title: LB-antibiotics

description: rRNA depleted

value: Tenfold diluted LB was supplemented with 2 µg/ml sulfamethoxazole and 0.4 µg/ml trimethoprim to tenfold diluted LB. This medium was inoculated with 2 ml of overnight culture. Cells cannot divide anymore in this medium and the increase in OD600 is due to massive cell elongation. We harvested the cells at the peak of OD600 at 0.194.


title: CGGA_671

status: Public on Jul 20 2014

type: SRA

city: Beijing

first: Wanlu

last: Ye

state: Beijing

address: Biodynamic Optical Imaging Center

department: Colleage of Life Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Remove duplications using picard-tools-1.80
Detect fusions using Tophat-2.0.6 with parameter -N 1 --read-gap-length 1 -r -50 --mate-std-dev 33 -p 4 -i 50 --bowtie1 --fusion-search --fusion-anchor-length 10 --solexa-quals
Detect fusions using defuse-0.6.1 with parameter --clustering_precision 0.90 --span_count_threshold 2 --split_min_anchor 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of a list of fusions tophat finds. Each row represents a fusion with detailed description of chromosome, break point, number of supporting reads…
Supplementary_files_format_and_content: tab-delimited text files of a list of fusions defuse finds.

molecule: total RNA

organism: Homo sapiens

source_name: Tumor cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions
RNA libraries were prepared using TruSeq RNA library perparation kit following standard Illumina protocols

tag: history

value: oligodendroastrocytomas


title: CGGA_D64

value: secondary Glioblastomas


title: LB-nitrite technical replicate 1

city: Freising

first: Richard

middle: B.

last: Landstorfer

address: Weihenstephaner Berg 3

department: Chair for Microbial Ecology

country: Germany

institute: Technische Universität München

description: rRNA depleted

data_processing:
SOLiD output as QUAL and CSFASTA files was converted to FASTQ with Galaxy. We mapped SOLiD and Illumina FASTQ files to the reference genome using Bowtie (settings for SOLiD data: 28 nt seed length, maximal two mismatches in the seed, a maximal threshold of 70 for the sum of the quality values at mismatched positions; Illumina data: 20 nt seed length, 0 mismatches in the seed) implemented in Galaxy. Using Samtools output SAM files were filtered for mappable reads only. We further converted SAM files to BAM files and indexed them to create BAM.BAI files.
The number of reads were normalized to reads per kilobase per million mapped reads (RPKM). Using this method, the number of reads is normalized with respect to the sequencing depth and the length of a given gene. For determination of counts and RPKM values, BAM files were imported into R (R Development Core Team) using Rsamtools. For further processing, the Bioconductor packages GenomicRanges and IRanges were used. Gene locations were determined by RefSeq and GenBank PTT files. The locations of the 16S rRNA and 23S rRNA are given by the RNT file from RefSeq. The method countOverlaps of IRanges was used to determine the remaining reads overlapping a 16S or 23S rRNA gene. We discarded these reads from further analysis due to the artificial removal of these rRNAs using the Ribominus kit as described above. countOverlaps is also used to determine the number of reads overlapping a gene on the same strand (counts). With these counts, we generated the RPKM values. For the value “million mapped reads”, the number of reads mapped to the genome minus the reads overlapping a 16S or 23S rRNA gene were used (see above). The differential gene expression was analyzed with the Bioconductor package edgeR (version 3.2.3) using the counts.
Genome_build: Escherichia coli (str. O157H7 substr. EDL933: 259
Supplementary_files_format_and_content: The xlsx file contains information for each annotated gene in each condition. For each gene, the first number indicates the logFC of a certain condition compared to LB; RPKM values are shown in parentheses. The magnitude of the absolute value of logFC is indicated by shades of grey. Significantly differentially expressed genes are in bold (i.e., p values ≤ 0.05 in edgeR).

organism: Escherichia coli O157:H7

source_name: whole organisms

extract_protocol:
RNA was extracted using Trizol, rRNA was removed with the Ribominus kit (life technologies).
The read fragments were phosphorylated and the library was constructed using the TruSeq smallRNA sample prep kit.

tag: strain

tag: growth phase

value: late logarthmic, early stationary phase

tag: growth condition and treatment

value: For nitrite, we added 200 mg/L sodium nitrite to 10-fold diluted LB and adjusted it to pH 6. Harvest was after 6.5 h at 2.9 x 108 cfu/ml.


title: CGGA_661

value: anaplastic astrocytomas


title: CGGA_659

value: oligodendrogliomas


title: CGGA_662


title: LB-15°C

description: rRNA depleted

value: Transcription was determined at 15°C in tenfold diluted LB medium and harvested at 3.1 x 108 cfu/ml (LB-15°C)


title: LB-pH4

description: rRNA depleted

value: Tenfold diluted LB medium at pH4 was adjusted to 4.0 at 37°C and filter sterilized. Cells were harvested at 2.0 x 108 cfu/ml (LB-pH4).


title: CGGA_658

value: primary Glioblastomas


title: LB-pH9

description: rRNA depleted

value: Tenfold diluted LB medium at alkaline pH was buffered with 10 mM CHES and the pH was adjusted to 9.0 at 37°C and was filter sterilized (LB-pH9). After 7 h, the cells reached 1.5 x 108 cfu/ml and were harvested.


title: feces

description: rRNA depleted

value: Cattle feces:The number of cultivatable bacteria of cattle feces was determined by serial platings on LB-agar plates after 12h at 37°C. The cattle feces was subsequently inoculated with 1000-fold number of EHEC, pre-grown in 1 L LB to stationary phase. When the bacteria had reached stationary phase, they were harvested by centrifugation and resuspended in 7 ml ¼-concentrated Ringer. We added this suspension to 10 g of cattle feces and mixed it thoroughly. After 6 h at 37°C, bacterial cells were harvested by adding 90 ml cold ¼ Ringer, shaking for 10 s, sedimentation for 30 s, decanting, and centrifugation.


title: LB medium biological replicate SOLiD

description: rRNA depleted

value: Tenfold diluted lysogeny broth was used as reference medium. Cells were harvested after 3.5 h at about 3.1 x 108 cfu/ml.


title: CGGA_655


title: CGGA_643

value: anaplastic oligodendroastrocytomas


title: CGGA_642

value: astrocytomas


title: CGGA_633


title: CGGA_635


title: CGGA_624

value: recurrent Glioblastomas


title: CGGA_630


title: CGGA_616


title: CGGA_607


title: CGGA_601


title: CGGA_604


title: CGGA_599


title: CGGA_605

value: recurrent anaplastic oligodendrogliomas


title: CGGA_603

value: recurrent anaplastic astrocytomas


title: CGGA_598

value: anaplastic oligodendrogliomas


title: CGGA_580

value: oligodendroastrocytomas


title: CGGA_666


title: CGGA_564


title: CGGA_578


title: CGGA_565


title: CGGA_591


title: CGGA_560


title: CGGA_538


title: CGGA_551


title: CGGA_543


title: CGGA_D63

value: secondary Glioblastomas


title: CGGA_510


title: CGGA_501


title: CGGA_495


title: CGGA_493


title: CGGA_499


title: CGGA_490


title: CGGA_494


title: CGGA_491


title: CGGA_488


title: CGGA_485


title: CGGA_446


title: CGGA_483


title: CGGA_458

value: recurrent oligodendroastrocytomas


title: CGGA_541


title: CGGA_545


title: CGGA_337


title: CGGA_413


title: CGGA_431


title: CGGA_323


title: CGGA_426

value: anaplastic astrocytomas


title: CGGA_400


title: CGGA_330


title: CGGA_374


title: CGGA_502


title: CGGA_318


title: CGGA_300


title: CGGA_314


title: CGGA_333


title: CGGA_309


title: CGGA_276

value: oligodendrogliomas


title: CGGA_274


title: CGGA_D61


title: CGGA_479


title: CGGA_448


title: CGGA_272


title: CGGA_269


title: CGGA_254


title: CGGA_256


title: CGGA_267


title: CGGA_252


title: CGGA_273


title: CGGA_251


title: CGGA_243


title: LB medium biological replicate Illumina

description: rRNA depleted

value: late logarthmic, early stationary phase


title: CGGA_171


title: CGGA_236


title: CGGA_241


title: CGGA_283


title: CGGA_235


title: radish sprouts biological replicate Illumina

description: rRNA depleted

value: Radish sprout seeds were sterilized (5 min 70% ethanol, 10 min 1% NaOCl with 0.1% Tween), then washed five times with sterile water and subsequently incubated in sterile MS medium without glucose in sterile plastic boxes (1 L total volume, passively aerated). After germination, seedlings were tested for sterility by plating a sample on LB agar. After 5 days of growth, the shoots were inoculated 10 min with 1 L ¼ concentrated Ringer solution containing 103 cfu/ml EHEC. The superfluous medium was decanted and cfu/g was periodically determined as follows:infected shoots were washed and bacterial numbers of the washing liquid were determined by serial dilution platings. After 120 hours, the transition from exponential to stationary phase could be determined. Bacteria were harvested by gently shaking the seedlings in cold ¼-concentrated Ringer (+1% Tween-20; 4°C) for 1 min. Bacteria were collected by centrifugation from the decanted Ringer as above.


title: CGGA_245

value: recurrent astrocytomas


title: Porphyromonas gingivalis ATCC 33277 ΔPGN_1524 mutant_1

status: Public on Jul 19 2014

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

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

department: ChemE & eScience Institute

country: USA

institute: University of Washington

data_processing:
Reads were aligned to Porphyromonas gingivalis ATCC 33277 scaffold using 0.7.4-r385 with default parameters.
Samtools 0.1.19-44428cd was used to post-process the alignments from SAM to BAM
htseq-count, part of the 'HTSeq' framework, version 0.5.4p5, was used to attribute reads to ORFs
The R package deseq2 was used to compute differential abundance measures and adjusted pvalues
Genome_build: ASM1050v1; AP009380.1
Supplementary_files_format_and_content: Tab delimited counts of reads for each ORF (generated by htseq-count)

organism: Porphyromonas gingivalis ATCC 33277

growth_protocol: Trypticase Soy Broth with hemin and menadione, anaerobic, 37C

extract_protocol:
RNA extraction was performed with TRIzol (Life Technologies, Carlsbad, CA, USA) and bead beating twice for 1 min at 50 Hz with a Qiagen Tissue Lyser LT (Valencia, CA, USA).  Sample cleanup was done with Zymo RNA Clean and Concentrator columns (Zymo Research, Irvine, CA, USA) per the kit instructions with the optional in-column DNase digestion.
Libraries were prepared according to Illumina's instructions for 36 bp reads.

treatment_protocol: harvested from mid-log phase

tag: genotype/variation

value: ΔPGN_1524 mutant


title: Wild-type Porphyromonas gingivalis ATCC 33277_2

value: wild-type


title: Porphyromonas gingivalis ATCC 33277 ΔPGN_1524 mutant_2


title: Wild-type Porphyromonas gingivalis ATCC 33277_1


title: Larix leptolepis synchronous embryos

city: beijing

first: junhong

last: zhang

address: Xiangshan Road

institute: Chinese Academy of Forestry

description: Calli were cultured in abscisic acid-removing medium for 45 days.

