseq


title: E6.5_P0_embryo1_cell39_RNAseq


title: E6.5_P0_embryo1_cell28_RNAseq


title: E6.5_P0_embryo1_cell2_RNAseq


title: E6.5_P0_embryo1_cell27_RNAseq


title: E6.5_P0_embryo1_cell64_RNAseq


title: E6.5_P0_embryo1_cell29_RNAseq


title: E6.5_P0_embryo1_cell25_RNAseq


title: E6.5_P0_embryo1_cell62_RNAseq


title: E6.5_P0_embryo1_cell38_RNAseq


title: E6.5_P0_embryo1_cell26_RNAseq


title: E6.5_P0_embryo1_cell1_RNAseq


title: E6.5_P0_embryo1_cell17_RNAseq


title: E6.5_P0_embryo1_cell16_RNAseq


title: E6.5_P0_embryo1_cell13_RNAseq


title: E6.5_P0_embryo1_cell14_RNAseq


title: E6.5_P0_embryo1_cell15_RNAseq


title: E6.5_P0_embryo2_cell95_BSseq


title: E6.5_P0_embryo2_cell96_BSseq


title: E6.5_P0_embryo2_cell94_BSseq


title: E6.5_P0_embryo2_cell92_BSseq


title: E6.5_P0_embryo2_cell90_BSseq


title: E6.5_P0_embryo2_cell93_BSseq


title: E6.5_P0_embryo2_cell91_BSseq


title: E6.5_P0_embryo2_cell84_BSseq


title: E6.5_P0_embryo2_cell82_BSseq


title: E6.5_P0_embryo2_cell7_BSseq


title: E6.5_P0_embryo2_cell81_BSseq


title: E6.5_P0_embryo2_cell78_BSseq


title: E6.5_P0_embryo2_cell79_BSseq


title: E6.5_P0_embryo2_cell80_BSseq


title: E6.5_P0_embryo2_cell72_BSseq


title: E6.5_P0_embryo2_cell70_BSseq


title: E6.5_P0_embryo1_cell74_RNAseq


title: E6.5_P0_embryo2_cell71_BSseq


title: E6.5_P0_embryo2_cell9_BSseq


title: E6.5_P0_embryo2_cell69_BSseq


title: E6.5_P0_embryo2_cell67_BSseq


title: E6.5_P0_embryo2_cell66_BSseq


title: E6.5_P0_embryo2_cell60_BSseq


title: E6.5_P0_embryo2_cell59_BSseq


title: E6.5_P0_embryo1_cell37_RNAseq


title: E6.5_P0_embryo2_cell58_BSseq


title: E6.5_P0_embryo2_cell8_BSseq


title: E6.5_P0_embryo2_cell56_BSseq


title: E6.5_P0_embryo2_cell57_BSseq


title: E6.5_P0_embryo2_cell55_BSseq


title: E6.5_P0_embryo2_cell54_BSseq


title: E6.5_P0_embryo2_cell47_BSseq


title: E6.5_P0_embryo2_cell46_BSseq


title: E6.5_P0_embryo2_cell45_BSseq


title: E6.5_P0_embryo2_cell43_BSseq


title: E6.5_P0_embryo2_cell44_BSseq


title: E6.5_P0_embryo2_cell42_BSseq


title: E6.5_P0_embryo2_cell36_BSseq


title: E6.5_P0_embryo2_cell34_BSseq


title: E6.5_P0_embryo2_cell6_BSseq


title: E6.5_P0_embryo2_cell33_BSseq


title: E6.5_P0_embryo2_cell68_BSseq


title: E6.5_P0_embryo2_cell31_BSseq


title: E6.5_P0_embryo2_cell23_BSseq


title: E6.5_P0_embryo2_cell30_BSseq


title: E6.5_P0_embryo2_cell24_BSseq


title: E6.5_P0_embryo2_cell32_BSseq


title: E6.5_P0_embryo2_cell22_BSseq


title: E6.5_P0_embryo2_cell21_BSseq


title: E6.5_P0_embryo2_cell20_BSseq


title: E6.5_P0_embryo2_cell48_BSseq


title: E6.5_P0_embryo2_cell19_BSseq


title: E6.5_P0_embryo2_cell18_BSseq


title: E6.5_P0_embryo2_cell11_BSseq


title: E6.5_P0_embryo2_cell83_BSseq


title: E6.5_P0_embryo2_cell12_BSseq


title: E6.5_P0_embryo1_cell88_BSseq


title: E6.5_P0_embryo2_cell10_BSseq


title: E6.5_P0_embryo1_cell89_BSseq


title: E6.5_P0_embryo1_cell87_BSseq


title: E6.5_P0_embryo2_cell35_BSseq


title: E6.5_P0_embryo1_cell85_BSseq


title: E6.5_P0_embryo1_cell75_BSseq


title: E6.5_P0_embryo1_cell64_BSseq


title: E6.5_P0_embryo1_cell74_BSseq


title: E6.5_P0_embryo1_cell65_BSseq


title: E6.5_P0_embryo1_cell62_BSseq


title: E6.5_P0_embryo1_cell51_BSseq


title: E6.5_P0_embryo1_cell73_BSseq


title: E6.5_P0_embryo1_cell77_BSseq


title: E6.5_P0_embryo1_cell76_BSseq


title: E6.5_P0_embryo1_cell53_BSseq


title: E6.5_P0_embryo1_cell61_BSseq


title: E6.5_P0_embryo1_cell5_BSseq


title: E6.5_P0_embryo1_cell52_BSseq


title: E6.5_P0_embryo1_cell50_BSseq


title: E6.5_P0_embryo1_cell86_BSseq


title: E6.5_P0_embryo1_cell63_BSseq


title: E6.5_P0_embryo1_cell4_BSseq


title: E6.5_P0_embryo1_cell40_BSseq


title: E6.5_P0_embryo1_cell3_BSseq


title: E6.5_P0_embryo1_cell38_BSseq


title: E6.5_P0_embryo1_cell39_BSseq


title: E6.5_P0_embryo1_cell37_BSseq


title: E6.5_P0_embryo1_cell29_BSseq


title: E6.5_P0_embryo1_cell2_BSseq


title: E6.5_P0_embryo1_cell27_BSseq


title: E6.5_P0_embryo1_cell28_BSseq


title: E6.5_P0_embryo1_cell25_BSseq


title: E6.5_P0_embryo1_cell17_BSseq


title: E6.5_P0_embryo1_cell16_BSseq


title: E6.5_P0_embryo1_cell15_BSseq


title: E6.5_P0_embryo1_cell14_BSseq


title: E5.5_P11.P6.P10_embryo7_cell9_RNAseq


title: E6.5_P0_embryo1_cell13_BSseq


title: E5.5_P11.P6.P10_embryo7_cell93_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell92_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell90_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell89_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell91_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell88_RNAseq


title: E6.5_P0_embryo1_cell49_BSseq


title: E5.5_P11.P6.P10_embryo7_cell87_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell86_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell81_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell7_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell85_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell80_RNAseq


title: E6.5_P0_embryo1_cell26_BSseq


title: E5.5_P11.P6.P10_embryo7_cell78_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell84_RNAseq


title: E6.5_P0_embryo1_cell1_BSseq


title: E5.5_P11.P6.P10_embryo7_cell77_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell79_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell74_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell75_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell76_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell96_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell73_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell72_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell69_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell6_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell67_RNAseq


title: E6.5_P0_embryo1_cell41_BSseq


title: E5.5_P11.P6.P10_embryo7_cell68_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell8_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell65_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell66_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell64_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell63_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell62_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell61_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell60_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell5_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell57_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell56_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell54_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell52_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell53_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell4_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell51_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell50_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell43_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell49_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell48_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell44_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell40_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell45_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell41_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell42_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell37_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell3_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell39_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell36_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell32_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell55_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell31_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell30_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell38_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell2_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell33_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell27_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell28_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell26_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell21_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell24_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell25_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell20_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell1_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell19_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell18_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell17_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell13_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell15_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell14_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell16_RNAseq


title: E4.5_P2_embryo5_cell9_RNAseq


title: E4.5_P2_embryo5_cell93_RNAseq


title: E4.5_P2_embryo5_cell8_RNAseq


title: E4.5_P2_embryo5_cell92_RNAseq


title: E4.5_P2_embryo5_cell81_RNAseq


title: E4.5_P2_embryo5_cell80_RNAseq


title: E4.5_P2_embryo5_cell69_RNAseq


title: E4.5_P2_embryo5_cell70_RNAseq


title: E4.5_P2_embryo5_cell58_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell29_RNAseq


