title: PCB126 BRAIN3 RNA-Seq

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark.
CpG methylation calls were extracted from Bismark aligned bam files using MethylKit.
Differential methylation analysis was carried out by SLIM method using methylKit
RNAseq data was pre-processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts
Genome_build: GRCz10
Supplementary_files_format_and_content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.

organism: Danio rerio

source_name: brain

extract_protocol:
Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit.
Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.

treatment_protocol: Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for 24 hours. After the exposure period, fish were reared in clean water for 7 days before sampling the tissues.

tag: treatment

tag: life history stage


title: PCB126 BRAIN4 RNA-Seq

status: Public on Sep 30 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

value: Adult


title: PCB126 BRAIN2 RNA-Seq


title: CHL1_H3K27Acq_01_DMSO

city: Berlin

first: Ralf

last: Lesche

address: Muellerstr 178

country: Germany

institute: Bayer Pharma AG

library_source: genomic

data_processing:
paired-end genome wide sequencing data were aligned to the human reference genome (assembly hg19) using Bowtie2 software and sorted and indexed using SAMtools
Peak calling was done using the Model-bases analysis for ChIP-seq (MACS2) software. Broad peaks from H3K27Ac were called using MACS2 broad mode. MACS2 was used to generate enrichment pileups (log likelihood ratio (logLR)) of treatment vs. input control samples. A pseudocount of 0.00001 was added to avoid log10(0) during logLR calculation.
ChIP-seq tracks were generated using the Integrative Genomics Viewer software (Thorvaldsdottir et al. 2013). Heatmaps and line plots were generated using the seqplots software (http://przemol.github.io/seqplots).
Genome_build: hg19
Supplementary_files_format_and_content: bw (see UCSC file format FAQ http://www.genome.ucsc.edu/FAQ/FAQformat.html) files reporting enrichment pileup as log likelihood ratio

molecule: genomic DNA

organism: Homo sapiens

source_name: melanoma cancer cell line CHL-1

growth_protocol: CHL-1 melanoma cells were obtained from the American Type Culture Collection (ATCC) and were routinely grown DMEM medium in the presence of 10% (v/v) fetal calf serum (Life Technologies) at 37 °C and in 5% CO2 atmosphere.

extract_protocol:
One 15 cm cell culture dish with 80% confluent cells was used per IP. ChIP DNA preparation for sequencing was carried out as described previously in Nagarajan  et al. (Cell Rep. 2014 Jul 24;8(2):460-9) with the following changes: cross-linked chromatin was sheared to 200-800 base pair fragments using sonication (30 sec on/30 sec off, high power, 2 x 7.5 minutes with a water bath change between the two cycles) in a Biorupter sonicator UCD-200. 1.5 µg antibodies (anti-BRD4 [Bethyl Labs, A301-985A100]; anti-H3K27ac [Diagenode, C15410174]) were used per IP. DNA was purified  using a PCR purification kit (Qiagen)
TrueSeq® ChIP Sample Preparation Guide (Illumina).

treatment_protocol: CHL-1 cells were treated for 4 hr with 500 nM BAY 1238097, OTX-015, or DMSO

tag: cell line

tag: tumor type

value: melanoma

tag: tissue

value: skin

tag: chip antibody

value: anti-H3K27Ac (Diagenode, C15410174)


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 3

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Reads were aligned to the mouse genome (mm9) using TopHat2 (Kim et al., 2013) with the following additional parameters: --no-coverage-search –max-multihits=10 –p 16.
Gene expression was quantified using cuffquant (Trapnell et al., 2013) against a previously-assembled reference transcriptome consisting of UCSC genes supplemented with mouse cortical lncRNAs (Molyneaux et al., 2015).
Differential expression testing was performed using cuffdiff v2.2.1 (RRID:SCRͺ001622), and data were analyzed and visualized using cummeRbund (Trapnell et al., 2013). Additional custom scripts and visualizations were also developed using the cummeRbund framework in R/Bioconductor.
Genome_build: mm9
Supplementary_files_format_and_content: CummeRbund output table containing per-condition gene expression estimates and results of differential tests.

molecule: polyA RNA

organism: Mus musculus

source_name: Ctip2+ sorted corticospinal neurons

extract_protocol:
RNA was recovered from the FACS-purified cells as previously described (Molyneaux et al., 2015), quantified by spectral absorbance on the NanoDrop, and qualitatively assessed on the Agilent Bioanalyzer RNA-6000 Pico chip. RNA integrity numbers (RINs) for all samples ranged between 8.3 and 10.
For each enriched sample, 10 ng of total RNA was reverse transcribed to synthesize cDNA using the Smart seq2 V4 kit (Clontech). Amplified cDNA was used as input for high-throughput RNA sequencing library preparation using the Nextera XT library kit (Illumina). Individual libraries were indexed, pooled, and sequenced to a mean depth of 5.466 x 107-125 bp paired-end reads per sample.

treatment_protocol: hSOD1G93A and hSOD1WT P5-7 mice were used for expression profiling. For each biological replicate, the cortex was isolated and dissociated into a single-cell suspension as previously described (Molyneaux et al., 2015). Cells were then immediately fixed in 4% PFA, incubated in RNase free conditions with antibodies against the nuclear markers CTIP2 and SATB2 (Rat anti-CTIP2, 1:100, Abcam, Cat. No. ab18465, RRID:AB_2064130; Mouse anti-SATB2, 1:250, Abcam, Cat. No. ab51502, RRID:AB_882455; Alexa 546 goat anti-rat, 1:1000, Molecular Probes, Cat. No. A11081, RRID:AB_141738; Alexa 488 goat anti-mouse, 1:1000, Molecular Probes, Cat. No. A11011, RRID:AB_2534069), and FACS-sorted as previously described to isolate SATB2-positive and CTIP2-positive neurons (Molyneaux et al., 2015).

value: cortex

tag: cell type

value: corticospinal neurons

tag: strain

tag: transgene

tag: developmental age

tag: enrichment


title: 3mo_Ret-EGFP_F_L6S1_A

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
URL: http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A22280
GUDMAP ID: 22280

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b (GRCm38.76 using the GRCm38.p2 assembly).  Low base quality reads and adaptors are clipped.  The 7 bp index used is AATACGC, the reverse complement is in the reverse primers used in library preparation denoted by "N" (CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA). Enumerate all known genes with raw counts to the matching gtf file from the same reference build from Ensembl with Subread:featureCounts (version 1.4.5) using the Ensembl gene ID as the key. Use the Sailfish package to estimate known transcript/isoform expression if needed. Use the counts listed in the output in the Subread:featureCounts files to generate Countsper-Million (CPM) normalized values for heat map generation (Sailfish/Salmon already produces CPM values in it’s output) if needed.
assembly: mm10
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
format and content:  Text file with raw gene counts

source_name: 3 month female Ret-EGFP mouse L6S1 DRG sample A

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest).  We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9uL) was reverse transcribed and amplified using the SMARTer Ultra Low Input RNA for Illumina  Sequencing - HV (Clontech, cat# 634828) according to the manufacturer's instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeq ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA.  Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 28 pooled DRGs dissected from 7 Ret-EGFP mice at spinal segment  levels L6 & S1. Following DRG dissection, cells were FACS sorted (Adult mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

tag: genotype

value: Tg(Ret-EGFP)SJ

value: L6S1 dorsal root ganglion

tag: age

tag: Sex

value: female

tag: pooled sample

value: yes

tag: pool size

value: Pooled sample of 28 DRGs from 7 mice


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 2


title: CONTROL BRAIN4 RNA-Seq

value: DMSO


title: CHL1_H3K27Acq_01_BAY


title: CHL1_BRD4_OTX_01

value: anti-BRD4 (Bethyl Labs, A301-985A100)


title: CHL1_input_D4_01


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 0


title: CONTROL BRAIN3 RNA-Seq


title: PCB126 BRAIN1 RNA-Seq


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*WT)2Gur/J replicate 1


title: CONTROL BRAIN2 RNA-Seq


title: siEZH2-3

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCh38.p2 (hg38) + Gencode-23 Annotation
Supplementary_files_format_and_content: raw count matrix in tab-delimited text file, one column for each sample

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For fluid shear stress experiments, HUVECs were exposed to atheroprotective flow (fluid shear stress) for 48 h, n=2. For EZH2 depletion experiments, HUVECs at 80% confluence were transfected with 20 nM Silencer® Select Negative Control #1 siRNA (#S25503, Thermo Fisher Scientific) (siCon) or Silencer® Select EZH2 siRNA (#s4916, Thermo Fisher Scientific) (siEZH2) using Lipofectamine 2000 (Thermo Fisher Scientific) for 48 h, n=3. Then, total RNA was harvested for RNA-sequencing study.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: passage

value: passage 3 to passage 5

tag: transfected with

value: EZH2 siRNA for 48 hrs


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 3


title: CHL1_BRD4_D4_01


title: CONTROL BRAIN1 RNA-Seq

tag: treatment

tag: life history stage


title: Corticocotical Neurons (Satb2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 2

source_name: Satb2+ sorted corticocortical neurons


title: siEZH2-2


title: PCB126 LIVER4 RNA-Seq

source_name: liver


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 2


title: CHL1_H3K27Acq_01_OTX

tag: cell line

tag: tumor type


title: siEZH2-1


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 1

tag: tissue


title: PCB126 LIVER3 RNA-Seq


title: siCon-3

tag: cell type

value: control siRNA for 48hrs


title: Corticospinal Neurons (Ctip2+) B6SJL-Tg(hSOD1*G93A)1Gur/J replicate 0

tag: strain


title: PCB126 LIVER2 RNA-Seq

value: Adult


title: siCon-2


title: PCB126 LIVER1 RNA-Seq


title: siCon-1


title: CONTROL LIVER3 RNA-Seq


title: s-flow-2

tag: exposed to

value: atheroprotective laminar flow (shear stress=12 dyne/cm2) for 48 h


title: CONTROL LIVER4 RNA-Seq


title: CONTROL LIVER1 RNA-Seq


title: s-flow-1


title: static-1


title: static-2


title: Rep3_2Days_AplusN

city: Portland

first: James

middle: Christopher

last: McGann

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Vollum Institute

institute: Oregon Health and Science University

data_processing:
Sequenced reads were trimmed of first 11 nucleotides which were of low read quality, then mapped to the mouse mm9 genome using Subread (default settings)
Raw gene level counts were calculated using FeatureCounts (default settings)
Genome_build: mm9
Supplementary_files_format_and_content: raw read counts for each gene in comma-separated values (.csv) format

source_name: Dissected P0 cortical astrocytes in culture for 2 weeks

growth_protocol: Astrocytes were dissected and grown in culture in DMEM with 10% FBS and 2mM glutamate with pen/strep and expanded at 80% confluency with TrypLE. When confluent, astrocytes were treated by plating 1x10^6 dissected hippocampal neurons from TdTomato+ P0 mice