data_processing:
The raw data were obtained using Illumina's Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by pipeline Bustard Module.
After the raw sequence reads were extracted from image data, a series of digital filters, namely ACGT101-miR program (Version 3.5, LC Sciences), were employed to remove various un-mappable sequencing reads. Specifically, 533ADT, 53ADT, and junk sequences (>=80% A, C, G or T; >=3 N; only A, C, or only G, T) were initially filtered out.
miRBase 19.0 was used for mapping.
Genome_build: miRBase 19.0
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each Sample.

organism: Larix kaempferi

source_name: synchronous embryos

growth_protocol: Embryogenic callus tissues were induced from immature embryos of L. leptolepis on induction medium, followed by sub-culture, and culture on differentiation medium in dark environment with the temperature of 25±2℃.

extract_protocol:
Total RNA was extracted from the materials as described above using Total RNA Purification Kit according to the manufacturer's instructions (NORGEN biotec corporation, Canada). Purity/concentration and integrity of RNA were evaluated by NanoDrop 1000 and electrophoresis, respectively.
The RNA was pooled for Illumina Genome Analyzer GA-IIx sequencing. The library construction, sequencing and initial data analysis were performed by LC Sciences.

tag: cell line

tag: cell type

value: embryogenic callus cells


title: Ribo-seq [PSI+] rep2

status: Public on Jul 18 2014

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.2.1 with 0.12 allowed error rate
Unique mapping using Bowtie2 with defaults parameters in very-sensitive mode
Measuring differential gene expression by assigning reads with Htseq-count version 0.5.3p3 using intersection-nonempty mode
Differential expression analysis with DESeq version 1.6.1 using default parameters
Genome_build: SacCer3
Supplementary_files_format_and_content: differential gene expression file (DESeq results)
Supplementary_files_format_and_content: The file named DE_cter_complete.tab.txt is differential expression values for ribosome profiling data from DESeq R library. This file contains 9 columns where the first two columns are gene number and gene name (id). For each gene, the file reports its mean expression level (at the base scale) as a joint estimate from both conditions, and estimated separately for each condition, the fold change from the first to the second condition, the logarithm (to basis 2) of the fold change, and the p value for the statistical significance of this change. The padj column contains the p values, adjusted for multiple testing with the Benjamini-Hochberg procedure. Only genes with padj < 0.1 are included in the file. Conditions described in the file are "PSI" for [PSI+] and "CTER" for [PSI+]-Cter, ie yeast infected by prion [PSI+] with overexpression of SUP35 Cter or not

organism: Saccharomyces cerevisiae

source_name: ribosome protected fragments

growth_protocol: OD600 of 0.6-0.8 at 30°C in YNB+CSM-U medium (2 % glucose)

extract_protocol:
As previously published by Ingolia et al, Science 324, 218-223 (2009).
Directional RNA-Seq library preparation was carried out with the Small RNA Sample Prep Kit and the v1.5 sRNA 3' Adaptor (Illumina), according to the manufacturer’s protocol.

treatment_protocol: Cells are treated with cycloheximide

tag: strain background

value: [PSI+] strain

tag: molecule subtype

value: ribosome protected fragments


title: Ribo-seq [PSI+] with  overexpression Cter of  SUP35 rep1

value: [PSI+] overexpressing SUP35-Cter strain


title: Ribo-seq [PSI+] rep1


title: Larix leptolepis germinated embryos

description: The whole embryo turned into yellow-green, especially for cotyledons, after cultured for 12 days on abscisic acid-removing medium.

source_name: germinated embryos


title: CGGA_261

value: astrocytomas


title: Larix leptolepis desynchronous embryos

source_name: desynchronous embryos


title: Larix leptolepis dormant embryos

description: After mature somatic embryos continued to stay for 12 days on abscisic acid-containing medium, the embryos entered into dormant or quiescent status, when the embryos were faint yellow.

source_name: dormant embryos


title: Ribo-seq [PSI+] with  overexpression Cter of  SUP35 rep2


title: human_hESC_input

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Reads were initially mapped against a set of human or mouse ribosomal RNA (rRNA) sequences using Bowtie (version 0.12.7), and all reads aligning to the rRNA were discarded. All remaining reads were aligned against the human (hg19) or mouse (mm9) genome using Tophat (version 1.4.1). Parameters used were ‘--max-multihits 1 –prefilter-multihits’ and ‘–transcriptome-index’, for which we assigned a pre-indexed version of the relevant transcriptomes, based on the UCSC Known Genes set of annotations. An in-house script was then used to project all reads aligning to the genome upon the human and mouse transcriptomes. Only reads fully matching a transcript structure, as defined by the ‘UCSC Known Genes’ transcriptome annotation, were retained. Such reads were computationally extended in transcriptome space from the beginning of the first read to the end of its mate, and coverage in transcriptome-space was calculated for each nucleotide across all transcripts.
Putative m6A sites were identified using a 3 step-approach, consisting of: (1) Examination of the IP sample, to identify regions within genes in the IP samples that were enriched in comparison to background gene levels; (2) Comparison of IP sample with input sample, to ensure that these regions were not enriched in corresponding input samples; and (3) Comparison across multiple replicates of IP and input samples. Below we provide a detailed description of these steps, which is very similar to the approach used in (Schwartz et al., 2013), with a few extensions and modifications.
(1) Peak detection within genes. To search for enriched peaks in the m6A IP samples, we scanned each gene using sliding windows of 100 nucleotides with 50 nucleotides overlap. Each window was assigned a Peak Over Median (POM) score, defined as mean coverage in the window / median coverage across the gene. Windows with POM scores greater than 4 (i.e., greater than 4-fold enrichment) and with a mean coverage >10 reads were retained. Overlapping windows were merged together, and for each disjoint set of windows in transcriptome space we recorded its start, end, and peak position, corresponding to the position with the maximal coverage across the window.
(2) Ensuring that peaks were absent in input. We repeated the procedure in step (1) for the input sample. We eliminated from all subsequent analysis all windows that were detected in both step (1) and (2).
(3) Comparison of multiple samples and criteria for WTAP-dependence. To compare between different perturbations and/or conditions, we applied the following strategy. We first merged the coordinates of all windows from all samples passing step (1) and (2), to define a set of disjoint windows passing these filters in at least one of the samples. For each such window, we recalculated the peak start, end, peak position, and POM score (as defined above) across each of the samples using the approach in step (1). In addition, for each window we calculated a Peak Over Input (POI) score, corresponding to the fold-change of coverage across the window in the IP sample over the coverage in the input sample. To account for differences in sample depth, we estimated the mean difference between IP and input samples across the 500 most highly expressed genes, which we used as an estimate for background. We subtracted this background from the POI score. Of note, the POM and POI scores generally correlated well with each other; nevertheless, we empirically found that in some cases it was more informative to filter based on the one than on the other.
The provided bed files are provided to facilitate easy browsing of the data. The were produced by first extending each read until the end of its mate in genomic space. Coverage was then calculated individually for the + and - strands using bedtools. The bed files were not used for the data analysis.  TDF files, similarly provided for facilitating browsing via IGV genome browser, were generated using the 'count' command in IGV tools, with parameters `-z 7 -w 5 -e 70`. The tdf files (binary format, summarizing coverage genome-wide) were used for the data analysis.
Genome_build: hg19
Supplementary_files_format_and_content: .bed
Supplementary_files_format_and_content: .tdf

molecule: polyA RNA

extract_protocol:
RNA was extracted from cells using a standard hot acid phenol protocol. Briefly, cell pellets were resuspended in equal volumes of acid phenol:chloroform 5:1 pH 4.3-4.7 (Sigma), buffer AE (50 mM sodium acetate, 10mM EDTA 1% SDS) and glass beads. This mixture was vortexed for 15 minutes, followed by a 15 minute incubation at 65°C. Samples were centrifuged for 10 minutes (12,000g, 4°C); the supernatant isolated, re-extracted with phenol:chloroform::5:1, and precipitated with sodium acetate and isopropanol. Enrichment of polyadenylated RNA (polyA+ RNA) from total RNA was performed using Oligo(dT) dynabeads (Invitrogen) according to the manufacturer’s protocol. The mRNA was chemically fragmented into ~80-nt-long fragments using RNA fragmentation reagent (Ambion). The sample was then subjected to Turbo DNAse treatment (Ambion), followed by a phenol-chloroform extraction, and resuspension in 20 μl of  IPP buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5). 25 μl of protein-G magnetic beads were washed and resuspended in 200 μl of IPP buffer, and tumbled with 3 μl of affinity purified anti-m6A polyclonal antibody (Synaptic Systems) at room temperature for 30 minutes. Following 2 washes in IPP buffer, RNA was added to the antibody-bead mixture, and incubated for 2 h at 4°C. The RNA was then washed twice in 200 μl of IPP buffer, twice in low-salt IPP buffer (50 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5), and twice in high-salt IPP buffer (500 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5), and eluted in 30 μl RLT (Qiagen). To purify the RNA, 20 μl MyOne Silane Dynabeads (Life Technologies) were washed in 100 μl RLT, resuspended in 30 μl RLT, and added to the eluted RNA. 60 μl 100% ethanol was added to the mixture, the mixture attached to the magnet and the supernantant discarded. Following two washes in 100 μl of 70% ethanol, the RNA was eluted from the beads in 160 μl IPP buffer. Eluted RNA was subjected to an additional round of IP, by re-incubating it with protein-A magnetic beads coupled to anti-m6A antibody, followed by washes, elution from the protein-A beads and purification as above, followed by elution from the MyOne silane dynabeads in 10 μl H20.
Strand-specific m6A RNA-seq libraries were generated as described in (Engreitz et al., 2013). Briefly, RNA was first subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3’ ligation of an RNA adapter using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed using AffinityScript Multiple Temperature Reverse Transcriptase (Agilent), and the cDNA was subjected to a 3’ ligation with a second adapter using T4 ligase. The single-stranded cDNA product was then amplified for 9-14 cycles in a PCR reaction. Libraries were sequenced on Illumina Miseq, HiSeq 2000 and/or HiSeq 2500 platforms generating paired end reads (25 or 30 bp from each end, depending on the platform).

tag: knockdown

value: human embryonic stem cells

tag: antibody

tag: dynamic program

value: hESC->NPC


title: human_hESC


title: human_hNPC_input

value: human neural progenitor cells


title: human_hNPC


title: transcriptome PSI+

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence unsing perl script
Unique mapping using Bowtie v0.12.7 with parameters -q -S -m 1 –un (unique mapping mode)
Measuring differential gene expression by assigning reads with Htseq-count version 0.5.3p3 using intersection-nonempty mode
Differential expression analysis with DESeq version 1.6.1 using default parameters
Genome_build: sacCer2
Supplementary_files_format_and_content: Count file from HTseq-count and differential gene expression file

source_name: RNA

growth_protocol: OD600 of 0.6-0.8 at 30°C in YPD medium

tag: isogenic variation

value: PSI+


title: traductome PSI- rep 1

description: polysome

value: PSI-


title: traductome PSI- rep 2

description: polysome


title: traductome PSI+ rep 2

description: polysome


title: transcriptome PSI-


title: MII_2 (deeper)