title: E4.5_P2_embryo5_cell57_RNAseq


title: E4.5_P2_embryo5_cell68_RNAseq


title: E4.5_P2_embryo5_cell56_RNAseq


title: E4.5_P2_embryo5_cell46_RNAseq


title: E4.5_P2_embryo5_cell44_RNAseq


title: E4.5_P2_embryo5_cell33_RNAseq


title: E4.5_P2_embryo5_cell45_RNAseq


title: E4.5_P2_embryo5_cell34_RNAseq


title: E4.5_P2_embryo5_cell21_RNAseq


title: E4.5_P2_embryo5_cell22_RNAseq


title: E4.5_P2_embryo5_cell32_RNAseq


title: E4.5_P2_embryo4_cell89_RNAseq


title: E4.5_P2_embryo5_cell10_RNAseq


title: E5.5_P11.P6.P10_embryo7_cell12_RNAseq


title: E4.5_P2_embryo4_cell88_RNAseq


title: E4.5_P2_embryo4_cell87_RNAseq


title: E4.5_P2_embryo4_cell76_RNAseq


title: E4.5_P2_embryo5_cell20_RNAseq


title: E4.5_P2_embryo4_cell6_RNAseq


title: E4.5_P2_embryo4_cell75_RNAseq


title: E4.5_P2_embryo4_cell65_RNAseq


title: E4.5_P2_embryo4_cell64_RNAseq


title: E4.5_P2_embryo4_cell63_RNAseq


title: E4.5_P2_embryo4_cell53_RNAseq


title: E4.5_P2_embryo4_cell5_RNAseq


title: E4.5_P2_embryo4_cell4_RNAseq


title: E4.5_P2_embryo4_cell52_RNAseq


title: E4.5_P2_embryo4_cell51_RNAseq


title: E4.5_P2_embryo4_cell39_RNAseq


title: E4.5_P2_embryo4_cell3_RNAseq


title: E4.5_P2_embryo4_cell41_RNAseq


title: E4.5_P2_embryo4_cell40_RNAseq


title: E4.5_P2_embryo4_cell29_RNAseq


title: E4.5_P2_embryo4_cell28_RNAseq


title: E4.5_P2_embryo4_cell77_RNAseq


title: E4.5_P2_embryo4_cell16_RNAseq


title: E4.5_P2_embryo4_cell27_RNAseq


title: E4.5_P2_embryo4_cell18_RNAseq


title: E4.5_P2_embryo4_cell17_RNAseq


title: E4.5_P2_embryo3_cell85_RNAseq


title: E4.5_P2_embryo3_cell73_RNAseq


title: E4.5_P2_embryo3_cell26_RNAseq


title: E4.5_P2_embryo3_cell49_RNAseq


title: E4.5_P2_embryo4_cell15_RNAseq


title: E4.5_P2_embryo3_cell37_RNAseq


title: E4.5_P2_embryo3_cell61_RNAseq


title: E4.5_P2_embryo3_cell2_RNAseq


title: E4.5_P2_embryo3_cell14_RNAseq


title: E4.5_P1_embryo2_cell91_RNAseq


title: E4.5_P2_embryo3_cell13_RNAseq


title: E4.5_P2_embryo3_cell25_RNAseq


title: E4.5_P1_embryo2_cell90_RNAseq


title: P0617


title: P0729


title: P1118


title: P1202


title: E4.5_P1_embryo2_cell78_RNAseq


title: E4.5_P1_embryo2_cell79_RNAseq


title: E4.5_P1_embryo2_cell6_RNAseq


title: E4.5_P1_embryo2_cell55_RNAseq


title: E4.5_P2_embryo3_cell1_RNAseq


title: E4.5_P1_embryo2_cell66_RNAseq


title: E4.5_P1_embryo2_cell43_RNAseq


title: WTC_PARE

city: Norwich

first: Josh

last: Thody

state: Norfolk

address: Norwich Research Park

institute: University of East Anglia

data_processing:
We processed the raw data using tools provided within the UEA sRNA Workbench Stocks et al. (2012). The adapter trimming tool was used to trim the adaptor sequences in each of the three degradome replicates.
Next, using the Filter tool, we discarded sequences that contained any ambiguous bases and aligned the remaining sequences to the genome (TAIR10) with no mismatches allowed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files contain non-redundant reads and their abundance

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis Col-0 seeds were stratified and then grown in soil at constant 22 C and 16 hours light until plants reached stage 5, as defined by Boyes et al. (2001)

extract_protocol:
All leaf tissue from nine Col-0 plants that were at stage 5 according to Boyes et al. (2001) was harvested, pulled together and frozen in liquid nitrogen to construct each library replicate. Frozen leaf tissue was immediately grinded and RNA extracted by TRI Reagent following to manufacturer's instructions.
One degradome library was constructed from each one of the three biological replicate RNA samples. Zhai et al. (2014) protocol was followed for library preparation, but SuperScript II reverse transcriptase was used instead of Superscript III unlike in the original protocol. Purified DNA fragments were sequenced on Illumina HiSeq in High Output mode using 50 bp single-end reads.

tag: genotype

value: wild type

value: Leaf

tag: ecotype

value: Columbia


title: E4.5_P1_embryo2_cell42_RNAseq


title: E4.5_P1_embryo2_cell31_RNAseq


title: E4.5_P1_embryo2_cell19_RNAseq


title: E4.5_P1_embryo2_cell18_RNAseq


title: WTB_PARE


title: E4.5_P1_embryo1_cell86_RNAseq


title: E4.5_P1_embryo1_cell85_RNAseq


title: E4.5_P1_embryo1_cell74_RNAseq


title: E4.5_P1_embryo1_cell73_RNAseq


title: H3 IP in glycerol, replicate 1

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Fastq files for chip-seq samples were generated with bcl2fastq 1.8.3 from Illumina.
ChIP-seq data was aligned to sacCer3 genome from UCSC with bowtie2 (2.2.0) using -k 1.
bigWig files were created in R (3.2.2) by reading in bam files, normalizing to reads per million by multiplying by 1 million and dividing by the total number of alignments for each sample.
Genome_build: sacCer3
Supplementary_files_format_and_content: rpm normalized bigWig files

organism: Saccharomyces cerevisiae

source_name: H3 IP in glycerol

growth_protocol: Cells were grown in YPD until mid-log phase, then culture media were shifted to YPD or YPglycerol for 2 hours.

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against H3pT11 (ab5168,  Abcam) or H3 (ab1791, Abcam)
Libraries were prepared using the HTP KAPA kit.

tag: media

value: YP with 3% glycerol

tag: chip antibody

value: H3 (ab1791, Abcam)


title: E4.5_P1_embryo2_cell67_RNAseq


title: H3 IP in YPD, replicate 1

source_name: H3 IP in YPD

value: YPD


title: E4.5_P1_embryo1_cell62_RNAseq


title: H3 T11 phosphorylation IP in glycerol, replicate 1

source_name: H3 T11 phosphorylation IP in glycerol

value: H3pT11 (ab5168,  Abcam)


title: E4.5_P1_embryo2_cell30_RNAseq


title: WTA_PARE


title: H3 T11 phosphorylation IP in YPD, replicate 3

source_name: H3 T11 phosphorylation IP in YPD


title: H3 T11 phosphorylation IP in glycerol, replicate 3


title: OVCA432 with miR-200 cluster 2 knockdown

type: RNA

city: Boston

first: pui wah

last: Choi

state: MA

address: 221 longwood Ave

department: OB/GYB

institute: Brigham and Women's Hospital

description: Gene expression data from OVCA432 with knockdown of miR-200 cluster 2 (miR-200c, miR-141) grown in Matrigel for 7 days

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 48C on GeneChip Gene 1.1 ST Array in GeneAtlas Hybridization Station. GeneChip was washed and stained according to GeneAtlas TM System User’s Guide (P/N 08-0246)

scan_protocol: GeneChips were scanned using the GeneAtlas Instrument.

data_processing: All gene expression data was normalized and summarized with Robust Multi-array Average method RMA algorithm with with Affymetrix Power Tools package using Affymetrix default analysis settings.

label: biotin

source_name: Seour ovarian cancer cells OVCA432 with knockdown of miR-200 cluster 2 (miR-200c, miR-141) grown in Matrigel for 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip WT Terminal Labling User Manual, 2009-2010, Affymetrix).

growth_protocol: Eight-well glass-chambered slides (BD Biosciences)  were coated with growth factor-reduced Matrigel matrix without phenol red (BD Biosciences) . Primary cultures of normal OSE and cancer cells were trypsinized and resuspended as single cells in complete medium with 10% FBS and 2% Matrigel. Fifty thousand single cells were seeded into each Matrigel-coated well. Complete medium with 2% Matrigel was replaced every 4 days. 3D structures would be formed after 4 to 7 days after seeding.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions with subsequent purification by chloroform extraction and isopropanol precipitation

treatment_protocol: The day for collecion, culture medium were removed and the cysts formed were rinsed with PBS and Trizol solution (Ambion) was added to the culture.

value: Ovarian epithelial tumor cell (serous subtype)

value: Serous invasive


title: OVCA432 transduced by virus carry vector inserted with a random sequence

description: Gene expression data from OVCA432 with random sequence inserted grown in Matrigel for 7 days

source_name: Seour ovarian cancer cells OVCA432 with random sequence inserted grown in Matrigel for 7 days


title: OVCA432 with miR-200 cluster 1 knockdown

description: Gene expression data from OVCA432 with knockdown of miR-200 cluster 1 (miR-200a, miR-200b and miR-429) grown in Matrigel for 7 days

source_name: Seour ovarian cancer cells OVCA432 with knockdown of miR-200 cluster 1 (miR-200a, miR-200b and miR-429) grown in Matrigel for 7 days


title: t11a YBL574 in YP with 3% glycerol, replicate 3

data_processing:
Fastq files for rna-seq samples were generated with bcl2fastq2 from Illumina.
RNA-seq data was aligned to sacCer3 genome from UCSC with tophat2 (2.0.13) using -x 1 -g 1 with annotation from Ensembl 84.
Reads were counted on genes (unioned exon space) using bedtools coverage (2.26.0).
Read counts were normalized using TMM normalization in edgeR (3.14.0).
Genome_build: sacCer3
Supplementary_files_format_and_content: rpkms calculated using edgeR from unioned exon space counts calculated using bedtools coverage (2.26.0) and normalized with TMM normalization in edgeR (3.14.0).

