title: Adjacent normal tissues_patient3

city: Tianjin

first: Renjie

last: Wang

state: State...

address: No 220, Chenglin Road, Hedong strict.

institute: Pingjin Hospital

description: Biological replicate 3 of 3 Adjacent normal tissues_patient3

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3‐labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Adjacent normal tissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US). Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: All these tissues were immediately put in liquid nitrogen after removal from glioma patients, and stored in -80 °C until used.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease state

value: Adjacent normal

value: brain

tag: gender

value: female

tag: age

tag: Stage

value: IV glioma


title: Bile_WT_14

status: Public on Dec 25 2018

type: SRA

city: Nashville

first: Ryan

middle: M

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt University Medical Center

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2_sig.csv
miRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_Bile_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

library_source: transcriptomic

data_processing:
Analysis Pipeline: TIGER
https://www.biorxiv.org/content/early/2018/01/23/246900
Step 1: Pre-processing
To assess raw data quality, FastQC was performed at the raw read level to check for base quality, total read counts, and adapter identification. Cutadapt was then used to trim 3’ adapters from processed reads (-a TGGAATTCTCGGGTGCCAAGG). Cutadapt was then used to remove the first and last 4 bases from the trimmed reads and all trimmed reads <16 nts in length were removed (-m 16 -u 4 -u -4). After trimming, read length distributions were plotted and FastQC was performed on trimmed reads to validate the efficiency of adapter trimming. To generate identical read files, trimmed reads in each sample were collapsed into non-redundant “identical” reads in FASTQ format and copy numbers were recorded for downstream analysis.
Step 2: Host-Genome Alignment (Mouse)
In the Host Genome & Database alignment module, bowtie (v1.1.2) was used to map reads to a costumed database with option (-a -m 100 --best - strata -v 1) which allows 1 mismatch (MM) and 100 multi-mapped loci, and only the best matches were recorded. The costumed database was constructed by the host genome and known sequences of host mature transcripts curated in specific library databases – tRNAs (http://gtrnadb.ucsc.edu/GtRNAdb2/) and rRNA (http://archive.broadinstitute.org/cancer/cga/rnaseqc_download). Counting and differential expression analysis of miRNAs, tDRs, rDRs, snDRs, snoDRs, and other miscellaneous sRNAs (miscRNA), including yDRs and lincDRs, were performed. All prepossessed quality reads were assigned to different classes of annotated sRNAs using distinct rules -- miRNA: 1 MM, ≥16nt, offset -2, -1, 0, 1, 2 and tDR, snDRs, snoDRs, yDRs, and miscRNAs: 1 MM, ≥16nt, overlap ≥0.9 overlap. Based on the extensive genomic coverage of lncRNAs and repetitive elements and conservation of rRNAs, the TIGER pipeline applies more stringent assignment rules for lncDRs and rDRs – perfect match, ≥20 nt, and ≥90% overlap with parent lncRNAs or rRNAs. Furthermore, reads assigned to lncDRs must only be aligned to lncRNA coordinates and not to any other loci in the genome. All reads ≥20 nts in length and not aligned to the costumed database were extracted and tested for alignment as non-host reads. Differential expression of tabulated read counts were performed by DEseq2.
Step 3: Non-Host Alignment Module
Non-host reads were then analyzed using the Non-Host Genome and Non-Host Library modules in parallel. In the Non-Host Genome module, reads were aligned in parallel to two collections of bacterial genomes: a human microbiome (HMB) collection and a hand-curated list of environmental bacteria observed during sequencing of human and mouse lipoproteins. Due to high conservation between bacterial genomes and multi-mapping issues, a different bowtie option (-a -m 1000 --best -strata -v 0) was used which allowed perfect match only and 1000 multi-mapped loci. Reads were aligned to the HMB, ENV, and fungal groups in parallel and, thus, the same reads could have been counted in multiple groups. The fraction of reads that align to both databases (HMB, ENV) and the reads that are unique to specific databases were plotted. Differential expression and high-end analyses, as described above, were performed at the genome level (total normalized read count for each genome) and at the individual read level. In parallel, non-host reads were also analyzed by the Non-Host Library (Gold) module where they were aligned to non-coding RNA databases with same bowtie option as non-host genome analysis. To identify possible non-host miRNAs (xenomiRs) in sRNA-seq datasets, all non-host reads were aligned perfectly to annotated miRNAs in miRBase (miRBase.org) and tabulated. Similarly, non-host reads were aligned to all tRNAs in the GtRNAdb database (GtRNAdb2). Extensive categorical analysis of parent non-host tRNAs were performed at the kingdom, genome (species), amino acid, anti-codon, and fragment (read) levels. All assigned non-host tDRs underwent differential expression analysis, high-end analysis, and data visualization, as described above. Non-host reads were also aligned to prokaryotic and eukaryotic rRNA transcripts in SILVA database (https://www.arb-silva.de). TIGER limits the analysis of non-host rDR to the kingdom level for counting, differential expression analysis and high- end analysis.
Genome_build: mm9
Supplementary_files_format_and_content:
Identical.fastq files are fastq files that contain all reads that survive processing (Step 1),
Count files are comma separated value spreadsheets that list all annotated features (.count.txt) or fragment reads (read.count.txt) or total categorical counts (category.count.txt) for associated with a given category
CSV files are outputs from differential expression analysis using DeSeq2 comparing Wild-type vs SRBIKO

molecule: total RNA

organism: Mus musculus

growth_protocol: Conventional Housing

extract_protocol:
Plasma, basal bile, urine, and livers were collected from wild-type (WT) and SR-BI-deficient (B6;129S2-Scarb1tm1Kri/J, SR-BI KO) mice. Mice were anesthetized with urethane (1g/kg, i.p.). The common bile duct was ligated and the gall bladder cannulated to divert bile into collection tubes. Basal bile was collected for a period of 30 min. Mice were then exsanguinated, blood was collected from the abdominal aorta in EDTA coated tubes and placed on wet ice, and tissues were dissected and snap frozen in liquid nitrogen. Plasma and tissues were stored at -80oC prior to analysis.  All animal procedures were completed under active and approved IACUC protocols. To separate HDL and apolipoprotein B (APOB)-containing lipoproteins from mouse plasma, 200 µL of 0.22-µm filtered-plasma samples were diluted to 500 µL in size-exclusion chromatography (SEC) running buffer (10 mM Tris-HCl, 0.15 M NaCl, 0.2% NaN3) and injected an ÄKTA SEC system (GE Healthcare) with three in-series Superdex-200 Increase gel filtration columns (10/300 GL; GE Healthcare). Samples were applied to the column with a flow rate of 0.3 mL/min at room temperature and eluate collected as 72 x 1.5 mL fractions using a F9-C 96-well plate fraction collector (GE Healthcare). Each fraction was analyzed for total protein (BCA; Pierce), total cholesterol (Raichem), and triglycerides (Raichem) to identify fractions corresponding with HDL and APOB particles. Due to the SEC set-up, we were not able to separate VLDL from LDL particles, and thus, we collected fractions covering both lipoprotein classes, referred to here as APOB. Fractions corresponding with each lipoprotein group were pooled, concentrated with Amicon Ultra-4 10 kDa centrifugal filters (Millipore) to <200 µL volume, and protein concentrations were quantified by BCA assays (Pierce). Based on the distribution of total cholesterol, triglycerides, and protein, fractions corresponding to HDL and APOB were collected, pooled, and concentrated. To differentiate lipoprotein sRNA signatures from liver and biofluids, and determine the impact of SR-BI-deficiency, samples were collected from Scarb1-/- (SR-BI KO) and wild-type (WT) mice. Total RNA was extracted from HDL (WT N=7, SR-BI KO N=7) and APOB (WT N=7, SR-BI KO N=7) particles, as well as livers (WT N=7, SR-BI KO N=7), bile (WT N=7, SR-BI KO N=6), and urine (WT N=5, SR-BI KO N=6). RNA was isolated from equal inputs of either bile (volume), liver (mg), HDL (protein) or APOB (protein) using miRNAEasy Mini kits (Qiagen). Specifically, 30 µL of primary bile, 120 μg of APOB, 180 μg of HDL or 20 mg of liver were added to 1 mL of Qiazol. Livers were homogenized in Qiazol with High-Impact Zirconium beads using a Bead Bug Homogenizer (Benchmark Scientific).  After removal of beads, subsequent steps for liver RNA extraction were followed according to manufacturer’s protocol. Bile, APOB and HDL RNA isolations were processed according to manufacturer’s protocol, except that after addition of ethanol, samples were incubated at -80oC overnight before application to isolation columns, and were eluted with a volume of 50 μL. Liver RNA samples were quantified by Take3 plates (BioTek).
NEXTflex Small RNA Library Preparation Kits v3 for Illumina® Platforms (BioO Scientific) were used to generate cDNA libraries for sRNA-seq. Briefly, 1 µg of liver total RNA was used as input for adapter ligation, as per manufacturer’s protocol. For bile, APOB and HDL RNA, 10.5 μL (21%) of the RNA isolation eluate was used as input for adapter ligation. Library generation was performed according to manufacturer’s protocol (BioO Scientific) with a modification to the amplification step, as liver libraries received 18 cycles and bile, APOB and HDL libraries received 25 cycles. After amplification, samples were size-selected using a Pippin-Prep (Sage Science) -- set for a range of 135-200 nts in length -- and subsequently purified and concentrated using DNA Clean and Concentrator 5 kit (Zymo). Individual libraries were then screened for quality by High-Sensitivity DNA chips using a 2100 Bioanalyzer (Agilent) and quantified using High-Sensitivity DNA assays with Qubit (Life Technologies). Equal concentrations of all individual libraries were pooled for multiplex sequencing runs, and concentrated using DNA Clean and Concentrator 5 kit (Zymo). For rigor in down-stream comparisons, all 66 sequencing libraries were randomized and run independently on three individual sequencing lanes. Single-end sequencing (75 cycles) of multiplexed libraries were performed on an Illumina NextSEQ 500 at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core laboratory. Each library was sequenced at an average depth of 16.28 million reads/sample.