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads had the first 9 base pairs clipped off and were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.3.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 9 --clip_r2 9 --paired).unmapped). Remaining sequences were then aligned to the mouse genome (build NCBIM37) in single-end mode (parameters: --bowtie2 --non_directional). Methylation calls were extracted after duplicate sequences had been excluded. Regions that were covered by a disproportionally high read number and were most likely mapping artefacts were excluded from subsequent analysis.
To deplete single-cell libraries of potential human contamination, trimmed sequences were first mapped to the human genome (build GRCh37) in paired-end mode using Bismark (v0.12.2; Krueger and Andrews, 2011, parameters: --bowtie2 --non_directional
Genome_build: NCBIM37
Supplementary_files_format_and_content: *CpG.txt: Genome-wide CpG methylation reports are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>
Supplementary_files_format_and_content: *cov.txt: Bismark CpG coverage report files are tab-delimited, use 1-based genomic coordinates (for the genome build GRCm38) for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: 161110_scBS_src.zip: Zip file with R source code for statistical analysis.

molecule: genomic DNA

organism: Mus musculus

source_name: oocytes

growth_protocol: ESCs were cultured in serum/LIF or 2i/LIF conditions as described previously (Ficz et al., Cell Stem Cell 13, 351–359)

extract_protocol:
N/A for single cells and MII bulk as the BS treatment was performed on cell lysate. For 2i/serum bulk: DNA was purified from cell pellets using the QIAamp micro kit (QIAGEN), according to the manufacturer’s instructions.
single cells: Bisulfite conversion was performed on cell lysates using the Imprint DNA Modification Kit (Sigma) with the following modifications: all volumes were halved, and chemical denaturation was followed by incubation at 65°C for 90min, 95°C for 3min and 65°C for 20min. Purification was performed as described previously (Miura et al., Nucleic Acids Research 40, e136–e136. 2012), and DNA eluted in 10mM Tris-Cl (pH 8.5) and combined with with 0.4mM dNTPs, 0.4µM oligo1 ([Btn]CTACACGACGCTCTTCCGATCTNNNNNNNNN) and 1x Blue Buffer (24µl final) before incubation at 65°C for 3min followed by 4°C pause. 50U of Klenow exo- (Sigma) was added and the samples were incubated at 4°C for 5min, +1°C/15s to 37°C, 37°C for 30min. Samples were incubated at 95°C for 1 min and transferred immediately to ice before addition of fresh oligo1 (10pmol), Klenow exo- (25U), and  dNTPs (1nmol) in 2.5µl total. The samples were incubated at 4°C for 5min, +1°C/15s to 37°C, 37°C for 30min. This random priming and extension was repeated a further 3 times (5 repeats in total). Samples were then incubated with 40U exonuclease I (NEB) for 1h at 37°C before DNA was purified using 0.8x Agencourt Ampure XP beads (Beckman Coulter) according to the manufacturer’s guidelines. Samples were eluted in 10mM Tris-Cl (pH 8.5) and incubated with washed M-280 Streptavidin Dynabeads (Life Technologies) for 20min with rotation at room temperature. Beads were washed twice with 0.1N NaOH, and twice with 10mM Tris-Cl (pH 8.5) and re-suspended in 48µl of 0.4mM dNTPs, 0.4µM oligo2 (TGCTGAACCGCTCTTCCGATCTNNNNNNNNN) and 1x Blue Buffer. Samples were incubated at 95°C for 45s and transferred immediately to ice before addition of 100U Klenow exo- (Sigma) and incubation at 4°C for 5min, +1°C/15s to 37°C, 37°C for 90min. Beads were washed with 10mM Tris-Cl (pH 8.5) and resuspended in 50µl of 0.4mM dNTPs, 0.4µM PE1.0 forward primer AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT), 0.4µM indexed iPCRTag reverse primer (Quail et al. Nat Methods. 2011 9(1):10-1), 1U KAPA HiFI HotStart DNA Polymerase (KAPA Biosystems) in 1x HiFi Fidelity Buffer. Libraries were then amplified by PCR as follows: 95°C 2min, 12-13 repeats of (94°C 80s, 65°C 30s, 72°C 30s), 72°C 3min, 4°C hold. Amplified libraries were purified using 0.8x Agencourt Ampure XP beads, according to the manufacturer’s guidelines.
bulk samples: Samples from bulk cell populations were prepared according to the protocol above, with the some modifications. For the bulk oocyte sample, 120 MII oocytes cells were collected and lysed as described above. For ESC bulk cell samples, DNA was purified from cell pellets using the QIAamp micro kit (QIAGEN), according to the manufacturer’s instructions, and 50ng of purified DNA was used in the library preparation. One round of first strand synthesis was performed using 0.8mM dNTPs and 4µM oligo1, and second strand synthesis also used 0.8mM dNTPs and 4µM oligo2. Bulk cell libraries were amplified as above with 9-12 cycles of PCR.

value: MII (ovulated) oocytes

value: C57BL/6 wild-type


title: MII_5 (deeper)


title: Ser_16

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads had the first 9 base pairs clipped off and were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.3.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 9 --clip_r2 9 --paired).unmapped). Remaining sequences were then aligned to the mouse genome (build NCBIM37) in single-end mode (parameters: --bowtie2 --non_directional). Methylation calls were extracted after duplicate sequences had been excluded. Regions that were covered by a disproportionally high read number and were most likely mapping artefacts were excluded from subsequent analysis.
To deplete single-cell libraries of potential human contamination, trimmed sequences were first mapped to the human genome (build GRCh37) in paired-end mode using Bismark (v0.10.1; Krueger and Andrews, 2011, parameters: --bowtie2 --non_directional --
Genome_build: NCBIM37
Supplementary_files_format_and_content: *CpG.txt: Genome-wide CpG methylation reports are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>
Supplementary_files_format_and_content: *cov.txt: Bismark CpG coverage report files are tab-delimited, use 1-based genomic coordinates (for the genome build GRCm38) for every covered cytosine position in the experiment and are in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: 161110_scBS_src.zip: Zip file with R source code for statistical analysis.

source_name: ES cells

value: mouse ESCs (E14)

tag: treatment

value: cultured in serum/LIF


title: traductome PSI+ rep 1

description: polysome


title: Ser_20


title: Ser_18


title: Ser_19


title: Salmonella_infected_3

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (TRAPL)
Read mapping using segemehl version 0.13 (TRAPL)
Coverage calculation and normalisation (TRAPL)
Genome_build: hs37d5
Supplementary_files_format_and_content: wiggle; Normalized read coverages multiplied by 1M  in wiggle format (*_forward.wig = forward strand; *_minus.wig= forward strand)

source_name: HeLa-229_Salmonella infected

growth_protocol: HeLa cells grown in standard conditions  (DMEM 1 g/L glucose (Life Technologies) supplemented with 10% fetal bovine serum (Biochrom), maintained in a 5% CO2, humidified atmosphere, at 37°C)

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, using standard Illumina protocols

treatment_protocol: Infection with Salmonella enterica serovar Typhimurium strain SL1344 constitutively expressing GFP (MOI 100), analysed 20hpi

value: HeLa-229 cells

tag: infection

value: Salmonella Typhimurium, MOI 100


title: Serum_ESCs_bulk


title: Ser_17


title: Ser_14


title: Mock_3

value: mock


title: Ser_13


title: Salmonella_infected_1


title: Mock_2


title: Ser_11


title: Ser_12


title: Ser_10


title: Salmonella_infected_2


title: miR-503

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Removal of polyA-tails from Fasta sequences (RAPL)
Size filtering: discarding reads shorter than 12 nt (RAPL)
Read mapping using segemehl version 0.13 (RAPL)
Coverage calculation and normalisation (RAPL)
Genome_build: hs37d5
Supplementary_files_format_and_content: wiggle

treatment_protocol: MicroRNAs were transfected into HeLa-229 cells using a standard reverse transfection protocol (Lipofectamine RNAiMAX, Life Technologies), at a final miRNA concentration of 50 nM. Cells were collected 72h post-transfection.

tag: transfected with

value: miR-503 (final conc. of 50nM)

tag: sample collection time

value: 72h post-transfection


title: Ser_8


title: Ser_9


title: RNA-Seq-Th17-Donor11

city: La Jolla

first: Anna

last: Gerasimova

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

data_processing:
The 35bp single end reads were aligned to human hg19 reference genome using the Tophat alignment program (Trapnell et al., 2009) allowing reads to span a splice junction. The alignment results were parsed via the samtools package (Li et al., 2009) to generate SAM files.
In order to quantitatively analyzing the gene expression levels under various cell types and disease types, we only counted the short reads uniquely mapping to an annotated features of the hg19 genome by using htseq-count (Anders et al., 2014). Here we selected “union” option in htseq-count to deal with reads overlapping more than one feature. After removing absent features (zero counts in all samples), we employed R/Bioconductor package “aroma.light” (Bengtsson et al., 2009) to perform quantile normalization on the samples for each test (comparison) of differential gene expression.
The quantile normalized raw counts were then imported to R/Bioconductor package “DESeq” (Anders and Huber, 2010) to identify differentially expressed genes among distinct cell types. We considered genes differentially expressed between two groups of samples if the DESeq analysis resulted in an adjusted p-value < 0.05 and in addition if the fold-change in gene expression was greater two-fold. For genes with low expression close to the detection threshold, normalized counts <3 were set equal to 3 when calculating fold-change values.
Genome_build: hg19
Supplementary_files_format_and_content: For visualization of the RNA-seq data in public genome browsers bw files were created using bedGraphToBigWig program from UCSC browser. The source BedGraph files were created by utilizing genomcov function of BEDTools Version 2.14.1-3 (Quinlan  and Hall, 2010)