source_name: t11a YBL574 in YP with 3% glycerol

growth_protocol: Cells were grown in YPD until mid-log phase, then culture media were shifted to YPD (YP media with 2% glucose) or YP with 3% glycerol for 2 hours.

extract_protocol:
Total RNA was extracted from cell pellets using a hot phenol method described in Schmitt et al. (1990)
Libraries were prepared using the Illumina (Epicentre) yeast ribo-kit (MRZY1324) and TruSeq Stranded Total RNA (w/ Ribo-zero gold) (RS-122-2302)


title: E4.5_P1_embryo2_cell7_RNAseq


title: H3 T11 phosphorylation IP in YPD, replicate 1


title: E4.5_P1_embryo2_cell54_RNAseq


title: MCAS with miR-200 cluster 1 and 2 knockdown

description: Gene expression data from MCAS with knockdown of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days

source_name: Mucinous ovarian cancer cells MCAS with knockdown of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days

value: Ovarian epithelial tumor cell (mucinous subtype)

value: Mucinous invasive


title: H3 IP in glycerol, replicate 3


title: E4.5_P1_embryo1_cell50_RNAseq


title: H3 IP in YPD, replicate 3


title: MCAS with miR-200 cluster 1 knockdown

description: Gene expression data from MCAS with knockdown of miR-200 cluster 1 (miR-200a, miR-200b and miR-429) grown in Matrigel for 7 days

source_name: Mucinous ovarian cancer cells MCAS with knockdown of miR-200 cluster 1 (miR-200a, miR-200b and miR-429) grown in Matrigel for 7 days


title: MCAS transduced by virus carry vector inserted with a random sequence

description: Gene expression data from MCAS with random sequence inserted grown in Matrigel for 7 days

source_name: Mucinous ovarian cancer cells MCAS with random sequence inserted grown in Matrigel for 7 days


title: Wild type OVCA432

description: Gene expression data from wild type OVCA432 cells grown in Matrigel for 7 days

source_name: Seour ovarian cancer cells OVCA432 cells grown in Matrigel for 7 days


title: t11a YBL574 in YP with 3% glycerol, replicate 2


title: E4.5_P1_embryo1_cell61_RNAseq


title: E4.5_P1_embryo1_cell49_RNAseq


title: E4.5_P1_embryo1_cell38_RNAseq


title: E4.5_P1_embryo1_cell37_RNAseq


title: cka1 BY4741 in YP with 3% glycerol, replicate 2

source_name: cka1 BY4741 in YP with 3% glycerol


title: cka1 BY4741 in YP with 3% glycerol, replicate 3


title: E4.5_P1_embryo1_cell2_RNAseq


title: E4.5_P1_embryo1_cell26_RNAseq


title: wt YBL574 in YP with 3% glycerol, replicate 2

source_name: wt YBL574 in YP with 3% glycerol

value: wt


title: wt YBL574 in YP with 3% glycerol, replicate 1


title: wt BY4741 in YP with 3% glycerol, replicate 3

source_name: wt BY4741 in YP with 3% glycerol


title: wt BY4741 in YP with 3% glycerol, replicate 2


title: t11a YBL574 in YP with 3% glycerol, replicate 1


title: wt BY4741 in YP with 3% glycerol, replicate 1


title: t11a YBL574 in YPD, replicate 1

source_name: t11a YBL574 in YPD


title: t11a YBL574 in YPD, replicate 2


title: MCAS with miR-200 cluster 2 knockdown

description: Gene expression data from MCAS with knockdown of miR-200 cluster 2 (miR-200c, miR-141) grown in Matrigel for 7 days

source_name: Mucinous ovarian cancer cells MCAS with knockdown of miR-200 cluster 2 (miR-200c, miR-141) grown in Matrigel for 7 days


title: wt YBL574 in YP with 3% glycerol, replicate 3


title: wt YBL574 in YPD, replicate 3

source_name: wt YBL574 in YPD


title: wt YBL574 in YPD, replicate 2


title: Wild type OSE7

description: Gene expression data from wild type OSE7 cells grown in Matrigel for 7 days

source_name: Normal ovarian surface epithelial cells OSE7  grown in Matrigel for 7 days

value: Ovarian surface epithelial cells

value: Normal

tag: age

value: immortalized


title: OSE7 transduced by virus carry vector inserted with a random sequence

description: Gene expression data from OSE7 with random sequence inserted grown in Matrigel for 7 days

source_name: Normal ovarian surface epithelial cells OSE7 with random sequence inserted grown in Matrigel for 7 days


title: OSE7 with miR-200 cluster 1 overexpressed

description: Gene expression data from OSE7 with over-expression of miR-200 cluster 1 (miR-200a, miR-200b and miR-429) grown in Matrigel for 7 days

source_name: Normal ovarian surface epithelial cells OSE7 with over-expression of miR-200 cluster 1 (miR-200a, miR-200b and miR-429) grown in Matrigel for 7 days


title: E4.5_P1_embryo1_cell1_RNAseq

source_name: Embryo


title: E4.5_P1_embryo1_cell25_RNAseq


title: OSE7 with miR-200 cluster 1 and 2 overexpressed

description: Gene expression data from OSE7 with over-expression of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days

source_name: Normal ovarian surface epithelial cells OSE7 with over-expression of miR-200 cluster 1 and 2 (miR-200a, miR-200b, miR-200c, miR-141 and miR-429) grown in Matrigel for 7 days


title: E4.5_P1_embryo1_cell14_RNAseq


title: t11a YBL574 in YPD, replicate 3


title: wt YBL574 in YPD, replicate 1


title: E4.5_P1_embryo1_cell13_RNAseq


title: cka1 BY4741 in YPD, replicate 1

source_name: cka1 BY4741 in YPD


title: E5.5_P11.P6.P10_embryo7_cell9_BSseq


title: wt BY4741 in YPD, replicate 3

source_name: wt BY4741 in YPD


title: wt BY4741 in YPD, replicate 2


title: OSE7 with miR-200 cluster 2 overexpressed

description: Gene expression data from OSE7 with over-expression of miR-200 cluster 2 (miR-200c, miR-141) grown in Matrigel for 7 days

source_name: Normal ovarian surface epithelial cells with over-expression of miR-200 cluster 2 (miR-200c, miR-141) grown in Matrigel for 7 days


title: cka1 BY4741 in YP with 3% glycerol, replicate 1


title: E5.5_P11.P6.P10_embryo7_cell96_BSseq


title: wt BY4741 in YPD, replicate 1


title: BT35

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho. Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: Total RNA depleted with rRNA

data_processing:
Type of Sequencer: HiSeq4000
Sequencing Control Software: HCS v3.3
The raw Illumina reads were trimmed with fqtrim (http://ccb.jhu.edu/software/fqtrim/index.shtml) with the parameters “-A –D –q 20 –l 50”. The trimmed reads were then mapped to a combined microbiome-host genome database using BWA mem (version 0.7.12-r1039). To generate the reference database, the combined microbiome reference genome database 1253 species of bacteria, 97 species of archaea, 326 species of lower eukaryotes and 1420 species of viruses were downloaded from Human Microbiome Project Site, and concatenated with the complete sequence sets of Mouse genome database (GRCm38/mm10 : Dec.2011) downloaded at UCSC Genome Bioinformatics Site (http://genome.ucsc.edu/) to create  the final reference database.
The sequences which mapped to coding regions of the B. theta genome were counted using Htseq Count.
For the functional abundance profiles of Firmicutes, the raw reads were uploaded on MG-RAST (Meyer et al., 2008), processed by default settings, and the counting of the functional annotations were retrieved at the level 3 of SEED Subsystems.
Supplementary_files_format_and_content: Sample1-38: htseq count data for sequences mapped on B. theta genome. Sample39-45: Counts for genes mapped on Firmicutes for level3 annotation (SEED Subsystems) by MG-RAST.

organism: mouse gut metagenome

source_name: mouse Cecal content

extract_protocol:
Total RNA was subjected to DNase digestion (Baseline-ZERO; Epicentre), passed through a MEGAClear column (Ambion) to deplete RNAs <200 nt (removing most 5S rRNA and tRNA). The samples were subjected to another round of DNase digestion (DNA-free TURBO; Ambion), passed through another MEGAClear column, and finally subjected to bacterial rRNA depletion (Ribo-Zero Magnetic kit Bacteria; Epicentre).
Double-stranded cDNA (dscDNA) was synthesized by SuperScript II (Invitrogen), and then the library was prepared using TruSeq Stranded RNA HT Kit (Illumina).

treatment_protocol: Germ free mice or SPF mice were used for the experiments. The SPF mice were given 100 mg/kg metronidazole by oral gavage every 24 h for 7 days, in addition to 0.66 mg/ml ciprofloxacin (Wako) and 10mg/ml of artificial sweetener (Palsweet; Ajinomoto) administered in the drinking water. To colonize B. theta, 1X108 c.f.u. of cultured bacteria were gavaged 2 days after antibiotic withdrawal. To generate backpack mice, 2×106 of cultured cells in 0.3 ml of PBS were injected subcutaneously beneath the dorsal skin of rag1-/- recipients.