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) followed by Ribogone treatment for mammalian cells (Clontech)
cDNA synthesis and indexed Illumina libraries were made using the SMARTer Universal Low Input RNA kit for Sequencing and the SMARTer Low Input Library Prep Kit. Six libraries were mixed at equal concentration and sequenced by an Illumina HiSeq 2000 sequencer at the OSU Center for Genome Research and Biocomputing

treatment_protocol: Cells were incubated in TrypLE for 10mins and centrifuged to collect cells, then resuspended in PBS and subjected to FACS sorting by TdTomato fluorescence.

value: Astrocye

value: P0-dissected hippocampal neurons

tag: days grown


title: Rep3_2DaysAonly


title: Rep2_7Days_AplusN


title: Rep3_7DaysAonly


title: Ta3_2_BL

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.8 software used for basecalling.
Illumina reads were mapped to the EnsemblProtists release of the Phaeodactylum tricornutum genome using CLC workbench with default parameters.
The resulting raw read counts were used for downstream analyses.
RNAseq data were statistically evaluated using edgeR on raw read counts as implemented in Bioconductor. Genes were called significantly differentially expressed if the FDR (q) value was below 0.01.
Transcripts per million (TPM) and Reads Per Kilobase per Million mapped reads (RPKM) were reported for all transcripts. TPM and RPKM values were averaged for the replicates of each condition.
Supplementary_files_format_and_content: Excel sheet (Supplemental Table S1.xls) file including gene name, gene length, raw counts, TPM for each sample and mean TPM for biological replicates, log2 fold-changes between blue light and dark values and mutants and wildtype, and edgeR results (q-values) of differential gene expression analysis comparing blue light versus dark and mutants versus wild type transcript abundances of each diatom line,  RPKM values for each sample and average RPKM values.

organism: Phaeodactylum tricornutum

source_name: Ta3, 1 h Blue light

growth_protocol: Phaeodactylum strains were grown in batch cultures under controlled conditions (16/8-h light/dark cycle, 18 °C, 40 µmol photons m-2 s-1, start cell density of 1 miliion cells ml-1).

extract_protocol:
Cells were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground cells using TRIzol. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared from 1 µg RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed  and sequenced in single-end mode (100 bp read length) on an Illumina HiSeq 2000 platform.

treatment_protocol: After 4 days growth under standard conditions cells were kept in constant darkness for 72 h and the "dark" (dark) sample harvested. Afterwards the strains were illuminated with blue light (SuperFlux LED, Lumitronix, 465 nm, 10 µmol m-2 s-1) for 1 h and the "blue light" (BL) sample harvested. Besides the change in light condtions all other growth parameters were kept constant.

value: UTEX 646

tag: light condition

value: 1 h Blue light

value: whole cell


title: Rep2_4Days_AplusN


title: Rep3_4DaysAonly


title: Rep3_7Days_AplusN


title: Na1_2_BL

source_name: Na1, 1 h Blue light

tag: genotype


title: Rep2_4DaysAonly


title: Na1_1_BL


title: WT_3_BL

source_name: Wildtype, 1 h Blue light

value: Wildtype


title: WT_2_BL


title: Rep3_4Days_AplusN


title: Ta3_1_BL


title: Rep2_2DaysAonly


title: CONTROL LIVER2 RNA-Seq


title: Rep2_2Days_AplusN


title: Rep1_7Days_AplusN


title: WT_1_BL


title: Rep1_7DaysAonly


title: Ta3_2_dark

source_name: Ta3, dark

value: dark


title: Rep2_7DaysAonly


title: Na1_3_BL


title: Ta3_1_dark


title: Rep1_4DaysAonly


title: PCB126 BRAIN4 Bisulfite-Seq (reduced representation)


title: Na1_2_dark

source_name: Na1, dark


title: Na1_1_dark


title: WT_3_dark

source_name: Wildtype, dark


title: WT_1_dark


title: Rep1_2DaysAonly


title: PCB126 BRAIN2 Bisulfite-Seq (reduced representation)


title: WT_2_dark


title: PCB126 BRAIN1 Bisulfite-Seq (reduced representation)


title: Rep1_4Days_AplusN


title: CONTROL BRAIN2 Bisulfite-Seq (reduced representation)


title: CONTROL BRAIN1 Bisulfite-Seq (reduced representation)


title: CONTROL LIVER3 Bisulfite-Seq (reduced representation)


title: PCB126 LIVER1 Bisulfite-Seq (reduced representation)


title: Rep1_2Days_AplusN


title: PCB126 LIVER2 Bisulfite-Seq (reduced representation)


title: 0.2% γ-T rep 4

city: Piscataway

first: Nanjoo

last: Suh

state: NJ

address: 164 Frelinghuysen Road

institute: Rutgers University

description:
processed data file:
E2_vs_gamma-T_gene_exp.diff

data_processing:
Align fastq files to the reference genome (rn6) using tophat2
Assemble transcripts using cufflinks for each samples
Run cuffmerge on all assemblies to create a single merged transcriptome annotation
Run cuffdiff to compare experimental group to E2 control
Genome_build: rn6
Supplementary_files_format_and_content: Diff file represting differentially gene genes, RPKM, p-value, q-value and significance from comparison of E2 control vs 0.2% δ-T, 0.2% γ-T, 0.2% α-T, or 0.2% γ-Tm

organism: Rattus norvegicus

source_name: Mammary tumor

extract_protocol:
Mammary tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats are treated with 0.2% δ-T, 0.2% γ-T, 0.2% α-T, or 0.2% γ-TmT for 30 weeks

value: ACI

value: Mammary tumor

tag: age

value: 40 weeks old


title: CONTROL LIVER4 Bisulfite-Seq (reduced representation)

value: DMSO


title: CONTROL LIVER2 Bisulfite-Seq (reduced representation)


title: 0.2% γ-T rep 3


title: PCB126 LIVER4 Bisulfite-Seq (reduced representation)


title: PCB126 LIVER3 Bisulfite-Seq (reduced representation)


title: 0.2% δ-T rep 1

description:
processed data file:
E2_vs_delta-T_gene_exp.diff


title: 0.2% γ-T rep 2


title: 0.2% α-T rep 4

description:
processed data file:
E2_vs_alpha-T_gene_exp.diff


title: 0.2% δ-T rep 2


title: 0.2% γ-T rep 1


title: CONTROL LIVER1 Bisulfite-Seq (reduced representation)


title: 0.2% α-T rep 3


title: 0.2% δ-T rep 4


title: 0.2% α-T rep 1


title: CONTROL BRAIN4 Bisulfite-Seq (reduced representation)


title: 0.2% δ-T rep 3


title: CONTROL BRAIN3 Bisulfite-Seq (reduced representation)


title: 0.2% γ-TmT rep 4

description:
processed data file:
E2_vs_gamma-TmT_gene_exp.diff


title: 0.2% γ-TmT rep 3


title: 0.2% α-T rep 2


title: 0.2% γ-TmT rep 2


title: 0.2% γ-TmT rep 1


title: Estrogen (E2) control rep 4

description: processed data file:


title: Estrogen (E2) control rep 3

description: processed data file:


title: Estrogen (E2) control rep 1

description: processed data file:


title: PCB126 BRAIN3 Bisulfite-Seq (reduced representation)


title: Estrogen (E2) control rep 2

description: processed data file:


title: Arundinella. anomala

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

description: FPKM.xlsx

data_processing:
quality control
assemble contig using trinity
blastx contigs to maize protein to annotate the assembled contigs
Calclate the transcipt abundance of contig using RSEM method
Supplementary_files_format_and_content: FPKM.xlsx contains the transcript abundance of all genes

organism: Arundinella anomala

source_name: Whole Leaf

growth_protocol: Plants were grown in the environmentally controlled growth room with a long photoperiod (16 h light/8 h dark) at 22°C

extract_protocol:
Total RNA were extracted on fresh 3rd leaf tissue by commercial PureLink® RNA Mini Kit followed company’s protocol
The cDNA libraries were constructed following Illumina TruSeqTM RNA sample preparation version 2 guide (catalog # RS-930–1021)

tag: development stage

value: mature

value: Wild type

value: Leaf


title: LIB014416_TRA00035336

city: Boston

first: Jessica

last: Whited

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Trinity was used for de novo transcriptome assembly performed by Stirplate.
Counts of RNA-seq fragments mapping to transcripts in our assembly were determined for each tissue type using RSEM .
Genome_build: n/a currently for axoltol
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TMM-normalized FPKMs for each Sample
Supplementary_files_format_and_content: Trinity_transcripts.counts.matrix: abundance measurements (fragment counts)
Supplementary_files_format_and_content: Trinity_transcripts.TMM.fpkm.matrix: abundance measurements (FPKM)

organism: Ambystoma mexicanum

source_name: Limb stump

extract_protocol:
RNA was harvested using Trizol reagent. The Illumina TruSeq v2 protocol was used to generate barcoded sequencing libraries. Paired-end, 50bp sequencing was performed on the Illumina HiSeq 2500 at Harvard Medical School's Biopolymers facility.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 protocol.

tag: condition

value: Control

value: Limb stump

value: wild-type

value: leucistic


title: LIB014416_TRA00035337


title: Arundinella. fluviatilis

description: FPKM.xlsx

organism: Arundinella fluviatilis


title: LIB014416_TRA00035335


title: LIB014416_TRA00035333

value: Multi-amp


title: Arundinella. pubescens

description: FPKM.xlsx

organism: Arundinella pubescens


title: LIB014416_TRA00035334


title: Imperata. cylindrica

description: FPKM.xlsx

organism: Imperata cylindrica


title: LIB014416_TRA00035330


title: CHL1_input_DMSO_02

value: melanoma

value: skin

tag: chip antibody


title: Capillipedium. parviflorum

description: FPKM.xlsx

organism: Capillipedium parviflorum


title: Bothriochloa. ischaemum

description: FPKM.xlsx

organism: Bothriochloa ischaemum


title: LIB014416_TRA00035332


title: LIB014416_TRA00035331


title: Arundinella. hirta

description: FPKM.xlsx

organism: Arundinella hirta


title: Arundinella. nepalensis

description: FPKM.xlsx

organism: Arundinella nepalensis


title: Non-targeting control siRNA on A375

status: Public on Sep 29 2017

city: Leuven

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
Raw Fastq files of the same sample were merged and adapter sequences were removed using fastq-mcf
RNA-seq reads were mapped to the genome (hg19) using STAR (v2.5.1b)
Reads with high mapping quality (Q4) were selected using SAMtools (v1.4)
Read counts per gene were obtained from the aligned reads using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including gene-sumarized counts for each sample (output from htseq-count)