source_name: Leukapheresis PBMCs

growth_protocol: No treatment post isolation was applied

extract_protocol:
From PBMC fraction of leukapheresis pouch, CD4 T cells were purified using the Miltenyi T cell isolation kit II according to manufacturer’s instructions. Purified cells were incubated in PBS containing 0.5% BSA and 2 mM EDTA pH 8.0 (MACS buffer) with a dilution of class II tetramer (10ml tetramer per 50x106 CD4 T cells) for 2 h at room temperature (HLA class II tetramers conjugated using PE labeled streptavidin were provided by the Tetramer Core Laboratory at Benaroya Research Institute).  Cells were then stained for cell surface antigens using anti-CD4-APC EFluor780 (RPA-T4), anti-CD45RA-EFluor450 (HI100) (both from Affymetrix eBioscience), anti-CD3-Alexa Fluor 700 (UCHT1), anti-CXCR3(CD183)-APC or CXCR3-Alexa Fluor 488 (1C6/CXCR3), anti-CD19-V500 (HIB19), anti-CD14-V500 (M5E2), anti-CD8-V500 (RPA-T8), anti-CD25-FITC (M-A251), anti-CCR4-PECy7 or CCR4-PE (1G1), anti-CCR6(CD196)-biotinylated (11A9) (all from BD Biosciences) followed by streptavidin-BV605 (BioLegend), anti-CCR7(CD197)-PerCPCy5.5 (G043H7) (BioLegend) and Live/Dead Aqua (Affymetrix eBiosciences) to exclude dead cells. Cells were sorted into six separate CD4+CD3+CD8/14/19−CD25- populations; tetramer+, CXCR3+CCR6+CCR4− (Th*), CXCR3+CCR6−CCR4− (Th1), CXCR3−CCR6+CCR4− (Th17), CXCR3−CCR6−CCR4+ (Th2) and CD4+CD3+CD8/14/19− CD45RA+CD25−CCR7+CXCR3−CCR6−CCR4− (naïve) cells directly in Trizol LS reagents. For RNAseq of activated cells; Th* cells were sorted from purified CD4+ T cells on a BD Aria flow cytometer. These and remaining cells (used as antigen presenting cells, APC) were rested over night in complete RPMI medium at 37°C in 5% CO2. APCs were stained with CFSE according to manufacturer’s instruction (Affymetrix eBioscience). Cells were cultured at a ratio of 2:1 CD4+ T cells:APC in the presence of 5 μg/ml MTB peptide pool or 0.1 μg/ml PMA with 1 μg/ml Ionomycin for 6 h in complete RPMI medium at 37°C in 5% CO2. Unstimulated cells were used to assess nonspecific/background activation. After 6 h, cells were harvested and CFSE negative cells (Th*) were sorted from the APCs on a BD Aria flow cytometer directly in Trizol LS cell lysis reagent. RNA was extracted using miRNease kit from Qiagen following manufacturer's instructions.
Total RNA was purified using miRNAeasy kit (Qiagen) and quantified as described previously (Seumois et al, 2012). 10-15ng of purified total RNA was used for poly A section (Poly(A)Purist Mag kit, Lifetechnologies). Poly A selected RNA was amplified with the Whole Transcriptome Amplification Sequencing Technology kit (SEQR, Sigma) as per manufacturers recommendation. One μg of this amplified cDNA was treated with restriction enzyme (SEQR, Sigma), to remove the primer sequences and then purified using AmpureXP beads (Beckman Coulter). Efficiency of removal of SEQR primer sequences was assessed by PCR. From this step, 250 ng of purified DNA was diluted with Te to obtain a total volume of 65 ul. Diluted cDNA was sonicated with E220 Covaris multiplex sonicator (Covaris) to generate 100-250bp DNA fragments. ~ 250 ng of DNA was used for preparing standard SOLiD sequencing library (5500 SOLiD® Fragment 48 Library Core Kit & Fragment Library Barcode Adaptors 1-96). Following emulsion PCR samples were sequenced on the SOLiD 5500 sequencer to obtain 35bp single end reads (SOLiD™ EZ Bead™ E120 System kits). Both, whole transcriptome amplification and sequencing library preparation were performed in a 96-well format, which significantly reduced hands-on time, besides reducing technical and assay-to-assay variability.

treatment_protocol: Most of samples are directly sorted in Trizol LS. For stimulated samples: complete RPMI medium at 37°C in 5% CO2. APCs were stained with CFSE according to manufacturer’s instruction (Affymetrix eBioscience). Cells were cultured at a ratio of 2:1 CD4+ T cells:APC in the presence of 0.1ug/ml PMA / 1ug/mlIonomycin for 6 h in complete RPMI medium at 37°C in 5% CO2.

value: Th17 cells

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6+, CCR4+, CXCR3- T cells

tag: disease

value: Healthy


title: Ser_15

tag: strain


title: miR-15a

value: miR-15a (final conc. of 50nM)


title: Ser_7


title: control-miR

value: control miR (final conc. of 50nM)


title: Ser_4


title: miR-16

value: miR-16 (final conc. of 50nM)


title: miRNA Salmonella +

source_name: HeLa-229 cells_infected_GFP+

extract_protocol:
Total RNA, including small RNA fraction was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, using standard Illumina protocols

treatment_protocol: Infection with Salmonella enterica serovar Typhimurium strain SL1344 constitutively expressing GFP (MOI 25), analysed 20hpi

value: Salmonella Typhimurium, MOI 25

tag: cell population

value: GFP positive fraction

value: small RNA fraction


title: Ser_5


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor5-PMA-ionomycin

data_processing: Supplementary_files_format_and_content: For visualization of the RNA-seq data in public genome browsers bw files were created using bedGraphToBigWig program from UCSC browser. The source BedGraph files were created by utilizing genomcov function of BEDTools Version 2.14.1-3 (Quinlan  and Hall, 2010)

value: Th* cells (persistent multifunctional memory CD4)

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6+, CCR4-, CXCR3+ T cells - stimulated with PMA/ionomycin

value: Latent tuberculosis infection (LTBI)


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor3-PMA-ionomycin


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor1-PMA-ionomycin


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor1-Medium

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6+, CCR4-, CXCR3+ T cells - stimulated with medium


title: miRNA Salmonella -

source_name: HeLa-229 cells_infected_GFP-

value: HeLa-229 cells

value: GFP negative fraction


title: miRNA mock 2

value: mock

value: non-sorted


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor5-Medium


title: Mock_1


title: Ser_2

value: mouse ESCs (E14)

value: cultured in serum/LIF


title: Ser_3


title: RNA-Seq-Th-TET-Donor2

value: TB antigen tetramer+ cells

value: CD3+, CD4+, CCR7+, CD45RA+, TB Antigenic Tetramer+ T cells


title: miRNA mock 1


title: CT_8

description: Empty MIIs

source_name: Empty MIIs


title: CT_7

description: Empty MIIs


title: CB-ECFCs

city: New York

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were aligned to hg18 using TopHat with default parameters
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript

source_name: cord blood-derived Endothelial colony forming cells

extract_protocol: Illumina TruSeq, PE 51x2 and 101x2


title: RNA-Seq-Th-TET-Donor3


title: H9-ECFCs

source_name: Day 12 H9-hES-derived NRP-1+CD31+ cells

value: Day 12 H9-hES-derived NRP-1+CD31+ cells


title: Ser_6


title: CT_6

description: Empty ESCs

source_name: Empty ESCs


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor1_2

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6+, CCR4-, CXCR3+ T cells


title: human_Exp2siMETTL14


title: hiPS D3

source_name: Day 3 differentiated hiPS-derived mesoderm proginator cells


title: human_Exp2siControl_input

value: siControl


title: miRNA total population

source_name: HeLa-229 cells_infected_total

value: Salmonella Typhimurium, MOI 25


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor2_2


title: CT_5

description: Empty ESCs


title: Ser_1


title: hiPS-ECFCs

source_name: Day 12 hiPS-derived NRP-1+CD31+ cells

value: Day 12 hiPS-derived NRP-1+CD31+ cells


title: RNA-Seq-Th-TET-Donor5


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor3_2

value: Th* cells (persistent multifunctional memory CD4)


title: RNA-Seq-Th-TET-Donor1


title: hiPS D0

source_name: undifferentiated day 0 hiPS cells

value: undifferentiated day 0 hiPS cells


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor5_2

value: Latent tuberculosis infection (LTBI)


title: human_Exp2siControl


title: SynH_LT_Stat1_CHBW

city: Madison

first: Robert

middle: C

last: Landick

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
Basecalling was done on the sequencers using the sequencer's Real-Time Analysis (RTA) software.  CASAVA was used to process the basecalled data into FASTQ format.
FASTQ formatted sequence files from strand-specific Illumina RNA-Seq reads were aligned to the GLBRCE1 reference genome NC_000913 using Bowtie version 0.12.7(Langmead et al., 2009) with '--nofw' strand-specific parameter and maximal distance between the paired reads of 1000 bp. NOTE: Genome NC_000913 (ASM584v2) represents the parental strain.  The strain used in our study was modified from the parental strain by replacing gene pflB with an insertion that contained 3 different genes.
Probabilistic expression counting was performed using the RNA-Seq by Expectation-Maximization (RSEM) version 1.2.4 (Li and Dewey, 2011)
Genome_build: ASM584v2
Supplementary_files_format_and_content: CSV file contains counts generated using RSEM software.  Ribosomal RNA transcripts excluded.

organism: Escherichia coli

source_name: Escherichia coli GLBRCE1

growth_protocol: Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2

extract_protocol:
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C
Total RNA (2ug) was subjected to rRNA depletion using Ribozero rRNA removal kit – Bacteria (Epicenter, illumina). rRNA-depleted RNA was purified using Ampure XP beads. Purified RNA was then fragmented using RNA Fragmentation Reagents (Ambion) at 70C for 2mins, targeting fragments ranging from 200-300bp. Fragmented RNA was then purified using Ampure XP beads (Agencourt). Reverse transcription was performed using SuperScript II Reverse Transcription (Invitrogen) with an initial annealing of random hexamers (Fermentas) at 65C for 5mins, follow by an incubation of 42C for 50mins and an inactivation step at 70C for 10mins. cDNA was then purified with Ampure XP beads. This was followed by second strand synthesis using dNTP mix where dTTP is replaced by dUTP. Reaction was performed at 16C for 1h. Double stranded cDNA fragments were purified and selected for targeted fragments (200-300bp) using Ampure XP beads. The dscDNA were then blunt-ended, the 3' ends were adenylated with a single A, and ligated with library adapters using Kapa Library Amplification Kit (Kapa Biosystems). Adapter-ligated DNA was purified using Ampure XP beads. Digestion of dUTP was then performed using AmpErase UNG (Applied Biosystems) to remove second strand cDNA. Digested cDNA was again cleaned up with Ampure SPRI beads. This was followed by amplification by 10 cycles of PCR using Kapa Library Amplification Kit (Kapa Biosystems). The final library was cleaned up with Ampure SPRI beads. Sequencing was done on the Illumina HiSeq platform generating paired end reads of 100bp each. Note: Target fragments here refers to the insert only, that is the cDNA.  The actual size we use in selection will be larger, typically the target fragment size + 125bp adaptors (~300-450bp).

treatment_protocol: Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C.