tag: bacteria

value: SPF-BT[delta]AFF

tag: host

value: originally SPF C57BL6 mice treated with antibiotics and colonized with B. theta

tag: sample type

value: cecal content


title: BT34

description: Total RNA depleted with rRNA

value: SPF-BTWT


title: BT33

description: Total RNA depleted with rRNA


title: BT36

description: Total RNA depleted with rRNA


title: BT37

description: Total RNA depleted with rRNA


title: BT32

description: Total RNA depleted with rRNA


title: BT31

description: Total RNA depleted with rRNA


title: CHD7_OPC_chIP-seq

organism: Rattus norvegicus

source_name: rat OPC

value: Sprague Dawley

value: primary cultured

value: Rabbit anti-Chd7: Cell signaling Technology; #6505; 1


title: E5.5_P11.P6.P10_embryo7_cell92_BSseq


title: BT30

description: Total RNA depleted with rRNA

value: originally germ free C57BL6 mice


title: cka1 BY4741 in YPD, replicate 3

value: YPD


title: cka1 BY4741 in YPD, replicate 2


title: E5.5_P11.P6.P10_embryo7_cell91_BSseq


title: E4.5_P2_embryo5_cell9_BSseq


title: E4.5_P2_embryo5_cell81_BSseq


title: E4.5_P2_embryo5_cell93_BSseq


title: BT29

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo5_cell8_BSseq


title: E4.5_P2_embryo5_cell80_BSseq


title: BT28

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo5_cell92_BSseq


title: E4.5_P2_embryo5_cell70_BSseq


title: BT27

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell90_BSseq


title: BT26

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell89_BSseq


title: E4.5_P2_embryo5_cell69_BSseq


title: E5.5_P11.P6.P10_embryo7_cell93_BSseq


title: E4.5_P2_embryo5_cell68_BSseq


title: E4.5_P2_embryo5_cell57_BSseq


title: E4.5_P2_embryo5_cell45_BSseq


title: E4.5_P2_embryo5_cell46_BSseq


title: E4.5_P2_embryo5_cell56_BSseq


title: E5.5_P11.P6.P10_embryo7_cell88_BSseq


title: BT24

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell87_BSseq


title: BT23

description: Total RNA depleted with rRNA


title: BT25

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell8_BSseq


title: E4.5_P2_embryo5_cell32_BSseq


title: E4.5_P2_embryo5_cell34_BSseq


title: E4.5_P2_embryo5_cell44_BSseq


title: E4.5_P2_embryo5_cell22_BSseq


title: BT21

description: Total RNA depleted with rRNA


title: BT22

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo5_cell21_BSseq


title: E5.5_P11.P6.P10_embryo7_cell84_BSseq


title: E4.5_P2_embryo5_cell33_BSseq


title: E4.5_P2_embryo5_cell58_BSseq


title: E5.5_P11.P6.P10_embryo7_cell85_BSseq


title: BT20

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo5_cell10_BSseq


title: E5.5_P11.P6.P10_embryo7_cell81_BSseq


title: E4.5_P2_embryo4_cell89_BSseq


title: BT19

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell80_BSseq


title: E4.5_P2_embryo4_cell87_BSseq


title: E4.5_P2_embryo4_cell77_BSseq


title: E5.5_P11.P6.P10_embryo7_cell86_BSseq


title: E5.5_P11.P6.P10_embryo7_cell7_BSseq


title: BT18

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell76_BSseq


title: E4.5_P2_embryo4_cell6_BSseq


title: BT16

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell65_BSseq


title: E4.5_P2_embryo5_cell20_BSseq


title: E5.5_P11.P6.P10_embryo7_cell77_BSseq


title: BT15

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell78_BSseq


title: E4.5_P2_embryo4_cell88_BSseq


title: E4.5_P2_embryo4_cell75_BSseq


title: BT17

description: Total RNA depleted with rRNA


title: BT14

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell64_BSseq


title: E4.5_P2_embryo4_cell5_BSseq


title: E5.5_P11.P6.P10_embryo7_cell76_BSseq


title: E4.5_P2_embryo4_cell53_BSseq


title: BT13

description: Total RNA depleted with rRNA


title: BT12

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell40_BSseq


title: E4.5_P2_embryo4_cell4_BSseq


title: E5.5_P11.P6.P10_embryo7_cell74_BSseq


title: BT11

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell3_BSseq


title: E5.5_P11.P6.P10_embryo7_cell73_BSseq


title: E4.5_P2_embryo4_cell63_BSseq


title: BT10

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell39_BSseq


title: E4.5_P2_embryo4_cell29_BSseq


title: BT9

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell72_BSseq


title: E4.5_P2_embryo4_cell28_BSseq


title: BT8

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell52_BSseq


title: E4.5_P2_embryo4_cell27_BSseq


title: E4.5_P2_embryo4_cell18_BSseq


title: BT7

description: Total RNA depleted with rRNA


title: E5.5_P11.P6.P10_embryo7_cell6_BSseq


title: E4.5_P2_embryo4_cell16_BSseq


title: E5.5_P11.P6.P10_embryo7_cell69_BSseq


title: E4.5_P2_embryo4_cell51_BSseq


title: E4.5_P2_embryo4_cell41_BSseq


title: E5.5_P11.P6.P10_embryo7_cell68_BSseq


title: E4.5_P2_embryo4_cell15_BSseq


title: E5.5_P11.P6.P10_embryo7_cell79_BSseq


title: E4.5_P2_embryo3_cell73_BSseq


title: BT6

description: Total RNA depleted with rRNA


title: Amplicon_BS_2i_90

description: library strategy: Bisulfite-Seq amplicon-Seq

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
The first 8 bp of Read 2, representing unique molecular identifiers (UMIs), were removed and written into the sequence IDs reads instead. The reads were then subjected to adapter and quality trimming using Trim Galore (v0.4.2; default parameters) and aligned to the mouse genome (build GRCm38) using Bismark (v0.16.3, parameters: --non_directional). After mapping reads were deduplicated using the UMI-mode of deduplicate_bismark (options --bam --barcode).
Genome_build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: E14 ESC

growth_protocol: Naïve ESCs were cultured in serum free media with 2i inhibitors (Neurobasal, N2, B27, 103 U/ml LIF, 1 μM Mek inhibitor PD0325901 and 3 μM Gsk3β inhibitor CHIR99021) without feeders at 37°C and 5% CO2. Primed ESCs were cultured in serum containing media (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1 mM nonessential amino acids, 50 μM β-mercaptoethanol, and 103 U/ml LIF ESGRO) without feeders at 37°C and 5% CO2.

extract_protocol:
Cells were lysed by removing media from culture dishes and adding 200ul of RLT plus buffer (Qiagen) supplemented with 0.5mM 2-mercaptoethanol. . Total nucleic acid was purified from cell lysates with RNAdvance magnetic beads (Beckman Coulter, A32649) using a Bravo Workstation pipetting robot (Agilent Technologies) following the manufacturers protocol. RNA was subsequently purified by treating the total nucleic acid with DNase I.
KAPA HiFi Uracil+ Master Mix (Kapa Biosystems) was used to amplify regions of interest using 30nM primers (Table S3), with the reverse primer including an 8N unique molecular identifier (UMI). The PCR program was: 95C 5min; 35 repeats of 98C 20s, 60C 15s, 72C 60s; 72C 10min. Amplicons were pooled for each sample and purified using Ampure XP beads (Agencourt), before a second round of PCR was used to incorporate Illumina Adaptor sequences and index samples. The PCR reaction included 11ul pooled amplicons, 200nM indexed PE1.0 (Table S5) and iPCRTag primers (Quail et al., 2012), and KAPA HiFi Master Mix (Kapa Biosystems). The PCR program was: 98C 45s; 5 repeats of 98C 15s, 65C 30s, 72C 30s; 72C 5min. Samples were then pooled and purified before library QC and sequencing was performed with up to 144 samples included on a 150bp paired-end MiSeq run.