growth_protocol: A375 cells were obtained from the ATCC and were cultured in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Lonza) and penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol:
Total RNA was extracted 72 hours after knockdown, using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions.
Quality checks were performed using the Bioanalyzer 1,000 DNA chip (Agilent) after which libraries were constructed:  After total RNA purification, mRNA was enriched using the Dynabeads mRNA purification kit (Invitrogen). To make cDNA, 1 µl of oligo(dT) primers (500ng/µl; Ambion) and 1 µl of 10 mM dNTP (Promega) was added to 10 µl of polyA-selected mRNA; incubated at 65°C for 5 min and placed on ice. First-strand cDNA synthesis was performed by adding 4 µl of first strand buffer (Invitrogen), 2 µl of 100 mM DTT (Invitrogen) and 1 µl of Superscript II (Invitrogen) and incubating the mix at 42°C for 50 min, then 70°C for 15 min. The second strand of cDNA was filled in by adding 35 µl of water, 15 µl of 5x second strand buffer (Invitrogen), 1.5 µl of 10 mM dNTP, 0.5 µl of 10 U/µl E Coli DNA ligase (Bioke), 2 µl of 10 U/µl E Coli DNA polymerase I (Bioke), 1 µl of 2 U/µl E Coli RNaseH and then incubating at 16°C for 2 hours. The cDNA was purified on a MinElute column (Qiagen) and eluted in 15 µl EB buffer. To incorporate sequencing adapters, we combined the purified cDNA with 4 µl of Nextera TD buffer (Illumina) and 1 µl of Nextera Tn5 enzyme (Illumina) on ice and incubated at 55°C for 5 min. The tagmented cDNA was purified again on a MinElute column and eluted in 20 µl EB buffer. To PCR amplify the fragments, we added 25 µl of NEBnext PCR master mix (Bioke), 5 µl of Nextera primer mix and incubated at 72°C for 5 min, then at 98°C for 30 sec, followed by 15 cycles of 98°C for 10 sec, 63°C for 30 sec and 72°C for 3 min. We purified the PCR amplicons with 55 µl AMPure beads (Analis).

treatment_protocol: Knockdown of NFATC2 was performed using the ON-TARGETplus NFATC2 siRNA SMARTpool (Dharmacon) at a final concentration of 40nM in opti-MEM medium (ThermoFisher Scientific).

value: melanoma cell line

tag: treated with

value: Non-targeting control siRNA


title: NFATC2 siRNA on A375

value: NFATC2 siRNA


title: Medicago / Rhizophagus replicate 2

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

description:
RAW Ri Mt vs ERM
32_AGTCAA_L004

data_processing:
Reads from R. irregularis symbiotic samples and extraradical mycelium (ERM) samples were mapped back to the Gloin1 genre repertoire to calculate gene expression as RPKM, using RNA-seq functionality in CLC software with the settings of minimum mapped read length fraction at 0.95 and minimum similarity at 0.98. To find the NRVTs significantly upregulated during symbiosis, the RPKM of R. irregularis gene in symbiotic samples were compared to their respective ERM using proportion-based test statistics with a False Discovery Rate (FDR) correction for multiple testing. R. irregularis genes were considered as significantly upregulated when meeting the requirements of RPKM fold change>5 and FDR corrected p value<0.05.
Genome_build: GCA_000439145.2

organism: Medicago truncatula

source_name: M. truncatula roots associated with R. irregularis

growth_protocol: To increase colonization of M. truncatula and B. distachyon, a nursery system was used: Leek seeds (Allium porum cv. Elboeuf) were germinated on vermiculite for 2 weeks at room temperature, and then transferred to 4L pots with sterile charred clay (Oil-dri, Klasmann, France) as substrate, mixed with 400sp/L of R. irregularis. Leeks were grown for 3 months at 25/22°C under a long day photoperiod (16h/8h) with 80% humidity. Seeds of M. truncatula A17 were surface sterilized with 3.2% sodium hypochlorite for 10 min, 95% ethanol for 2 min and washed four times with sterile distiled water. Seeds were germinated on water agar 1% for 5 days at 4°C in the dark. Seeds of B. distachyon were surface sterilized with Ethanol 70% for 30 seconds, rinsed with water and treated with 10% sodium hypochlorite added with a drop of tween 20 for 20 minutes under agitation. Seeds were rinsed 3 times for 5 minutes with sterile water, and soaked in water for 1 hour. They were finaly rinsed 3 times and germinated for 3 days on water agar 0,7% at 22°C under 16h photoperiod. Seedlings were than transferred to pots containing mycorrhized Leeks to increase fungal colonization. Plantlets were removed after 3 weeks, they were transferred in 250mL pots with sterile charred clay as substrate and grown for 2 weeks. Root colonization reached 67% and 42% for M. truncatula and B. distachyon respectively. Lunulari cruciata (liverwort) subcultures were cultivated in vitro on solid M medium (4% phytagel) + sucrose, in association with R. irregularis under a long day photoperiod (16h/8h). After 6 weeks, thalli were harvested and distal parts were cut with a scalpel and discarded, as these zone are not colonized by the fungus. To generate extra radical mycelium, R. irregularis was cultivated in association with Daucus carota in split plate on solid M medium (4g/L phytagel) at 22°C in the dark. Once the fungal compartment was colonized, the gel was removed with a scalpel and replaced by liquid M medium without sucrose. After two weeks of growth in the same previous conditions, ERM were collected with forceps and frozen with liquid nitrogen.

extract_protocol:
Plant roots and extra radical mycelium were collected and crushed with a motar and a pestle in liquid nitrogen and mRNA were extracted using RNeasy plant kit (Qiagen), according to the manufacturer instructions.
Samples were sequenced at the Genome and Transriptome platform (Toulouse, France). mRNA were isolated with polyT beads before processing, libraries were constructed according to the manufacturer's protocol.

treatment_protocol: no treatment was applied

tag: fungal strain

tag: plant specie

value: Medicago truncatula A17

value: Roots


title: Lunularia / Rhizophagus replicate 2

description:
RAW Ri Lc vs ERM
62_TTAGGC_L001

organism: Lunularia cruciata

source_name: L. cruciata thalli associated with R. irregularis

value: Lunularia cruciata


title: Lunularia / Rhizophagus replicate 1

description:
RAW Ri Lc vs ERM
61_ATCACG_L001


title: Lunularia / Rhizophagus replicate 3

description:
RAW Ri Lc vs ERM
63_ACTTGA_L001


title: Medicago / Rhizophagus replicate 1

description:
RAW Ri Mt vs ERM
31etoile_AGTTCC_L004


title: RNA-seq_QK_27c_4hr

city: Cambridge

first: Sandra

last: Cortijo

address: Bateman Street

institute: Sainsbury Laboratory, Cambridge University

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: QK hsfa1abde mutant

growth_protocol: Seedlings were grown at 17c in long days for 10 days and collected after 15min, 1hr or 4hrs of shift at 17c, 27c or 37c. Shifts were done at ZT1

extract_protocol:
Total RNA was isolated from 30 mg of grinded seedlings using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using 1 ug of high integrity total RNA (RIN>8) using the TruSeq Stranded mRNA library preparation kit and TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2101 and RS-122-2001), following manufacturer’s instruction. The libraries were sequenced on a HiSeq2000 using paired-end sequencing of 100 bp in length at Max Planck Institute (MPI) Tubingen and the Beijing Genomics Institute (BGI) sequencing centres.

tag: shift experiment

tag: temperature

tag: incubation time

tag: replicate


title: RNA-seq_QK_17c_1hr


title: RNA-seq_QK_17c_4hr


title: Medicago / Rhizophagus replicate 3

description:
RAW Ri Mt vs ERM
33_ATGTCA_L004

tag: tissue


title: RNA-seq_QK_17c_0min


title: RNA-seq_TK_27c_1hr

source_name: TK Wild Type


title: RNA-seq_QK_27c_1hr


title: RNA-seq_TK_27c_4hr


title: RNA-seq_QK_27c_15min


title: RNA-seq_TK_17c_1hr


title: RNA-seq_TK_17c_15min


title: RNA-seq_TK_17c_0min


title: RNA-seq_QK_17c_15min


title: RNA-seq_TK_17c_4hr


title: HSFA1A_ChIP-seq_37c_15min

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC  (www.bioinformatics.babraham.ac.uk/projects/fastqc/).   Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 reference genome using Bowtie2 (Langmead et al., 2009). Potential optical duplicates were removed using Picard, as described earlier. The read counts mapped to each bp in each sample was normalised by the sample’s genome-wide mappable reads coverage per bp, and used in the subsequent statistical analyses. The nucleosome and ChIP profiles were binned to generate a “pileup” ChIP profiles for different groups of genes/promoters using in-house R and Perl scripts. Nucleosome positioning and occupancy was determined using DANPOS (Chen et al., 2013). HSF1 peaks were analysed using MACS (Zhang et al., 2008) and PeakAnalyzer (Salmon-Divon et al., 2010).
The nucleosome and ChIP profiles were binned to generate “pileup” ChIP profiles at TSS  using in-house R and Perl scripts. We restricted the analyse to the genes of 750 bp or longer in length, and with at least 500 bp upstream intergenic region between the adjacent genes, in order to avoid false gene body H2A.Z signal influenced by H2A.Z that marks the start or stop of the adjacent genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: text files with binned reads at TSS.

source_name: Col0 HSFA1A::HSFA1A:FLAG seedlings

growth_protocol: Seedlings were grown at 17c in long days for 12 days and collected after 15min, 1hr or 4hrs of shift 17c, 27c or 37c.

extract_protocol:
ChIP was performed as described (Gendrel et al., 2002) with minor modifications. In brief, chromatin was extracted from 1 g of crosslinked materials. For HTA11 (a highly expressed H2A.Z gene) and H3, the chromatin was resuspended in MNase digestion buffer (20mM Tris-HCl [pH8], 50mM NaCl, 1mM DTT, 0.5% NP-40, 1mM CaCl2, 0.5mM phenylmethylsulfonyl fluoride (PMSF) and 1X protease inhibitor cocktail [Roche]), and digested with 0.4U/ml of Micrococcal nuclease (MNase, Sigma, N3755) for 15 min. Digestion was stopped with 5 mM EDTA. For HSF1, chromatin was fragmented by sonication using a bioruptor (Diagenode) in lysis buffer (10 mM Tris-HCl [pH 8], 150 mM NaCl, 1 mM EDTA [pH 8], 0.1% deoxycholate, and 1X protease inhibitor cocktail). All ChIPs were performed in a buffer containing 20mM Tris-HCl (pH8), 150mM NaCl, 2mM EDTA, 1% triton X-100 and 1X protease inhibitor cocktail. ChIP were performed for HTA11 and HSF1 using FLAG M2 magnetic beads (Sigma, M8823) and for H3 using H3 antibody (Abcam, ab1791) coupled to a 1/1 mix of protein-A and protein-G Dynabeads (life technologies, 10001D and 10003D). All ChIPs were performed in a buffer containing 10 mM Tris-HCl [pH 8.0], 5 mM EDTA [pH 8.0], 150 mM NaCl, 1% Triton X-100, and 1× protease inhibitor cocktail. The elution was done for HTA11 and HSF1 ChIP with 100ng/ul of 3XFLAG in TE buffer and for H3 ChIP with elution buffer (1% SDS, 0.1M NaHCO3).
The efficiency of ChIP materials was assessed by qPCR in prior to in-house library preparation, using the TruSeq ChIP sample preparation kit (Illumina, IP-202-1012) following the manufacturer’s instructions. The libraries were sequenced on HiSeq2000 by MPI Tubingen and BGI using paired-end 100bp length reads, and on NextSeq500 at the Cambridge Genomic Services sequencing facility, Department of Pathology, University of Cambridge and at the Sainsbury Laboratory Cambridge University using paired-end 75 bp length reads .