tag: medium

tag: growth phase


title: 2i_ESCs_bulk

tag: cell line

value: cultured in 2i/LIF


title: human_Exp2siMETTL3andsiMETTL14


title: 2i_12


title: CT_1

description: FACS Beads

source_name: FACS Beads


title: human_Exp2siMETTL3andsiMETTL14_input


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor9

tag: cell type

value: Healthy


title: SynH_LT_Stat1_BXNZ


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor11


title: SynH_LT_Stat1_BXNB


title: human_Exp2siMETTL3_input


title: SynH_Stat1_CUOC

value: SynH


title: CT_4

description: Empty ESCs


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor8


title: CT_2

description: FACS Beads


title: SynH_Stat1_CBYN


title: human_Exp2siMETTL3


title: 2i_11


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor7


title: 2i_10


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor6


title: 2i_9


title: human_Exp2siKIAA1429_input


title: human_Exp2siKIAA1429


title: SynH_LT_Trans_CBYW

value: Trans


title: SynH_LT_Trans_BXXC


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor10


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor5


title: SynH_LT_Trans_BXNC


title: human_Exp2siWTAP_input

value: siWTAP


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor4


title: SynH_Trans_CUOB


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor3


title: 2i_7

value: mouse ESCs (E14)


title: human_shGFP_1_rep2_input

value: shGFP


title: human_Exp2siWTAP


title: 2i_5


title: 2i_6


title: human_shGFP_1_rep2


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor2


title: SynH_LT_Exp_CBYU

value: Exp


title: 2i_4


title: RNA-Seq_CCR6+CXCR3+CCR4-_Donor1


title: SynH_LT_Exp_BXNX


title: 2i_8


title: RNA-Seq-Th17-Donor10

value: Th17 cells

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6+, CCR4+, CXCR3- T cells


title: human_shGFP_1_rep1_input


title: 2i_3


title: human_shGFP_2_input


title: human_shGFP_1_rep1


title: 2i_2


title: SynH_LT_Exp_CCOG


title: SynH_Exp_BXHU


title: RNA-Seq-Th17-Donor9


title: human_shGFP_2


title: SynH_Exp_CBYS


title: SynH_Trans_CUNZ


title: 2i_1


title: RNA-Seq-Th17-Donor8


title: MII_oocytes_bulk

value: MII (ovulated) oocytes


title: RNA-Seq-Th17-Donor7


title: human_shMETTL3_rep2_input


title: human_shMETTL3_rep2


title: human_shMETTL3_rep1_input


title: RNA-Seq-Th17-Donor5


title: MII_11


title: MII_12


title: RNA-Seq-Th17-Donor4


title: MII_9


title: human_shMETTL3_rep1


title: MII_10


title: human_shMETTL14_3_rep2_input


title: MII_8


title: RNA-Seq-Th17-Donor3


title: human_shMETTL14_1_rep2_input


title: RNA-Seq-Th17-Donor1


title: human_shMETTL14_3_rep2


title: human_Exp2siMETTL14_input


title: RNA-Seq-Th2-Donor10

value: Th2 cells

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6-, CCR4+, CXCR3- T cells


title: human_shMETTL14_1_rep2


title: MII_6


title: human_shMETTL14_3_rep1_input


title: MII_7


title: MII_5


title: mouse_e17Brain

data_processing:
Reads were initially mapped against a set of human or mouse ribosomal RNA (rRNA) sequences using Bowtie (version 0.12.7), and all reads aligning to the rRNA were discarded. All remaining reads were aligned against the human (hg19) or mouse (mm9) genome using Tophat (version 1.4.1). Parameters used were ‘--max-multihits 1 –prefilter-multihits’ and ‘–transcriptome-index’, for which we assigned a pre-indexed version of the relevant transcriptomes, based on the UCSC Known Genes set of annotations. An in-house script was then used to project all reads aligning to the genome upon the human and mouse transcriptomes. Only reads fully matching a transcript structure, as defined by the ‘UCSC Known Genes’ transcriptome annotation, were retained. Such reads were computationally extended in transcriptome space from the beginning of the first read to the end of its mate, and coverage in transcriptome-space was calculated for each nucleotide across all transcripts.
Putative m6A sites were identified using a 3 step-approach, consisting of: (1) Examination of the IP sample, to identify regions within genes in the IP samples that were enriched in comparison to background gene levels; (2) Comparison of IP sample with input sample, to ensure that these regions were not enriched in corresponding input samples; and (3) Comparison across multiple replicates of IP and input samples. Below we provide a detailed description of these steps, which is very similar to the approach used in (Schwartz et al., 2013), with a few extensions and modifications.
(1) Peak detection within genes. To search for enriched peaks in the m6A IP samples, we scanned each gene using sliding windows of 100 nucleotides with 50 nucleotides overlap. Each window was assigned a Peak Over Median (POM) score, defined as mean coverage in the window / median coverage across the gene. Windows with POM scores greater than 4 (i.e., greater than 4-fold enrichment) and with a mean coverage >10 reads were retained. Overlapping windows were merged together, and for each disjoint set of windows in transcriptome space we recorded its start, end, and peak position, corresponding to the position with the maximal coverage across the window.
(2) Ensuring that peaks were absent in input. We repeated the procedure in step (1) for the input sample. We eliminated from all subsequent analysis all windows that were detected in both step (1) and (2).
(3) Comparison of multiple samples and criteria for WTAP-dependence. To compare between different perturbations and/or conditions, we applied the following strategy. We first merged the coordinates of all windows from all samples passing step (1) and (2), to define a set of disjoint windows passing these filters in at least one of the samples. For each such window, we recalculated the peak start, end, peak position, and POM score (as defined above) across each of the samples using the approach in step (1). In addition, for each window we calculated a Peak Over Input (POI) score, corresponding to the fold-change of coverage across the window in the IP sample over the coverage in the input sample. To account for differences in sample depth, we estimated the mean difference between IP and input samples across the 500 most highly expressed genes, which we used as an estimate for background. We subtracted this background from the POI score. Of note, the POM and POI scores generally correlated well with each other; nevertheless, we empirically found that in some cases it was more informative to filter based on the one than on the other.
The provided bed files are provided to facilitate easy browsing of the data. The were produced by first extending each read until the end of its mate in genomic space. Coverage was then calculated individually for the + and - strands using bedtools. The bed files were not used for the data analysis.  TDF files, similarly provided for facilitating browsing via IGV genome browser, were generated using the 'count' command in IGV tools, with parameters `-z 7 -w 5 -e 70`. The tdf files (binary format, summarizing coverage genome-wide) were used for the data analysis.
Genome_build: mm9
Supplementary_files_format_and_content: .bed
Supplementary_files_format_and_content: .tdf

tag: tissue

value: embyronic brain (e17)

value: Brain (embryonic vs adult)


title: RNA-Seq-Th17-Donor6


title: RNA-Seq-Th2-Donor9


title: mouse_e17Brain_input


title: mouse_adultBrain_input

value: adult  Brain


title: RNA-Seq-Th2-Donor8


title: MII_3


title: MII_4


title: human_shMETTL14_1_rep1


title: human_shMETTL14_3_rep1


title: human_shMETTL14_1_rep1_input


title: RNA-Seq-Th2-Donor11


title: mouse_adultBrain


title: MII_2


title: mouse_shGFP

value: Mouse embryonic fibroblasts (MEF)


title: RNA-Seq-Th2-Donor5

value: Latent tuberculosis infection (LTBI)


title: MII_1


title: mouse_shRFP_input

value: shRFP


title: mouse_shGFP_input


title: mouse_DC6_input

value: Dendritic cells

tag: condition

value: 6 hours post LPS stimulation

value: DC stimulated with LPS


title: RNA-Seq-Th2-Donor6

value: Healthy


title: human_shWTAP_rep1_input

tag: knockdown

value: shWTAP


title: human_shWTAP_rep2

tag: antibody


title: mouse_DC6

tag: dynamic program


title: mouse_shMETTL3_3_input


title: human_shWTAP_rep2_input


title: RNA-Seq-Th2-Donor4


title: mouse_shMETTL3_3


title: mouse_DC3

value: 3 hours post LPS stimulation


title: human_shWTAP_rep1


title: mouse_DC3_input


title: RNA-Seq-Th2-Donor7


title: mouse_shMETTL3_2_input


title: human_OKMSiPSC_input

value: OKMS inducible fibroblasts

value: Fully reprogrammed into iPSC

value: iPSC reprogramming


title: RNA-Seq-Th2-Donor1

value: Th2 cells


title: mouse_shMETTL3_2


title: human_OKMSiPSC


title: mouse_DC0

value: Non stimulated


title: RNA-Seq-Th1-Donor11

value: Th1 cells

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6-, CCR4-, CXCR3+ T cells


title: mouse_shRFP


title: RNA-Seq-Th1-Donor9


title: RNA-Seq-Th2-Donor3

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6-, CCR4+, CXCR3- T cells


title: human_OKMSfibrominusDox

value: 5 days after not inducing with Dox


title: human_OKMSfibrominusDox_input


title: RNA-Seq-Th2-Donor2

value: Latent tuberculosis infection (LTBI)


title: mouse_shWTAP_3_input

value: Mouse embryonic fibroblasts (MEF)


title: RNA-Seq-Th1-Donor7


title: RNA-Seq-Th1-Donor8


title: mouse_shWTAP_2_input


title: mouse_shWTAP_3


title: RNA-Seq-Th1-Donor6


title: human_OKMSfibroplusDox

value: 5 days post induction with Dox


title: human_OKMSfibroplusDox_input


title: mouse_shHRNPDL_4_input


title: human_Exp1siControl_input

value: siControl


title: RNA-Seq-Th1-Donor5


title: mouse_DC0_input

value: Dendritic cells

value: DC stimulated with LPS


title: mouse_shWTAP_2


title: RNA-Seq-Th1-Donor4


title: human_Exp1siMETTL3_input


title: human_Exp1siMETTL3


title: RNA-Seq-Th1-Donor10

value: Healthy


title: mouse_shHRNPDL_3_input

value: shHRNPDL


title: mouse_shHRNPDL_3

value: shHNRPDL


title: human_Exp1siWTAP_input

value: siWTAP


title: RNA-Seq-Th1-Donor3


title: ACSH_Stat1_CNFW

value: ACSH


title: ACSH_Stat1_CNGG


title: ACSH_Trans_CIYT

value: Trans


title: human_Exp1siWTAP


title: ACSH_Exp_CIYS

value: Exp


title: human_Exp1siControl


title: WT 0.05 µM AHL R2

description: NGR234 wild type supplemented with 0.05 µM AHLs in exponential phase

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (TRAPL)
Read mapping using segemehl version 0.13 (TRAPL)
Coverage calculation and normalisation (TRAPL)
Genome_build: ASM1854v1 [NC_012587.1, NC_000914.2, NC_012586.1]
Supplementary_files_format_and_content: wiggle file: Normalized  (by total number of aligned reads) read coverages multiplied by 1M  in wiggle format (*_forward.wig = forward strand; *_minus.wig= forward strand)

organism: Sinorhizobium fredii NGR234

growth_protocol: Sinorhizobium fredii NGR234 was grown at 30°C in liquid TY medium (0.5% tryptone, 0.25% yeast extract, 10 mM CaCl2, pH 7.0) at 200 rpm and supplemented with rifampicin (25 µg/ml). NGR234 QS deletion mutants were cultivated under same condition as the NGR234 wild type strain, but the TY medium was additionally supplemented with gentamycin (10 µg/ml).

extract_protocol:
Hot-phenol
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

treatment_protocol: Precultures were established from cryocultures in 5 mL liquid TY medium and cultivated at 30°C and 200 rpm. For early stationary growth phase cultures 200 mL liquid TY medium were inoculated with freshly grown precultures of NGR234 wild type as well as the mutant strains and cultivated for 34-40 h (OD600 3.1-3.3) at 30°C and 200 rpm as batch cultures. Cultures were then separated into fractions of 50 mL, which were transferred into falcon tubes with 10 mL ethanol/phenol (95:5). Samples were mixed well, directly frozen in liquid nitrogen and stored at -70°C until further use. For early exponential growth phase cultures 200 mL liquid TY medium were inoculated with a freshly grown preculture of NGR234 wild type and cultivated at 30°C, 200 rpm till an OD600 of 0.1. Cultures were then divided into two separate fractions of 100 mL; one was supplemented with either 0.05 µM or 50 µM of 3-oxo-C8-HSL (stock solution of 3-oxo-C8-HSL in ethyl acetate) and the control was treated with an equal aliquot of ethyl acetate. Cultures were allowed to grow for three additional hours, then harvested and treated as outlined before.