value: Embryonic stem cell

tag: cell line

value: E14 ESC


title: E5.5_P11.P6.P10_embryo7_cell67_BSseq


title: E4.5_P2_embryo3_cell85_BSseq


title: E4.5_P2_embryo3_cell61_BSseq


title: E4.5_P2_embryo3_cell49_BSseq


title: BT5

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo4_cell17_BSseq


title: E5.5_P11.P6.P10_embryo7_cell66_BSseq


title: BT4

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo3_cell2_BSseq


title: E4.5_P2_embryo3_cell26_BSseq


title: E5.5_P11.P6.P10_embryo7_cell75_BSseq


title: E5.5_P11.P6.P10_embryo7_cell65_BSseq


title: BT3

description: Total RNA depleted with rRNA


title: BT2

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo3_cell25_BSseq


title: E4.5_P2_embryo3_cell1_BSseq


title: E5.5_P11.P6.P10_embryo7_cell64_BSseq


title: E4.5_P1_embryo2_cell91_BSseq


title: BT1

description: Total RNA depleted with rRNA


title: E4.5_P2_embryo3_cell37_BSseq


title: E5.5_P11.P6.P10_embryo7_cell62_BSseq


title: E4.5_P2_embryo3_cell14_BSseq


title: E5.5_P11.P6.P10_embryo7_cell63_BSseq


title: E4.5_P2_embryo3_cell13_BSseq


title: E4.5_P1_embryo2_cell79_BSseq


title: E4.5_P1_embryo2_cell90_BSseq


title: BP8

description: Total RNA depleted with rRNA

value: backpack in rag1-/- mice (SPF)


title: E5.5_P11.P6.P10_embryo7_cell60_BSseq


title: E5.5_P11.P6.P10_embryo7_cell61_BSseq


title: E4.5_P1_embryo2_cell7_BSseq


title: BP7

description: Total RNA depleted with rRNA


title: E4.5_P1_embryo2_cell78_BSseq


title: BP6

description: Total RNA depleted with rRNA


title: BP5

description: Total RNA depleted with rRNA


title: E4.5_P1_embryo2_cell55_BSseq


title: E4.5_P1_embryo2_cell66_BSseq


title: E5.5_P11.P6.P10_embryo7_cell5_BSseq


title: E4.5_P1_embryo2_cell43_BSseq


title: E5.5_P11.P6.P10_embryo7_cell57_BSseq


title: BP2

description: Total RNA depleted with rRNA


title: BP3

description: Total RNA depleted with rRNA


title: E4.5_P1_embryo2_cell30_BSseq


title: E5.5_P11.P6.P10_embryo7_cell56_BSseq


title: E4.5_P1_embryo2_cell54_BSseq


title: E4.5_P1_embryo2_cell67_BSseq


title: BP4

description: Total RNA depleted with rRNA


title: E4.5_P1_embryo2_cell18_BSseq


title: E5.5_P11.P6.P10_embryo7_cell55_BSseq


title: E5.5_P11.P6.P10_embryo7_cell54_BSseq


title: E4.5_P1_embryo2_cell19_BSseq


title: E4.5_P1_embryo1_cell86_BSseq


title: BP1

description: Total RNA depleted with rRNA


title: E4.5_P1_embryo2_cell6_BSseq


title: E4.5_P1_embryo2_cell31_BSseq


title: E5.5_P11.P6.P10_embryo7_cell53_BSseq


title: E5.5_P11.P6.P10_embryo7_cell52_BSseq


title: E4.5_P1_embryo1_cell74_BSseq


title: E4.5_P1_embryo1_cell85_BSseq


title: E5.5_P11.P6.P10_embryo7_cell51_BSseq


title: E4.5_P1_embryo1_cell73_BSseq


title: E4.5_P1_embryo1_cell61_BSseq


title: E5.5_P11.P6.P10_embryo7_cell50_BSseq


title: E4.5_P1_embryo1_cell50_BSseq


title: E4.5_P1_embryo1_cell49_BSseq


title: E4.5_P1_embryo1_cell62_BSseq


title: E4.5_P1_embryo1_cell38_BSseq


title: E4.5_P1_embryo1_cell37_BSseq


title: E5.5_P11.P6.P10_embryo7_cell4_BSseq


title: E4.5_P1_embryo1_cell25_BSseq


title: E4.5_P1_embryo1_cell2_BSseq


title: E4.5_P1_embryo2_cell42_BSseq


title: E4.5_P1_embryo1_cell26_BSseq


title: E4.5_P1_embryo1_cell14_BSseq


title: E5.5_P11.P6.P10_embryo7_cell49_BSseq


title: E5.5_P11.P6.P10_embryo7_cell48_BSseq


title: E4.5_P1_embryo1_cell13_BSseq


title: E4.5_P1_embryo1_cell1_BSseq


title: E5.5_P11.P6.P10_embryo7_cell45_BSseq


title: E5.5_P11.P6.P10_embryo7_cell44_BSseq


title: E5.5_P11.P6.P10_embryo7_cell43_BSseq


title: E5.5_P11.P6.P10_embryo7_cell42_BSseq


title: E5.5_P11.P6.P10_embryo7_cell41_BSseq


title: E5.5_P11.P6.P10_embryo7_cell40_BSseq


title: E5.5_P11.P6.P10_embryo7_cell39_BSseq


title: E5.5_P11.P6.P10_embryo7_cell3_BSseq


title: E5.5_P11.P6.P10_embryo7_cell38_BSseq


title: JTG155_mut

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software.
Sequenced reads were trimmed for adaptor sequence and filtered in order to keep reads with a Q33 quality score or higher, then mapped to GRCm38 transcriptome using TopHat 2.1.0 using parameters -p 6 and b2-sensitive. Remaining unmapped reads were mapped to genome of the same version.
HTSeq 0.6 .1 was used for feature counting read counts mapped on exons with parameters -stranded=reverse and -m intersection strict
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes cpm read counts using normalized library sizes for all samples

source_name: Pneumocytes

growth_protocol: Pneumocytes were freshly isolated from the lung, and no growth protocol was followed

extract_protocol:
Pneumocytes were collected directly in Tris Reagent and stored at -80ºC. RNA was then isolated using PicoPureTM RNA isolation kit.
1 µg of total RNA samples was used as provided by the user. Sample RNA Integrity Numbers were in the range 7.5-9 (average 8.0) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Mice had been treated with tamoxifen for 4 weeks when they were sacrificed, their lungs were excised and mechanically and enzymatically dissociated. Lung dissociated cells were then stained with CD31 and CD45 surface markers prior to FACS sorting.

value: CD31-/CD45-, KRasG12V-FDG+ sorted pneumocytes

tag: Sex

value: Female


title: JTG147_wt


title: JTG178_mut

value: Male


title: JTG185_wt


title: JTG192_wt


title: JTG153_wt


title: JTG135_mut


title: JTG156_mut


title: HV_7-2_ET

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: HV n°7, triplicate 2, condition ET

hyb_protocol: 5 micrograms of purified DNA were fragmented into 50-200 bp fragments and were 3-labeled using Encore Biotin Module kit (Nugen). The resulting target was mixed with standard hybridization controls and B2 oligonucleotides following recommendations of manufacturer. The hybridization cocktail was heat-denatured at 99°C for 2 minutes, incubated at 50°C for 5 minutes and centrifuged at 16,000 g for 5 minutes to pellet the residual salts. The HERV-V3 microarrays were prehybridized with 200 µL of hybridization buffer and placed under stirring (60 rpm) in an oven at 50°C for 10 minutes. The hybridization buffer was then replaced by the denatured hybridization cocktail. Hybridization was performed at 50°C for 18 hours in the oven under constant stirring (60 rpm). Washing and staining were carried out according to the protocol supplied by the manufacturer, using a fluidic station: GeneChip fluidic station 450 (Affymetrix).

scan_protocol: The arrays were finally scanned using a fluorometric scanner: GeneChip scanner 3000 7G (Affymetrix)

data_processing: CEL files were transformed into matrix, normalized, adjusted for background noise (RMA normalization) and probes were summarized into probesets  with command apt-probeset-summarize (V 1.18.0)  with rma option . Batch effects were removed using COMBAT. Probesets were filtered when log2 signal was under 5.5 in more than 68% of samples.

source_name: HV n°7, triplicate 2, condition ET

label_protocol: The cDNA synthesis and amplification steps were performed from 16 ng of RNA using the Ovation Pico WTA System V2 kit (Nugen). Briefly, cDNA synthesis was done using a mixture of random and polydT primers, followed by the synthesis of the complementary strand. The Single Primer Isothermal Amplification (SPIA) was then performed with hybrid DNA/RNA primers sensitive to RNAse-H digestion, in the presence of a DNA polymerase with strong strand displacement activity. The resulting amplified cDNA was purified using the QIAquick purification kit (Qiagen), from which, total DNA concentration was measured using the NanoDrop 1000 spectrophotometer (Thermo Scientific) and the product quality was checked on the Bioanalyser 2100 (Agilent).

extract_protocol: Total RNA was extracted from PBMCs using RNeasy Plus Mini kits (Qiagen). For each RNA extraction, the residual genomic DNA was digested using the gDNA Eliminator spin column (Qiagen) and directly on RNeasy spin column using RNase-Free DNase Set (Qiagen). RNA was eluted in 30 µL of RNase Free Water. RNA quantity was determined for each sample using Nanodrop (Thermo Scientific) according to the manufacturer’s instructions. RNA quality was assessed on a Bioanalyser 2100 (Agilent) according to the manufacturer’s instructions. All samples have a RIN greater than 7.

treatment_protocol: Citrated blood from healthy volunteers was obtained from EFS (Etablissement Français du Sang) and used immediately. According to EFS standardized procedures for blood donation, informed consent was obtained from healthy volunteers and personal data for blood donors were anonymized at time of blood donation and before blood transfer to our research lab. Peripheral blood mononuclear cells (PBMCs) were isolated from citrated venous blood with Unisep tubes density gradient centrifugation (Eurobio) and washed with PBS. Cell were cultured in 24-well plates at 2×106 cell/mL in X-Vivo 20 Medium (Lonza). As shown in Figure 3A, to induce the LPS-primed state, PBMCs were cultured in the presence or absence (control group) of 2 ng/mL LPS mix from Escherichia coli O55:B5, O127:B8 and O11:B4 (Sigma-Aldrich) and incubated overnight at 37°C and 5% CO2 (15 hours). Following a washing step, in order to induce reverse tolerance, PBMCs were incubated for an additional 24 hours in the presence or absence of 100 ng/mL of human IFN-g1b (Miltenyi Biotec). Finally PBMCs were stimulated a second time by adding 100 ng/mL of LPS for another six hours. To achieve a classical ex vivo endotoxin tolerance model, the step with IFNg stimulation is not carried out. For each conditions,  supernatants were recovered and stored at -80°C. Cells were harvested, lysed in RLT buffer supplemented with β mercaptoéthanol and stored at -80°C until further processing.