tag: cultivar

value: seedling

tag: shift experiment type (17>27c or 17c>37c)

tag: fragmentation method (mnase digestion or sonication)

value: sonication

value: Anti-FLAG® M2 Magnetic Beads (M8823 SIGMA)


title: HSFA1A_ChIP-seq_INPUT

source_name: Col0 WT seedlings

value: wildtype


title: H2B_ChIP-seq_27c_4hr

description: This sample was not analyzed; no processed data available.

value: MNase (mononucleosome)

value: Anti Histone H2B antibody (Abcam ab1790)


title: PolII_ChIP_seq_17c_15min

value: Anti PolII antibody (Abca, ab817)


title: RNA-seq_TK_27c_15min


title: HSFA1A_ChIP-seq_27c_15min


title: PolII_ChIP_seq_27c_15min


title: H2B_ChIP-seq_27c_1hr


title: H2B_ChIP-seq_27c_15min


title: H2B_ChIP-seq_17c_15min


title: H3_ChIP-seq_27c_4hr_rep2

value: Anti Histone H3 antibody (Abcam ab1791)


title: H3_ChIP-seq_27c_1hr_rep2


title: H3_ChIP-seq_17c_4hr_rep2


title: H2B_ChIP-seq_17c_4hr


title: H2B_ChIP-seq_17c_1hr


title: H3_ChIP-seq_17c_1hr_rep2


title: MNase-seq_37c_4hr_37Exp

source_name: Col0 HTA11::HTA11:FLAG seedlings


title: MNase-seq_37c_1hr_37Exp


title: H3_ChIP-seq_17c_15min_rep2


title: HSFA1A_ChIP-seq_17c_15min


title: MNase-seq_17c_4hr_37Exp


title: MNase-seq_37c_15min_37Exp


title: HTA11_ChIP-seq_37c_4hr_37Exp


title: HTA11_ChIP-seq_37c_15min_37Exp


title: HTA11_ChIP-seq_37c_1hr_37Exp


title: HTA11_ChIP-seq_17c_4hr_37Exp


title: HTA11_ChIP-seq_17c_15min_37Exp


title: HTA11_ChIP-seq_27c_15min_rep3


title: HTA11_ChIP-seq_27c_4hr_rep3


title: HTA11_ChIP-seq_27c_1hr_rep3


title: H3_ChIP-seq_27c_15min_rep2


title: HTA11_ChIP-seq_17c_1hr_rep3


title: HTA11_ChIP-seq_17c_4hr_rep3


title: RNA-seq_22to27c_4hr

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed.
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with gene ID, FPKM, TPM and raw counts.

value: seedlings


title: RNA-seq_22to27c_1hr


title: THP1 MΦ, pS469-GRIP1(Ncoa2), Dex, 100nm, 1hour, rep 2

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description: differentiated THP1 MΦ

data_processing:
Paired-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500.  Read quality was evaluated using FASTQC.
50 bp single-end reads were aligned to the human genome (GRCh37/hg19) or mouse genome (mm10) with bowtie2.
Peak calling for all other data sets was performed with MACS2 with the following  parameters:   for GR in THP1 MΦ --format=BAM --gsize 2451960000 --bw=300 ---slocal 1000 --llocal 10000 --keep-dup 1 -qvalue 0.01;   for GRIP1 in BMMΦ --format=BAM --gsize 2150570000 --bw=200 --to-large --ratio 1.0 --slocal 1000 --llocal 10000 --keep-dup 1 –pvalue 0.0001;   for GRIP1 in THP1 MΦ --format=BAM --gsize 2451960000 --bw=200 --ratio 1.0 --slocal 3000 --llocal 15000 --keep-dup 1 --pvalue 1e-05   with a matching input file to estimate background read distribution. pS469 peaks in Dex-treated samples were called vs. pS469 untreated samples to only obtain Dex-induced peaks with the following   parameters: --format=BAM --gsize 2451960000 --bw=200 --to-large --ratio 1.0 --slocal 1000 --llocal 100000 --keep-dup 1 --pvalue 0.0001.
Genome_build: human genome (GRCh37/hg19) or mouse genome (mm10)
Supplementary_files_format_and_content: bigwig files

source_name: THP1 MΦ

growth_protocol: C57BL/6 mice (NCI, Charles River Laboratories)  were maintained in the Hospital for Special Surgery and Weill Cornell Animal Facility in full compliance with guidelines approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Cells were dual cross-linked in 2 mM disuccinimidyl glutarate solution followed by 1% methanol-free formaldehyde for 40 min total at room temperature and quenched in 0.125 M glycine for 10 min. Cells were then washed with PBS, scraped and lysed for 10 min at 4°C in lysis buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) with protease inhibitor cocktail (Sigma) and the crude nuclear extract was collected by centrifugation at 600 g for 5 min at 4°C. Nuclei were washed for 10 min at 4°C in wash buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with protease inhibitors) and collected as above. Nuclei were lysed (0.1% SDS, 10 mM EDTA, 50 mM Tris, pH 8.1 with protease inhibitors) and sonicated using a Bioruptor Pico (Diagenode) for THP1 M and hMΦ or an S220 Ultrasonicator (Covaris) for BMMΦ to generate DNA fragments approximately 150-600 bp. Inputs were taken from cleared lysates or incubated for 4 h at 4°C with the following antibodies to precipitate protein:DNA complexes: GR (Santa Cruz, M20x, sc-1004x or N499), GRIP1 (Abcam, ab10491 or Bethyl A300-346A), phospho-specific GRIP1 antibodies, or CDK9 (Santa Cruz, H169x, sc-8338x). 40-50 μl of pre-washed Dynabeads Protein A were added per IP and incubated O/N at 4°C. Beads were washed 8x in modified RIPA wash buffer (50 mM HEPES [pH 7.6], 100 mM LiCl [for H3Ac, H4Ac, H4K5/K8/K12Ac, BRD2/3/4 and P-TEFb (CDK9)] or  300 mM LiCl [H3, H3K4me3, Pol II and Pol II S2], 1mM EDTA, 1% NP-40 and 0.7% Nadeoxycholate) and 1x in TE containing 50 mM NaCl. Elution of DNA was performed in TE buffer containing 1% SDS After 6h cross-link reversal at 65 C, RNase digestion and Proteinase K digestion, ChIP DNA and input DNA were purified using the QIAGEN Quiaquick PCR purification kit. The amount and sonication quality of DNA was tested with Qubit (Thermo) and Bionalyzer 2100 (Agilent Technologies)
Sequencing libraries were constructed using Illumina TruSeq ChIP-Seq Library Prep Kit and sequencing by a HiSeq 2500 system (4-6 samples/SR lane, 50 bp reads).

treatment_protocol: 1.Human THP1 cells were maintained in RPMI-1640  supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals) and 5-10 nM beta-mercapto ethanol. THP1 were differentiated by 25 ng/ml phorbol myristate acetate (PMA, Sigma) for 18-24 h followed by a 48 h rest before treatment to obtain THP1 MΦ. 2. BMMΦ were isolated from 8-10 week old male mice C57BL/6 mice (NCI, Charles River Laboratories) and  cultured in DMEM-20% FBS supplemented with L1-cell conditioned media  for the 6-day MΦ expansion; cells were then scraped, incubated in DMEM-20% FBS overnight and were treated with 100 nM Dex for 45(BMMΦ) or 60(THP1) minutes.

tag: cell line

tag: cell type

value: macrophage

tag: antibody

value: peripheral blood-derived

tag: Sex

value: male


title: RNA-seq_22c_1hr


title: THP1 Input

description: differentiated THP1 MΦ

value: none (input)


title: RNA-seq_22c_4hr


title: THP1 MΦ, pS469-GRIP1(Ncoa2), Dex, 100nm, 1hour, rep 1

description: differentiated THP1 MΦ


title: MNase-seq_17c_1hr_37Exp

tag: genotype


title: RNA-seq_22to27c_15min


title: RNA-seq_22c_15min


title: THP1 MΦ, pS469-GRIP1(Ncoa2), untreated, rep 2

description: differentiated THP1 MΦ


title: MNase-seq_17c_15min_37Exp

tag: chip antibody


title: THP1 MΦ, GRIP1(Ncoa2), Dex, 100nm, 1hour, rep 1

description: differentiated THP1 MΦ


title: HTA11_ChIP-seq_17c_1hr_37Exp


title: RNA-seq_22c_0min


title: THP1 MΦ, pS469-GRIP1(Ncoa2), untreated, rep 1

description: differentiated THP1 MΦ


title: THP1 MΦ, GR, Dex, 100nm, 1hour, rep 2

description: differentiated THP1 MΦ

value: GR


title: THP1 MΦ, GRIP1(Ncoa2), untreated, rep 2

description: differentiated THP1 MΦ


title: THP1 MΦ, GRIP1(Ncoa2), Dex, 100nm, 1hour, rep 2

description: differentiated THP1 MΦ


title: THP1 MΦ, GRIP1(Ncoa2), untreated, rep 1

description: differentiated THP1 MΦ


title: HTA11_ChIP-seq_17c_15min_rep3


title: H3_ChIP-seq_27c_1hr_rep1


title: THP1 MΦ, GR, Dex, 100nm, 1hour, rep 1

description: differentiated THP1 MΦ


title: THP1 MΦ, GR, untreated, rep 1

description: differentiated THP1 MΦ


title: H3_ChIP-seq_27c_4hr_rep1


title: H3_ChIP-seq_17c_4hr_rep1


title: MNase-seq_27c_4hr_rep1


title: MNase-seq_27c_4hr_rep2


title: H3_ChIP-seq_17c_15min_rep1


title: MNase-seq_27c_1hr_rep2


title: MNase-seq_27c_15min_rep2


title: MNase-seq_27c_1hr_rep1


title: ESCs with no extra Myc and EYFP copies from induced homozygous iMOST1-Myc ESC mosaic cultures (replica 3)