tag: genotype/variation

value: wild type

value: exponential phase

tag: agent

value: 0.05 µM AHLs


title: WT 50 µM AHL R2

description: NGR234 wild type supplemented with 50 µM AHLs in exponential phase

value: 50 µM AHLs


title: RNA-Seq-Th1-Donor2

value: Th1 cells

value: CD3+, CD4+, CCR7+, CD45RA+, CCR6-, CCR4-, CXCR3+ T cells

value: Latent tuberculosis infection (LTBI)


title: RNA-Seq-Th1-Donor1


title: mouse_shHRNPDL_4

value: Mouse embryonic fibroblasts (MEF)


title: WT 50 µM AHL R1


title: MCF7WS84OHT

city: Washington

first: V

middle: Craig

last: Jordan

state: DC

address: 3800 Reservoir Road NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University

data_processing:
Analysis was performed with the ALEXA-seq software package [PMID: 20835245 and 23704208]
Genome_build: hg18
Supplementary_files_format_and_content: Text file with FPKM measurement per gene

source_name: MCF-7 wild type

extract_protocol:
Total RNA was isolated with an RNeasy Micro kit (Qiagen, Valencia, CA).
These RNA samples were first converted into a library of cDNA fragments. Sequencing adaptors were subsequently added to each cDNA fragment and a 2x100 bp paired-end sequence was obtained from each cDNA using high-throughput sequencing technology (Illumina GAII).

treatment_protocol: Wild-type MCF-7 cells were treated with vehicle control (0.1% ethanol), E2 (10-9 mol/L) and 4-OHT (10-6 mol/L) respectively for 24 hours.

value: breast cancer cell line

tag: treated with

value: 4-OHT (10-6mol/L) for 24 hrs


title: ACSH_Exp_CNFT


title: ACSH_Trans_CNFU


title: WT 0.05 µM AHL R1


title: MCF7WS8E29

value: E2 (10-9mol/L)for 24 hrs


title: WT (exp. Phase) R2

description: NGR234 wild type strain in exponential phase


title: MCF7WS8CON

value: vehicle (0.1% EtOH) as control for 24hrs


title: MCF75CE29PP2V2

data_processing:
The resulting sequence reads were aligned to reference genome build hg19 using TopHat 1.3.0
Aligned sequences were assembled into transcripts. Transcript abundance were estimated as Fragments Per Kilobase of exon per Million fragments mapped (FPKM), using Cufflinks 1.0.3
Differential expression at the level of transcripts was examined using Cuffdiff 1.1.0
Additional analysis was performed with the alternative expression analysis by sequencing (Alexa-seq) software package as previously described [PMID: 20835245].
Genome_build: hg18
Supplementary_files_format_and_content: Text file with FPKM measurement per gene

source_name: MCF-7:5C cells

growth_protocol: MCF-7:5C cells were seeded in 10cm dishes.

extract_protocol:
Cells were harvested in TRIzol. Total RNA was isolated with an RNeasy Micro kit.
These long RNA samples were first converted into a library of cDNA fragments. Sequencing adaptors were subsequently added to each cDNA fragment and a 2x100 bp paired-end sequence was obtained from each cDNA using high-throughput sequencing technology (Illumina GAII).

treatment_protocol: The next day, cells were treated with vehicle (0.1% EtOH) as control, E2 (10-9mol/L), 4-OHT (10-6mol/L), E2 (10-9mol/L) plus 4-OHT (10-6mol/L), PP2 (5x10-6mol/L), and E2 (10-9mol/L) plus PP2 (5x10-6mol/L) respectively for 72 hours.

value: E2 (10-9mol/L) plus PP2 (5x10-6mol/L) for 72 hrs


title: WT (exp. Phase) R1


title: MCF75CPP2V2

value: PP2 (5x10-6mol/L) for 72 hrs


title: ngrl Mutante R2

description: NGR234 ngrI-mutant strain in stationary phase

value: ngrI-mutant

value: stationary phase


title: MCF75C4OHTV2

value: 4-OHT (10-6mol/L) for 72 hrs


title: MCF75CE29V2

value: E2 (10-9mol/L)for 72 hrs


title: ngrl Mutante R1


title: MCF75CCONV2

value: vehicle (0.1% EtOH) as control for 72hrs


title: traI Mutante R2

description: NGR234 traI-mutant strain in stationary phase

value: traI-mutant


title: WT (stat. Phase) R2

description: NGR234 wild type strain in stationary phase

value: wild type


title: WT (stat. Phase) R1


title: C57BL/6J RNA HF Replicate 1

status: Public on Jul 17 2014

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

description: rRNA-depleted RNA

data_processing:
RNA-seq:RNAs were extracted from livers using Trizol (Invitrogen). RNAs were depleted of ribosomal RNA (Epicentre Ribo-Zero™ Magnetic Kit, Cat. MRZH11124). Eluted RNAs were prepared for sequencing using Illumina protocols and sequenced on the HiSeq 2500 (Illumina) to generate 2x100bp paired-end reads. The reads were aligned to the mm9 reference genome with Tophat using the RefSeq gene annotation for transcript reference. Cuffdiff was used to identify differentially expressed transcripts from the RefSeq gene annotation.
RNA-seq: Cuffdiff output format
Genome_build: mm9

source_name: Liver

growth_protocol: Livers were harvested from humanely euthanized mice

extract_protocol: Libraries were prepared according to Illumina instructions for RNA-seq or DNA-seq

treatment_protocol: Mice were fed control or high fat diet

tag: chip antibody

value: liver

tag: diet

value: High Fat


title: C57BL/6J RNA HF Replicate 2

description: rRNA-depleted RNA


title: DBA/2J RNA HF Replicate 1

description: rRNA-depleted RNA


title: DBA/2J RNA Con Replicate 2

description: rRNA-depleted RNA

value: Control


title: C57BL/6J H3K4me1 Con Replicate 1

description: ChIP-seq

data_processing:
ChIP-seq: ChIPs were performed with an anti-H3K4me1 antibody (Abcam, ab8895) using standard ChIP and our published protocols (Leung et al., 2013). Sequencing libraries compatible with Illumina HiSeq 2500 technology was generated using Illumina protocols. We obtained 55M million tags for livers of C57BL/6J control and 71M million reads for tags of C57BL/6J HF. Sequences were aligned to the mm9 reference genome as with FAIRE-seq tags.
ChIP-seq: BEDPE file format
Genome_build: mm9

value: Abcam, ab8895


title: C57BL/6J H3K4me1 Con Replicate 2

description: ChIP-seq


title: C57BL/6J H3K4me1 HF Replicate 1

description: ChIP-seq


title: DBA/2J RNA HF Replicate 2

description: rRNA-depleted RNA

data_processing:
RNA-seq:RNAs were extracted from livers using Trizol (Invitrogen). RNAs were depleted of ribosomal RNA (Epicentre Ribo-Zero™ Magnetic Kit, Cat. MRZH11124). Eluted RNAs were prepared for sequencing using Illumina protocols and sequenced on the HiSeq 2500 (Illumina) to generate 2x100bp paired-end reads. The reads were aligned to the mm9 reference genome with Tophat using the RefSeq gene annotation for transcript reference. Cuffdiff was used to identify differentially expressed transcripts from the RefSeq gene annotation.
ChIP-seq: BEDPE file format
Genome_build: mm9


title: genomic DNA of U2OS cells infected with pRS empty vector

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description: osteosarcoma

data_processing: Alignment: Sequence reads were obtained and mapped to the human hg18 (March, 2006) genomes using the Illumina Genome Analyzer Pipeline.

source_name: Bone

growth_protocol: U2Os cells were maintained in Dubelcco’s modified Eagle’s medium (DMEM, Gibco BRL) supplemented with 10% fetal bovine serum and grown at 37°C under 5% CO2. They are splited three times a week with a 1/4 dilution.

extract_protocol: Genomic DNA was extracted and purified from U2Os cells using Qiagen QiaAMP Kit according to standard instructions. The recommended RNase treatment was performed.

treatment_protocol: After retroviral infection, cells were maitained 6 days in presence of 1µg/ml of puromycin,

tag: transfection

value: pRS empty vector


title: C57BL/6J H3K4me1 HF Replicate 2

description: ChIP-seq

tag: strain


title: C57BL/6J FAIRE Con Replicate 2

description: FAIRE-seq

data_processing:
FAIRE-seq: FAIRE was performed as previously described (Giresi et al., 2007). Isolated DNAs were barcoded and sequenced on the Illumina HiSeq 2500 to produced 100bp x 100bp paired-end reads. Reads were aligned to the mouse genome (version mm9, from the UCSC Genome Browser) using Bowtie2 with default options except for local alignment allowing for 1 mismatch in the seed sequence (Langmead and Salzberg, 2012). To assess the effect of sequence variation on the ability to map tags from DBA/2J liver to the mm9 reference genome, we generated a pseudo DBA/2J reference genome by substituting SNVs into the mm9 genome and performed the same analysis.
FAIRE-seq: narrowPeaks format
Genome_build: mm9


title: DBA/2J FAIRE Con Replicate 1

description: FAIRE-seq


title: DBA/2J FAIRE Con Replicate 2

description: FAIRE-seq


title: DBA/2J FAIRE HF Replicate 2

description: FAIRE-seq


title: C57BL/6J RNA Con Replicate 2

description: rRNA-depleted RNA


title: mRNA-seq MicL-S t10

city: San Francisco

first: Carol

middle: A

last: Gross

institute: UCSF

description: Fragmented, then size selected 25-40bp fragments, for mRNA-seq

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme.
Genome_build: NC000913.2
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

source_name: bacteria

growth_protocol: Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014).

treatment_protocol: At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time.

tag: media

value: fully supplemented MOPS glucose media

tag: plasmid

value: pMicL-S


title: mRNA-seq MicL-S t20


title: mRNA-seq MicL-S t4


title: mRNA-seq MicL-S t0


title: genomic DNA of U2OS cells infected with pRS-CK2 vector

description: osteosarcoma

value: pRS-CK2 vector


title: traI Mutante R1

tag: growth phase


title: DBA/2J FAIRE HF Replicate 1

description: FAIRE-seq


title: C57BL/6J FAIRE HF Replicate 2

description: FAIRE-seq


title: mRNA-seq WT t10

value: empty vector


title: C57BL/6J RNA Con Replicate 1

description: rRNA-depleted RNA


title: mRNA-seq MicL t10

value: pMicL


title: mRNA-seq MicL t4


title: DBA/2J RNA Con Replicate 1

description: rRNA-depleted RNA


title: mRNA-seq Vector t20

source_name: mRNA-seq in rich defined media

tag: molecule subtype

value: mRNA


title: mRNA-seq WT t4


title: ribosome profiling MicL t20

source_name: ribosome profiling in rich defined media

value: ribosome protected mRNA


title: 110

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Paired-end 101bp length output reads were aligned to the human reference genome (UCSC hg19) with TopHat v.2.0.2 (PMID: 19289445) using Bowtie v.0.12.8 (PMID: 19261174). The TopHat parameters explicitly used are tophat -p 30 -G genes.gtf --library-type fr-unstranded -r 100 -F 0.05 --microexon-search.
The annotated RefSeq GTF transcript and fasta genome files were from UCSC and were downloaded from http://cufflinks.cbcb.umd.edu/igenomes.html.  Gene expression was measured as the normalized sum of expression of all its exons. The dexseq_count python script (PMID: 22722343) was used by counting uniquely mapped reads in each exon.
Gene and exon expression normalizations were then performed using the TMM method (PMID: 20196867), and further normalization was applied by adjusting the expression to gene or exon length respectively.
In addition, only the genes and exons that had reads mapped to them in at least 5% of the samples were kept.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM gene and exon values normalized for each Sample (and also normalized by gene and exon length respectively). The processed files also include the genomic coordinates of the genes and exons annotated