value: blood

value: PBMC

value: ET


title: HV_7-2_LPS

description: HV n°7, triplicate 2, condition LPS

source_name: HV n°7, triplicate 2, condition LPS

value: LPS


title: HV_7-3_LPS

description: HV n°7, triplicate 3, condition LPS

source_name: HV n°7, triplicate 3, condition LPS


title: HV_7-1_LPS

description: HV n°7, triplicate 1, condition LPS

source_name: HV n°7, triplicate 1, condition LPS


title: HV_7-2_NS

description: HV n°7, triplicate 2, condition NS

source_name: HV n°7, triplicate 2, condition NS

value: NS


title: E5.5_P11.P6.P10_embryo7_cell33_BSseq


title: HV_7-3_NS

description: HV n°7, triplicate 3, condition NS

source_name: HV n°7, triplicate 3, condition NS


title: HV_7-3_ET

description: HV n°7, triplicate 3, condition ET

source_name: HV n°7, triplicate 3, condition ET


title: E5.5_P11.P6.P10_embryo7_cell32_BSseq


title: E5.5_P11.P6.P10_embryo7_cell37_BSseq


title: E5.5_P11.P6.P10_embryo7_cell31_BSseq


title: HV_7-1_ET

description: HV n°7, triplicate 1, condition ET

source_name: HV n°7, triplicate 1, condition ET


title: HV_6-3_ET

description: HV n°6, triplicate 3, condition ET

source_name: HV n°6, triplicate 3, condition ET


title: HV_7-1_NS

description: HV n°7, triplicate 1, condition NS

source_name: HV n°7, triplicate 1, condition NS


title: E5.5_P11.P6.P10_embryo7_cell30_BSseq

source_name: Embryo


title: HV_6-1_ET

description: HV n°6, triplicate 1, condition ET

source_name: HV n°6, triplicate 1, condition ET


title: E5.5_P11.P6.P10_embryo7_cell29_BSseq


title: E5.5_P11.P6.P10_embryo7_cell2_BSseq


title: HV_6-2_LPS

description: HV n°6, triplicate 2, condition LPS

source_name: HV n°6, triplicate 2, condition LPS


title: HV_6-2_ET

description: HV n°6, triplicate 2, condition ET

source_name: HV n°6, triplicate 2, condition ET


title: HV_6-3_NS

description: HV n°6, triplicate 3, condition NS

source_name: HV n°6, triplicate 3, condition NS


title: HV_6-3_LPS

description: HV n°6, triplicate 3, condition LPS

source_name: HV n°6, triplicate 3, condition LPS


title: HV_6-1_LPS

description: HV n°6, triplicate 1, condition LPS

source_name: HV n°6, triplicate 1, condition LPS


title: E5.5_P11.P6.P10_embryo7_cell28_BSseq


title: E5.5_P11.P6.P10_embryo7_cell26_BSseq


title: E5.5_P11.P6.P10_embryo7_cell27_BSseq


title: E5.5_P11.P6.P10_embryo7_cell24_BSseq


title: E5.5_P11.P6.P10_embryo7_cell25_BSseq


title: E5.5_P11.P6.P10_embryo7_cell21_BSseq


title: E5.5_P11.P6.P10_embryo7_cell20_BSseq


title: HV_6-1_NS

description: HV n°6, triplicate 1, condition NS

source_name: HV n°6, triplicate 1, condition NS


title: HV_4-2_ET

description: HV n°4, triplicate 2, condition ET

source_name: HV n°4, triplicate 2, condition ET


title: HV_ 4-2_LPS

description: HV n°4, triplicate 2, condition LPS

source_name: HV n°4, triplicate 2, condition LPS


title: E5.5_P11.P6.P10_embryo7_cell19_BSseq


title: HV_4-1_ET

description: HV n°4, triplicate 1, condition ET

source_name: HV n°4, triplicate 1, condition ET


title: E5.5_P11.P6.P10_embryo7_cell1_BSseq


title: E5.5_P11.P6.P10_embryo7_cell17_BSseq


title: E5.5_P11.P6.P10_embryo7_cell16_BSseq


title: HV_4-1_LPS

description: HV n°4, triplicate 1, condition LPS

source_name: HV n°4, triplicate 1, condition LPS


title: HV_6-2_NS

description: HV n°6, triplicate 2, condition NS

source_name: HV n°6, triplicate 2, condition NS


title: E5.5_P11.P6.P10_embryo7_cell18_BSseq


title: E5.5_P11.P6.P10_embryo7_cell15_BSseq


title: E5.5_P11.P6.P10_embryo7_cell14_BSseq


title: E5.5_P11.P6.P10_embryo7_cell13_BSseq


title: HV_4-3_NS

description: HV n°4, triplicate 3, condition NS

source_name: HV n°4, triplicate 3, condition NS


title: E5.5_P11.P6.P10_embryo7_cell12_BSseq


title: HV_3-1_LPS

description: HV n°3, triplicate 1, condition LPS

source_name: HV n°3, triplicate 1, condition LPS


title: HV_3-2_LPS

description: HV n°3, triplicate 2, condition LPS

source_name: HV n°3, triplicate 2, condition LPS


title: HV_4-2_NS

description: HV n°4, triplicate 2, condition NS

source_name: HV n°4, triplicate 2, condition NS


title: E5.5_P11.P6.P10_embryo7_cell36_BSseq

source_name: Embryo


title: HV_4-1_NS

description: HV n°4, triplicate 1, condition NS

source_name: HV n°4, triplicate 1, condition NS


title: HV_3-1_ET

description: HV n°3, triplicate 1, condition ET

source_name: HV n°3, triplicate 1, condition ET


title: HV_3-3_ET

description: HV n°3, triplicate 3, condition ET

source_name: HV n°3, triplicate 3, condition ET


title: HV_3-3_LPS

description: HV n°3, triplicate 3, condition LPS

source_name: HV n°3, triplicate 3, condition LPS


title: JTG00319_mut

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software.
Sequence reads were mapped to GRCm38 transcriptome using TopHat 2.1.0 using parameters -p 6, b2-sensitive and -r for the average insert size. Remaining unmapped reads were mapped to genome of the same version.
HTSeq 0.6 .1 was used for feature counting (exons) with parameters -stranded=no and -m intersection strict
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes cpm read counts using normalized library sizes for all samples

source_name: Pneumocytes

extract_protocol:
Pneumocytes were collected directly in Tris Reagent and stored at -80ºC. RNA was then isolated using PicoPureTM RNA isolation kit.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2013) with some modifications. Briefly, RNA quality (the RIN value) and quantity was estimated from the Agilent RNA 6000 Nano assay and 1.8ul of RNA was used for cDNA synthesis. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), template-switching oligonucleotides (1µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), 100 nM ISPCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 8 or 20 cycles of amplification, in function of the starting material quantities. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent). 200 ng of the amplified cDNA was fragmented for 10 min at 55 ºC using Nextera® XT (Illumina) and amplified for 12 cycles with indexed Nextera® PCR primers. The Nextera® libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4 and TruSeq Dual Index of 8bp+8bp. We generated in a mean 20 million paired-end reads for each sample in a fraction of a sequencing v4 flow cell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of FASTQ sequence files by CASAVA.Products were purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified again on a Bioanalyzer using a High Sensitvity DNA Kit.

treatment_protocol: Mice had been treated with tamoxifen for 4 weeks when they were sacrificed, their lungs were excised and mechanically and enzymatically dissociated. Lung dissociated cells were then loaded with FDG by treatment with a hypotonic buffer, and stained with CD31 and CD45 surface markers prior to FACS sorting.


title: JTG00321_mut


title: JTG00335_mut


title: JOP00404_mut


title: JTG00339_wt


title: HV_3-2_ET

description: HV n°3, triplicate 2, condition ET

source_name: HV n°3, triplicate 2, condition ET


title: HV_3-2_NS

description: HV n°3, triplicate 2, condition NS

source_name: HV n°3, triplicate 2, condition NS


title: HV_2-2_ET

description: HV n°2, triplicate 2, condition ET

source_name: HV n°2, triplicate 2, condition ET


title: HV_3-3_NS

description: HV n°3, triplicate 3, condition NS

source_name: HV n°3, triplicate 3, condition NS


title: JTG00333_wt


title: JTG00320_wt


title: JTG00326_wt


title: HV_3-1_NS

description: HV n°3, triplicate 1, condition NS

source_name: HV n°3, triplicate 1, condition NS


title: HV_2-3_ET

description: HV n°2, triplicate 3, condition ET

source_name: HV n°2, triplicate 3, condition ET


title: HV_2-1_LPS

description: HV n°2, triplicate 1, condition LPS

source_name: HV n°2, triplicate 1, condition LPS


title: HV_2-1_ET

description: HV n°2, triplicate 1, condition ET

source_name: HV n°2, triplicate 1, condition ET


title: HV_2-3_LPS

description: HV n°2, triplicate 3, condition LPS

source_name: HV n°2, triplicate 3, condition LPS


title: HV_4-3_LPS

description: HV n°4, triplicate 3, condition LPS

source_name: HV n°4, triplicate 3, condition LPS


title: HV_2-2_LPS

description: HV n°2, triplicate 2, condition LPS

source_name: HV n°2, triplicate 2, condition LPS


title: BP_P3U1_4

data_processing:
Type of Sequencer:Illumina MiSeq, paired end
USEARCH algorithm was used to filter the high quality reads, cluster into operational taxonomic units (OTUs) and remove chimeras based on the database in RDP classifier.
Minimum identity of 97% was set to identify OTUs. The QIIME scripts (version 1.9.1) were then used to assign taxonomy, align sequences to the greengenes reference database, perform alpha and beta diversity analysis and summarize taxonomy.
16Sana1,2,4: taxa summary data at the family level
16Sana3: OUT table for sequence counts

organism: Bacteria

source_name: mouse cecal content

extract_protocol:
Genomic DNA was isolated from fecal samples using the PowerSoil bacterial DNA extraction kit (MoBio). DNA samples were amplified using the following barcoded primers targeting V1–V2 region of the 16SrRNA gene.
The amplicons were purified with AMPure XP beads (Beckman), indices and sequencing adaptors were introduced  using the Nextera XT Index kit (Illumina), quantified by using THUNDERBIRD SYBR qPCR mix (TOYOBO) and pooled according to the Illumina protocol.