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description:
Myc_TAMOX_WT_3
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt

data_processing:
Libraries sequenced using Illumina GAII single end 75nt.
Base-calling was produced by Illumina RTA Software v 1.13.48.
Demultiplexed fastq files were generated from the bcl files using picard tools.
Sequencing adaptor contaminations were removed using cutadapt.
Reads were mapped and gene expression quantified using rsem v1.17.
Counts were normalized using voom from Limma R package.
Genome_build: GRCm38 v84
Supplementary_files_format_and_content: ALL.GRCm38.84.rsem.genes.results.txt: Tab-delimited text file includes RSEM estimated counts per sample per gene. Samples in columns, Genes in rows.

source_name: Embryonic stem cells (ESCs)

growth_protocol: ESCs were cultured on gelatin-coated plates in 2xLIF SR-ESC medium.

extract_protocol:
ESCs were sorted according to their EYFP expression levels. Total RNA was purified from ESCs using RNeasy Mini Kit (Qiagen).
A cDNA library was prepared according to Illumina recommendations and sequenced in a GAII analyzer using the single-end 75bp protocol.

treatment_protocol: ESC cultures were treated with 20μM 4-hydroxytamoxifen for 24 hours.

tag: strain/background

value: mixed background

tag: genotype/variation

value: Homozygous iMOS T1-Myc; RERT

tag: cell population


title: MNase-seq_27c_15min_rep1


title: ESCs with no extra Myc and EYFP copies from induced homozygous iMOST1-Myc ESC mosaic cultures (replica 2)

description:
Myc_TAMOX_WT_2
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: ESCs with no extra Myc and EYFP copies from induced homozygous iMOST1-Myc ESC mosaic cultures (replica 1)

description:
Myc_TAMOX_WT_1
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: MNase-seq_17c_4hr_rep1


title: ESCs with two extra Myc and EYFP copies from induced homozygous iMOST1-Myc ESC mosaic cultures (replica 3)

description:
Myc_TAMOX_2EYFP_3
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: MNase-seq_17c_4hr_rep2


title: THP1 MΦ, GR, untreated, rep 2

description: differentiated THP1 MΦ


title: ESCs with two extra Myc and EYFP copies from induced homozygous iMOST1-Myc ESC mosaic cultures (replica 2)

description:
Myc_TAMOX_2EYFP_2
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: MNase-seq_17c_15min_rep2


title: HTA11_ChIP-seq_27c_4hr_rep2


title: ESCs with two extra Myc and EYFP copies from induced homozygous iMOST1-Myc ESC mosaic cultures (replica 1)

description:
Myc_TAMOX_2EYFP_1
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: H3_ChIP-seq_27c_15min_rep1


title: Uninduced homozygous iMOS T1-Myc ESCs (replica 3)

description:
Myc_3
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt

value: Uninduced homozygous iMOS T1-Myc ESCs


title: H3_ChIP-seq_17c_1hr_rep1

value: seedling


title: RNA-seq_17c_15min_arp6_rep2

source_name: Col0 arp6-1 mutant seedlings

tag: shift experiment


title: RNA-seq_17c_15min_arp6_rep1

tag: temperature


title: Uninduced homozygous iMOS T1-Myc ESCs (replica 2)

description:
Myc_2
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: Uninduced homozygous iMOS T1-Myc ESCs (replica 1)

description:
Myc_1
Processed data file: ALL.GRCm38.84.rsem.genes.results.txt


title: HTA11_ChIP-seq_27c_4hr_rep1

tag: incubation time


title: HTA11_ChIP-seq_27c_1hr_rep1

tag: replicate


title: Control pAN1201 replicate 2 (IPTG-/aTc-/Ara-)

city: Bristol

first: Thomas

middle: Edward

last: Gorochowski

address: 24 Tyndall Avenue

department: Biological Sciences

institute: University of Bristol

data_processing:
Reads mapped to reference using BWA versiopn 0.7.4 with default settings
Read counts for each host and circuit gene was carried out using the htseq-count command of the HTSeq toolkit with user-defined GFF annotations of the reference sequences and the options '-s reverse -a 10 -m union'.
Normalized FPKM values were generated from the raw gene counts by custom scripts that calculated and applied a trimmed mean of M-values (TMM) factor using edgeR version 3.8.6.
Genome_build: NC_010473.1
Supplementary_files_format_and_content: CSV files of raw read counts and normalized gene expression in FPKM units.

organism: Escherichia coli

source_name: Culture grown in 14 ml tube

growth_protocol: Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours.

extract_protocol:
Cultures were spun down at 4 °C, 15,000 × g for 3 minutes. Supernatants were discarded after centrifugation and cell pellets were flash frozen in liquid nitrogen for storage at -80 °C. Cells were lysed with 1 mg of lysozme (Sigma Aldrich L6871) in 10 mM Tris-HCl (pH 8.0) (USB 75825) supplemented with 0.1 mM EDTA (USB 15694). RNA was extracted with PureLink RNA Mini Kit (Life Technologies) and further purified and concentrated with RNA Clean & Concentrator-5 (Zymo Research) to assure sample quality. The purified RNA samples were analyzed using a Bioanalyzer (Agilent) and Ribo-Zero rRNA Removal Kit for bacteria (Illumina) was used to deplete rRNA from the samples.
Strand specific RNAtag-seq libraries were created by the Broad Technology Labs specialized service facility (SSF) using the standard protocol described in Shishkin et al. Nature Methods 2016.

tag: strain

value: NEB 10-beta


title: Control pAN1201 replicate 1 (IPTG-/aTc-/Ara-)


title: 10X E14.5 wildtype kidney

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: The barcodes are contained within the BAM file.

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v1.3.0 using default parameters to obtain the bam files.
Cellranger produced two expression matrices, raw reads and counts-per-million normalized
genome build: mm10
processed data files format and content: tab delimited raw or normalized gene counts per cell

source_name: kidney

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: mixed with mostly CD-1, and 129

tag: age

tag: tissue

value: kidney


title: Dropseq E14.5 wildtype kidney

description: The barcodes are in the first read of the pair of fastq files for the Dropseq data.

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Reads were normalized by dividing the read count of each gene by the total number of reads per cell and multiplying by 10000
genome build: mm10
processed data files format and content: tab delimited file with raw or normalized gene counts per cell


title: Modified 0x58 state 3 (IPTG-/aTc+/Ara-)


title: MNase-seq_17c_1hr_rep1

tag: cultivar

tag: shift experiment type (17>27c or 17c>37c)

tag: fragmentation method (mnase digestion or sonication)

value: MNase (mononucleosome)


title: mRNA_day16

first: Elena

last: Torlai Triglia

state: Deutschland

address: Robert Rössle Str 10

department: BIMSB

institute: Max Delbrück Center for Molecular Medicine

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie 2.0.5 with default parameters. The reference for Bowtie was produced from the Mouse Genome version mm10.
ChIP-seq data were filtered using a 95% quantile threshold for read duplication.
mRNA-seq reads were aligned against using TopHat (Trapnell et al., 2009) v2.0.8. The reference for Tophat was produced from the Mouse Genome version mm10, providing gtf annotation from UCSC Known Genes (mm10, version 6) and associated isoform-gene relationship information from the Known Isoforms table (UCSC). Both tables were downloaded from the UCSC Table browser (http://genome.ucsc.edu/cgi-bin/hgTables).
Bam files were converted to Bed and then to Bedgraph using bedtools v2.17.0 (bamToBed and genomeCoverageBed, respectively)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig from UCSC, format described in http://genome.ucsc.edu/goldenpath/help/bigWig.html

growth_protocol: The day before starting the differentiation protocol (day ‘-1’), growing EpiSC were plated on Nunc plates coated with 15 μg/ml human plasma fibronectin (Millipore, # FC010) and cultured in N2B27 basal medium containing Activin and FGF2, to reach 70-80% confluency after 24h. Differentiation was started by rinsing cells twice with PBS, and culturing in N2B27 basal medium plus 1μM PD 0325901 (Axon, # 1408) for 2 days. Medium was refreshed every day. On day 2, cells were washed with PBS, scraped, replated on Nunc 10 cm dishes coated with 15 μg/ml human plasma fibronectin (Millipore, # FC010) and cultured in N2B27 basal medium for 3 days. At this stage, medium was refreshed every day by removing ½ volume and adding ½ volume of freshly prepared medium.  After 72h, the medium was replaced with N2B27 basal medium plus 100 ng/ml FGF8 (Peprotech, # 100-25-25) and 200 ng/ml Shh (R&D, # 464-sh-025). Medium was refreshed every day by removing ½ volume and adding ½ volume of freshly prepared medium.  After 96h, cells were washed with PBS, and the medium replaced with N2B27 basal medium plus 10 ng/ml BDNF (R&D, # 450-02-10), 10 ng/ml GDNF (R&D, # 450-10-10) and 200 μM L-ascorbic acid (Sigma, # A4544). Medium was refreshed every day by removing ½ volume and adding ½ volume of freshly prepared medium until day 16

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen # 15596-018) extraction following the manufacturer's instructions.
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated genomic DNA (quantified by Picogreen and Qubit) using the Next ChIP-Seq Library Prep Master Mix Set from Illumina (NEB, # E6240) following NEB protocol with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent).
mRNA libraries were made using TruSeq RNA Sample Preparation Kits v2 setA (Illumina, # RS-122-2001) following the manufacturer's instructions. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent)

tag: cells

value: day16 diff

tag: source

value: cDNA


title: HTA11_ChIP-seq_27c_15min_rep1

tag: genotype

value: Anti-FLAG® M2 Magnetic Beads (M8823 SIGMA)


title: 0x58 replicate 3 state 8 (IPTG+/aTc+/Ara+)


title: mRNA_day30

growth_protocol: The day before starting the differentiation protocol (day ‘-1’), growing EpiSC were plated on Nunc plates coated with 15 μg/ml human plasma fibronectin (Millipore, # FC010) and cultured in N2B27 basal medium containing Activin and FGF2, to reach 70-80% confluency after 24h. Differentiation was started by rinsing cells twice with PBS, and culturing in N2B27 basal medium plus 1μM PD 0325901 (Axon, # 1408) for 2 days. Medium was refreshed every day. On day 2, cells were washed with PBS, scraped, replated on Nunc 10 cm dishes coated with 15 μg/ml human plasma fibronectin (Millipore, # FC010) and cultured in N2B27 basal medium for 3 days. At this stage, medium was refreshed every day by removing ½ volume and adding ½ volume of freshly prepared medium.  After 72h, the medium was replaced with N2B27 basal medium plus 100 ng/ml FGF8 (Peprotech, # 100-25-25) and 200 ng/ml Shh (R&D, # 464-sh-025). Medium was refreshed every day by removing ½ volume and adding ½ volume of freshly prepared medium.  After 96h, cells were washed with PBS, and the medium replaced with N2B27 basal medium plus 10 ng/ml BDNF (R&D, # 450-02-10), 10 ng/ml GDNF (R&D, # 450-10-10) and 200 μM L-ascorbic acid (Sigma, # A4544). Medium was refreshed every day by removing ½ volume and adding ½ volume of freshly prepared medium until day 30