source_name: pancreatic islets

extract_protocol:
Pancreatic islets were isolated according to the isolation protocol described from Nordic Islet Transplantation Programme (http://www.nordicislets.org). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets

tag: age

tag: bmi

tag: gender

value: Male

tag: year of birth


title: 108

tag: tissue


title: ribosome profiling MicL t0


title: mRNA-seq MicL t20


title: mRNA-seq MicL t0


title: C57BL/6J FAIRE HF Replicate 1

description: FAIRE-seq


title: 109


title: 101

value: Female


title: C57BL/6J FAIRE Con Replicate 1

description: FAIRE-seq


title: mRNA-seq Vector t0


title: 107


title: 105


title: 85


title: 106


title: 103


title: 102


title: 91


title: 100


title: 89


title: 88


title: 90


title: 80


title: 104


title: 87


title: 86


title: 78


title: 84


title: 82


title: 67


title: 76


title: 71


title: 79


title: 66


title: 73


title: 75


title: 70


title: 81


title: 77


title: 72


title: 64


title: 65


title: 59


title: MCF75CE294OHTV2

tag: cell line

tag: cell type

value: breast cancer cell line

value: E2 (10-9mol/L) plus 4-OHT (10-6mol/L) for 72 hrs


title: 58


title: 52


title: 60


title: 50


title: 62


title: 57


title: 54


title: 55


title: 45


title: 53


title: 44


title: 43


title: 49


title: 40


title: 63


title: 48


title: 33


title: 46


title: 56


title: 42


title: 32


title: 39


title: 37


title: 36


title: 35


title: 38


title: 34


title: 51


title: 24


title: 23


title: 22


title: 30


title: 26


title: 25


title: 21


title: 16


title: ChIP-Seq of Atf3 HDL+CpG BMDM (Atf3 +/+)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
processed data file:
Atf3_HDL_CpG_KOIN_corrected_MACS_peaks_annot.txt,
Atf3_HDL_CpG_wildtype_MACS_peaks_annot.txt

data_processing:
Basecalls performed using CASAVA software version 1.8
ChIP-seq reads were aligned to the NCBI Build 37 (mm9) genome assembly using Bowtie v0.12.8 with following options: -t -q -e 70 -l 28 -n 2 --best  --maxbts 125 -S
After ChIP-seq quality control using HOMER v4.3, reads of biological replicates were pooled, and peaks were called using MACS v1.4.2 without Atf3-deficient BMDMs (standard method) or with Atf3-deficient dataset (KO implemented normalization = KOIN) set as background with following options: -p 1e-4 -g 1.87e9 --on-auto
Annotation of peak positions and counting of normalized Atf3 tag counts in called regions was performed with HOMER v4.3 (annotatePeaks). Peak regions with less than 2 fold change for normalized tag counts in Atf3 +/+ dataset to Atf3 -/- dataset were filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: Annotated MACS peak positions in tab-delimited text format

growth_protocol: BMDMs were obtained by culturing bone marrow cells from 6- to 8-week old WT C57BL/6 mice in DMEM supplemented with 10% (vol/vol) FCS, 10 μg/ml Ciprobay-500 and 40 ng/ml M-CSF (R&D Systems). Six days later, BMDMs were collected and plated. Age- and sex-matched WT control mice were used to derive BMDMs for comparative experiments with Atf3-deficient BMDMs. Immortalized BMDMs were cultured in DMEM supplemented with 10% FCS and 10 μg/ml Ciprobay-500 (D. De Nardo et al.; Nature Immunology 2013)

extract_protocol:
ChIP for Atf3 was performed using the EZ-Magna ChIP G Kit (Millipore) according to the manufacturer's instructions. In brief, three biological replicates of BMDMs from WT and Atf3-deficient mice were treated with HDL, CpG, HDL then CpG or left untreated. Cells were then cross-linked with 1% paraformaldehyde, before they were lysed and chromatin was sheared by sonication for 30 min with the Covaris S220. Immunoprecipitation was performed over night at 4 °C using 2.5 μg of rabbit polyclonal anti-Atf3 antibody (C-19X, Santa Cruz). After washing, eluted samples were reverse cross-linked and treated with RNase A and proteinase K per the manufacturer's recommendations.
ChIP fragments were ligated to NEXTflex ChIP-Seq barcode adaptors using the NEXTflex ChIP-Seq Kit (both BioO Scientific). Adaptor ligated DNA fragments were size-selected (150–250 bp), PCR-amplified, further size selected (150–250 bp), pooled and sequenced on an Illumina HiSeq-1000 sequencer according to the manufacturer's instructions.

treatment_protocol: BMDMs were pretreated with medium alone (ctrl) or 2 mg/ml HDL for 6 h or 2 mg/ml HDL for 6 h followed by stimulation with 100 nM CpG for 4 h

tag: strain background

tag: genotype/variation

value: bone marrow derived macrophage

value: 2 mg/ml HDL for 6 h + 100nM CpG for 4 h

value: rabbit polyclonal anti-Atf3 antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: ChIP-Seq of Atf3 HDL+CpG BMDM (Atf3 -/-)

tag: treated with

tag: chip antibody


title: 20


title: 19


title: 15


title: ChIP-Seq of Atf3 HDL BMDM (Atf3 +/+)

description:
processed data file:
Atf3_HDL_KOIN_corrected_MACS_peaks_annot.txt,
Atf3_HDL_wildtype_MACS_peaks_annot.txt

value: 2 mg/ml HDL for 6 h


title: 14


title: 7


title: 13


title: ChIP-Seq of Atf3 Unstim BMDM (Atf3 -/-)

description:
processed data file:
Atf3_Unstim_KOIN_corrected_MACS_peaks_annot.txt,
Atf3_Unstim_wildtype_MACS_peaks_annot.txt


title: 10


title: 31


title: 6


title: 9


title: 8


title: 4


title: PID 4

city: Yangling

first: Zhao

last: Xing

state: (Click to Select US State)

address: No.3 Taicheng Road, Yangling, Shaanxi, China

department: College of Veterinary Medicine

institute: NORTHWEST A&F UNIVERSITY

data_processing:
Libraries were sequenced using Solexa's proprietary sequencing-by-synthesis method.
After masking of adaptor sequences and removal of contaminated reads, we got the clean reads of full-length small RNA sequences for further analysis.
Genome_build: Sscrofa9
Supplementary_files_format_and_content: tab-delimited text files include non-coding RNA sequences for each sample

organism: Sus scrofa

source_name: pulmonary alveolar macrophages

growth_protocol: Pulmonary alveolar macrophages from pigs infected with H1N1 SwIV were respectively collected  on PID 0, PID4, and PID7.

extract_protocol:
Total RNA from PAM samples was extracted using the mirVana™ miRNA Isolation Kit.
18-30 nt size range of RNA was enriched by polyacrylamide gel electrophoresis and then 20 µg of the purified small RNA from each sample was subject to DNA sequencing with an Illumina Genome Analyzer

value: pulmonary alveolar macrophages

tag: infection

value: H1N1 SwIV

tag: time

value: 4 dpi


title: PID 7

value: 7 dpi


title: ChIP-Seq of Atf3 HDL BMDM (Atf3 -/-)


title: 3


title: PID 0

value: 0 dpi


title: 5


title: 2


title: 12


title: 1


title: MV01_Kar9L

status: Public on Jul 16 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: Sample 3

data_processing:
At Baseclear FASTQ sequence reads were generated using Illumina Casava pipeline version 1.8.2
Quality assesment was based on data passing the Ilumina Chastity filtering. Subsequently, reads containing adapters and/or PhiX control signal were removed using an in-house (At Baseclear) filtering protocol.
RNA-seq reads were mapped with BWA (version 0.5.9-r16) to Kluyveromyces lactis NRRL Y-1140 whole genome
samtools (version 0.1.7-r510) was used to convert the BWA sam output to sorted bam format
cuffdiff, from the cufflinks packages (version 1.0.3), was used to calculate the differential expression between WT (MV01_Kar18L and _18R) and Mutant (MV01_Kar9L and _Kar9R).
Genome_build: Kluyveromyces lactis strain CLIB210/NRRL Y-1140 GCF_000002515.2
Supplementary_files_format_and_content: differential expression between WT and Mutant

organism: Kluyveromyces lactis

source_name: Aerobic batch fermentor

growth_protocol: Growth experiments were conducted in synthetic medium containing salts, trace elements and vitamins, prepared and sterilized as described previously (Verduyn et al., 1992). Glucose was added to a final concentration of 20.0 g L-1 and 3.3g/l arginine was used. Moreover, 3.3 g L-1 potassium sulfate was added to compensate for the removal of ammonium sulfate. Controlled aerobic batch cultures were grown in 2 L laboratory bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.2 L. Culture pH was maintained at pH 6.0 by automatic addition of 2 M KOH (ADI 1030 Biocontroller, Applikon) and temperature was kept constant at 30C (Lauda E300 thermostat, Lauda DR. R. Wosber Gmbh & Co. KG Lauda-Königshofen, Germany). Aeration was achieved by sparging air through the cultures at a flow rate of 0.5 L min-1 continuously stirring at 700 rpm. The exhaust gas of the bioreactor was cooled in a condenser using a cryostat set at 4C (Lauda E100 cryostat). CO2 and O2 concentrations in the off gas were measured with an NGA 2000 analyzer (Rosemount Analytical, Solon, OH).

extract_protocol:
Biomass samples for RNA extractions were sampled from mid-exponential phase of K. lactis strains GG and IMS0367 grown in batch cultivations in bioreactors with chemically defined medium with glucose and arginine as sole N-source. The sampling, the extract
cDNA libraries for the Illumina platform were generated and sequenced at BaseClear BV (Leiden, The Netherlands). cDNA was used as input for library preparation using the Illumina TruSeq DNA library preparation kit (Illumina). Briefly, the DNA was fragmented by nebulization and subjected to end-repair, A-tailing, ligation of adaptors including sample-specific barcodes and size-selection to obtain a library with median insert-size around 200-400 bp. After PCR enrichment, the resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2500 with paired-end protocol
library with a 350 insert size were prepared and sequenced with an Illumina Genome Analyzer II.

treatment_protocol: Broth was directly quenched in liquid nitrogen.

tag: strain

value: Klcar1Δ Arg+; arginase mutant

tag: culture condition

value: aerobic bioreactor batch cultures on glucose chemically defined medium with arginine as sole nitrogen source


title: ChIP-Seq of Atf3 Unstim BMDM (Atf3 +/+)


title: MV01_Kar9R

description: Sample 4


title: MV01_Kar18R

description: Sample 2

value: Klku80Δ KlCAR; reference strain


title: MV01_Kar18L

description: Sample 1


title: meDIP-seq_data_CTRL1

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

institute: University of Cambridge

data_processing:
preprocessing of the raw reads were performed using FastQC and TrimGalore to remove poor quality bases and adapter sequences
reads post-QC were mapped to mouse reference genome NCBIM37/mm9 using BWA v0.6.2
mapped reads were subject to further QC by SAMtools to remove unmapped, unpaired reads and reads with mapping quality score less than 10
differentially methylated regions (DMRs) were identified using MEDIPS
DNA methylation levels across the whole genome were assessed using sliding windows (size 500bp and 200bp to shift the window)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files, scores represent methylation levels

source_name: Sperm

growth_protocol: Sperm was isolated from 2 month old male offspring of control dams or dams undernourished by 50% during the last week of gestation.