tag: strain background

tag: genotype/variation

value: WT

tag: animal id#

tag: tissue

value: Bile

tag: barcode


title: HDL_SRBIKO_4

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
miRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_HDL_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

value: SRBIKO; Srbi-/-

value: HDL


title: Bile_SRBIKO_13


title: Bile_WT_10


title: Urine_WT_14

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
miRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

value: Urine


title: Urine_SRBIKO_13


title: Bile_WT_12


title: Liver_SRBIKO_13

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
miRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_Liver_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

value: Liver


title: Liver_WT_14


title: Liver_WT_12


title: Adjacent normal tissues_patient2

status: Public on Dec 26 2018

type: RNA

country: China

description: Biological replicate 2 of 3 Adjacent normal tissues_patient2

organism: Homo sapiens

value: male


title: Liver_SRBIKO_11


title: Liver_WT_10


title: Adjacent normal tissues_patient1

description: Biological replicate 1 of 3 Adjacent normal tissues_patient1


title: GBM tissues_patient3

description: Biological replicate 3 of 3 GBM tissues_patient3

source_name: GBM tissue

value: GBM


title: GBM tissues_patient1

description: Biological replicate 1 of 3 GBM tissues_patient1


title: APOB_WT_14

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
miRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_APOB_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

value: APOB


title: APOB_WT_12


title: GBM tissues_patient2

description: Biological replicate 2 of 3 GBM tissues_patient2


title: APOB_SRBIKO_11


title: APOB_WT_10


title: APOB_WT_5


title: APOB_SRBIKO_7


title: HDL_WT_10


title: APOB_SRBIKO_6


title: HDL_WT_5


title: Urine_WT_8


title: Urine_SRBIKO_9


title: Bile_SRBIKO_7


title: Bile_SRBIKO_9


title: HDL_SRBIKO_9


title: Bile_WT_8


title: HDL_WT_8


title: HDL_WT_14


title: Urine_SRBIKO_11


title: Urine_SRBIKO_7


title: Urine_SRBIKO_6


title: Urine_WT_5


title: Liver_SRBIKO_9


title: Liver_WT_8


title: Liver_SRBIKO_6


title: APOB_SRBIKO_9


title: Bile_SRBIKO_6


title: Liver_SRBIKO_7


title: HDL_SRBIKO_6


title: APOB_WT_1


title: APOB_SRBIKO_4


title: APOB_WT_3


title: HDL_WT_3


title: APOB_SRBIKO_2


title: HDL_SRBIKO_2


title: HDL_WT_1


title: Bile_SRBIKO_4


title: Bile_WT_5


title: Bile_SRBIKO_2


title: Bile_WT_3


title: Urine_WT_3


title: APOB_SRBIKO_13


title: Bile_WT_1


title: Liver_WT_5


title: HSR-GBM1+5azacitidine replicate 3

type: genomic

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

description: Genomic DNA extracted from HSR-GBM1cells and the cells treated with vitamin C/5-azacitidine were genotyped using Infinium Global Screening Array-24 (Illumina).

hyb_protocol: The fragmented, resuspended DNA was loaded onto a BeadChip and incubated for 18 hours at 48°C. After incubation, single-base extension and allele-specific staining was performed on a Te-Flow Chamber Rack (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining, the BeadChip was coated with XC4/EtOH, dried in a vacuum desiccator for approximately 1 hour and scanned on an iScan System (Illumina) using the Infinium LCG scan setting.

data_processing: DNA samples were genotyped using Infinium Global Screening Array-24 (Illumina). Data were analyzed usign GenomeStudio 2.0 Genotyping Module (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Glioblastoma

label_protocol: Approximately 200ng of genomic DNA was whole-genome amplified using neutralisation mix (MA2) and amplification master mix (MSM) and incubated for 22 hours at 37°C. After incubation, the amplified DNA was fragmented with fragmentation solution (FMS), precipitated with precipitation solution (PM1) and 2-propanol and resuspended in resuspension/hybridisation solution (RA1).

growth_protocol: HSR-GBM1 cells were cultured as neurospheres on ultra-low attachment plates (Sigma) in Dulbecco's Modified Eagle Medium /Nutrient Mixture (DMEM/F-12) Media (Gibco) containing 2% StemPro neural supplement (Invitrogen Life Technologies), 20 ng/ml basic fibroblast growth factor (bFGF; Millipore) and 20 ng/ml epidermal growth factor (EGF; Millipore) at 37 °C, 5% CO2 and 95% humidity.

extract_protocol: Total genomic DNA were extracted from cultured cell pellets using the ISOLATE II Genomic DNA Kit (Bioline) according to manufacturer’s protocols . The DNA samples were treated with 3 μL of RNase solution (Qiagen) and Proteinase K Solution (20 μg/μL; Qiagen) at 65 °C for 10 minutes.

treatment_protocol: HSR-GBM1 cells were cultured in the presence of 0.5 μM of 5-azacytidine (Sigma-Aldrich) for 48 hours or 100 μg/mL of Vitamin C (L-ascorbic acid, Sigma-Aldrich) for 72 hours. Culture media was changed every 24 hours.

value: Male

value: brain tumor

value: Glioblastoma

tag: cell line


title: Liver_WT_1


title: Liver_WT_3


title: HDL_SRBIKO_11


title: 2N

city: shanghai

first: wang

last: yu

address: zhizaoju Road NO.639

institute: Shanghai Ninth People’s Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and Homo sapiens genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: normal salivary gland tissues

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
miRNA Library Construction and RNA Sequencing:  The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA library had been size selected by PAGE Gel electrophoresis for miRNA sequencing. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

value: normal salivary gland tissues


title: 1N


title: 2T

source_name: salivary adenoid cystic caricnoma

value: salivary adenoid cystic caricnoma


title: 3N


title: 3T


title: HDL_SRBIKO_7


title: 1T


title: Urine_SRBIKO_2


title: 18_16wk_ASNase

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers, The State University of New Jersey

data_processing:
RNA sequencing reads were aligned with TopHat (version 2.0.9). Differential gene analysis and discovery of new transcripts was performed by DESeq2.
Genome_build: Mus musculus, GRCm38 mm10
Supplementary_files_format_and_content: The matrix of read count was produced using DESeq2 pipeline on the BAM files generated with the TopHat software

molecule: polyA RNA

source_name: Liver

growth_protocol: 2, 8, and 16 week old mice

extract_protocol:
Total RNA was extracted from the frozen murine livers using TriReagent protocol. Liver RNA from 2 and 16 week old mice were sent Sulzberger Columbia Genome Center for cDNA library preparation and sequencing at the same time as liver RNA from 8 week old mice (GSE92364).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were once daily intraperitoneally injected with either L-asparaginase (Elspar) at 3 international units per gram body weight or equivolume phosphate buffered saline for 7 days for 2 and 16 week old mice and for 8 day for 8 week old mice.  Mice were injected in the morning each day (~8:00 AM) and were killed by decapitation 7.5 hours later.

value: 16 week old

tag: Sex

value: Female

tag: treatment

value: 7 daily injections of asparaginase

tag: genetic background


title: 16_16wk_ASNase


title: Liver_SRBIKO_2


title: HSR-GBM1 untreated replicate 2


title: 17_16wk_ASNase


title: HSR-GBM1+Vitamin C replicate 3


title: 14_8wk_ASNase

description: same as GSM2428120

value: 8 week old

value: 8 daily injections of asparaginase


title: APOB_WT_8

value: WT


title: TT_Input

city: Columbus

first: Matthew

last: Ringel

state: Oh

address: 565 McCampbell Hal

department: Division of Endocrinology, Diabetes, and Metabolism

institute: The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center

library_source: genomic

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1e-5.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: TT medullary thyroid cancer cells

growth_protocol: Cells were cultured in RPMI media supplemented with 20% heat-inactivated FBS, 1% non-essential amino acids, and 1% glutamine, at 37deg celcius and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500/NextSeq 500.

value: TT medullary thyroid cancer cells

tag: chip antibody


title: 15_8wk_ASNase

description: same as GSM2428121


title: TT_BRD4


title: 13_8wk_ASNase

description: same as GSM2428119


title: 10_16wk_PBS

value: 7 daily injections of PBS


title: 12_16wk_PBS

value: Liver


title: HSR-GBM1+5azacitidine replicate 1


title: 09_8wk_PBS

description: same as GSM2428118

value: 8 daily injections of PBS


title: 11_16wk_PBS


title: 08_8wk_PBS

description: same as GSM2428117


title: 05_2wk_ASNase

value: 2 week old


title: 04_2wk_ASNase


title: HSR-GBM1 untreated replicate 3


title: HSR-GBM1+Vitamin C replicate 2


title: 03_2wk_PBS


title: 07_8wk_PBS

description: same as GSM2428116


title: HSR-GBM1+5azacitidine replicate 2


title: 01_2wk_PBS


title: 02_2wk_PBS


title: 06_2wk_ASNase


title: HSR-GBM1+Vitamin C replicate 1


title: PD09

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter.
Additional quality filtering used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to keep only reads that have at least 80% of bases with a quality score of 20 or more (conducted by fastq_quality_filter function) and reads left with 10 bases or longer after being end-trimmed with a base quality score of 20 (conducted by fastq_quality_trimmer function).
A bowtie2 index was built for the mouse reference genome (GRCm38) using bowtie version 2.1.0. The RNA-seq reads of each of the 38 samples were mapped using Tophat version 2.0.9(Trapnell and Salzberg, 2009) supplied by Ensembl annotation file; GRCm38.78.gtf. Gene expression values were computed using fragments per kilo base per million mapped reads (FPKM) values.
Differential gene expression was determined using Cuffdiff tool which is available in Cufflinks version 2.2.1(Trapnell et al., 2010) supplied by GRCm38.78.gtf.
Normalization was performed via the median of the geometric means of fragment counts across all libraries, as described in(Anders and Huber, 2010). Statistical significance was assessed using a false discovery rate (FDR) threshold of 0.05.
Genome_build: mm10

source_name: Splenocytes

growth_protocol: The transgenic B6.Sle1b.IFNaR1-/- mice and B6.Sle1b control mice were bred on the wild-type C57BL/6J background. All mice were maintained on an ad libitum feeding.

extract_protocol:
Single cell suspensions were obtained total splenocytes  in aged (6Mo) mice. Single cell suspensions from spleens were placed at 4C and then surface stained in FACS buffer (1X PBS with 3% BSA) containing fluorochrome-conjugated monoclonal antibodies and then stained with a fixable viability dye prior to fluorescence activated cell sorting (FACs). Germinal Center B cells (GC B cells) were defined as Live/Dead-neg, B220-pos, GL7-pos and CD95-pos, whereas non-germinal center B cells (Non-GC B cells) were defined as Live/Dead-neg, B220-pos, GL7-neg, CD95-neg.  All FACS-sorting was performed using a FACSAria (BD) High Speed cell sorter. Cells were sorted directly into Trizol reagent to isolate RNA for further RNA-sequencing (RNA-seq).   RNA was phase separated using chloroform and the aqueous phase containing RNA was removed following centrifugation and precipitated overnight at -20C using ice cold isopropanol. RNA was washed with 75% ethanol then solubilized in RNase-free water. Optical density values of extracted RNA were measured using NanoDrop (Thermo Fisher Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was measured using BioAnalyzer (Agilent) RNA 6000 Pico Kit to confirm RIN above 7. The cDNA libraries were prepared using the SMARTer® Ultra® Low Input RNA Kit for Sequencing - v3 (Clontech) followed by Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
Single cell suspensions were obtained total splenocytes  in aged (6Mo) mice. Single cell suspensions from spleens were placed at 4C and then surface stained in FACS buffer (1X PBS with 3% BSA) containing fluorochrome-conjugated monoclonal antibodies and then stained with a fixable viability dye prior to fluorescence activated cell sorting (FACs). Germinal Center B cells (GC B cells) were defined as Live/Dead-neg, B220-pos, GL7-pos and CD95-pos, whereas non-germinal center B cells (Non-GC B cells) were defined as Live/Dead-neg, B220-pos, GL7-neg, CD95-neg.  All FACS-sorting was performed using a FACSAria (BD) High Speed cell sorter. Cells were sorted directly into Trizol reagent to isolate RNA for further RNA-sequencing (RNA-seq).   RNA was phase separated using chloroform and the aqueous phase containing RNA was removed following centrifugation and precipitated overnight at -20C using ice cold isopropanol. RNA was washed with 75% ethanol then solubilized in RNase-free water. Optical density values of extracted RNA were measured using NanoDrop (Thermo Fisher Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was measured using BioAnalyzer (Agilent) RNA 6000 Pico Kit to confirm RIN above 7. The cDNA libraries were prepared using the SMARTer® Ultra® Low Input RNA Kit for Sequencing - v3 (Clontech) followed by Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
Single cell suspensions were obtained total splenocytes  in aged (6Mo) mice. Single cell suspensions from spleens were placed at 4C and then surface stained in FACS buffer (1X PBS with 3% BSA) containing fluorochrome-conjugated monoclonal antibodies and then stained with a fixable viability dye prior to fluorescence activated cell sorting (FACs). Germinal Center B cells (GC B cells) were defined as Live/Dead-neg, B220-pos, GL7-pos and CD95-pos, whereas non-germinal center B cells (Non-GC B cells) were defined as Live/Dead-neg, B220-pos, GL7-neg, CD95-neg.  All FACS-sorting was performed using a FACSAria (BD) High Speed cell sorter. Cells were sorted directly into Trizol reagent to isolate RNA for further RNA-sequencing (RNA-seq).   RNA was phase separated using chloroform and the aqueous phase containing RNA was removed following centrifugation and precipitated overnight at -20C using ice cold isopropanol. RNA was washed with 75% ethanol then solubilized in RNase-free water. Optical density values of extracted RNA were measured using NanoDrop (Thermo Fisher Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was measured using BioAnalyzer (Agilent) RNA 6000 Pico Kit to confirm RIN above 7. The cDNA libraries were prepared using the Ovation RNA-seq System V2 (NuGEN, San Carlos, CA) as per the manufacturer’s instructions.  The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies) and then loaded onto TruSeq SR v3 flow cells on an Illumina HiSeq 2500 (Illumina, San Diego, CA) and run for 100 cycles using a paired-read recipe (TruSeq SBS Kit v3, Illumina) according to the manufacturer's instructions.

treatment_protocol: Spleens were isolated from aged female mice (6Mo old) of the indicated genotypes. Non-germinal center and germinal center B cells were sorted from total splenocyte pools. Only female mice were used for all experiments; all mice were sex- and age-matched to control mice.

value: Splenocytes

tag: cell type

value: Non-germinal center B cells (B220+GL7-CD95-)

tag: genotype

value: F

tag: strain


title: PD19


title: TS193_Teff4

city: San Francisco

first: Hsin-Wen

last: Chang

state: CA

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

description:
TS193_Teff4_L3
TS193_Teff4_STAR.cufflinks

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and were aligned to UCSC GRCm38/mm10 reference genome with STAR software (2.4.2a)
SAM files were generated with SAMtools from alignment results
Read counts were obtained with htseq-count (0.6.1p1) with the union option
Differential expression was determined using the R/Bioconducter package DESeq2
FPKM table was generated using Cufflink(2.2.1)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Cutaneous Teff cells_SPF

growth_protocol: Specific-pathogen-free newborn C57BL6 mice were colonized with either strains Staphylococcus epidermidis Tü3298 and Staphylococcus aureus SF8300 starting on day 3 of life and every other day thereafter until post-natal day 19 by pipetting 100 μl of bacterial suspension onto their skin and distributing evenly using a sterile PBS-soaked cotton-tipped swab.

extract_protocol:
RNA isolation was performed by Expression Analysis Q2 Solutions using QIAGEN RNeasy Spin columns and was quantified via Nanodrop ND-8000 spectrophotometer. RNA quality was checked by Agilent Bioanalyzer Pico Chip.
The SMARTer Ultra Low input kit was used to generate cDNA libraries

treatment_protocol: To isolate skin T cells for staining and FACS sorting, mice were sacrificed at 21 days of age and the entire trunk skin harvested and lightly defatted. Skin was then minced with scissors and re-suspended in a 50ml conical with 1-2 ml of digestion media comprised of 2mg/ml collagenase XI, 0.5mg/ml hyaluronidase and 0.1 mg/ml DNase in RPMI with 1% HEPES, 1% penicillin-streptomycin and 10% fetal calf serum. This mixture was incubated in a shaking incubated at 37°C at 250 rpm for 45 min. An additional 15 ml of RPMI/HEPES/P-S/FCS media was then added and the 50 ml conical was shaken vigorously by hand for 30 s. Another 15 ml of media was added and then the entire suspension was filtered through a sterile 100 mm cell strainer followed by a 40 mm cell strainer into a new 50 ml conical. The suspension was then pelleted and the cell pellet was re-suspended in sort buffer (RPMI, 2 mM EDTA, 25mM HEPES, 2% FBS) with U/ml RiboLock RNase inhibitor (Thermo Scientific) for staining for 30 min at 4°C with fluorophore-conjugated antibodies specific for CD3, CD4, CD8, CD25, CD45, ICOS, TCRβ, and Tonbo Live-dead Ghost Dye. Teff (Live, CD45+, CD3int, CD4+, CD8neg, TCRβ+ CD25neg, ICOSneg) cells were then isolated via cell sorting on a MoFlo XDP (Beckman Coulter) in the UCSF Flow Cytometry Core. Cells were pelleted and flash frozen.

value: post natal day 21

tag: bacteria colonized

value: no additional colonization (SPF)

value: cutaneous CD4+ T effector cells


title: TS193_Teff3

description:
TS193_Teff3_L7.N712
TS193_Teff3_STAR.cufflinks

source_name: Cutaneous Teff cells_SE+SPF

value: early colonization of S. epidermidis (SE+SPF)


title: PD31

value: Germinal center B cells (B220+GL7+CD95+)


title: PD20


title: PD21


title: PD12


title: PD29


title: PD10


title: TT_H3K27Ac

value: H3K27Ac (Active Motif, cat:39133, lot:8)


title: PD28


title: PD30


title: TS190_Teff6

description:
TS190_Teff6_L7.N709
TS190_Teff6_STAR.cufflinks

source_name: Cutaneous Teff cells_SA+SPF

value: early colonization of S. aureus (SA+SPF)


title: PD22


title: PD11


title: TS190_Teff5

description:
TS190_Teff5_L7.N708
TS190_Teff5_STAR.cufflinks


title: TS193_Teff6

description:
TS193_Teff6_L7.N703
TS193_Teff6_STAR.cufflinks


title: TS190_Teff4

description:
TS190_Teff4_L6.N707
TS190_Teff4_STAR.cufflinks


title: TS193_Teff1

description:
TS193_Teff1_L7.N710
TS193_Teff1_STAR.cufflinks


title: Liver_SRBIKO_4

value: SRBIKO; Srbi-/-


title: TS190_Teff2

description:
TS190_Teff2_L6.N706
TS190_Teff2_STAR.cufflinks


title: HSR-GBM1 untreated replicate 1

tag: gender

value: Male

value: brain tumor

tag: disease state

value: Glioblastoma


title: TS193_Teff5

description:
TS193_Teff5_L7.N702
TS193_Teff5_STAR.cufflinks

tag: age


title: TS189_Teff2

description:
TS189_Teff2_L6.N704
TS189_Teff2_STAR.cufflinks


title: TS189_Teff1

description:
TS189_Teff1_L6.N703
TS189_Teff1_STAR.cufflinks


title: Urine_WT_1

description:
Small RNA Seq-fastq, demultiplexed, NextFlex V3
processed data file:
ENV_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
Fungus_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
HMB_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_rRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
ex_tRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
isomiR_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
miRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
othersRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
rRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snoRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
snRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
tRNA_Urine_SRBIKO_vs_WT_detectedInBothGroup_min5_DESeq2.csv
bacteria_group1_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group1_pm_KCV_3018_77_78_79.read.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.category.count.txt
bacteria_group2_pm_KCV_3018_77_78_79.read.count.txt
fungus_group4_pm_KCV_3018_77_78_79.category.count.txt
fungus_group4_pm_KCV_3018_77_78_79.read.count.txt
KCV_3018_77_78_79.Category.Table.csv
rRNA_pm_KCV_3018_77_78_79.count.txt
tRNA_pm_KCV_3018_77_78_79.read.count.txt
tRNA_pm_KCV_3018_77_78_79.category.count.txt
tRNA_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.count.txt
miRBase_pm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.isomiR.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.base.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.NTA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.miRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.count.txt
smallRNA_1mm_KCV_3018_77_78_79.other.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.rRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snoRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.snRNA.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.aminoacid.read.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.count.txt
smallRNA_1mm_KCV_3018_77_78_79.tRNA.NTA.count.txt
rRNA_pm_KCV_3018_77_78_79.read.count.txt

tag: strain background

value: WT

value: Urine


title: TS180_Teff3

description:
TS180_Teff3_L6.N701
TS180_Teff3_STAR.cufflinks

value: specific pathogen free (SPF)


title: TS180_Teff4

description:
TS180_Teff4_L6.N702
TS180_Teff4_STAR.cufflinks


title: TS193_Teff2

description:
TS193_Teff2_L7.N711
TS193_Teff2_STAR.cufflinks


title: TS190_Teff1

description:
TS190_Teff1_L6.N705
TS190_Teff1_STAR.cufflinks


title: set2, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 8a

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b+_8a

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the standard Ensembl gtf annotation and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.1.1.
htseq-count (authored by Simon Anders) was used in union mode to assign tophat-aligned reads to gene entries in the standard Ensembl gtf annotation supplied with the bowtie2 iGenome.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
For downstream analysis, mRNAs were filtered at 1 cpm (read per million aligned reads). Batch-correction was performed via edgeR / limma-voom using batch as a blocking factor.
Genome_build: GRCm38 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene.  The file labeled ‘depth-normalized_batch-corrected_cpm-filtered’ contains adjusted htseq-count values used in a manuscript submitted in conjunction with this study.

source_name: Myocardial DTR transgenic, no DT, no PFD

extract_protocol:
myocardial CD19+ cells were FACS sorted directly into lysis buffer and RNA was extracted with the Zymo Research QuickRNA MicroPrep (Zymo Research, Irvine, CA, USA), according to the manufacturer’s instructions
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using duty cycle 10, intensity 5, cycles/burst 200, time 180 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
non-strand-specific, single-end RNA-Seq

value: FACS-sorted myocardial B cells

tag: cd19 status

tag: cd11b status

value: no DT, no PFD

tag: study batch


title: set2, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 8a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b-_8a


title: preB_1

city: Baltimore

first: Alan

middle: D

last: Friedman

state: MD

address: 1650 Orleans St.

department: Oncology

institute: Johns Hopkins University

hyb_protocol: 0.825 ug of each Cy3-labeled sample was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

scan_protocol: Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software.  Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

data_processing: Agilent FE processed signal intensities were imported into GeneSpring GX 10 (Agilent Technologies). Normalization was done by setting intensity thresheld to 5 and log2 transformation.

source_name: Cebpa-Enh prom mouse preB replicate 1

label_protocol: Sample amplification and labeling  were carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The labeled cRNA were purified using RNeasy mini kit (Qiagen).

extract_protocol: RNA from hematopoietic cells was prepared using NucleoSpin RNA II, with use of RNase-free DNase (Machery-Nagel)

tag: tissue

value: bone marrow

value: female

value: 16 weeks

tag: genotype/variation

value: preB


title: preproB hCD4-_2

source_name: Cebpa-Enh prom mouse preproB hCD4- replicate 2

value: hCD4- preproB


title: proB hCD4-_1

source_name: Cebpa-Enh prom mouse proB hCD4- replicate 1

value: hCD4- proB


title: WT-biofilm-replicate2

city: Tokyo

first: Shinya

last: Sugimoto

address: 3-25-8 Nishi-Shimbashi

department: Department of Bacteriology

country: Japan

institute: The Jikei University School of Medicine

description: Gene expression under biofilm growth conditions

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to E.coli Gene Expression Microarray, 8x15K (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Escherichia coli

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp WT Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: All overnight cultures were grown in LB at 30°C with shaking. Aliquots (5 μl) of the cultures were diluted into 5 ml fresh YESCA medium in 6-well plate and grown for 48 hours at 30°C.

extract_protocol: Total RNA extraction was carried out based on the protocols given in the manual of QIAGEN - RNAprotect Bacteria Reagent Handbook, QIAGEN - RNeasy Mini Kit and QIAGEN - RNase-free DNase set. The concentration of each RNA sample was measured by Agilent 2100 BioAnalyzer.

value: wild type

tag: culture duration

tag: growth condition

value: biofilm


title: set2, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 7a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b+_7a

tag: treatment


title: proB hCD4+_1

source_name: Cebpa-Enh prom mouse proB hCD4+ replicate 1

value: hCD4+ proB


title: KO-biofilm-replicate1


title: KO-biofilm-replicate2


title: proBhCD4-_2

source_name: Cebpa-Enh prom mouse proB hCD4- replicate 2


title: GMP hCD4+_1

source_name: Cebpa-Enh/prom mouse GMP hCD4+ replicate 1

value: hCD4+ GMP


title: preproB_rep2

description: Gene expression, no deletion

source_name: preproB replicate 2

extract_protocol: cells were sorted into Trizol, chloroform extracted, and upper phase added to equal volume ethanol and then applied to RNA Clean and Concentrator-5 (Zymo Research) columns and Eluted with 15 ml water to isolate RNA.

treatment_protocol: pIpC 300 mg s.q. every other day for 3 doses, then wait 5 wks to isolate marrow and then preproB cells

value: male

value: 24 wks

value: with the +37 kb Cebpa enhancer


title: proB hCD4+_2

source_name: Cebpa-Enh prom mouse proB hCD4+ replicate 2


title: WT TFH, biological rep1

city: Chongqing

first: Xiangyu

last: Chen

address: 30 Gaotanyan Street

department: Institute of Immunology, PLA

institute: Third Military Medical University

description: Gene expression data from TFH cells in spleen of WT mice at day 8-post LCMV Armstrong infection

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

source_name: WT mice, LCMV Armstrong D8

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Spleen

value: WT

value: follicular T helper cells

tag: time-point

value: day 8-post LCMV Armstrong infection


title: WT TFH, biological rep2

tag: cell type


title: preproB hCD4+_1

source_name: Cebpa-Enh prom mouse preproB hCD4+ replicate 1

value: bone marrow

value: hCD4+ preproB


title: SIPA1_ChIPSeq

city: Wuhan

first: Li

last: Su

state: -- None selected --

address: 1037 Luoyu Road

department: College of Life Science and Technology

institute: Huazhong University of Science and Technology

data_processing:
Illumina 1.9 software used for basecalling.
Linker sequence and low quality reads were removed by using fastx (version:0.0.13) software.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie (version: 0.12.8) software.
Peaks were analised by using MACS (version:1.4.2) software.
Genome_build: hg19
Supplementary_files_format_and_content: SIPA1CHIP_macs_peaks.xls includes the peaks information about position, length, p-value and fold enrichment.

source_name: breast cancer cell

growth_protocol: Human breast cancer cell line MDA-MB-231 was routinely cultured (typically 2–3 × 106 cells into a T75 flask) in RIPM-1640 medium (Gibco, USA) supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and SIPA1-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: MDA-MB-231 cell line

tag: chip antibody

value: SIPA1 (Santa Cruz SC-137043)


title: preproB_EnhDel_rep1

description: Gene expression, enhancer deletion

source_name: preproB Cebpa enhancer-deleted replicate 1

tag: strain

value: without the +37 kb Cebpa enhancer


title: preB_2

source_name: Cebpa-Enh prom mouse preB replicate 2

tag: gender

value: female

value: 16 weeks

value: preB


title: preproB hCD4+_2

source_name: Cebpa-Enh prom mouse preproB hCD4+ replicate 2


title: EZH2-null TFH, biological rep1

description: Gene expression data from TFH cells in spleen of EZH2-null mice at day 8-post LCMV Armstrong infection

source_name: EZH2-null mice, LCMV Armstrong D8

tag: genotype


title: preproB_EnhDel_rep2

description: Gene expression, enhancer deletion

source_name: preproB Cebpa enhancer-deleted replicate 2

tag: age


title: EZH2-null TFH, biological rep2


title: WT-biofilm-replicate1

value: wild type

value: biofilm


title: set2, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 7a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b-_7a

source_name: Myocardial DTR transgenic, no DT, no PFD

value: FACS-sorted myocardial B cells

value: no DT, no PFD


title: preproB hCD4-_1

source_name: Cebpa-Enh/prom mouse preproB hCD4- replicate 1

value: hCD4- preproB


title: GMP hCD4+_2

source_name: Cebpa-Enh/prom mouse GMP hCD4+ replicate 2

value: hCD4+ GMP


title: preproB_rep1

description: Gene expression, no deletion

source_name: preproB replicate 1

value: 26 wks

value: with the +37 kb Cebpa enhancer


title: set2, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 6a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b+_6a


title: SB20

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

description: NXTGNTpool18_index6_GCCAAT_L008_R*_001_AC0P9YACXX.filt

data_processing:
Data were mapped using BOWTIE.
For each nucleotide, the amount of mapped fragments was considered (= coverage).
Data files were compressed by merging neighbouring nucleotides with equal coverages into single rows, with indication of start and end position of nucleotides with that specific coverage.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MBD2.txt containing resp. region id, version, Ensembl gene id, Entrez Gene id, gene label, gene description, chromosome, begin position, end position (nucleotide), location, location info, middle difference and amount of mapped fragments per sample.

source_name: Control_mammary gland

extract_protocol:
DNA extracted extracted using the Invitrogen PureLink Genomic DNA Mini kit. ). Briefly, 50-85 mg of manually dissected glandular tissue was lysed with proteinase K (20 g/L) for 4 h at 55 °C and 300 rpm. The lysate was centrifuged (3 min at 17968 g, room temperature) and treated with RNase A (20 g/L in 50 mM Tris-HCl (pH 8.0), 10 mM EDTA; 2 min at room temperature). The sample was purified through a silica-based membrane and gDNA was eluted twice with 50 µL of water. DNA quantity and fragment length were measured using Qubit dsDNA HS assay (Invitrogen, Merelbeke, Belgium) and 1% agarose gelelectrophoresis, respectively, and all samples were diluted to a final concentration of 500 ng gDNA/75 µL water.
MBD2 protein methyl-CpG binding domain

tag: subject status

value: generally healthy Belgian or Dutch volunteer

tag: disease

tag: dietary treatment group

value: Control

value: mammary gland


title: SB17

description:
NXTGNTpool17_index1_ATCACG_L007_R*_001_AC0P9YACXX.filt
Technical replicate

source_name: Soymilk_mammary gland

value: Soymilk


title: SB22

description: NXTGNTpool18_index8_ACTTGA_L008_R*_001_AC0P9YACXX.filt


title: SB18

description: NXTGNTpool17_index2_CGATGT_L007_R*_001_AC0P9YACXX.filt


title: SB21

description: NXTGNTpool18_index7_CAGATC_L008_R*_001_AC0P9YACXX.filt


title: SB19

description: NXTGNTpool18_index5_ACAGTG_L008_R*_001_AC0P9YACXX.filt


title: set2, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 6a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b-_6a

tag: cd19 status

tag: cd11b status

tag: study batch


title: SB15

description: NXTGNTpool17_index11_GGCTAC_L007_R*_001_AC0P9YACXX.filt

tag: tissue


title: SB14

description: NXTGNTpool17_index10_TAGCTT_L007_R*_001_AC0P9YACXX.filt


title: SB16

description: NXTGNTpool17_index12_CTTGTA_L007_R*_001_AC0P9YACXX.filt


title: SB12

description: NXTGNTpool16_index8_ACTTGA_L006_R*_001_AC0P9YACXX.filt


title: SB11

description: NXTGNTpool16_index7_CAGATC_L006_R*_001_AC0P9YACXX.filt


title: set2, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 5a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b-_5a


title: SB10

description: NXTGNTpool16_index6_GCCAAT_L006_R*_001_AC0P9YACXX.filt


title: SB8

description: NXTGNTpool16_index4_TGACCA_L006_R*_001_AC0P9YACXX.filt


title: set2, Myocardial DTR transgenic, CD19+CD11b-, DT-treated, 2

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_DTR_CD19+CD11b-_2

source_name: Myocardial DTR transgenic, DT-treated

value: DT-treated


title: set2, Myocardial DTR transgenic, CD19+CD11b+, DT-treated, 2

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_DTR_CD19+CD11b+_2


title: SB4

description: NXTGNTpool15_index12_CTTGTA_L005_R*_001_AC0P9YACXX.filt


title: SB5

description: NXTGNTpool15_index1_ATCACG_L005_R*_001_AC0P9YACXX.filt


title: SB2

description: NXTGNTpool15_index10_TAGCTT_L005_R*_001_AC0P9YACXX.filt


title: SB6

description: NXTGNTpool15_index2_CGATGT_L005_R*_001_AC0P9YACXX.filt


title: SB7

description: NXTGNTpool15_index3_TTAGGC_L005_R*_001_AC0P9YACXX.filt


title: set2, Myocardial DTR transgenic, CD19+CD11b-, DT-treated, 1

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_DTR_CD19+CD11b-_1


title: set1, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 8

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b-_8


title: SB13

description: NXTGNTpool16_index9_GATCAG_L006_R*_001_AC0P9YACXX.filt


title: SB1

description: NXTGNTpool14_index9_GATCAG_L003_R*_001_AC0P9YACXX.filt


title: set1, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 6

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b-_6


title: SP4_RRBS

city: Auckland

first: Teena

last: Gamage

state: Scotland

country: New Zealand

institute: Grafton

data_processing:
Single-end (100bp) sequencing using Illumina HiSeq2000
Reads were aligned to human GRCh37 reference genome assembly using  Bismark aligner
bam files were sorted and Bismark methylation extractor  was used to determine DNA methylation status and to yield CpG report files
Analysis of these report files was performed with R package “methylKit”
Genome_build: human GRCh37
Supplementary_files_format_and_content: CpG report files

source_name: Hoechst-low side-population

extract_protocol:
DNA was extracted using Qiagen DNA Mini Kit (Qiagen, Germany)
RRBS was undertaken on 500ng of DNA per sample as previously described (Chatterjee et al., 2012a). MspI  restriction enzyme was used in the RRBS library preparation  with one size selection step (150-325bp). Libraries were amplified with 15–18 cycles.

value: First Trimester Placenta (villous tissue)

tag: gestation

value: 8.2 weeks

tag: facs isolation characteristic

value: Hoechst-low side-population


title: CTB4_RRBS

source_name: B4 integrin positive

value: B4 integrin positive


title: SP2_RRBS

value: 8.0 weeks


title: set1, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 4

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b-_4

tag: treatment


title: set2, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 5a

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_naive_CD19+CD11b+_5a

tag: cell type


title: EVT4_RRBS

source_name: HLA-G positive

value: HLA-G positive


title: set1, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 3

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b+_3

value: FACS-sorted myocardial B cells


title: set2, Myocardial DTR transgenic, CD19+CD11b+, DT-treated, 1

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set2_DTR_CD19+CD11b+_1


title: EVT3_RRBS

value: 12.1 weeks


title: CTB1_RRBS


title: EVT2_RRBS


title: SP1_RRBS


title: SP3_RRBS


title: EVT1_RRBS


title: set1, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 5

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b+_5

value: no DT, no PFD


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT+PFD-treated, 22

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR+PFD_CD19+CD11b-_22

source_name: Myocardial DTR transgenic, DT+PFD-treated

value: DT+PFD-treated


title: SB9

description:
NXTGNTpool16_index5_ACAGTG_L006_R*_001_AC0P9YACXX.filt
Technical replicate

value: female


title: set1, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 1

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b+_1


title: SB3

description: NXTGNTpool15_index11_GGCTAC_L005_R*_001_AC0P9YACXX.filt


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT+PFD-treated, 21

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR+PFD_CD19+CD11b+_21


title: set1, Myocardial DTR transgenic, CD19+CD11b+, no DT, no PFD, 7

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b+_7


title: CTB3_RRBS


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT+PFD-treated, 20

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR+PFD_CD19+CD11b-_20


title: set1, Myocardial DTR transgenic, CD19+CD11b-, no DT, no PFD, 2

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_naive_CD19+CD11b-_2


title: CTB2_RRBS


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT+PFD-treated, 19

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR+PFD_CD19+CD11b+_19


title: KTB42-2_S94_non-immortalized

first: Harikrishna

last: Nakshatri

address: 980 W. Walnut St.,R3 C218C

institute: IU School of Medicine

description: mRNA-seq

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg19 refGene genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: *_Aligned.sortedByCoord.out.bam.counts.txt: Tab-delimited text files include raw counts in the last column.

source_name: non-Immortalized normal breast epithelial cell  line

growth_protocol: Cells were cultured in low glucose (1 gm/liter) DMEM and F12 medium (1:3), supplemented with 5% fetal bovine serum (FBS; Gibco, USA), 1% penicillin/streptomycin (Corning, USA), 5µg/ml insulin, 0.4µg/ml hydrocortisone, 24µg/ml adenine (Sigma, USA), 10ng/ml EGF (Millipore, USA) and 10mM ROCK inhibitor.

extract_protocol:
Total RNA extraction and purification were done with Qiagen Rneasy Plus Mini Kit
Roche KAPA mRNA Hyperprep Kit (KK8581)


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT+PFD-treated, 18

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR+PFD_CD19+CD11b-_18


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT+PFD-treated, 17

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR+PFD_CD19+CD11b+_17


title: KTB42-1_S93_non-immortalized

description: mRNA-seq

value: non-Immortalized normal breast epithelial cell line


title: KTB40-2_S92_non-immortalized

description: mRNA-seq


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT-treated, 9

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b+_9


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT-treated, 15

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b+_15


title: KTB39-2_S90_non-immortalized

description: mRNA-seq


title: KTB40-1_S91_non-immortalized

description: mRNA-seq


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT-treated, 14

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b-_14


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT-treated, 16

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b-_16


title: KTB39-1_S89_non-immortalized

description: mRNA-seq


title: KTB37-2_S88_non-immortalized

description: mRNA-seq


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT-treated, 13

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b+_13


title: KTB37-1_S87_non-immortalized

description: mRNA-seq


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT-treated, 12

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b-_12


title: CjCutting_Needle_6wpi_rep1

city: Hitachi

first: Yuki

last: Fukuda

state: Ibaraki

department: Breeding Department, Breeding Division

institute: Forestry and Forest Products Research Institute, Forest Tree Breeding Center

description:
Gene expression at 6 weeks post insertion in needle of C. japonica cutting
Needle, 6 weeks post insertion, replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to 8×60k microarrays for 17 hours at 65°C in a rotating microarray hybridization oven (Agilent Technologies). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C with GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Region full agilent slide, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (protocol: GE1_1105_Oct12 and Grid: 069025_D_F_20140811) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Cryptomeria japonica

source_name: Needle, 6 weeks post insertion

label_protocol: Cyanine-3 (Cy3) labeled cRNA were synthesized from 200 ng of total RNA from each sample using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop 2000C (Thermo Fisher Scientific).

growth_protocol: Stem cuttings were excised from 18-year-old donor trees of C. japonica in the field and inserted into soil in a greenhouse with an automatic irrigation and no regulation of environment condition.

extract_protocol: Total RNA from each sample was extracted using RNeasy Plant Mini kit (Qiagen, Hilden, Germany) with a DNase digestion on-column using RNase-Free DNase Set (Qiagen). RNA concentration was measured by NanoDrop 2000C (Thermo Fisher Scientific, Waltham, MA, USA) and RNA integrity was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using Agilent RNA 6000 Nano Kit (Agilent Technologies).

tag: clone

value: Tsukuba 1

tag: cutting

value: needle

tag: time

value: 6 weeks post insertion


title: CjCutting_Needle_6wpi_rep3

description:
Gene expression at 6 weeks post insertion in needle of C. japonica cutting
Needle, 6 weeks post insertion, replicate 3


title: CjCutting_Needle_3wpi_rep1

description:
Gene expression at 3 weeks post insertion in needle of C. japonica cutting
Needle, 3 weeks hour post insertion, replicate 1

source_name: Needle, 3 weeks hour post insertion

value: 3 weeks post insertion


title: CjCutting_Needle_6wpi_rep2

description:
Gene expression at 6 weeks post insertion in needle of C. japonica cutting
Needle, 6 weeks post insertion, replicate 2


title: CjCutting_Needle_3wpi_rep2

description:
Gene expression at 3 weeks post insertion in needle of C. japonica cutting
Needle, 3 weeks hour post insertion, replicate 2


title: CjCutting_Needle_1wpi_rep1

description:
Gene expression at 1 week post insertion in needle of C. japonica cutting
Needle, 1 week post insertion, replicate 1

source_name: Needle, 1 week post insertion

value: 1 week post insertion


title: CjCutting_Needle_1wpi_rep3

description:
Gene expression at 1 week post insertion in needle of C. japonica cutting
Needle, 1 week post insertion, replicate 3


title: CjCutting_Needle_1wpi_rep2

description:
Gene expression at 1 week post insertion in needle of C. japonica cutting
Needle, 1 week post insertion, replicate 2


title: CjCutting_Needle_3dpi_rep1

description:
Gene expression at 3 days post insertion in needle of C. japonica cutting
Needle, 3 days post insertion, replicate 1

source_name: Needle, 3 days post insertion

value: 3 days post insertion


title: CjCutting_Needle_3wpi_rep3

description:
Gene expression at 3 weeks post insertion in needle of C. japonica cutting
Needle, 3 weeks hour post insertion, replicate 3


title: CjCutting_Needle_3dpi_rep3

description:
Gene expression at 3 days post insertion in needle of C. japonica cutting
Needle, 3 days post insertion, replicate 3


title: CjCutting_Needle_3dpi_rep2

description:
Gene expression at 3 days post insertion in needle of C. japonica cutting
Needle, 3 days post insertion, replicate 2


title: set1, Myocardial DTR transgenic, CD19+CD11b+, DT-treated, 11

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b+_11

value: DT-treated


title: KTB36-1_S85_non-immortalized

description: mRNA-seq


title: set1, Myocardial DTR transgenic, CD19+CD11b-, DT-treated, 10

description:
unprocessed_HTSeq-data.txt
depth-normalized_batch-corrected_cpm-filtered_HTSeq-data.txt
set1_DTR_CD19+CD11b-_10


title: KTB34-1_S83_non-immortalized

description: mRNA-seq


title: KTB26-2_S82_non-immortalized

description: mRNA-seq


title: KTB26-1_S81_non-immortalized

description: mRNA-seq


title: CjCutting_Needle_1dpi_rep3

description:
Gene expression at 1 day post insertion in needle of C. japonica cutting
Needle, 1 day post insertion, replicate 3

source_name: Needle, 1 day post insertion

value: 1 day post insertion


title: KTB22-2_S80_non-immortalized

description: mRNA-seq


title: CjCutting_Needle_1dpi_rep1

description:
Gene expression at 1 day post insertion in needle of C. japonica cutting
Needle, 1 day post insertion, replicate 1


title: KTB36-2_S86_non-immortalized

description: mRNA-seq


title: KTB22-1_S79_non-immortalized

description: mRNA-seq


title: KTB21-2_S78_non-immortalized

description: mRNA-seq


title: KTB21-1_S77_non-immortalized

description: mRNA-seq


title: KTB34-2_S84_non-immortalized

description: mRNA-seq


title: 1505-10B-2-S96_non-immortalized

description: mRNA-seq


title: CjCutting_Needle_3hpi_rep3

description:
Gene expression at 3 hours post insertion in needle of C. japonica cutting
Needle, 3 hours post insertion, replicate 3

source_name: Needle, 3 hours post insertion

value: 3 hours post insertion


title: 1505-10B-1-S95_non-immortalized

description: mRNA-seq


title: CjCutting_Needle_0hpi_rep2

description:
Gene expression at 0 hour post insertion in needle of C. japonica cutting
Needle, 0 hour post insertion, replicate 2

source_name: Needle, 0 hour post insertion

value: 0 hour post insertion


title: SinR1-cy3_WT1-cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 1 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: sinR mutant grown 7h TY

label_protocol: 5 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E WT and sinR mutant were grown in TY

extract_protocol: Total RNA was extracted using QIAgen RNAeasy kit.

tag: genotype/variation

value: C630E Mullany sinR::erm

source_name: WT grown 7h TY

value: C630E Mullany


title: SinR2-cy3_WT2-cy5

description: Biological replicate 2 of 4.


title: CjCutting_Needle_1dpi_rep2

description:
Gene expression at 1 day post insertion in needle of C. japonica cutting
Needle, 1 day post insertion, replicate 2


title: CjCutting_Needle_0hpi_rep3

description:
Gene expression at 0 hour post insertion in needle of C. japonica cutting
Needle, 0 hour post insertion, replicate 3


title: SinR4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: MCF7_RNA2_S24

description: mRNA-seq

data_processing:
Base calling and quality scoring were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg19 refGene genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *_Aligned.sortedByCoord.out.bam.counts.txt: Tab-delimited text files include raw counts in the last column.

source_name: Immortalized normal breast epithelial cell line

extract_protocol:
Total RNA extraction and purification were done with Qiagen RNeasy Plus Mini Kit.
Illumina TruSeq Stranded mRNA Lib Prep Kit.

tag: cell line


title: MCF7_RNA1_S23

description: mRNA-seq

value: Immortalized normal breast epithelial cell line


title: CjCutting_Needle_0hpi_rep1

description:
Gene expression at 0 hour post insertion in needle of C. japonica cutting
Needle, 0 hour post insertion, replicate 1


title: CjCutting_Needle_0hpe_rep1

description:
Gene expression at 0 hour post excision in needle of C. japonica cutting
Needle, 0 hour post excision, replicate 1

source_name: Needle, 0 hour post excision

value: 0 hour post excision


title: MCF10A-3_S36

description: mRNA-seq


title: CjCutting_Needle_0hpe_rep3

description:
Gene expression at 0 hour post excision in needle of C. japonica cutting
Needle, 0 hour post excision, replicate 3


title: CjCutting_Needle_0hpe_rep2

description:
Gene expression at 0 hour post excision in needle of C. japonica cutting
Needle, 0 hour post excision, replicate 2


title: Biofilm4-cy3_Planktonic4-cy5

description: Biological replicate 4 of 4.

source_name: Biofilm in Bioreactor

growth_protocol: C.difficile strain C630E Biofilm in Bioreactor and in Planktonic growth at 24H in TY

tag: strain

source_name: Planktonic grown 24h TY


title: DM2_14.5

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: S094_TruSeq_mm10_UCSC_20140923_093222_TS6

data_processing:
Read quality filtering: Every read that was considered valid by the Illumina control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; c) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. Any reads with no alignments were re-aligned against an artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incomplete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation:  Reads that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more mappings to exons, it was assigned randomly to one of the exons, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. The expression level of each transcript model was taken as the total number of reads at all its possible mapping positions, normalized as Reads Per Kilobase mRNA Per Million (RPKM).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-separated file with RPKM.

source_name: dorsal midbrain

growth_protocol: Mouse embryos were obtained from  TH-GFP animals  (Matsushita et al, J Neurochem. 82: 295, 2002) that were mated overnight, and noon of the plug day was considered  E0.5.  Embryos were dissected out of the uterine horns at E11.5 - E14.5 and placed in ice cold sterile PBS where brain regions were dissected under a stereomicroscope with a UV attachment to detect GFP. VM samples corresponded to domains M3 to M7 of the floor and basal plate (Nakatani et al, Development 134: 2783, 2007). Tissue samples were collected in separate tubes and stored at  - 80 ̊C until RNA isolation.

extract_protocol:
Total RNA isolation was performed with the RNeasy kit  (Qiagen). The RNA  integrity and concentration was checked using Qubit and 2200 TapeStation (Agilent).
Illumina TruSeq libraries were prepared using the kit and standard protocol from Illumina.

value: dorsal midbrain

tag: developmental stage

tag: genotype

value: TH-GFP


title: DM3_14.5

description: S094_TruSeq_mm10_UCSC_20140923_093222_TS7


title: MCF7_RNA3_S25

description: mRNA-seq


title: Biofilm3-cy5_Planktonic3-cy3

description: Biological replicate 3 of 4.


title: Biofilm2-cy3_Planktonic2-cy5

description: Biological replicate 2 of 4.


title: SinR3-cy5_WT3-cy3

description: Biological replicate 3 of 4.


title: CjCutting_Middle_6wpi_rep2

description:
Gene expression at 6 weeks post insertion in middle of C. japonica cutting
Middle of Cutting, 6 weeks post insertion, replicate 2

value: middle


title: CjCutting_Middle_6wpi_rep3

description:
Gene expression at 6 weeks post insertion in middle of C. japonica cutting
Middle of Cutting, 6 weeks post insertion, replicate 3

value: Tsukuba 1


title: VM4_14.5

description: S094_TruSeq_mm10_UCSC_20140923_093222_TS5

source_name: ventral midbrain

value: ventral midbrain


title: MCF10A-1_S23

description: mRNA-seq


title: KTB42-hTERT3_S33

description: mRNA-seq


title: VM3_14.5

description: S094_TruSeq_mm10_UCSC_20140923_093222_TS4


title: CjCutting_Middle_3wpi_rep2

description:
Gene expression at 3 weeks post insertion in middle of C. japonica cutting
Middle of Cutting, 3 weeks hour post insertion, replicate 2


title: Biofilm1-cy5_Planktonic1-cy3

description: Biological replicate 1 of 4.


title: CjCutting_Middle_6wpi_rep1

description:
Gene expression at 6 weeks post insertion in middle of C. japonica cutting
Middle of Cutting, 6 weeks post insertion, replicate 1

value: 6 weeks post insertion


title: CjCutting_Middle_3wpi_rep3

description:
Gene expression at 3 weeks post insertion in middle of C. japonica cutting
Middle of Cutting, 3 weeks hour post insertion, replicate 3

value: 3 weeks post insertion


title: MCF10A-2_S24

description: mRNA-seq


title: KTB42-hTERT2_S18

description: mRNA-seq


title: KTB42-hTERT1_S17

description: mRNA-seq


title: CM3_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS7

source_name: ventral hindbrain

value: ventral hindbrain


title: KTB40-hTERT2_S16

description: mRNA-seq


title: CM2_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS6


title: CjCutting_Middle_1wpi_rep2

description:
Gene expression at 1 week post insertion in middle of C. japonica cutting
Middle of Cutting, 1 week post insertion, replicate 2

value: 1 week post insertion


title: KTB40-hTERT1_S15

description: mRNA-seq


title: DM6_11.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS5


title: KTB39-hTERT3_S31

description: mRNA-seq


title: CjCutting_Middle_1wpi_rep3

description:
Gene expression at 1 week post insertion in middle of C. japonica cutting
Middle of Cutting, 1 week post insertion, replicate 3


title: DM4_11.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS4


title: CjCutting_Middle_1wpi_rep1

description:
Gene expression at 1 week post insertion in middle of C. japonica cutting
Middle of Cutting, 1 week post insertion, replicate 1


title: VM2_14.5

description: S094_TruSeq_mm10_UCSC_20140923_093222_TS2


title: CjCutting_Needle_3hpi_rep2

description:
Gene expression at 3 hours post insertion in needle of C. japonica cutting
Needle, 3 hours post insertion, replicate 2

value: needle


title: KTB39-hTERT2_S14

description: mRNA-seq


title: DM2_11.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS2


title: L4_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS19

source_name: alar plate

value: alar plate


title: CjCutting_Middle_3wpi_rep1

description:
Gene expression at 3 weeks post insertion in middle of C. japonica cutting
Middle of Cutting, 3 weeks hour post insertion, replicate 1


title: CjCutting_Middle_3dpi_rep3

description:
Gene expression at 3 days post insertion in middle of C. japonica cutting
Middle of Cutting, 3 days post insertion, replicate 3

value: 3 days post insertion


title: DM4_14.5

description: S094_TruSeq_mm10_UCSC_20140923_093222_TS12


title: KTB39-hTERT1_S13

description: mRNA-seq


title: KTB37-hTERT3_S30

description: mRNA-seq


title: KTB40-hTERT3_S32

description: mRNA-seq


title: L3_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS18


title: L2_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS16


title: CjCutting_Middle_3dpi_rep2

description:
Gene expression at 3 days post insertion in middle of C. japonica cutting
Middle of Cutting, 3 days post insertion, replicate 2


title: CjCutting_Middle_3dpi_rep1

description:
Gene expression at 3 days post insertion in middle of C. japonica cutting
Middle of Cutting, 3 days post insertion, replicate 1


title: CjCutting_Middle_1dpi_rep3

description:
Gene expression at 1 day post insertion in middle of C. japonica cutting
Middle of Cutting, 1 day post insertion, replicate 3

source_name: Middle of Cutting, 1 day post insertion

value: 1 day post insertion


title: KTB37-hTERT2_S12

description: mRNA-seq


title: CjCutting_Middle_1dpi_rep1

description:
Gene expression at 1 day post insertion in middle of C. japonica cutting
Middle of Cutting, 1 day post insertion, replicate 1


title: CjCutting_Middle_1dpi_rep2

description:
Gene expression at 1 day post insertion in middle of C. japonica cutting
Middle of Cutting, 1 day post insertion, replicate 2


title: CjCutting_Middle_3hpi_rep3

description:
Gene expression at 3 hours post insertion in middle of C. japonica cutting
Middle of Cutting, 3 hours post insertion, replicate 3

value: 3 hours post insertion


title: RM4_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS15

source_name: ventral forebrain

value: ventral forebrain


title: KTB37-hTERT1_S11

description: mRNA-seq

value: Immortalized normal breast epithelial cell line


title: KTB36-hTERT3_S29

description: mRNA-seq


title: RM2_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS14


title: CjCutting_Middle_3hpi_rep1

description:
Gene expression at 3 hours post insertion in middle of C. japonica cutting
Middle of Cutting, 3 hours post insertion, replicate 1


title: KTB36-hTERT2_S10

description: mRNA-seq


title: CM4_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS12


title: RM4_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS7


title: RM3_14.5

description: S093_TruSeq_mm10_UCSC_20140929_163905_TS13


title: RM2_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS6


title: KTB34-hTERT3_S28

description: mRNA-seq


title: KTB34-hTERT2_S8

description: mRNA-seq


title: CM6_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS5


title: KTB34-hTERT1_S7

description: mRNA-seq


title: CjCutting_Middle_0hpi_rep3

description:
Gene expression at 0 hour post insertion in middle of C. japonica cutting
Middle of Cutting, 0 hour post insertion, replicate 3

value: 0 hour post insertion


title: CjCutting_Middle_3hpi_rep2

description:
Gene expression at 3 hours post insertion in middle of C. japonica cutting
Middle of Cutting, 3 hours post insertion, replicate 2


title: CjCutting_Middle_0hpe_rep3

description:
Gene expression at 0 hour post excision in middle of C. japonica cutting
Middle of Cutting, 0 hour post excision, replicate 3

source_name: Middle of Cutting, 0 hour post excision

value: 0 hour post excision


title: CjCutting_Middle_0hpi_rep1

description:
Gene expression at 0 hour post insertion in middle of C. japonica cutting
Middle of Cutting, 0 hour post insertion, replicate 1


title: CjCutting_Middle_0hpi_rep2

description:
Gene expression at 0 hour post insertion in middle of C. japonica cutting
Middle of Cutting, 0 hour post insertion, replicate 2


title: CjCutting_Middle_0hpe_rep2

description:
Gene expression at 0 hour post excision in middle of C. japonica cutting
Middle of Cutting, 0 hour post excision, replicate 2


title: CM4_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS4

value: TH-GFP


title: KTB26-hTERT3_S27

description: mRNA-seq


title: VM6_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS19


title: CM2_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS2


title: KTB26-hTERT1_S5

description: mRNA-seq


title: KTB26-hTERT2_S6

description: mRNA-seq


title: KTB36-hTERT1_S9

description: mRNA-seq


title: CjCutting_Middle_0hpe_rep1

description:
Gene expression at 0 hour post excision in middle of C. japonica cutting
Middle of Cutting, 0 hour post excision, replicate 1

value: middle


title: VM4_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS18


title: KTB22-hTERT3_S26

description: mRNA-seq


title: VM2_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS16


title: L4_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS15


title: CjCutting_Base_6wpi_rep3

description:
Gene expression at 6 weeks post insertion in base of C. japonica cutting
Base of Cutting, 6 weeks post insertion, replicate 3

source_name: Base of Cutting, 6 weeks post insertion

value: Tsukuba 1

value: base


title: KTB22-hTERT2_S4

description: mRNA-seq


title: CjCutting_Base_6wpi_rep2

description:
Gene expression at 6 weeks post insertion in base of C. japonica cutting
Base of Cutting, 6 weeks post insertion, replicate 2

value: 6 weeks post insertion


title: KTB22-hTERT1_S3

description: mRNA-seq