tag: treatment

value: backpack in rag1-/- mice (SPF), treated with metronidazole and ciprofloxacin for 7 days, and then colonized with B. theta

value: fecal content

tag: molecule


title: BP_P3U1_5


title: BP_P3U1_3


title: BP_P3U1_2


title: BP_7.6_4


title: BP_7.6_5


title: BP_7.6_3


title: BP_7.6_2


title: HV_4-3_ET

description: HV n°4, triplicate 3, condition ET

source_name: HV n°4, triplicate 3, condition ET

tag: tissue


title: Bvul17

source_name: mouse feces

value: metronidazole+ciprofloxacin, 4 weeks after colonization

tag: genotype/variation

value: BV[delta]MAFF


title: BP_P3U1_1


title: HV_2-2_NS

description: HV n°2, triplicate 2, condition NS

source_name: HV n°2, triplicate 2, condition NS

tag: cell type


title: lgs301315_CTCF HiChIP-seq

city: Oklahoma City

first: Patrick

middle: M

last: Gaffney

state: OK

address: 825 NE 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

description:
CTCF-mediated HiChIP-Seq
processed data: CTCF_HiChIP_connectome.txt.gz

data_processing:
For ChIP-seq, raw FASTQ reads were quality filtered and trimmed for Illumina adapters using Trimmomatic v0.35
To assess the quality of the ChIP-seq data, we calculated the fraction of reads in peaks (FRiP) for acCBP/p300 and RNAPII enrichment peaks and scrutinized experiments with FRiP scores <1%. We also used strand cross-correlation to calculate the normalized strand coefficient (NSC) and relative strand coefficient (RSC), and repeated experiments with NSC < 1.05 and RSC < 0.8.
Reads aligning to Poly-A, Poly-C, ribosomal, mitochondrial, or Phi-X sequences were excluded using Bowtie v2.2.4 with option -L 10.
Filtered reads were aligned using the Burrows Wheeler Aligner (BWA) to the human hg19 genome with the following options: -n 2 –o 0 –l 20.
To reduce reference genome bias on read mappability, we used the WASP pipeline to relocate reads potentially biased by genetic variation.  Only reads overlapping single nucleotide polymorphisms (SNPs) which were segregating in the genotyping data (≥2 minor alleles across population) were targeted by the realignment procedure.
For RNA-seq, post-sequence reads were quality filtered and trimmed for Illumina adapters using Trimmomatic v0.35
Resulting reads were aligned to the hg38 genome using Kallisto v0.43.0 with the following options: --bias enabled, 50 bootstraps.
Transcript expression values were summarized at the gene level to transcript-length adjusted, library-size scaled counts per million (CPM) with the R package tximport (PMID:26925227)
RNA-seq expression data were normalized with PEER using K=10 latent factors on genes with positive expression in >50% of individuals. The PEER-derived weights were then scaled by the mean of each gene.
For HiChIP-seq, sequenced reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
Loop calling was performed with hichipper (PMID: 29489746) for each sample
Alignment was performed on the entire hg19 genome, and also to custom genomes of the hg19 COX and hg19 PGF Major Histocompatibility Complex loci.
Genome_build: hg19 (ChIP-seq, HiChIP-seq), hg38 (RNA-seq)
Supplementary_files_format_and_content: Adjusted.hetp.txt (Output of the Combined Haplotype Test software after WASP alignment bias correction),
Supplementary_files_format_and_content: connectome.txt (High-confidence loop calls  and paired-end tag counts from genome-wide alignment of HiChIP-seq data to the hg19 genome)
Supplementary_files_format_and_content: interactions.all.mango (High-confidence loop calls from custom haplotype alignment of HiChIP-seq data to the COX and PGF sequences)
Supplementary_files_format_and_content: Kallisto_expression_25cellLines_filtered_PEERnormalized+scaled_lengthScaledTPM.txt (Matrix of normalized gene-level abundances from RNA-seq data)

source_name: CTCF HiChIP-seq

growth_protocol: LCLs were maintained in RPMI 1640 medium supplemented with 10% FBS, penicillin, streptomycin, and L-glutamine.

extract_protocol:
For ChIP-seq, we crosslinked 10 million Epstein-Barr Virus (EBV)-transformed B cells with 1% formaldehyde for 5 minutes followed by careful cell lysis using the truChIP Chromatin Shearing Kit (Covaris).  Nuclei were isolated and fragmented using a Covaris E220e sonicator   with the following operating conditions: Peak Incident Power: 140 Watts; duty cycle: 5%; cycles per burst: 200; treatment time: 15 minutes; setpoint temperature: 6°C).  Crosslinked protein/DNA was immunoprecipitated using H3K27ac (rabbit polyclonal, Abcam #ab4729, 20ug/ml)  or H3K4me1 (rabbit polyclonal, Abcam #ab8895, 20ug/ml) antibodies on Protein A + G immunomagnetic beads.  Anti-acetyl histone H3 antibodies and isotype matched IgG antibodies were included as positive and negative controls, respectively.  An aliquot of the fragmented chromatin, not subjected to immunoprecipitation, was also used as an input control.  Chromatin crosslinks were reversed, then protein was digested with proteinase K and DNA fragments were purified using Ampure XP beads (Beckman Coulter).  For HiChIP-sequencing, We crosslinked 10 million EBV-transformed B cells using 1% formaldehyde for 10 minutes at room temperature.  Intact nuclei were isolated and digested using the MboI restriction enzyme for 4 hours at 37C.  DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature overnight.  Following the in situ ligation, we fragmented the ligated chromatin as previously described64.  Crosslinked protein/DNA was immunoprecipitated using antibodies to H3K27ac (rabbit polyclonal, Abcam #ab4729, 20ug/ml) and CTCF (rabbit mAb, clone D31H2, Cell Signaling #3418, 20ug/ml) and then purified by Protein A+G immunomagnetic beads.  The amount of MboI enzyme, antibody, and beads are determined by the number of cells in each sample64. After immunoprecipitation, DNA was eluted from the beads by incubating at 65C for 4 hours with 5% Proteinase K. DNA was purified by Zymo DNA Clean & Concentrator Column and quantified by Qubit High Sensitivity Assay Kit.  RNA was isolated from each LCL using TRIzol.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols. DNA libraries were sequenced on the Illumina NextSeq 500 using 75bp single-end reads.  RNA libraries were sequenced on the Illumina HiSeq 3000 using 75bp paired-end reads with 10 samples per lane, yielding 30 million reads per sample.

value: lymphoblastoid cell lines (LCLs)

tag: disease

value: Systemic lupus erythematosus

tag: race

value: European-American

tag: gender

value: CTCF (Cell Signaling #3418, clone D31H2)


title: BP_7.6_1

value: backpack in rag1-/- mice (SPF)


title: lgs301283_CTCF HiChIP-seq


title: lgs102580_CTCF HiChIP-seq


title: lgs101645_CTCF HiChIP-seq


title: lgs102943_CTCF HiChIP-seq


title: HV_2-3_NS

description: HV n°2, triplicate 3, condition NS

source_name: HV n°2, triplicate 3, condition NS


title: Bvul16


title: lgs000379_CTCF HiChIP-seq


title: lgs301283_H3K27ac HiChIP-seq

description:
H3K27ac-mediated HiChIP-Seq
processed data: H3K27ac_HiChIP_connectome.txt.gz

source_name: H3K27ac HiChIP-seq

value: H3K27ac (Abcam, #ab4729)


title: Bvul15


title: HV_2-1_NS

description: HV n°2, triplicate 1, condition NS

source_name: HV n°2, triplicate 1, condition NS


title: Bvul14


title: Bvul18


title: Bvul13


title: lgs102580_H3K27ac HiChIP-seq

value: Female


title: lgs101645_H3K27ac HiChIP-seq

value: Male


title: Bvul11


title: lgs100524_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control

source_name: Input Chromatin ChIP-seq control


title: lgs301315_H3K27ac HiChIP-seq


title: lgs102943_H3K27ac HiChIP-seq


title: Bvul10


title: Bvul9

value: BVWT


title: lgs000379_H3K27ac HiChIP-seq


title: Bvul7


title: Bvul6


title: lgs000502_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs102943_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs000379_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: Bvul5