extract_protocol:
Sperm DNA was extracted by standard phenol-chloroform extraction, with an overnight proteinase K reaction at 55 degrees.
DNA was sonicated, paired end adaptors ligated and 12 cycles of whole-genome amplification employed using PhusionTM High-Fidelity Taq and paired end Illumina primers.  Libraries were electrophoresed in 2% 1x TAE agarose gels at 95V in 1x TAE buffer followed by excision of a 200bp range band either 200-400bp to 300-500bp according to the peak fragment size.  Identical size ranges were obtained for control and UN libraries.  qPCR for known methylated and unmethylated regions confirmed library quality.

treatment_protocol: Serial centrifugations were used to purify sperm from potential contaminating cells (such as epithelium or white blood cells).

value: ICR

tag: antibody

value: anti-5methyl-cytosine antibody

tag: age

value: two month

tag: treatment

value: control dams


title: WT1_2

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

institute: UCL

description: Healthy control (HC) volunteer.

data_processing:
Primary data analysis: SOLiD 3 System software analysis was used for primary data analysis including image analysis, bead finding, quality metrices and color calls. The software applications used to set and control data analysis included the SOLiD software suite under license agreement. The suite included: Instrument Control Software (ICS), SOLiD Experimental Tracking System (SETS), and SOLiD Analysis Tools (SAT) V3.0. The jobs were managed by the Job Manager. The Corona-Lite v4.0 platform was used. Sequencing was run on the Applied Biosystems SOLiD 3 System to generate sequencing data. Images of each cycle were analyzed, data was clustered and normalized. For each tag, a sequential (sequence-ordered) set of color space calls was produced. Quality metrices were produced through normalization. Two probe sets were used to maximize the fraction of "mappable" amplified beads, read length and sequencing throughput for sequencing of the 50-bp reads. Five rounds of primers (A, B, C, D and E) were used to sequence template by ligation of di-base labeled probes. As the libraries were size fragmented, the set of primers used was specific to the P1 Adaptor. For each library, three types of raw data files were created: .csfasta (the sequenced reads in color space), .qual and .stats. The quality values given in the .qual files are estimate of confidences given for each color call. The quality value q for a particular xcall is mathematically related to its probability of error p. q=-10log10p. The SOLiD QVs are similar to those generated by Phred and the KB basecaller for capillary electrophoresis (references: I. Ewing B., green p., 1998, Base-calling of automated sequencer traces using Phred. II. Error probabilities: Genome Research 8:186-194). The algorithm relies on training (calibration) to a large set of control data and color calls for which the correct call is known. In the SOLiD 3 system, the correct call is determined by mapping the read to a known reference sequence.
Color space conversion: Through color space analysis, sequential ligation of dye-labeled oligonucleotides enabled massively parallel sequencing of clonally amplified DNA fragments through the SOLiD 3 system. Each color represented 4 potential two-base combinations. The conversion into nucleotide base space was conducted during the secondary analysis data phase.
Secondary data analysis: The SOLID secondary data analysis included matching of the reads to the reference genome and generation of base space sequences. The .gff and .sam files were created during this analysis step. The reads were mapped to the human genome version homo_sapiens.GRCh37.56.dna.toplevel.fa database. The alignment software Mapreads was used. Count merging was performed in both pipelines. It employs discontiguous word pattern search algorithms.
Tertiary data analysis: Exon- and junction-level mapping was conducted using Applied BioScope V1.2 software through cloud computing. The analysis was conducted on the ordered genome. Junction mapping was conducted using the splice junction extractor tool. Exon-level mapping was conducted using the counttag BioScope tool.
Genome_build: GRCh37
Supplementary_files_format_and_content: .gff, .bed, and .tab files were created using BioScope.
Supplementary_files_format_and_content: GFF (General Feature Format) is a record-based file format where each line describes a single feature (i.e., read) with a list of tab-delimited fields in a fixed order specified by the GFF specifications. The file type created by the SOLiD 3 system is the .gff v3 file.
Supplementary_files_format_and_content: The .bed files are tab-delimited text files that define a feature track.
Supplementary_files_format_and_content: For each library, .tab files were generated for junctions. The file includes the following fields: Exon-1 (the gene id followed by the exon order on the gene), Exon-1-reference, Exon-1 strand (+/-), Exon-1 start position, Exon-1 end position, Exon-2, Exon-2-reference, Exon-2 strand, Exon-2 start, Exon-2 end, Exon-1-size, Exon-2-size, Exon-1-readcount, Exon-2-readcount, Exon-1-F3-RPKM, Exon-2-F3-RPKM, Exon-distance (distance between two exons; the exon distance is not applicable if it is on a different chromosome), Total-SR-evidence (the total single-read evidence for the junction), Unique-SR-evidence, JCV (a Junction confidence value), Known ("K"  if a junction is known, and "P" if a junction is putative), E1-all-genes (the list of all genes to which exon-1 was mapped), E2-all-genes (the list of all genes to which exon-1 was mapped), Other (other information provided about the junction).
Supplementary_files_format_and_content: RPKM in the .tab files is computed by 10^9x(ExonReadCount/TotalReadCount ExonLength).

source_name: Blood leukocytes, healthy

growth_protocol: Leukocytes were filtered from total blood samples (collected with EDTA vaccutainer tubes) with Ambion Inc. LeukoLOCK™ filters within up to 10 minutes of blood extraction.

extract_protocol:
The captured leukocytes were treated with RNAlater immediately after filtration of the blood and were maintained frozen until RNA extraction.
RNA quality was assessed by running the samples on Agilent RNA 6000 Nano gels (#5067-1511). For each library, ribosomal RNA of 5 ug total RNA was removed using the Invitrogen RiboMinus kit (# A10837-08), and then the sample was concentrated using the RiboMinus™ Concentration Module (Invitrogen). Ribosomal RNA removal was verified by RNA 6000 Nano gel analysis. Library construction was done according to the SOLiD™ Whole Transcriptome Analysis Kit (PN 4425680) protocol. Fragmentation (by RNase III) was verified on Agilent RNA 6000 Pico Kit (#5067-1513), and 150 ng fragmented RNA were used for further protocol. cDNA samples were run on 4% agarose gel, 150-250bp fragments were cut and extracted using the Qiagen Min-Elute Gel Extraction Kit (#28604), and the gel was dissolved by intensive vortexing and not by heating. Libraries were barcoded and amplified for 12 cycles using barcoded primers supplied in the SOLiD™ Transcriptome Multiplexing Kit (Ambion 4427046). Libraries were quantified using the Kapa ABI SOLiD Library Quantification Kit (KK4833) and diluted for final analysis on Agilent High Sensitivity DNA Kit (#5067-4626). 500 uM libraries were used for emulsion PCR according to the Applied Biosystems SOLiD™ 3 System Templated Bead Preparation Guide (4407421 ) to prepare for sequencing on the SOLiD 3 platform.

tag: disease status

value: healthy

tag: gender

value: male

value: blood leukocytes

tag: control volunteer/patient number


title: WT3

description: Healthy control (HC) volunteer.

tag: cell type


title: WT4

description: Parkinson's Disease (PD) patient, pre-DBS.

source_name: Blood leukocytes, PD, pre-DBS

value: Parkinson's Disease (PD)

value: pre-deep brain stimulation (DBS)


title: WT7


title: WT6

description: Parkinson's Disease (PD) patient, post-DBS following 1 hour off electrical stimulation (OFF-Stim).

source_name: Blood leukocytes, PD, post-DBS, OFF-Stim

value: post-deep brain stimulation (DBS) off electrical stimulation 1 hr


title: WT10


title: WT1_1

description: Healthy control (HC) volunteer.


title: WT8

description: Parkinson's Disease (PD) patient, post-DBS on electrical stimulation (ON-Stim).

source_name: Blood leukocytes, PD, post-DBS, ON-Stim

value: post-deep brain stimulation (DBS) on electrical stimulation


title: WT9


title: Kat2a_cKO_C3

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

data_processing:
Base calling was achieved through Illumina's CASAVA pipeline.
Alignment was achieved using BLAST against the miRBase database
Small RNAs were then counted and microRNAs compared using Excel
Genome_build: miRBase release 20
Supplementary_files_format_and_content: CA1_smallRNAome.xls, Excle sheet, Counted reads for each sample

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the suppliers manual. Following DNase1 (life Technologies) treatment for 20 min at 37 °C, RNA was again purified using phenol-chloroform extraction.
Library was constructed using standard Illumina smallRNA sequencing kits. The size of the band excised from the gel was 150bp.

tag: strain background

value: Kat2afl/fl ; CamKIIα-cre+

value: 3-5 months

tag: tissue

value: dissected CA1 hippocampal subfield


title: Kat2a_cKO_C5

tag: genotype/variation


title: Kat2a_cKO_C6


title: WT5


title: meDIP-seq_data_UN1

value: dams undernourished by 50% during the last week of gestation


title: WT12


title: Control_A3


title: Kat2a_cKO_C2


title: WT2

description: Healthy control (HC) volunteer.


title: Kat2a_cKO_novelty-exposed_D7

description:
processed data file: FilteredDifferentialExpression_min_10reads_C-D.txt
processed data file: FilteredDifferentialExpression_min_10reads_B-D.txt

data_processing:
Base calling was achieved through Illumina HiSeq2000 standard pipeline
Alignment was achieved by using STAR aligner version 2.3.0 with following non-default parameters: --outFilterMismatchNmax 2,  --outSAMstrandField intronMotif
Read counting in genes was achieved using HTSeq with the following non-default parameters:  -m intersection-nonempty, –stranded=no
Differential expression calling for pairwise comparisons was done using DESeq2 with the following non-default parameters: cooksCutoff=FALSE
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: *geneCounts.txt: tab delimited text file with read counts
Supplementary_files_format_and_content: FilteredDifferentialExpression*.txt - tab delimited text file with expression values, fold change, p-values and gene annotation

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the suppliers manual. Following DNase1 (life Technologies) treatment for 20 min at 37 °C, RNA was again purified using phenol-chloroform extraction.
Library preparation and cluster generation for mRNA sequencing was performed according to Illumina standard protocols using the TruSeq RNA Sample Prep Kit v2 and the TruSeq Paired-End Cluster Generation Kit v3-cBot-HS (for PE mRNA-seq) with subsequent use of the corresponding TruSeq Cluster Generation Kit 3-cBot-HS (for SE mRNA-seq). Libraries were quality controlled and quantified using a Nanodrop 2000 (Thermo Scientific), an Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit (life Technologies).

value: Kat2afl/fl ; CamKII_alpha-cre+

tag: exposure

value: 15 min novetlty exposure


title: Kat2a_cKO_C4


title: Control_A6


title: Control_A4


title: Control_A5


title: WT11


title: Kat2a_cKO_C1