value: day30 diff


title: WT_distal_aorta_3

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

data_processing:
The raw FASTQ files were split into files containing 4,000,000 reads and checked for quality using FASTX toolbox
Based on the quality results, the reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed (3 nucleotides at the left end of R1 and 3 nucleotides off the left end of R2).
Sequence alignment to the mm10 mouse reference genome was performed using TopHat v2.1.0 with fr-unstranded as the library type.  The mate-inner-distance and mate-std-dev settings were determined for each sample by non-gapped alignment of a portion of the reads to the mouse mRNA reference using Bowtie2.  All other TopHat settings were left as default.
Exon- and gene-level read counts were calculated using the easyRNASeq function of the easyRNASeq R package version 2.4.7 running on R version 3.2.2.  For gene-level read counts, the summarization method used was geneModels. For annotation, an RDA file was generated from the Ensembl Mouse Release 83 gene transfer format (GTF) file using the annotation file generation function of easyRNASeq.
Gene-level read counts were adjusted for library size and gene length by calculating the reads per kilobase transcript length per million mapped reads (RPKM).  A reliable quantification threshold (RQT) was calculated for each sample according to the formula RQT = (50 / 2) / (total mapped reads / 1,000,000), which would be equal to an RPKM equivalent of 50 reads assuming an average gene length of 2 kb. The RPKM values were filtered to retain a list of genes whose RPKM values were above RQT in one or more samples.  To avoid reporting large fold changes due to random variation of counts from low abundance mRNA,  RPKM values equivalent to a count of <= 10 reads per gene were replaced with the average RPKM value equivalent to 10 reads/gene across all the samples in the experiment.
A 2-way ANOVA was performed on the log2 RPKM data for the 21,954 detectable mouse genes to examine the effect of Genotype (Wildtype and Notch1+/-) and Location (Proximal and Distal) as well as their interaction on gene expression. Tukey honestly significant difference tests were performed to determine the effect of genotype within each location and the effect of location within each genotype.  No Tukey test was run if the average log2 RPKM value for both groups in the pairwise comparison was less than RQT. ANOVA and Tukey p values across all genes were adjusted to control the false discovery rate (FDR).  Differentially expressed genes were defined as those having a Tukey P value < 0.05 and  an expression fold change ≥ 1.5. All statistical analysis was performed using R version 3.2.2 statistical computing software.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is an xlsx format, and contains the differential gene expression information, and includes information on the Gene ID, Related pubmed links, description, Tukey P values, Tukey FDR values, fold changes, and RPKM for each gene for each sample. Within this file, there is also the correlation matrix as a tab, thresholds as a tab, and sample info as a tab.

source_name: distal aorta

growth_protocol: Proximal and distal aortic tissue samples were collected from 3 wildtype and 3 Notch1.129S6+/- mice at 2 months of age.

extract_protocol:
RNA was isolated using a combination of Trizol and Total RNA Purification Kit (Norgen Biotek). Twelve (12) total RNA samples from mouse aorta tissues (n=3 of each group), were submitted to ORB for mRNA-Sequencing. The RNA was digested with RNase free DNase I (Epicentre; Part # D9905K) and re-purified on RNeasy MinElute columns (Qiagen; Part #: 74204) using an alternative high-ethanol binding condition to preserve Low Molecular Weight (LMW) RNAs. The newly prepared digested total RNA samples were then quantified by Quant-iT RiboGreen RNA fluorometric assay (Thermo Fisher Scientific; Part # R11491) and assessed for quality by Agilent2100 Bioanalyzer RNA 6000 Pico Assay (Agilent Technologies; Part # 5067-1513).
Amplified cDNA was prepared from a total of 10 nanograms (ng) of the digested total RNA samples using the NuGen Ovation RNA-Seq System v2 (NuGen: Part # 7102-A01) and fragmented using NEBNext dsDNA Fragmentase (NEB: Part # M0348L). Template DNA molecules suitable for cluster generation were then prepared from the fragmented cDNA using the Illumina TruSeq DNA Nano HT Library Preparation Kit (Illumina Inc.: Part # FC-121-4003). The quality and size distribution of the amplified cDNA libraries were determined by chip-based capillary electrophoresis using an Agilent 2100 Bioanalyzer DNA 1000 Chip assay (Agilent Technologies: Part # 5067-1504). The libraries were then quantified using the KAPA Library Quantification Kit (Kapa Biosystems; Boston MA).  The libraries were pooled at equimolar concentrations and diluted prior to loading onto the flow cell of the Illumina cBot cluster station. The libraries were extended and bridge amplified to create sequence clusters using the Illumina HiSeq PE Cluster Kit v4 and sequenced on an Illumina HiSeq Flow Cell v4 with 50-bp paired-end reads plus dual index read using the Illumina HiSeq SBS Kit v4. Real time image analysis and base calling were performed on the HiSeq2500 using the HiSeq Sequencing Control Software version 2.2.68.

value: wildtype

value: distal aorta

value: 2 months


title: HTA11_ChIP-seq_17c_4hr_rep2

tag: chip antibody


title: MNase-seq_17c_15min_rep1


title: 0x58 replicate 3 state 7 (IPTG-/aTc+/Ara+)


title: mRNA_day3

city: Berlin

growth_protocol: ESCs were plated with high density (1.5 x 10^5 cells/cm2) in serum-free ESGRO Complete Clonal Grade Medium (Millipore, # SF001-B) to which 1000U/ml LIF was added. After 24 hours, ESCs were washed 3 times with PBS without magnesium and calcium, incubated in PBS for 3 min at room temperature and then dissociated by incubating in 0.05% (v/v) Trypsin (Gibco #25300-054) for 2 minutes at 37°C. ESCs were plated onto 0.1% (v/v) gelatin-coated 10 cm dishes (Nunc) at 1.6 x 10^6 cells/dish in RHB-A (Takara-Clontech. #Y40001), changing media every day.  Cells were collected after 3 days.

value: day3 diff


title: WT_distal_aorta_2


title: HTA11_ChIP-seq_27c_1hr_rep2


title: 0x58 replicate 3 state 6 (IPTG+/aTc-/Ara+)


title: HTA11_ChIP-seq_17c_1hr_rep2


title: mRNA_day1

growth_protocol: ESCs were plated with high density (1.5 x 10^5 cells/cm2) in serum-free ESGRO Complete Clonal Grade Medium (Millipore, # SF001-B) to which 1000U/ml LIF was added. After 24 hours, ESCs were washed 3 times with PBS without magnesium and calcium, incubated in PBS for 3 min at room temperature and then dissociated by incubating in 0.05% (v/v) Trypsin (Gibco #25300-054) for 2 minutes at 37°C. ESCs were plated onto 0.1% (v/v) gelatin-coated 10 cm dishes (Nunc) at 1.6 x 10^6 cells/dish in RHB-A (Takara-Clontech. #Y40001). Cells were collected after 24h.

value: day1 diff


title: mRNA_ESC

source_name: ES cells

growth_protocol: 46C mouseESCs were plated on gelatin-coated (0.1% (v/v)) Nunc 10 cm dishes in serum-free ESGRO Complete Clonal Grade Medium (Millipore, # SF001-B) to which was added 1000U/ml LIF (Millipore, # ESG1107). Cells were grown for 48h, with a medium change at 24h.

value: 46c ES cells


title: HTA11_ChIP-seq_17c_4hr_rep1


title: 0x58 replicate 3 state 5 (IPTG-/aTc-/Ara+)


title: ChIP_controlChIP(anti-digoxigenin)_day16_B

description:
technical replicate number 2
46c_58_day16_dig_AB.mm10.nodup.bw

extract_protocol:
ChIP for Digoxigenin was performed using chromatin from ESCs fixed in 1% formaldehyde (Sigma) at 37°C for 10 min, as described (associated paper, Brookes et al., 2012; Stock et al., 2007).  600-700 μg of chromatin were used for immunoprecipitation.
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated genomic DNA (quantified by Picogreen and Qubit) using the Next ChIP-Seq Library Prep Master Mix Set from Illumina (NEB, # E6240) following NEB protocol with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent).
mRNA libraries were made using TruSeq RNA Sample Preparation Kits v2 setA (Illumina, # RS-122-2001) following the manufacturer's instructions. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent)

tag: antibody

value: anti-Digoxigenin (Jackson Immunoresearch # 200-002-156)

value: Fixed chromatin


title: HTA11_ChIP-seq_17c_1hr_rep1

value: seedling


title: Fluidigm E14.5 wildtype kidney

description: The cells in the matrices are identified by the raw file name in the column header. A supplementary file available at the foot of this page lists the SRR ID and its associated raw file name.

data_processing:
The fastq for each cell was aligned with bowtie2-2.2.7 using the -k 1 option.
Reads were counted by using summarizeOverlaps in the R package GenomicAlignments using the mode "Union"
Reads were normalized by dividing the read count of each gene by the total number of reads per cell and multiplying by 10000
The expression matrices from the two fluidigm runs were merged.
genome build: mm10
processed data files format and content: tab delimited file with raw or normalized gene counts per cell. Column headers are the name of the associated raw data file. When archiving raw high throughput sequence data, SRA renames files with a SRR ID. Please see the file "Fluidigm_SRR_id.txt" available at the foot of this page for a key to raw file name and its SRR ID. Raw data are provided as 1580 fastq files but the expression matrices only reflect 894 cells. The Fluidigm chip was analyzed under a microscope and only those wells that had a single cell were kept for the analysis. Blank well, wells with debris, and wells containing more than one cell were removed.


title: WT_distal_aorta_1

tag: genotype/variation


title: WT_proximal_aorta_3

source_name: proximal aorta

value: proximal aorta


title: ChIP_controlChIP(anti-digoxigenin)_day16_A

description:
technical replicate number 1
46c_58_day16_dig_AB.mm10.nodup.bw


title: HTA11_ChIP-seq_17c_15min_rep2


title: HTA11_ChIP-seq_27c_15min_rep2


title: WT_proximal_aorta_2


title: HTA11_ChIP-seq_17c_15min_rep1


title: RNA-seq_37c_4hr_37cExp

value: seedlings


title: ChIP_controlChIP(anti-digoxigenin)_ESC


title: ChIP_H3K27me3_day30

extract_protocol:
ChIP for H3K27me3 was performed using chromatin from ESCs fixed in 1% formaldehyde (Sigma) at 37°C for 10 min, as described (associated paper, Brookes et al., 2012; Stock et al., 2007).  600-700 μg of chromatin were used for immunoprecipitation.
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated genomic DNA (quantified by Picogreen and Qubit) using the Next ChIP-Seq Library Prep Master Mix Set from Illumina (NEB, # E6240) following NEB protocol with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent).
mRNA libraries were made using TruSeq RNA Sample Preparation Kits v2 setA (Illumina, # RS-122-2001) following the manufacturer's instructions. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent)


title: WT_proximal_aorta_1


title: Notch1_distal_aorta_3


title: 0x58 replicate 3 state 2 (IPTG+/aTc-/Ara-)

value: NEB 10-beta


title: Notch1_distal_aorta_2


title: ChIP_RNAPII-S7p_day30_B

description:
technical replicate number 2
46c_59_day30_4e12_AB.mm10.nodup.bw

extract_protocol:
ChIP for RNAPII modifications was performed using chromatin from ESCs fixed in 1% formaldehyde (Sigma) at 37°C for 10 min, as described (associated paper, Brookes et al., 2012; Stock et al., 2007).  600-700 μg of chromatin were used for immunoprecipitation.
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated genomic DNA (quantified by Picogreen and Qubit) using the Next ChIP-Seq Library Prep Master Mix Set from Illumina (NEB, # E6240) following NEB protocol with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent).
mRNA libraries were made using TruSeq RNA Sample Preparation Kits v2 setA (Illumina, # RS-122-2001) following the manufacturer's instructions. Libraries were quantified by Qubit (Invitrogen) and qPCR Kapa Library Quantification Universal Kit (KapaBiosytems, # KK4824), and library size was assessed by Bioanalyzer (Agilent)

value: anti RNAPII-S7p 4E12 (Chapman et al. science 2007)


title: 0x58 replicate 3 state 1 (IPTG-/aTc-/Ara-)


title: 0x58 replicate 2 state 8 (IPTG+/aTc+/Ara+)


title: Notch1_proximal_aorta_3


title: Notch1_distal_aorta_1


title: 0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)


title: ChIP_RNAPII-S7p_day30_A

description:
technical replicate number 1
46c_59_day30_4e12_AB.mm10.nodup.bw


title: ChIP_RNAPII-S5p_day30

value: anti RNAPII-S5p CTD4H8, BioLegend, # 904001


title: 0x58 replicate 2 state 7 (IPTG-/aTc+/Ara+)


title: 0x58 replicate 2 state 6 (IPTG+/aTc-/Ara+)


title: RNA-seq_17c_4hr_37cExp


title: 0x58 replicate 2 state 5 (IPTG-/aTc-/Ara+)


title: Notch1_proximal_aorta_2


title: 0x58 replicate 3 state 3 (IPTG-/aTc+/Ara-)


title: RNA-seq_37c_15min_37cExp


title: RNA-seq_17c_1hr_37cExp


title: Notch1_proximal_aorta_1


title: ChIP_H3K27me3_day16

value: day16 diff


title: RNA-seq_17c_15min_37cExp


title: RNA-seq_17c_0min_37cExp


title: 0x58 replicate 2 state 4 (IPTG+/aTc+/Ara-)


title: RNA-seq_27c_4hr_rep2


title: 0x58 replicate 2 state 2 (IPTG+/aTc-/Ara-)


title: BMMΦ, input

source_name: BMMΦ

tag: cell type

value: macrophage

value: none (input)

value: bone marrow -derived

value: 8-10 weeks

tag: Sex

value: male


title: RNA-seq_37c_1hr_37cExp

tag: shift experiment

tag: temperature


title: ChIP_RNAPII-S7p_day16_A

description:
technical replicate number 1
46c_59_day16_4e12_AB.mm10.nodup.bw


title: 0x58 replicate 2 state 3 (IPTG-/aTc+/Ara-)


title: BMMΦ, GRIP1(Ncoa2), Dex, 100nm, 1hour, rep 2


title: ChIP_RNAPII-S5p_day16_A

description:
technical replicate number 1
46c_59_day16_4h8_AB.mm10.nodup.bw


title: RNA-seq_27c_4hr_rep1

tag: incubation time

tag: replicate


title: 0x58 replicate 2 state 1 (IPTG-/aTc-/Ara-)

tag: strain


title: BMMΦ, GRIP1(Ncoa2), Dex, 100nm, 1hour, rep 1

tag: tissue

tag: age


title: ChIP_H3K27me3_day3

growth_protocol: ESCs were plated with high density (1.5 x 10^5 cells/cm2) in serum-free ESGRO Complete Clonal Grade Medium (Millipore, # SF001-B) to which 1000U/ml LIF was added. After 24 hours, ESCs were washed 3 times with PBS without magnesium and calcium, incubated in PBS for 3 min at room temperature and then dissociated by incubating in 0.05% (v/v) Trypsin (Gibco #25300-054) for 2 minutes at 37°C. ESCs were plated onto 0.1% (v/v) gelatin-coated 10 cm dishes (Nunc) at 1.6 x 10^6 cells/dish in RHB-A (Takara-Clontech. #Y40001), changing media every day. Cells were collected after 3 days.

value: day3 diff


title: RNA-seq_27c_1hr_rep2

tag: cultivar


title: BMMΦ, GRIP1(Ncoa2), untreated, rep 1


title: RNA-seq_27c_1hr_rep1


title: Flask state 7 (IPTG-/aTc+/Ara+)

source_name: Culture grown in 250 ml Erlenmeyer flask

growth_protocol: Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours.


title: BMMΦ, GRIP1(Ncoa2), untreated, rep 2


title: ChIP_RNAPII-S7p_day3


title: BMMΦ, GR, Dex, 100nm, 45 min

value: GR


title: ChIP_RNAPII-S7p_day16_B

description:
technical replicate number 2
46c_59_day16_4e12_AB.mm10.nodup.bw


title: ChIP_RNAPII-S5p_day3


title: Flask state 6 (IPTG+/aTc-/Ara+)


title: ChIP_RNAPII-S5p_day16_B

description:
technical replicate number 2
46c_59_day16_4h8_AB.mm10.nodup.bw


title: ChIP_H3K27me3_day1

value: day1 diff


title: RNA-seq_27c_15min_rep1


title: Flask state 5 (IPTG-/aTc-/Ara+)


title: BMMΦ, GR, untreated


title: Medium C-myc rep3

data_processing:
libraries sequenced usign Illumina HiSeq 2500 single end 61nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using voom from Limma R package
Genome_build: GRXm38 v76
Supplementary_files_format_and_content: tab separated file. Contains log2 normalized counts. Samples in columns, Genes in rows

source_name: Embryonic Stem Cells

growth_protocol: mESC were cultured on gelatine-coated plate in 2xLIF SR-ES medium

extract_protocol:
total RNA was purified from ES cells sorted in a cytometer according to GFP-Myc or EYFP levels (three biological replicas)
A cDNA library was prepared according to Illumina recommendations and sequenced in a HiSeq 2500 single end 61nt.

value: mESCs

tag: cell population

value: Medium C-myc


title: ChIP_RNAPII-S7p_day1

tag: cells

value: Fixed chromatin


title: RNA-seq_17c_4hr_rep2


title: Flask state 8 (IPTG+/aTc+/Ara+)


title: RNA-seq_17c_1hr_rep2


title: High C-myc rep3

value: High C-myc


title: ChIP_H3K27me3_ESC

value: 46c ES cells

tag: source


title: ChIP_RNAPII-S7p_ESC


title: RNA-seq_17c_1hr_rep1

value: seedlings


title: Flask state 3 (IPTG-/aTc+/Ara-)

value: NEB 10-beta


title: Low C-myc rep3

value: Low C-myc


title: Medium C-myc rep2


title: ChIP_RNAPII-S5p_day1

value: anti RNAPII-S5p CTD4H8, BioLegend, # 904001


title: RNA-seq_17c_4hr_rep1


title: BMMΦ, GR, input

value: macrophage


title: RNA-seq_17c_15min_rep2


title: ChIP_RNAPII-S5p_ESC


title: Low C-myc rep2


title: Flask state 1 (IPTG-/aTc-/Ara-)


title: Flask state 2 (IPTG+/aTc-/Ara-)


title: High C-myc rep2


title: Tube state 7 (IPTG-/aTc+/Ara+)


title: RNA-seq_17c_15min_rep1


title: RNA-seq_27c_15min_rep2


title: Medium C-myc rep1


title: Tube state 8 (IPTG+/aTc+/Ara+)


title: 48 hpf hace1 MO-injected sample B

city: Ottawa

first: Sergey

middle: V

last: Prykhozhij

state: Ontario

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

data_processing:
Torrent_Suite 4.2.1 used for basecalling
Trimming with Cutadapt v1.2.1
Second pass trimming with home-made script in order to remove reads shorter than 17bp and larger than 300bp and Q<20
2 steps alignement for RNA with tophat v2.0.6 and bowtie2 v2.0.2
Quantification and normalization with StrandNGS Version 2.1 with the following settings
Strand specific reads: false
Consider partial reads: true
Max EM Iterations: 1000
Convergence criterion for EM: 0.0010
Normalization Type = DeSeq
Threshold for normalization = 1
Baseline type =  median of all samples
Genome_build: Danio_rerio_Zv9-78 Transcripts (2015.01.22)
Supplementary_files_format_and_content: tab-delimited text files include normalised values or raw counts for each sample

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish housing, breeding conditions, and developmental staging of larvae, were performed according to Westerfield (Westerfield, 2000).  Use of zebrafish in this study was approved by the Dalhousie University Committee on Laboratory Animals (Protocol 15-123).  All zebrafish embryos were maintained in E3 embryo medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in 10 cm Petri dishes at 28oC.

extract_protocol:
TRIzol Reagent RNA Extraction protocol (Ambion RNA Life technologies) was used to extract RNA from pooled samples of hace1 or control morphants (n=6 per group).  Approximately 100 embryos per sample were used.  Tubingen wild type strain (TU) fish were previously injected with either hace1 MO or control MO using the injection protocol noted above.  RNA samples were quantified using the NanoDrop Spectrophotometer ND-1000 (Thermo Fisher Scientific, Wilmington, DE).  RNA yields for this experiment were lower than the 100µg of RNA needed for RNA sequencing, so 3 samples were pooled into one, for a final n=2 for each of the hace1 MO and control MO groups.
Barcoded cDNA libraries were prepared using RNA-Seq Version 2 kit from Life Technologies following their recommended protocol. Library preparations were assayed for both quality control and quantity using Experion DNA 1K chip (Life Technologies) and diluted to 16 pM concentration. Samples were sequenced using a Proton Sequencer from Life Technologies on a PI chip following the manufacturer recommended protocol. Each chip was loaded with 2 samples.

treatment_protocol: The hace1-HECT (5’-CCCTCGAACTGTTAGACAGAATAAA-3’) and standard control morpholinos (5’-CCTCTTACCTCAGTTACAATTTATA-3’) were purchased from Genetools LLC (Philomath, OR).  The hace1 morpholino splice site resides within the catalytically active HECT domain, upstream of the critical cysteine residue required for hace1 ubiquitin ligase function.  Knockdown of hace1 was verified by RT-PCR as described in Daugaard et al (Daugaard et al., 2013).

tag: morpholino

value: Tubingen

tag: Stage

value: 48 hpf


title: Tube state 6 (IPTG+/aTc-/Ara+)


title: RNA-seq_17c_0min_rep1


title: Tube state 5 (IPTG-/aTc-/Ara+)


title: VAT_24mo_KO_rep4

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)

data_processing:
Signal intensities were converted to individual base calls during a run using the system's Real Time Analysis (RTA) software
Sequencing reads were retrieved as FASTQ files and then demultiplexed using CASAVA software suite version 1.8.2
Reads were aligned against the murine genome version mm10 using TopHat version v2.0.13 (Kim et al., 2013); all default options were used
BAM files were sorted according to the mapping position and then imported into Partek® Genomics Suite® software, version 6.6 Copyright©; 2016 (PGS)
Quantification of mRNA was performed against the mm10-RefSeq Transcripts database version 2015-05-07 to obtain read counts for each individual RefSeq gene; 18,719 genes were finally retrieved
Three datasets were generated out of the 20 samples
Dataset 1 contains macrophages isolated from both spleen and adipose tissue of wild type mice only (samples 1-13)
Dataset 2 contains macrophages isolated from adipose tissue of both wild type and Nlrp3-/- mice (samples 1-7 and 14-17)
Dataset 3 contains macrophages isolated from spleen of both wild type and Nlrp3-/- mice (samples 8-13 and 18-20)
The obtained read count tables for the three datasets were normalized separatley using the R package DESeq2 (Love et al., 2014) and were then imported back into PGS
Genes were reduced to those, which had a mean normalized read count of 20 in at least one of the investigated groups for the corresponding dataset; 13,954, 13,129 and 13,169 genes remained for the datasets 1, 2 and 3, respectively
All normalized count values smaller than 1 were set to 1 to avoid spurious Fold-Changes later on
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text files containing normalized abundance measurements for a filtered list of genes (see processing steps) for the three different datasets
Supplementary_files_format_and_content: Dataset1: contains samples 1-13
Supplementary_files_format_and_content: Dataset2: contains samples 1-7 and 14-17
Supplementary_files_format_and_content: Dataset3: contains samples 8-13 and 18-20

organism: Mus musculus

source_name: visceral adipose tissue (VAT)

extract_protocol:
RNA extraction and purification was performed using RNeasy kits (Qiagen) according to manufacturer’s instructions.  Total RNA quality is determined by estimating the A260/A280 and A260/A230 ratios by nanodrop.   RNA integrity is determined by running an Agilent Bioanalyzer gel, which measures the ratio of the ribosomal peaks.
mRNA was purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: Cells were sorted on a BD FACS Aria into RPMI+20%FBS, stored on ice until they could be pelleted and resuspended in trizol for RNA extraction

value: macrophages

value: 24 months

tag: gender

tag: genotype


title: VAT_24mo_KO_rep3

tag: cell type

value: male


title: Tube state 4 (IPTG+/aTc+/Ara-)


title: Tube state 3 (IPTG-/aTc+/Ara-)


title: 48 hpf control MO-injected sample A

value: control


title: Low C-myc rep1


title: VAT_24mo_KO_rep1


title: Spleen_24mo_KO_rep3

source_name: spleen


title: Spleen_24mo_KO_rep2


title: Spleen_24mo_WT_rep4

value: wild type


title: Spleen_24mo_WT_rep3


title: Flask state 4 (IPTG+/aTc+/Ara-)


title: Rhizophagus ERM replicate 3

description:
this sample is present as reference in the three processed data files
66_GGCTAC_L001

organism: Rhizophagus irregularis

source_name: Extra radical mycelium of Rhizophagus irregularis

tag: fungal strain

value: Fungus alone


title: Spleen_24mo_KO_rep1


title: Rhizophagus ERM replicate 2

description:
this sample is present as reference in the three processed data files
65_TAGCTT_L001


title: KO ESC #1

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

data_processing:
RRBS sequencing reads were mapped to the mouse genome (mm9) using Bismark v0.10.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics). The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are the coverage files generated by Bismark (chr, start, end, methylation%, number of reported C, number of reported T)

source_name: ESCs

growth_protocol: ESCs are cultured in in N2B27 supplemented with Mek inhibitor PD325901 (1 mM, Stemgen), Gsk3 inhibitor Chir99021 (3 mM, Stemgen), and LIF (1000 units/ml, ESGRO, Millipore) in the presence of irradiated MEF feeder.  Before harvesting ESCs for DNA extraction, ESCs were cultured for 5 passages without feeder cells.

extract_protocol:
Genomic DNA extraction was performed with QIAamp DNA mini kits (Qiagen) following manufacturer's instructions.
50 ng of genomic DNA was digested in 18 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) for 3 hours at 37 ℃. After 20 minutes of inactivation at 80 ℃, the digested DNA was filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 1.8 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 40 minutes of incubation at 37 ℃ and 15 minutes of inactivation at 75 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where * indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Fast Bisulfite Conversion Kit (QIAGEN) following manufacturer’s low-concentration protocol. The bisulfite converted DNA was immediately subjected to PCR amplification using KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Primers for Illumina (New England Biolabs). After amplification, final libraries were obtained by size selection of 150-500 bp DNA fragments using SPRIselect beads (Beckman Coulter).

value: Naa10 KO


title: KO ESC #2


title: WT ESC #2

value: WT


title: Spleen_24mo_WT_rep2


title: WT ESC #1


title: Rhizophagus ERM replicate 1

description:
this sample is present as reference in the three processed data files
64_GATCAG_L001

growth_protocol: To increase colonization of M. truncatula and B. distachyon, a nursery system was used: Leek seeds (Allium porum cv. Elboeuf) were germinated on vermiculite for 2 weeks at room temperature, and then transferred to 4L pots with sterile charred clay (Oil-dri, Klasmann, France) as substrate, mixed with 400sp/L of R. irregularis. Leeks were grown for 3 months at 25/22°C under a long day photoperiod (16h/8h) with 80% humidity. Seeds of M. truncatula A17 were surface sterilized with 3.2% sodium hypochlorite for 10 min, 95% ethanol for 2 min and washed four times with sterile distiled water. Seeds were germinated on water agar 1% for 5 days at 4°C in the dark. Seeds of B. distachyon were surface sterilized with Ethanol 70% for 30 seconds, rinsed with water and treated with 10% sodium hypochlorite added with a drop of tween 20 for 20 minutes under agitation. Seeds were rinsed 3 times for 5 minutes with sterile water, and soaked in water for 1 hour. They were finaly rinsed 3 times and germinated for 3 days on water agar 0,7% at 22°C under 16h photoperiod. Seedlings were than transferred to pots containing mycorrhized Leeks to increase fungal colonization. Plantlets were removed after 3 weeks, they were transferred in 250mL pots with sterile charred clay as substrate and grown for 2 weeks. Root colonization reached 67% and 42% for M. truncatula and B. distachyon respectively. Lunulari cruciata (liverwort) subcultures were cultivated in vitro on solid M medium (4% phytagel) + sucrose, in association with R. irregularis under a long day photoperiod (16h/8h). After 6 weeks, thalli were harvested and distal parts were cut with a scalpel and discarded, as these zone are not colonized by the fungus. To generate extra radical mycelium, R. irregularis was cultivated in association with Daucus carota in split plate on solid M medium (4g/L phytagel) at 22°C in the dark. Once the fungal compartment was colonized, the gel was removed with a scalpel and replaced by liquid M medium without sucrose. After two weeks of growth in the same previous conditions, ERM were collected with forceps and frozen with liquid nitrogen.


title: High C-myc rep1

value: mESCs

value: High C-myc


title: Brachypodium / Rhizophagus replicate 2

description:
RAW Ri Bd vs ERM
59_GTCCGC_L001

organism: Brachypodium distachyon

source_name: B. distachyon roots associated with R. irregularis

tag: plant specie

value: Brachypodium distachyon Bd21

value: Roots


title: 48 hpf control MO-injected sample B


title: VAT_24mo_KO_rep2


title: Tube state 2 (IPTG+/aTc-/Ara-)

value: NEB 10-beta


title: Brachypodium / Rhizophagus replicate 1

description:
RAW Ri Bd vs ERM
58_CCGTCC_L001


title: Spleen_24mo_WT_rep1


title: Spleen_3mo_WT_rep2

value: 3 months


title: VAT_24mo_WT_rep4


title: Tube state 1 (IPTG-/aTc-/Ara-)


title: Spleen_3mo_WT_rep1


title: VAT_24mo_WT_rep3


title: VAT_3mo_WT_rep2


title: VAT_24mo_WT_rep2


title: VAT_24mo_WT_rep1


title: VAT_3mo_WT_rep3


title: Brachypodium / Rhizophagus replicate 3

description:
RAW Ri Bd vs ERM
60_GTGAAA_L001


title: VAT_3mo_WT_rep1


title: SORT-Seq zebrafish fin (merged)

status: Public on Sep 28 2017

city: Utrecht

first: Susanne C

middle: van den

last: Brink

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using bwa (version 0.6.2-r126) with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel-specific barcode information (first 8 bases) followed by a UMI-sequence (4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data) and a polyT-stretch. Reads 1 were thus used to extract the cell-barcode sequences (see “Cel-seq_barcodes_96.csv” file for sequences used for unstained satellite cell data and see "Cel-seq_barcodes_384" for MitoTracker stained satellite cells and zebrafish data) and UMIs; see Supplementary Methods for details.
After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (see Supplementary Methods section for details). Note that processed files for satellite cell data here still contain ERCC Spike-in molecules, bulk samples (bulk samples are only included in CEL-Seq experiments; see “BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library) and mitochondrial reads (only for MitoTracker stained satellite cells).
Genome_build: mus musculus: mm10; danio rerio: Zv9 (Ensembl release 74); both were extended with spike-ins (see "ERCC92.fa")
Supplementary_files_format_and_content: *.coutt.csv, *TranscriptCounts.tsv and *count_table.csv: tab-separated data files listing how many reads of which transcripts were detected in all sequenced cells (after UMI-correction). Column names refer to cells sequenced in this library (numbers refer the the CEL-Seq primer barcode used for that cell). The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike-in molecules, bulk samples (bulk samples are only included in CEL-Seq experiments; see “BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library) and mitochondrial reads (only for MitoTracker stained satellite cells).

source_name: All cells from caudal fin

extract_protocol:
Cells were sorted into Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius, after which SORT-Seq (Muraro et al., 2016, with minor modifications as desribed in Supplementary Methods of van den Brink et al., 2017) was applied.
As in SORT-Seq protocol (Muraro et al., 2016), with minor modifications as desribed in Supplementary Methods of van den Brink et al., 2017.

value: Wildtype


title: SORT-Seq MitoTracker stained; Repeat; plate 2

description: mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France

source_name: Satellite cells from Tibialis Anterior muscle

value: female


title: SORT-Seq MitoTracker stained; Repeat; plate 4

value: Satellite cells from Tibialis Anterior muscle


title: SORT-Seq MitoTracker stained; Repeat; plate 1


title: SORT-Seq MitoTracker stained; Pilot