title: lgs303260_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: Bvul12


title: Bvul3


title: lgs304761_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs100111_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs301315_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs302096_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: Bvul1


title: Bvul8


title: lgs304082_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs303397_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: PBS30

value: metronidazole+ciprofloxacin, 4 weeks after PBS inoculation


title: lgs101301_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: Bvul4


title: PBS29


title: lgs304654_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: Bvul2


title: lgs304629_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: PBS26


title: PBS27


title: PBS28


title: PBS25


title: lgs100953_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: PBS24


title: lgs106435_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: PBS23


title: lgs000705_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: PBS22


title: lgs101645_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs304714_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: PBS20


title: lgs102580_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: lgs304050_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: 101103430130_R04C02

type: genomic

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

description: HumanMethylation450 BeadChip - standard protocol

scan_protocol: BeadStudio

data_processing: non-normalized, background subtracted. CpGAssoc package was used to filter out CpG sites that have a Detection P-Value greater than 0.001 in more than 10% of the samples and samples that have a Detection P-Value greater than 0.001 in more than 5% of the CpG sites. After this, cross-reactive probes were removed and normalization was performed using BMIQ and combat

source_name: Whole Blood

extract_protocol: Invitrogen Puregene Genomic DNA kit

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: W

tag: ga

value: CC

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: PBS18

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: PBS21


title: lgs301430_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: lgs301283_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control


title: 101103430130_R03C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: H

tag: ga

value: TC

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: 101103430068_R06C02

tag: sample

tag: subjectid

tag: tp

tag: race

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: PBS17

tag: treatment

tag: host

tag: sample type

value: fecal content

tag: molecule

tag: genotype/variation


title: 101103430130_R01C02

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl


title: 101103430130_R06C01

tag: sample

tag: subjectid

tag: tp

tag: race

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: PBS16

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: PBS15


title: lgs302096_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

source_name: H3K4me1 ChIP-seq

tag: cell line

tag: disease

tag: gender

tag: chip antibody

value: H3K4me1 (Abcam, #ab8895)


title: PBS14


title: lgs100524_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: race


title: PBS19


title: 101103430068_R01C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: lgs302634_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: PBS13

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: 101103430068_R03C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

value: TT

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: lgs102943_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

value: lymphoblastoid cell lines (LCLs)

tag: disease

tag: race

tag: gender

tag: chip antibody


title: PBS12

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: 100994770046_R03C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: PBS11

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: 100994770067_R01C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

tag: ga

tag: genocord

tag: logfolicacid

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: 101103430068_R04C01

value: Not disclosed

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: 100994770067_R03C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

value: AA

tag: ga

tag: genocord

tag: logfolicacid

tag: logmethioninebl


title: 100994770028_R03C02

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: lgs000502_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

value: Systemic lupus erythematosus

value: European-American

tag: gender

tag: chip antibody


title: 100994770046_R04C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

value: MIED

tag: ga

tag: genocord

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: 100994770067_R04C02

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: PBS9

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: PBS10


title: PBS8


title: lgs303260_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: lgs301315_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

value: Female


title: lgs304761_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: PBS7


title: 100994770046_R06C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: lgs101293_Input Chromatin ChIP-seq control

description: Input Chromatin ChIP-Seq control

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: 100994770028_R04C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: lgs100111_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: race


title: 100994770067_R06C01

tag: sample

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl


title: 100994770020_R03C02

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl


title: 100994770028_R06C02

tag: sample

tag: race

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logfolicacidbl


title: lgs304082_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: gender

tag: chip antibody


title: lgs303397_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: 100994770028_R01C01

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl


title: PBS5

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: lgs101301_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: PBS3


title: PBS2


title: PBS4


title: 101103430130_R06C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: 101103430130_R04C01

tag: sample

tag: subjectid

tag: tp

tag: race

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl


title: 100994770020_R04C01

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa


title: PBS1

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: lgs000379_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: B.theta37

value: metronidazole+ciprofloxacin, 4 weeks after colonization

value: BT[delta]MAFF


title: 100994770020_R06C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: lgs100953_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: lgs000705_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: lgs304629_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

value: Male


title: 101103430130_R03C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine


title: B.theta36

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: lgs106435_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: B.theta35


title: lgs102580_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: 101103430130_R01C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: W

tag: ga

tag: genocord

tag: logfolicacid

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: 101103430068_R06C01

tag: sample

tag: subjectid

tag: tp

tag: race

value: CC

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine


title: lgs101645_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

tag: gender

tag: chip antibody


title: B.theta33

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: lgs304714_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: B.theta32


title: lgs302634_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: lgs304050_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: B.theta30


title: B.theta31


title: lgs304654_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: PBS6

value: metronidazole+ciprofloxacin, 4 weeks after PBS inoculation


title: lgs301430_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment


title: 100994770020_R01C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: 100994770067_R06C02

tag: sample

tag: subjectid

tag: tp

tag: race

value: H

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine


title: B.theta29

tag: treatment

tag: host

tag: sample type

value: fecal content

tag: molecule

tag: genotype/variation


title: VqmR rep3

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

country: Germany

institute: Friedrich-Schiller-Universität Jena

description:
dvqmR_pVqmR_3_ACTGAT
ΔvqmR + pBAD-vqmR
processed data file: VqmR_pulse_read_counts.xlsx

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3' adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4.
The trimmed reads were checked for quality and mapped to the V. cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1.
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 2.5 and a Bonerroni adjusted p-value < 1E-10 were considered to be differentially expressed.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: VqmR_pulse_read_counts.xlsx: Read count table and edgeR (exact mode) analysis.

organism: Vibrio cholerae

source_name: whole bacterial cells

growth_protocol: Vibrio cholerae C6706 ΔvqmR strains carrying pBAD-ctr or pBAD-vqmR plasmids were grown to exponential phase (OD600=0.5) in 100ml LB media containing 50µg/ml kanamycin. At this point, 0.2% L-arabinose was added to induce vqmR expression and cells were harvested 15minutes after induction.

extract_protocol:
RNA was isolated using Tri-reagent according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) according to the manufacturer's instructions, and tested using a Bioanalyzer.

treatment_protocol: The cells were treated with 0.2% L-arabinose in mid-exponential growth phase (OD600=0.5). After 15 minutes of treatment 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethanol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

tag: strain/background

value: <delta>vqmR + pBAD-vqmR

tag: growth phase

value: exponential

value: 0.2% L-arabinose


title: VqmR rep2

description:
dvqmR_pVqmR_2_GTCCGC
ΔvqmR + pBAD-vqmR
processed data file: VqmR_pulse_read_counts.xlsx


title: lgs301283_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

value: lymphoblastoid cell lines (LCLs)

tag: disease

tag: gender

tag: chip antibody

value: H3K4me1 (Abcam, #ab8895)


title: 101103430068_R01C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: VqmR rep1

description:
dvqmR_pVqmR_1_CCGTCC
ΔvqmR + pBAD-vqmR
processed data file: VqmR_pulse_read_counts.xlsx

tag: strain/background

tag: genotype/variation

tag: growth phase

tag: treatment


title: B.theta27

tag: host

tag: sample type

tag: molecule


title: control rep3 [dvqmR_pCtrl]

description:
dvqmR_pCtrl_3_GAGTGG
ΔvqmR + pBAD-ctr
processed data file: VqmR_pulse_read_counts.xlsx

value: <delta>vqmR + pBAD-ctr


title: lgs101293_H3K4me1 ChIP-seq

description: H3K4me1 ChIP-Seq experiment

tag: cell line

tag: disease

value: Systemic lupus erythematosus

tag: race

value: European-American

tag: gender

tag: chip antibody


title: B.theta28


title: 101103430068_R03C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

value: TT

tag: genocord

value: TC

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl


title: B.theta26

tag: treatment

value: metronidazole+ciprofloxacin, 4 weeks after colonization

tag: host

tag: sample type

tag: molecule

tag: genotype/variation

value: BT[delta]MAFF


title: lgs302096_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

source_name: H3K27ac ChIP-seq

tag: cell line

tag: disease

tag: race

tag: gender

value: Female

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: control rep2 [dvqmR_pCtrl]

description:
dvqmR_pCtrl_2_AGTTCC
ΔvqmR + pBAD-ctr
processed data file: VqmR_pulse_read_counts.xlsx

tag: strain/background

tag: growth phase


title: 100994770046_R06C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

value: CC

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: 100994770067_R03C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

value: AA

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl


title: 100994770067_R04C01

value: W

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah


title: lgs100524_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

tag: cell line

tag: disease

tag: gender

tag: chip antibody


title: 100994770046_R03C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

value: H

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: lgs302096_RNA-seq

description: processed data: Kallisto_expression_25cellLines_filtered_PEERnormalized+scaled_lengthScaledTPM.txt.gz

source_name: RNA-seq

tag: cell line

tag: disease


title: lgs100524_RNA-seq

tag: gender

tag: chip antibody


title: lgs000379_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: B.theta24

tag: treatment

tag: host

tag: sample type

value: fecal content

tag: molecule

tag: genotype/variation


title: lgs102943_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

tag: race


title: 100994770028_R04C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logmethioninebl

tag: loghomocysteinebl


title: B.theta25

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation