title: yamuscle1

city: Cologne

first: Franziska

last: Metge

address: Joseph-Stelzmann-Str 9b

department: Bioinformatics Corefacility

institute: Max Planck Institute for Biology of Ageing

data_processing:
raw reads were trimmed and filtered using Flexbar (version 2.5)
reads were aligned in paired end mode using STAR (version 2.5.2b)
Unmapped reads were aligned in single end mode using STAR (version 2.5.2b)
circRNAs were detected using DCC (version 0.4.4)
differential circRNA expression was analyzed using R’s ibb package
Genome_build: NFZv2
Supplementary_files_format_and_content: excel workbooks representing circRNA coordinates, circRNA counts, linearRNA counts, differential circRNA statistics

organism: Nothobranchius furzeri

source_name: muscle

extract_protocol:
brain and muscle tissues were carefully dissected under a microscope. Isolates were briefly washed with PBS (1x) and frozen in liquid nitrogen. RNA was extracted with Trizol (10296028, Invitrogen, USA)
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit, after removing ribosomal RNA using Ribo-zero rRNA removal Kit against human, mouse and rat (Illumina, USA)
RNAseq, 2x250 BP paired end on a HiSeq 2500 (Illumina, USA)

value: 8.5 weeks

tag: strain

value: GRZ-AD


title: 4321

status: Public on Jul 31 2019

type: SRA

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Rd

department: Genetics

country: USA

institute: The University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Fastx toolkit was used to remove low quality reads; reads with phred quality > 20 for 80% of bases were retained.
Tagdust was used to identify and remove reads containing adapter and linker sequences.
STAR (version 2.4.2a) was used as the aligner, with hg19 and GENCODE v19 as annotation; STAR was run, using a 2-pass strategy, were splice locations from the first pass were used as additional annotation for the second pass.
salmon (version 0.7.2) was used to estimate isoform abundance from aligned BAM files; GENCODE 19 was used as annotation. --gcBias option was used.
tximport (version 1.0.3) was used to collapse isoform abundance estimates from salmon to gene abuddance estimates
Genome_build: hg19
Supplementary_files_format_and_content: Abundance measurements generated using salmon and tximport; values represent the transcripts per million (TPM) estimate of gene abundance.

molecule: polyA RNA

organism: Homo sapiens

source_name: subcutaneous adipose tissue

extract_protocol:
Subcutaneous adipose needle biopsies were obtained from near the umbilicus of men from the METSIM cohort. RNA was isolated using the QIAGEN miRNeasy kit.
Libraries were constructed using a polyA+ selection protocol (Illumina TruSeq RNA Sample Preparation Kit v2)

tag: Sex

value: male

tag: sequencing batch

value: batch 1

tag: transcript integrity number

tag: age

tag: bmi


title: yamuscle3

country: Germany

molecule: total RNA


title: obrain1

source_name: brain

value: 14 weeks


title: ymuscle3

value: 3.5 weeks


title: omuscle1


title: obrain3


title: STL002.AO2.ADS396

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description:
AO.pp.all.bz2
AO.po.all.bz2

library_source: genomic

data_processing:
Read pairs from Promoter Capture Hi-C library were independently mapped to human genome hg19 using BWA-mem and manually paired with in house script.
Unmapped, non-uniquely mapped, and PCR duplicates were removed.
Trans-chromosomal read pairs and putative self-ligated products (<15kb read pairs) were removed.
Off-target reads were removed when both read pairs did not match to capture probe sequences.
Genome_build: Hg19
Supplementary_files_format_and_content: *.po and *.pp provide interaction frequencies for promoter-promoter interactions or promoter-other interactions, respectively.  We combined multiple donors or replicates according to cell/tissue types.

molecule: genomic DNA

source_name: Human Aorta

extract_protocol:
Promoter Capture Hi-C library was constructed by performing a target enrichment protocol (enriching target promoter-centered proximity ligation fragments from Hi-C library using capture RNA probes). Briefly, we incubated 500ng Hi-C library 24h at 65 °C within a humidified hybridization chamber with 2.5ug human Cot-1 DNA (Life Technologies), 2.5ug salmon sperm DNA (Life Technologies), and p5/p7 blocking oligos with hybridization buffer mix (10X SSPE, 10mM EDTA, 10X Denhardts solution, and 0.26% SDS) and 500ng RNA probes. RNA:DNA hybrids were enriched using 50ul T1 streptavidin beads (Invitrogen) with 30min incubation at RT. Next, bead-bound hybrids were washed by a 15min incubation in wash buffer1 (1X SSC and 0.1% SDS) with frequent vortexing, and then washed three times with 500ul of pre-warmed (65 °C) wash buffer2 (0.1X SSC and 0.1% SDS), and resuspended in nuclease-free water. The resulting capture Hi-C libraries were amplified while bound to the T1 beads, and purified using AMPure XP beads, followed by sequencing.
Promoter Capture Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq2500 or HiSeq4000 protocols with minor modifications (Illumina, San Diego, CA).
Capture Hi-C

tag: tissue

value: Aorta


title: ymuscle1


title: omuscle2


title: STL002.AO2.ADS206

description:
AO.pp.all.bz2
AO.po.all.bz2


title: yabrain2


title: yabrain1


title: 2050


title: obrain2


title: Ct_3_60

city: Jena

first: Philipp

last: Kämmer

address: Adolf-Reichwein-Straße 23

department: Microbial Pathogenicity Mechanisms

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

data_processing:
RTA software version 1.18.64 were used for basecalling.
Read quality were checked with Fastqc. Reads were trimmed with trimmomatic version 0.32 and following parameters: SE threads 5 -phred33 FILE LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 15:20 MINLEN 30
Trimmed reads were mapped to reference genome of Candida tropicalis MYA-3404_features and of Homo sapiens GRCh38.77 using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version 1.4.5 and DeSeq2 were used for differential expression filtering.
Genome_build: GRCh38.77, MYA-3404_features
Supplementary_files_format_and_content: Comma-delimited text files include counts for each gene per sample

organism:
Candida tropicalis
Homo sapiens

source_name: whole blood, all

growth_protocol: Candida tropicalis cells grew at 37°C in Homo sapiens whole blood.

extract_protocol:
To isolate human RNA aliquots of infected or mock infected samples were added to a PAXgene® Blood RNA Tube (PreAnalytiX) and processed with the PAXgene® Blood RNA Kit (PreAnalytiX) according to the manufacturer’s protocol. For fungal RNA isolation aliquots were added to ice-cold water, centrifuged and immediately frozen in liquid nitrogen. The cell pellet was further processed with the RiboPure™-Yeast Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. RNA quantity was determined with NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and RNA quality was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies). Fungal and human RNA samples were pooled subsequently in a quantitative ratio of 1:10.
Library Preperation was performed by GATC Biotech using validated  standard procedures modified to optimize the method for automated  Preperation. Library Preparation consisted of the following steps:  Purification of poly-A containing mRNA molecules, mRNA fragmentation, Random primed cDNA synthesis (strand specific), Adapter ligation and adapter specific PCR amplification

treatment_protocol: Homo sapiens whole blood cells were treated with Candida tropicalis MYA 3404.

tag: c. tropicalis strain

tag: time point

value: 60 minutes


title: ybrain3


title: yabrain3


title: Ct_3_30

value: 30 minutes


title: 960


title: ybrain2


title: H3K4me3 ChIP-Seq Zygotene nuclei (Expt R1)

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

data_processing:
BigWig files were generated in one of four ways:
1. BIGWIG files named: monoCorrected.ws25bp.bigwig:
Coverage normalized by calibration with internal spike-in. We retained only sequencing reads with an alignment q-score >= 20, that were mapped in a “proper pair” (for paired-end data), that passed vendor QC and that were mapped as a primary alignment. For paired-end data, we only retained reads from fragments with an insert size between 100 bp and 200 bp. We first converted paired-end reads to fragments, then calculated the enrichment of fragments mapping to each spike-in sequence after ChIP. Normalization using the K-MetStat spike-in was performed as described previously (Grzybowski et al. 2015), with slight modification (see methods of the paper linked to this submission; Lam et al. 2019).
2. BIGWIG files named: ncisCorrectedByStablePromoters.ws25bp.bigwig
We retained only sequencing reads with an alignment q-score >= 20, that were mapped in a “proper pair” (for paired-end data), that passed vendor QC and that were mapped as a primary alignment. We also only retained reads from fragments with an insert size between 100 bp and 200 bp. We first converted paired-end reads to fragments. Read coverage in non-overlapping 25bp windows of the genome was calculated. NCIS and input DNA of a matched experiment were used to estimate a background normalization factor for each experiment. The NCIS-normalized input DNA coverage was subtracted from the count in each 25bp window. We next identified a subset of stable gene promoters that varied little across the five populations of meiotic prophase (see methods of the paper linked to this submission; Lam et al. 2019). The coverage in each 25bp window was divided by the mean coverage at stable promoters.
3. BIGWIG files named: 150bp.RPKM.bigwig
We used deeptools 3.0.1 and the following arguments: bamCoverage -b $bam -o $bigwig --binSize 150 --ignoreForNormalization chrX chrY chrM --normalizeUsing RPKM
4. BIGWIG files named: NCIS.ws25bp.bigwig
Read coverage in non-overlapping 25bp windows of the genome was calculated. NCIS and input DNA were used to estimate a background normalization factor for each experiment. The NCIS-normalized input DNA coverage was subtracted from the count in each 25bp window.
Genome_build: mm10
Supplementary_files_format_and_content: Peaks for H3K4me3 ChIP-Seq were called using MACS2 (version 2.1.2) with default parameters except (-q 0.1 --broad) and with a stage-matched input DNA sample as a control.
Supplementary_files_format_and_content: BigWig files were generated in one of four ways:   1. BIGWIG files named: monoCorrected.ws25bp.bigwig:   Coverage normalized by calibration with internal spike-in. We retained only sequencing reads with an alignment q-score >= 20, that were mapped in a “proper pair” (for paired-end data), that passed vendor QC and that were mapped as a primary alignment. For paired-end data, we only retained reads from fragments with an insert size between 100 bp and 200 bp. We first converted paired-end reads to fragments, then calculated the enrichment of fragments mapping to each spike-in sequence after ChIP. Normalization using the K-MetStat spike-in was performed as described previously (Grzybowski et al. 2015), with slight modification (see methods of the paper linked to this submission; Lam et al. 2019).    2. BIGWIG files named: ncisCorrectedByStablePromoters.ws25bp.bigwig  We retained only sequencing reads with an alignment q-score >= 20, that were mapped in a “proper pair” (for paired-end data), that passed vendor QC and that were mapped as a primary alignment. We also only retained reads from fragments with an insert size between 100 bp and 200 bp. We first converted paired-end reads to fragments. Read coverage in non-overlapping 25bp windows of the genome was calculated. NCIS and input DNA of a matched experiment were used to estimate a background normalization factor for each experiment. The NCIS-normalized input DNA coverage was subtracted from the count in each 25bp window. We next identified a subset of stable gene promoters that varied little across the five populations of meiotic prophase (see methods of the paper linked to this submission; Lam et al. 2019). The coverage in each 25bp window was divided by the mean coverage at stable promoters.    3. BIGWIG files named: 150bp.RPKM.bigwig  We used deeptools 3.0.1 and the following arguments: bamCoverage -b $bam -o $bigwig --binSize 150 --ignoreForNormalization chrX chrY chrM --normalizeUsing RPKM     4. BIGWIG files named: NCIS.ws25bp.bigwig  Read coverage in non-overlapping 25bp windows of the genome was calculated. NCIS and input DNA were used to estimate a background normalization factor for each experiment. The NCIS-normalized input DNA coverage was subtracted from the count in each 25bp window.

organism: Mus musculus

source_name: H3K4me3 ChIP-Seq Zygotene nuclei

extract_protocol:
Chromatin extracted for ChIP-Seq was either sheared by sonication or Micrococcal nuclease (MNase) digestion. Chromatin for all H3K4me3 ChIP-Seq for studying histone dynamics in stage-specific populations was sheared by sonication, whereas ChIP-Seq for identifying histone marks at hotspots were performed on MNase-digested chromatin. Experimental procedures are listed below in detail.
Shearing chromatin by sonication:
Frozen nuclei pellets were thawed at RT for 10 min. Nuclei were lysed with Lysis buffer 1 (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8) and incubated at RT for 10 min. Nuclei pellets were subsequently washed with Lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8) and lysed with RIPA buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 140 mM NaCl plus protease inhibitor). Chromatin was sheared into ~500−1000 bp fragments by sonication using Bioruptor (diagenode). Chromatin concentration was measured using a Qubit dsDNA HS Assay Kit (Thermo Fisher).
MNase digestion:
Frozen nuclei pellets were thawed at RT for 10 min. Nuclei pellets were resuspended with MNase buffer (50 mM Tris-HCl pH 8, 1 mM CaCl2, 4 mM MgCl2, 4% NP-40 plus protease inhibitor). MNase digestion was performed in a concentration of 3U MNase (USB, Affymetrix) per one million nuclei at 37°C for 5 min. The reaction was stopped by adding a final concentration of 10 mM EDTA and incubated at 4°C for 5 min. Chromatin was pelleted and resuspended in RIPA buffer. Chromatin concentration was measured.
For stage-specific H3K4me3-ChIP-Seq, modified mononucleosomes (SNAP-ChIP K-MetStat Panel, EpiCypher) were added at a spike-in volume of 1 μl per ~1.5 μg chromatin DNA. Chromatin was immunoprecipitated with 0.8-5 μg antibodies (or 5 μl unpurified serum) in 0.5-1 ml RIPA buffer at 4°C overnight (see Supplementary Table 1 for details). The immuno-complexes were captured using 20-75 μl Dynabeads Protein G (30 mg/ml, Novex) at 4°C for 2 hr. The beads were washed with buffers previously described27. ChIPed DNA was eluted using a IPure kit v2 (diagenode).
ChIP-seq libraries were constructed with a KAPA Hyper Prep Kit (Kapa Biosystems) following steps for generating 1 μg of library DNA. DNA libraries were cleaned up with an Agencourt AMPure XP system (Beckman Coulter). The DNA concentration and fragment size of these libraries were measured with a Qubit dsDNA HS Assay Kit (Thermo Fisher) and an Agilent High Sensitivity DNA Kit (Agilent), respectively.

treatment_protocol:
Testes from adult mice were de-capsulated and fixed with 1% formaldehyde for 10 min followed by 5 min of quenching at RT. Fixed tissues were homogenized and filtered through a 70- or 100-μm cell strainer. After washing with chilled 1 x PBS, nuclei were extracted using nucleus extraction buffer (15 mM Tris-HCl pH 7.4, 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA, 0.2 mM EGTA) on ice for 5 min and were homogenized with 20 strokes with loose pestle followed by 10 strokes with tight pestle. Nuclei were filtered through a 40-μm cell strainer and resuspended in chilled PBTB buffer (1 x PBS with 0.1% Triton X-100, 5% BSA and protease inhibitor).
Nuclei were incubated in 10% of normal serum at RT for 10 min. This blocking step helps reduce non-specific binding of antibodies. Nuclei were then labelled with different combinations of primary antibodies (1 μg of antibodies to 11 million events) in 10% of normal serum at 20°C for 40 min. Nuclei were washed, resuspended in PBTB, blocked with serum, and then labelled with secondary antibodies (1:250 dilution) in 10% of normal serum at 20°C for 30 min. Controls for each secondary antibody were also prepared for setting up the threshold of background fluorescent signal for FACS. Nuclei were washed, resuspended in PBTB, and stored at 4°C until sorting.
Nuclei were filtered through a 40-μm cell strainer, and stained with DAPI for 30 min or longer before sorting. All sorting experiments were performed on either a BD FACSAria II or a BD FACSAria Fusion flow cytometer at a flow rate of ~20,000 events/sec. Singlets were gated using both forward scatter and side scatter. Nuclei from primary spermatocytes (4C) were gated based on DNA content deduced from the DAPI signal, and sorted into populations of interest based on fluorochrome intensity into collection tubes containing PBTB. Sorted nuclei were collected by centrifugation. Nuclei were examined under microscope and counted with a hemocytometer. Finally, excess buffer was removed and nuclei pellets were stored at -80°C.

tag: genotype/variation

value: wild-type

value: adult

value: whole testis

tag: meiotic nuclei population

value: Zygotene nuclei

tag: chip antibody

value: Anti-H3K4me3 Epicypher 13-0028


title: 7517


title: Ct_3_240

value: 240 minutes


title: Ct_3_15

value: 15 minutes


title: 6907


title: 2481


title: 5307


title: 6548


title: 1964


title: 4311


title: Ct_3_120

value: 120 minutes


title: 5210


title: Ct_2_15


title: Ct_2_240


title: Ct_2_60


title: Ct_3_0

value: 0 minutes


title: Ct_2_120


title: Ct_2_30


title: 10377


title: 5633


title: Ct_1_60


title: 2363


title: Ct_1_30


title: ybrain1

value: GRZ-AD


title: Ct_1_240


title: 5084

value: male


title: Ct_1_15


title: 6055

value: batch 1


title: Ct_1_120


title: 5953


title: Ct_1_0


title: 1147


title: 4544


title: 2812


title: 6807


title: 4008


title: HS43m1

city: St. Louis

first: Malia

middle: A

last: Gehan

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Heated shoots treatment, sampled on day 1 of heat treatment

data_processing:
Sequencing data was processed by Novogene (https://en.novogene.com/): removed reads containing adapters, removed reads containing N > 10%, removed reads containing low quality (Qscore<= 5) base which is over 50% of the total base
Genome_build: ASM168347v1
Supplementary_files_format_and_content: Tab delimited text file contains p-values, q-values, and b values, as well as statistical analysis for every gene in the quinoa genome, for every treatment and day of heat sampled as obtained from Sleuth v 0.30.0. Also contains Arabidopsis ortholog gene names and Panther (http://www.pantherdb.org/) gene classification and GO annotation

organism: Chenopodium quinoa

source_name: Green healthy leaf from mid section of the plant

growth_protocol: Plants were grown at 22°C, 50% relative humidty, 400 µmol m-2 s-1 light intensity, with 12 hours of light, until first anthesis

extract_protocol:
Total RNA was extracted with Qiagen's RNeasy Plant Mini Kit, including the RNase-free DNase Set.
Libraries were constructed by Novogene (https://en.novogene.com/) with NEB Next® Ultra™ RNA Library Prep Kit: mRNA from eukaryotic organisms is enriched using oligo(dT) beads. the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment

treatment_protocol: At first anthesis, plants were transferred to their respective heat treatment: 1. control with both roots and shoots at 22°C, 2. heated roots with roots at 30°C and shoots at 22°C, 3. heated shoots with roots at 22 °C and shoots at 35°C, and 4. heated roots and shoots with roots at 30°C and shoots at 35°C.

tag: developmental stage

value: anthesis on main panicle

tag: accession

tag: treatment

value: Heated shoots treatment

tag: time

value: sampled on day 1 of treatment


title: Ct_2_0


title: HS41m11

description: Heated shoots treatment, sampled on day 11 of heat treatment

value: sampled on day 11 of treatment

value: Green healthy leaf from mid section of the plant


title: 7038


title: 7501


title: 6106


title: HS39m1


title: 4481


title: HS35m1


title: HS34m11


title: 2808


title: 2320


title: 780


title: 1947


title: HS31m11


title: HRS58m1

description: Heated roots and shoots treatment, sampled on day 1 of heat treatment

value: Heated roots and shoots treatment


title: HRS55m1


title: 10070


title: 2278


title: 493


title: HRS54m11

description: Heated roots and shoots treatment, sampled on day 11 of heat treatment


title: 1044


title: HRS59m11


title: 6689


title: 377


title: 2230


title: HRS47m11


title: HRS51m1


title: ACTA2eGFP- 1

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from day 30 ACTA2eGFP- candidate SMCs.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

label: biotin

source_name: human iPSCs differentiated towards SMCs

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Cells were treated with 24 hours of BMP4, ActivinA, VEGF, and FGF2, followed by 72 hours of BMP4, FGF2, and VEGF to reach a KDR+ mesodermal progenitor stage. Cells were then treated with PDGF-BB, TGF-B, and FGF2 to specify towards a smooth muscle-like ACTA2eGFP+ cell.

extract_protocol: QIAzol extraction of total RNA according to the manufacturer's instructions

treatment_protocol: Cells were dissociated and sorted based on viability (calcein blue+) and GFP expression.

tag: cell population


title: HR14m1

description: Heated roots treatment, sampled on day 1 of heat treatment

value: Heated roots treatment


title: F8-2

city: Wuhan

first: lvwei

middle: jian

last: jun

state: Hubei

address: shizishan street, NO.1

department: College of Animal science and technology

country: China

institute: huazhong agriculture university

description: lncRNA expression of 8 days after cells differentiation

hyb_protocol: 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: Mouse Skeletal muscle cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA) according to the manufacture, instructions

treatment_protocol: C2C12 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), and grown to 80-90% conflunce. Then, cells were transferred to DMEM medium contain 2% horse serum (HS), and differentiated to 2, 5 and 8 days

tag: cell line

value: C2C12 cells

tag: culture

value: differentiation for 8 days


title: HR11m11

description: Heated roots treatment, sampled on day 11 of heat treatment


title: ACTA2eGFP- 3


title: ACTA2eGFP+ 2

description: Gene expression data from day 30 ACTA2eGFP+ candidate SMCs.


title: F5-3

description: lncRNA expression of 5 days after cells differentiation

value: differentiation for 5 days


title: ACTA2eGFP+ 3


title: ACTA2eGFP- 2


title: F5-2


title: HR9m1


title: F8-3


title: HR7m1


title: F2-3

description: lncRNA expression of 2 days after cells differentiation

value: differentiation for 2 days


title: F5-1


title: ACTA2eGFP+ 1


title: F8-1


title: HR5m11


title: HR1m11


title: C30m11

description: Control treatment, sampled on day 11 of heat treatment

value: Control treatment


title: F2-2


title: C28m11


title: C27m1

description: Control treatment, sampled on day 1 of heat treatment


title: F2-1


title: C22m1


title: F0-3

description: lncRNA expression of proliferating myoblasts

value: proliferation


title: F0-2


title: F0-1


title: C20m1


title: C16m11


title: STL003.GA3.ADS391

description:
GA.pp.all.bz2
GA.po.all.bz2

source_name: Human Gastric

value: Gastric


title: Dux-KO_ mixture of liver and muscles

city: Shanghai

first: Mingyue

last: Guo

state: Shanghai

address: Siping

department: School of Life science and technology

institute: Tongji University

description: whole genome

data_processing:
Library strategy: DNA-Seq
The PacBio reads were aligned to the mouse genome (mm9) using pbmm2 (version 1.0.0), a wrapper of minimap2  with deault settings.
We used variantCaller (version 2.3.3 ) to get the consensus and variant calling using the algorithm “arrow”.
The positions with read coverage less than 5 were marked by Ns in the consensus sequence.
Genome_build: mm9
Supplementary_files_format_and_content: genomic consensus sequence of knockout Dux gene and its vicinity (30 kb upstream and 30kb downstream ),  fasta format

source_name: organs genome

extract_protocol:
High quality genome DNA was extracted from organs of Dux knockout mouse according to the standard protocol by phenol:chloroform extraction and ethanol precipitation.
Genome DNA library was prepared for sequencing using standard PacBio Sequel protocol
Third-generation whole-genome sequencing

tag: strain

tag: genotype

value: Dux KO

value: mixture of liver and muscles


title: IMR90.ADS116

description:
imr90.pp.all.bz2
imr90.po.all.bz2

source_name: Human Fibroblasts

value: Fibroblasts


title: CCMP160 Tsup rep3

city: Sackville

first: Yue

last: Liang

state: NB

address: 144 Main St

country: Canada

institute: Mount Allison University

data_processing:
Basecalling performed using CASAVA
Raw reads were then mapped to the PhiX genome using Bowtie2 (version 2.2.9) and the unmapped reads were outputted using samtools (version 1.3.1). The first 12nt from the 5' end of the reads and the 3’ adapter fragments were removed using cutadapt (version 1.10). Sequences between 25nt and 80nt were reserved and properly paired using Trimmomatic (version 0.36). Unpaired reads were attached to the end of the left reads of the paired fragments for assembly.
De novo transcriptome assembly was performed with Trinity (version 2.2.0).
The newly assembled transcriptomes were annotated using blastx for nucleotide sequences and blastp for peptide sequences generated from TransDecoder (version 3.0.0) against the uniprot_swiss-prot database (release 2016.08).
KEGG ids of each annotated genes were obtained from both uniprot database using uniprot ids and the GhostKOALA service from KEGG (http://www.kegg.jp/ghostkoala/).
Cleaned and trimmed reads of each sample were mapped to the corresponding assembled transcriptomes of each species using Bowtie2 (version 2.2.9). The counts of each genes were obtained with Trinity’s abundance_estimates_to_matrix module using eXpress method.
Differential gene expression were calculated using DESeq2 within the Trinity’s run_DE_analysis module. Genes at suboptimal or supra-optimal temperatures with adjusted P values less than 0.01 and log fold change unequal to 0 as compared to their expression level at the optimal temperature were determined as differentially expressed genes.
Supplementary_files_format_and_content: comma-delimited matrix tables of raw counts and KEGG ID for each contig.

organism: Chaetoceros sp.

source_name: microalgae

growth_protocol: Two strains of Chaetoceros sp., CCMP158 and CCMP160, were grown in f/2 + Si medium under continuous light of 389 ± 27 (SD) μmol photons m-2 s-1. Triplicate cultures of each species were then sampled in acclimated growth at three experimental temperatures for cell composition and transcriptomic analyses.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer instructions.
TruSeq mRNA stranded library preparation protocols for 100 bp paired-end reads

treatment_protocol: The experimental temperatures were the maximum growth rate (Tmax, 17°C for CCMP158 and 25°C for CCMP160) as well as sub-optimal (Tsub, 12°C for CCMP158 and 19°C for CCMP160) and supra-optimal temperatures (Tsup, 22°C for CCMP158 and 28°C for CCMP160) where growth rate was around 50 % of Tmax (except Tsup of CCMP160, where growth was 86% of Tmax).


title: CCMP160 Tsup rep1


title: GZ081_NS

city: Beijing

first: Han

last: Qi

institute: Beijing An Ding Hospital

hyb_protocol: In the hybridization, firstly we need to prepare the 10X blocking agent, then, we mixed the Cyanine 3-labeled cRNA, 10X blocking agent, nuclease-free water and 25X fragmentation buffer and placed the samples on ice after 13,000 centrifuge. The samples need to be manually added in clean slides and hybridized in oven at 65? for 17 hours.

scan_protocol: Profile AgilentG3_GX_1Color was selected for scan control program. The dye channel was "green", scan region was all scan areas, resolution was 3 um and tiff was 20bit. Then we started the scan using G2565CA Microarray Scanner. After generating the microarray scan images, we extracted tiff images using Agilent Feature Extraction software version 10.7.3. The details of the operations for feature extraction could be found in protocol of Agilent One-Color Microarray-Based Exon Analysis.

data_processing:
Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3?m, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by the Quantile algorithm of the limma package of R 3.2.2. software. The hypothesis was that several lncRNAs and mRNAs could be differentially expressed between salt-sensitive individuals and salt-resistant individuals, which may be related with pathogenesis mechanism of salt sensitivity of blood pressure.

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from whole blood samples. Then, NanoDrop ND-2000 spectrophotometer and Agilent Bioanalyzer 2100 were applied to inspect RNA concentrations and integrations. Qualified RNA was amplified and transcribed into cRNA. Labeled cRNA was purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

tag: gender

value: female

tag: age

tag: resistance

value: SSN


title: CCMP160 Tsub rep3


title: HDF_DNTGFBR2_2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Human Clariom D

scan_protocol: GeneChip scanner 7G System

data_processing: Data obtained for each set of samples were normalized by applying the SST-RMA algorithm using the TACv4.0 software (Thermo Fisher Scientific).

label: Biotin

source_name: human dermal fibroblasts lentivirally transduced with a dominant negative mutant TGFBR2 receptor (DNTGFBR2) expressing vector

label_protocol: 100 ng of total RNA were used as input for the preparation of single-strand cDNA using the GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific). Targets were then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Thermo Fisher Scientific)

growth_protocol: Two strains of primary HDFs (GP-HDF, PB-HDF) cultured in complete medium (DMEM enriched in Glutamine, Pyruvate and high Glucose level supplemented with 10% FBS and 1% Antibiotic Cocktail)

extract_protocol: RNA was extracted from HDFs through Direct-zol RNA MiniPrep kit (Zymo Research) coupled with DNase treatment and its quality verified by a Bioanalyzer (Agilent Technologies).

treatment_protocol: HDFs (GP-HDF, PB-HDF) were lentivirally transduced with either a dominant negative mutant FGFR1 receptor (DNFGFR1)- or a dominant negative mutant TGFBR2 receptor (DNTGFBR2)-expressing vector, versus empty vector control. RNA was collected 10 days after infection.

tag: cell type

value: human dermal fibroblasts


title: GZ396_NS


title: CCMP160 Tsup rep2


title: GZ045_NS

value: SRN


title: HL068_NS

value: male

value: SRH


title: NDC12-3

first: Jin

last: Liu

address: No. 5 Yiheyuan Rd

department: Department of Energy and Resources Engineering

institute: Peking University

data_processing:
To ensure quality, the raw data (2×125-bp paired-end reads) were modified as follows: First, adapter pollutions in reads and the reads with length less than 35 nt were removed, and second, all reads were trimmed from the 5′ and 3′ ends until the corresponding end most position with Phred quality score was 20 or greater. These filtered Illumina reads were aligned to the C. zofingiensis genome (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Czofingiensis_er) with TopHat2 with default parameters (Kim et al., 2013). Reads mapped to more than one location were excluded.
Determination of counts per gene and transcript abundance in terms of fragments per Kb of gene per million mapped fragments (FPKMs) were made with Cuffdiff (Trapnell et al., 2012).
Two-fold differentially-expressed genes and regularized log2-transformation were performed with the R DESeq2 package (Love et al., 2014).
Genome_build: Chromochloris zofingiensis v5.2.3.2 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Czofingiensis_er)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Chromochloris zofingiensis

source_name: Whole cell

growth_protocol: Chromochloris zofingiensis was maintained at 16°C on agar plates of the BG-11 medium. Briefly, the algal cells from agar plates were inoculated into liquid BG-11 medium and allowed to grow aerobically in flasks at 25°C for 6 days with orbital shaking at 150 rpm and illuminated with continuous light of 30 µE m−2 s−1. The cells were then inoculated at 10% (v/v) into columns provided with constant illumination of 70 µE m−2 s−1 and aeration of 1.5% CO2 enriched air

extract_protocol:
Total RNAs of algal samples under the above conditions were extracted using Trizol reagents (Invitrogen)
RNA libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New england biolabs) following manufacturer’s recommendations

treatment_protocol: The algal cells in exponential phase (designated as 0 h of ND) were harvested by centrifugation, washed with N-free BG-11 medium three times, and then re-suspended in the medium  in triplicate for ND treatment and ND plus cerulenin treatment, with constant illumination of 70 µE m−2 s−1 and aeration of 1.5% CO2 enriched air. Cells were sampled at 0, 3, 6, 12, and 24 h of ND, and at 6 and 12 of ND plus cerulenin for RNA-Seq.

tag: trophic mode

value: Autotrophy

value: ND plus 10 uM cerulenin for 12 h


title: GZ504_NS


title: CCMP160 Tsub rep2


title: HDF_CTRL_2

source_name: human dermal fibroblasts - control


title: HDF_DNFGFR1_2

source_name: human dermal fibroblasts lentivirally transduced with a dominant negative mutant FGFR1 receptor (DNFGFR1) expressing vector


title: GZ434_NS


title: GZ502_NS

value: SSH


title: GZ353_NS


title: GZ308_NS


title: GZ500_NS


title: GZ351_NS


title: HL126_NS


title: HDF_DNTGFBR2_1


title: CCMP160 Tsub rep1


title: NDC12-2


title: GZ149_NS


title: NDC12-1


title: HDF_CTRL_1


title: GZ078_NS


title: HL095_NS


title: NDC6-3

value: ND plus 10 uM cerulenin for 6 h


title: CCMP160 Tmax rep2


title: GZ338_NS


title: HL096_NS


title: GZ404_NS


title: HDF_DNFGFR1_1


title: GZ393_NS


title: GZ495_NS


title: CAF_16

source_name: skin SCC

label_protocol: 50 ng of total RNA were used as input for the preparation of single-strand cDNA using the GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific). Targets were then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Thermo Fisher Scientific)

growth_protocol: Skin cancer-associated fibroblast (CAF) strains were derived from surgically excised skin SCCs. Normal fibroblast strains were derived from flanking unaffected skin from matched donors. All fibroblasts were cultured in complete medium (DMEM enriched in Glutamine, Pyruvate and high Glucose level supplemented with 10% FBS and 1% Antibiotic Cocktail)

extract_protocol: RNA was extracted from normal fibroblasts and CAFs through Direct-zol RNA MiniPrep kit (Zymo Research) coupled with DNase treatment and its quality verified by a Bioanalyzer (Agilent Technologies).

tag: tissue

value: skin SCC

value: cancer-associated fibroblast (CAF)


title: 7H9_OADC3

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description:
Mtb_raw_counts_matrix.txt
Mtb_counts_normalized.csv

data_processing:
Flexbar (v. 3.4)  has been used to remove low quality reads and trim Illumina adapters.
rRNA reads have been  removed using Bowtie2 (--sensitive mode)
rRNA filtered fastq files were split using Bowtie2 (--very-sensitive mode) into species-specific  files using the two reference genomes, GRCm38.94 for Mus musculus and NCBI assembly  GCA_00668235.1 for Mtb Erdman
Hisat2 (v. 2.1.0) was used to align reads to the respective transcriptomes
Raw read counts for each sample were obtained using HTSeq (v. 0.11.0)
Genome_build: GRCm38.94 for Mus musculus and NCBI assembly GCA_00668235.1 for Mtb Erdman
Supplementary_files_format_and_content: 1) Mtb_counts_normalized.csv is a comma separated values file, containing the normalized counts from the DESeq2 pipeline for the Mtb transcriptome from the different samples.
2) Mtb_counts_normalized_am_im_only.csv is a comma separated values file, containing the normalized counts from the DESeq2 pipeline for the Mtb transcriptome from the in-vivo samples only.
3) Mtb_raw_counts_matrix.txt is a tabular text file containing the raw reads counts generated by the HTSeq software, for the Mtb transcriptome from each sample.
4) Mtb_raw_counts_matrix_am_im_only is a tabular text file containing the raw reads counts generated by the HTSeq software, for the Mtb transcriptome from the in-vivo samples only.
5) Mus_musculus_counts_normalized.csv is a comma separated values file, containing the normalized counts from the DESeq2 pipeline for the Mus Musculus transcriptome from in-vivo samples.
6) Mus_musculus_raw_counts.tsv is a tabular text file containing the raw reads counts generated by the HTSeq software, for the Mus Musculus transcriptome from in-vivo samples.

organism: Mycobacterium tuberculosis

source_name: Mtb mid-log 7h9-oadc cultures

growth_protocol: M.tuberculosis Erdman was grown in 7H9-OADC media until mid-log phase (OD600 = 0.4-0.6)

extract_protocol:
Bacterial RNA extraction was performed using the protocol previously described (Rohde et al., 2012). See manuscript for reference.
rRNA removal was performed using 50-100ng total RNA input and a modified protocol for the  Ribo-Zero Epidemiology Gold rRNA removal kit (Illumina). Briefly, 90 μl bead stock was used  per sample, together with 2 μl each of reaction buffer and removal solution in a 20 μl reaction  volume, as detailed in the manufacturer’s protocol. The rRNA-depleted samples were purified by  precipitating the RNA. Sequencing libraries were generated using the NEBNext Ultra™ II  Directional RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced  on a NextSeq500 (Illumina) in multiple rounds until the desired sequencing depth for bacterial  reads was reached (target 1M 85nt reads).
Rna-seq Directional Libraries

tag: infection

value: no infection (7H9-OADC broth culture)


title: 7H9_OADC2


title: NDC6-2


title: CCMP158 Tsup rep3


title: 7H9_OADC1


title: NDC6-1


title: CCMP160 Tmax rep1


title: S4_LI_Cp13

city: belo horizonte

first: Vasco

middle: Ariston

last: Azevedo

state: MINAS GERAIS

address: 6627 AVENIDA ANTONIO CARLOS

country: Brazil

institute: UFMG

data_processing:
The output raw data files generated by the Ion proton system were converted to FASTQ-sanger file format using the Torrent Suite Software v. 5.0.5 (Thermo Scientific). The software was also used to remove low quality bases at the 3’-end and the ion adaptor sequences
An additional quality trimming was performed using Trimmomatic v0.36  using the following command <trimmomatic-0.36.jar SE -trimlog  <output log file>  -phred33  <compressed raw fastq file>  <output file> SLIDINGWINDOW:4:10
Trimmed reads were mapped to the Corynebacterium pseudotuberculosis  genome using the Torrent Mapping Alignment Program v3.4.1. using the following command:  mapall -f  <fasta file> -r <fastq file> -a 2 -s <bam output file> -v -Y -u -o 1 stage1 map1 stage2 map3 map4. Available at <https://github.com/iontorrent/TMAP>
The output BAM files were sorted, indexed and combined using the SAMtools v.1.5 package. Samples with more than one sequenced replicate were first sorted using < samtools sort>. The replicates were then combined using < samtools merge> and sorted again < samtools sort>
Sorted bam files were used as input for the HTSeq-count script from the HTSeq v0.8.0 package, using the following command: python -m HTSeq.scripts.count [-f bam -r pos -o <samout> -s no -a 0 -t exon -i gene_id] <alignment_files> <gff_file>. The output was a tab txt file with gene identification and raw read counts.
Differential expression analysis was performed with the bicondoctor R package DESeq2 v.1.16.1. In short, using a generalized linear model (GLM) for each gene, the uniquely mapped read counts were modeled as following a negative binomial distribution with mean and dispersion, where the mean is proportional to the concentration of RNA fragments counted scale by a size factor normalization, which accounts for differences in sequencing depth between samples. The linear model fit applied generated coefficients that indicate the overall gene expression strength and the log2fold change between the two conditions (Low iron  vs Ct). Batch effect was addressed in the Cp13 strain samples by including into the DESeq2 design formula: ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = '<>', design= ~ batch + condition). Batch identification followed the processing description given in  the sample 'characteristics: Batch'. Batch identification followed the processing description given under the 'characteristics: Batch' of each sample.
Genome_build: C. pseudotuberculosis strain 1002B - NZ_CP012837.1
Supplementary_files_format_and_content: tab-delimited text files include unique aligned read counts

organism: Corynebacterium pseudotuberculosis

source_name: bacterial cultures

growth_protocol: Bacterial strains were grown in low iron (LI) BHI media prepared with 250uM of iron chelator 2,2’-dipyridyl (Sigma Aldrich). BHI incubation of control (Ct) samples were conducted in parallel and independent sets of paired samples (control and LI conditions) were prepared for each strain. Bacterial growth was monitored by optical density (OD600) and total RNA extractions were carried out after 6:30h of incubation.

extract_protocol:
Following 6:30 hours of incubation, each culture (LI and Ct) was centrifuged for 10 minutes at 5.000 rpm (4˚ C) in 50 mL conical tubes, and the supernatants were discarded. The bacterial pellets were kept on ice and resuspended in 300 µL of Tris/EDTA/SDS (Tris HCl pH8 50 mM/L–EDTA pH8 10 mM/L) lysis buffer per 10 mL of used initial culture volume. Cell suspensions were homogenized with 0,1% of SDS and 1 mL of TRIzol® Reagent (Invitrogen™) was added (1 volume per 10 mL of used initial culture). Pellets from each tube were divided into 2 new tubes filled with 1mm diameter glass microbeads (Bertin Thechnologies). The cells were mechanically lysed using Prescellys®24, set for 2 cycles (15 seconds per cycle) at 6200 rpm with 5 seconds interval between each cycle. The tubes were immediately placed on ice following the lysis. The cooled samples were centrifuged for 10 seconds at 14.000 rpm and the supernatants were carefully transferred to a new tube for total RNA extraction. Subsequent extraction steps were carried out following TRIzol® Reagent manufacturer’s recommended protocol and total RNA was eluted in 50ul of RNase free water. Traces of contaminating DNA were eliminated with the Ambion® TURBO DNA-free™ DNase kit (Invitrogen), following manufacturer’s protocol.
All RNA samples were subjected to ribosomal RNA depletion and purification using the RiboMinus™ Bacteria Transcriptome Isolation Kit with the RiboMinus™ and the Concentration Module (Invitrogen), as described in the manual. 5 µg of purified depleted RNA samples were used to prepare 14 individual single-end RNA-seq libraries with the Ion Total RNA-seq v2 for Whole Transcriptome Library kit (Thermo Scientific).

tag: experimental condition

value: Low Iron (LI)

tag: batch

value: Batch 3


title: CCMP158 Tsup rep2


title: ND24-3

value: ND for 24 h


title: ND24-2


title: CCMP158 Tsub rep3


title: ND24-1


title: ND12-3

value: ND for 12 h


title: S3_LI_T1

description: Sample eliminated due to the low number of sequenced reads

value: Batch 1


title: ND12-2


title: CCMP158 Tsub rep1


title: CCMP158 Tmax rep3


title: ND12-1


title: CCMP158 Tsup rep1


title: S4_Ct_Cp13

value: Control


title: CAF_14


title: Normal_fibroblasts_15

source_name: distal normal skin

value: distal normal skin

value: normal fibroblasts


title: Normal_fibroblasts_14


title: S2_Ct_T1


title: CAF_15


title: S2_LI_T1


title: CAF_13


title: CCMP158 Tmax rep2


title: Normal_fibroblasts_13


title: CAF_12


title: Normal_fibroblasts_16


title: CCMP158 Tsub rep2


title: S3_LI_Cp13


title: CCMP158 Tmax rep1


title: ND6-3

value: ND for 6 h


title: ND6-2


title: ND6-1


title: S3_Ct_Cp13


title: S3_Ct_T1

description: Control sample eliminated due to the low sequenced reads of paired low iron sample (38I)


title: S2_Ct_Cp13

value: Batch 2


title: ND3-2

value: Autotrophy

value: ND for 3 h


title: ND3-3


title: ND3-1


title: Yap CKO #2

city: Bunkyo-ku

first: Hideaki

last: Isago

state: Tokyo

department: Department of Respiratory Medicine

country: Japan

institute: The University of Tokyo Graduate School of Medicine

data_processing:
Sequence were read by BGISEQ500 and basecalling was processed.
Sequenced reads were aligned against mouse genome mm10 using Bowtie2 (v2.2.9; --local -x mm10)
Gene expression levels were measured by counting numbers of reads in all the exons using featureCounts (v1.5.0-p1; -p -t exon -g gene_id -F GTF )
Differential gene expression was measured using DESeq version 1.16.0 edgeR (v3.18.1):Normalization: Upper-quartile (UQ, Model: negative binomial assumption, Testing strategy: exact test, logFC>+-2, FDR q-value<0.05
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: a text file include TMM normalized values for each sample

source_name: total lung

extract_protocol:
Rneasy Mini (Qiagen)
RNA libraries were prepared for sequencing using standard BGI protocols

value: Yap conditional knockout (CKO)

value: embryonic day 14.5


title: S2_LI_Cp13


title: S1_LI_T1


title: ND0-3

value: ND for 0 h


title: S1_Ct_T1


title: Yap CKO #1


title: S1_LI_Cp13


title: Control #2

value: wild type


title: ND0-2


title: S1_Ct_Cp13


title: ND0-1


title: CAF_10

value: skin SCC

value: cancer-associated fibroblast (CAF)


title: p6374

city: LEEDS

first: Milene

last: Volpato

address: St James University Hospital

department: LIRM

country: United Kingdom

institute: University of Leeds

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalisation

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: RPMI, 10% foetal calf serum

extract_protocol: RNEasy kit QIAGEN

treatment_protocol: cell growth to 70% confluence in T75 flasks

tag: sample type

value: EPA resistant cells


title: Control #1


title: CAF_11


title: p6375

description: replicate 2


title: Normal_fibroblasts_11


title: p6373

description: replicate 1

value: EPA sensitive cells


title: p6372

description: replicate 2


title: Normal_fibroblasts_10


title: Normal_fibroblasts_8


title: p6371

description: replicate 3


title: yFR116_Thiolutin_Rpb3vsInput_SPIKE-IN_Rep2

status: Public on Jul 30 2019

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy in WT cells treated with 3µg/ml thiolutin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR116_Thiolutin_Rpb3vsInput_SPIKE-IN_Rep1-2__S.cerevisiaeApr11_873611.bed
BED description: A genome browser-ready file for RNAPII (Rpb3) occupancy (IP/Input) in WT cells treated with 3µg/ml thiolutin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

hyb_protocol: Hybridization: Resuspend colored pellet in 110 uL of hybridization mix (100 uL DIG Easy Hyb buffer, 5 uL 10mg/mL Salmon Sperm DNA, 5 uL 8mg/mL yeast tRNA). Put at 95°C for 5 min. Put at 42°C for 10 min (keep samples at 42°C while waiting for hybridization). Follow standard Agilent chamber hybridization protocol. Incubate overnight (16-24h) at 42°C in Agilent hybridization oven at 20 rpm rotation speed.  Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 min at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in Wash buffer #2 pre-warmed at 31°C for 5 min on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Stripping: Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 20 to 25 min. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. 1M Potassium phosphate buffer pH 6.6: mix 3.81 mL of 1M K2HPO4 + 6.19 mL of 1M KH2PO4. Dilute 5 mL of this 1M solution in 1 L Milli-Q water to obtain 5 mM Potassium phosphate buffer pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180K. Set the scan as follow: pixel size = 2µm; speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto. Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing:
Correction = Foreground-Background; Normalisation = median normalized
median normalized log2 (Cy5/Cy3) ratio (ChIP vs control); see file: GSE113025_Jan2019_NewSamples_median_norm_log2_ratios.xlsx

organism: Saccharomyces cerevisiae

label_protocol: Standard Yeast aa-dUTP Labeling. Blunting: Do everything on ice. Add 70 uL of the blunting solution (11 uL NEB Buffer #2, 0.5 uL BSA 10mg/mL, 0.5 uL 20mM dNTPs, 0.2 uL T4 DNA Polymerase 3U/uL, 57.8 uL ddH2O) to 40 uL of the resuspended DNA obtained at the end of the cleanup step. For Inputs, use 4uL + 36uL ddH2O. Incubate 20 min at 12°C. Precipitation: Add 11.5 uL 3M NaOAc pH 5.2 and 0.5 uL Glycogen 20mg/mL and vortex briefly. Extract with 120 uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110 uL to a new tube and add 230 uL of cold 100% EtOH (-20°C). Spin 20 min at 4°C. Wash the pellet with 700 uL of cold 70% EtOH (-20°C) and spin 5 min at 4°C. Resuspend the pellet in 25 uL ddH2O and place on ice. Ligation: Thaw everything and do all manipulations on ice. Add 25 uL of ligase mix (10 uL 5x T4 Ligase Buffer, 6.7 uL 15uM unidirectional linkers, 0.5 uL T4 DNA Ligase (5U/uL), 8 uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16°C. Precipitation: Add 6 uL 3M NaOAc pH 5.2 and vortex. Add 130 uL of cold 100% EtOH (-20°C) and incubate at least 30 min at -20°C. Centrifuge 20 min at 4°C at maximum speed. Wash the pellet (should be a smear on the side of the tube) with 500 uL cold 70% EtOH (-20°C). Spin 5 min at 4°C. Dry the pellet and resuspend in 25 uL ddH2O. Leave on ice for about 20 min, vortex, centrifuge briefly and put on ice. Labeling: Add 15 uL of PCR labeling mix (4 uL 10x ThermoPol Buffer, 2 uL 5mM aa-dUTP mix, 1.25 uL 40uM Oligo FR1, 7.75 uL ddH2O) to the pellet from the ligation step. Start the PCR program and during the first step (4 min at 55°C), add 10 uL of the polymerase mix (1 uL 10x ThermoPol buffer, 1 uL Taq Polymerase 5U/uL, 0.01 uL Pfu Polymerase Turbo 2.5U/uL, 8 uL ddH2O). PCR cycling conditions: 1) 4 min at 55°C; 2) 5 min at 72°C; 3) 2 min at 95°C; 4) 30 sec at 95°C; 5) 30 sec at 55°C; 6) 1 min at 72°C; 7) Repeat steps 4-6 31 more times; 8) 4 min at 72°C; 9) Forever at 4°C. Purify PCR reactions with QIAquick PCR purification kit (Qiagen), following manufacturer's protocol but use a Phosphate Wash buffer and a Phosphate Elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns twice and elute with 50 uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5 uL 0.1M Sodium Carbonate buffer pH 9.0. Add 4.5 uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dyes should be resuspended in 73 uL DMSO. Mix well and incubate at room temperature in the dark for one hour. Add 35 uL 0.1M NaOAc pH 5.2. Purify using the QIAquick PCR purification kit (Qiagen), wash twice and elute in 50 uL. Mix both samples of a pair (Cy5 and Cy3) in the same tube. Speed-vac until 10-20uL are left. Phosphate Wash buffer (100 mL): 0.5 mL 1M KPO4 pH 8.5, 15.25 mL ddH2O, 84.25 mL 95% EtOH. Solution will be cloudy upon mixing. Phosphate Elution buffer (10 mL): 0.04 mL 1M KPO4 pH 8.5, 9.96 mL ddH2O. 1M KPO4 pH 8.5 (10 mL): 9.5 mL 1M K2HPO4, 0.5 mL 1M KH2PO4. 1M Sodium Carbonate buffer pH 9.0 (100 mL): 10.8g Na2CO3, 80 mL ddH2O and pH to 9.0 with concentrated HCl. Adjust volume to 100 mL with ddH2O. Dilute 1:10 when using. Solution will change composition over time. Use only if less than a month old.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 around 0.6. Cell cultures are treated with 3µg/ml thiolutin for 30 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
Cells are thawed on ice and resuspended in 700 uL Lysis buffer with protease inhibitors. 500 uL of acid-washed glass beads (Sigma) are added and the cells are lysed using a bead-beater (4 x 5 min cycles, with 5 min breaks on ice). The tubes are pierced with an 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2 mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x20sec at output 7 Watts, with a 1 min break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4°C max speed and the supernatant used immediately for ChIP (or saved and frozen at -80°C). Lysis buffer: 50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM PMSF, 1mM Benzamidine, 10ug/mL Aprotinin, 1ug/mL Leupeptin, 1ug/mL Pepstatin.
Beads are spun down and supernatant is transferred to a new 1.5 mL tube. 350 uL of a mix of (345 uL TE, 3 uL RNAse A 10mg/mL, 2 uL Glycogen 20mg/mL) is added to the supernatant. Samples are vortexed and incubated at 37°C for 2 hr. 15 uL 10% SDS and 7.5 uL Proteinase K are then added, vortexed and incubated for another 2 hr at 37°C. The samples are then extracted twice with 400 uL phenol/chloroform/isoamyl alcohol (25:24:1). 14 uL of 5M NaCl is added to the final extract of about 350 uL. 1 mL of cold 100% EtOH (-20°C) is added and the samples are centrifuged at maximum speed for 20 min at 4°C. The supernatant is discarded and the pellet is washed with 700 uL of cold 70% EtOH (-20°C) and centrifuged 5 min at 4°C. The supernatant is discarded and the pellet resuspended in 50 uL TE and stored at -20°C.

treatment_protocol:
3µg/ml thiolutin for 30 min
RNAPII (Rpb3)  ChIP. Antibody from Neoclone (W0012). Pan anti-mouse  Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μl/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

tag: antibody

value: Rpb3 (W0012 Neoclone)

treatment_protocol:
3µg/ml thiolutin for 30 min
no IP


description:
Biological replicate 1 of 2. H3K4me3 occupancy in rpb1-G1097D (fast) cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR1252_G1097Dmutant-FastRNAPII_H3K4me3vsInput_20171012_rep1-2_MN__S.cerevisiaeApr11_651604.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in rpb1-G1097D (fast) cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 around 0.7. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
none
H3K4me3  ChIP. Antibody from Abcam (Ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, lys2-128∂, ura3-52, his3∆200, leu2∆0 or ∆1, trp1∆63, met15∆0, rpb1∆::CLONATMX, RPB3-3xFLAG::kanMX, [pRS315 (CEN, LEU2, rpb1-G1097D)]

treatment_protocol:
none
no IP


title: yFR1252_G1097Dmutant-FastRNAPII_H3K4me3vsInput_20171012_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in rpb1-G1097D (fast) cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR1252_G1097Dmutant-FastRNAPII_H3K4me3vsInput_20171012_rep1-2_MN__S.cerevisiaeApr11_651604.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in rpb1-G1097D (fast) cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


title: Normal_fibroblasts_12


description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy in WT cells treated with 3µg/ml thiolutin for 30 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR116_Thiolutin_Rpb3vsInput_SPIKE-IN_Rep1-2__S.cerevisiaeApr11_873611.bed
BED description: A genome browser-ready file for RNAPII (Rpb3) occupancy (IP/Input) in WT cells treated with 3µg/ml thiolutin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


title: p6376

description: replicate 3


title: yFR116_WT_Rpb3vsInput_SPIKE-IN_Rep1

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR116_WT_Rpb3vsInput_SPIKE-IN_Rep1-2__S.cerevisiaeApr11_861328.bed
BED description: A genome browser-ready file for RNAPII (Rpb3) occupancy (IP/Input) in WT cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 around 0.8. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
none
RNAPII (Rpb3)  ChIP. Antibody from Neoclone (W0012). Pan anti-mouse  Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μl/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.


title: yFR1240_WT-RNAPII_H3K4me3vsInput_20171012_rep2

description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR1240_WT-RNAPII_H3K4me3vsInput_20171012_rep1-2_MN__S.cerevisiaeApr11_400555.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

value: MATα, lys2-128∂, ura3-52, his3∆200, leu2∆0 or ∆1, trp1∆63, met15∆0, rpb1∆::CLONATMX, RPB3-3xFLAG::kanMX, [pRS315 (CEN, LEU2, RPB1)]


title: yFR3150_SWD1-AID_SPT16-FRB_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-FRB and swd1-AID cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3150_SWD1-AID_SPT16-FRB_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_511173.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in swd1-AID and spt16-FRB cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 around 0.5. Cell cultures are treated with 500µM IAA (Auxin) for 60 min and then with 1 μg/mL of rapamycin for additional 30 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min
H3K4me3  ChIP. Antibody from Abcam (Ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, his3-11,15::pADH1-AFB2-HIS3, SWD1-AID-6xHA::hphNT, SPT16-FRB::kanMX6

treatment_protocol:
500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min
no IP


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-FRB and swd1-AID cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3150_SWD1-AID_SPT16-FRB_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_511173.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in swd1-AID and spt16-FRB cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


title: CAF_8


title: yFR116_WT_Rpb3vsInput_SPIKE-IN_Rep2

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR116_WT_Rpb3vsInput_SPIKE-IN_Rep1-2__S.cerevisiaeApr11_861328.bed
BED description: A genome browser-ready file for RNAPII (Rpb3) occupancy (IP/Input) in WT cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-FRB cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL of rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3149_Spt16-FRB_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_356014.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt16-FRB cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, his3-11,15::pADH1-AFB2-HIS3, SPT16-FRB::kanMX6


title: yFR3147_SWD1-AID_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in swd1-AID cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3147_SWD1-AID_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_206111.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in swd1-AID cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, his3-11,15::pADH1-AFB2-HIS3, SWD1-AID-6xHA::hphNT


description:
Biological replicate 1 of 2. H3K4me3 occupancy in rpb1-H1085Y (slow) cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR1242_H1085Ymutant-SlowRNAPII_H3K4me3vsInput_20171012_rep1-2_MN__S.cerevisiaeApr11_985929.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in rpb1-H1085Y (slow) cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

value: MATα, lys2-128∂, ura3-52, his3∆200, leu2∆0 or ∆1, trp1∆63, met15∆0, rpb1∆::CLONATMX, RPB3-3xFLAG::kanMX, [pRS315 (CEN, LEU2, rpb1-H1085Y)]


title: yFR3149_Spt16-FRB_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-FRB cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3149_Spt16-FRB_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_356014.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt16-FRB cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


description:
Biological replicate 1 of 2. H3K4me3 occupancy in swd1-AID cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3147_SWD1-AID_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_206111.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in swd1-AID cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3143_WT_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_759661.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

value: MATα, ade2-1, trp1-1, can1-100, leu2-3,112, ura3, GAL, psi+, tor1-1, fpr1Δ::NAT, RPL13A-2xFKBP12::TRP1, his3-11,15::pADH1-AFB2-HIS3


title: yFR3143_WT_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated with 500 µM IAA (Auxin) for 60 min and then 1 μg/mL rapamycin for 30 min. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR3143_WT_IAA60min_Rapa30min_H3K4me3vsInput_20180924_rep1-2__S.cerevisiaeApr11_759661.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated with 500µM IAA (Auxin) for 60 min and 1 μg/mL rapamycin for 30 min.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


title: yFR1242_H1085Ymutant-SlowRNAPII_H3K4me3vsInput_20171012_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in rpb1-H1085Y (slow) cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR1242_H1085Ymutant-SlowRNAPII_H3K4me3vsInput_20171012_rep1-2_MN__S.cerevisiaeApr11_985929.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in rpb1-H1085Y (slow) cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
BED name: SmthBED_yFR1240_WT-RNAPII_H3K4me3vsInput_20171012_rep1-2_MN__S.cerevisiaeApr11_400555.bed
BED description: A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells.
BED method: The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).


title: RCMB24

first: Volker

last: Hovestadt

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: 137 high quality malignant cells

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by RSEM v1.2.3 in paired-end mode using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene were extracted.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing TPM values (transcript-per-million reads) for 23,686 analyzed genes (rows), across all high-quality malignant cells in a given sample (columns). Log2-transformed TPM values are provided (log2(TPM/10+1)).

growth_protocol: Patients and their parents at Boston Children’s Hospital, the Medical University of Vienna and St. Jude Children’s Research Hospital gave consent preoperatively according to Institutional Review Boards. Fresh tumours were collected at the time of surgery and processed directly.

extract_protocol:
Tumour samples from Boston Children’s Hospital and the Medical University of Vienna were mechanically and enzymatically dissociated using a papain-based brain tumour dissociation kit (Miltenyi Biotec). Tumour samples from St. Jude Children’s Research Hospital and low passage (<10) PDX models were precut and dissociated for 30 minutes in papain solution (Worthington, 10u/ml), rinsed in Neurobasal medium and filtered using a 40um strainer.
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter). Libraries were then generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications. oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 384 or 768 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina).

treatment_protocol: Diagnostic samples were resected prior to patient treatment.

value: M

tag: methylation subgroup

value: SHH-adult

tag: methylation subtype

tag: metastasis

tag: histology

tag: methylation idat id


title: RCMB18

description: 166 high quality malignant cells


title: RCMB20

description: 60 high quality malignant cells

value: Group 3

value: Subtype II


title: Exosomal RNA biological replicate_3

city: Fujisawa

first: Kentaro

last: Otake

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Neuroscience Drug Discovery Unit

institute: Takeda Pharmaceutical Company Limited

description:
Exo_3
Raw_Counts.txt
EdgeR_Results.txt

data_processing:
Base Calls were performed in NextSeq500 suquencing system.
Mapping to genome and counting the reads were performed by RNA-seq pipeline implemented in Omicsoft Array Studio (QIAGEN).
Genes with raw counts less than 10 were removed.
Differential analysis was performed by edgeR after TMM normalization
Genome_build: B37.3
Supplementary_files_format_and_content: Tab-delimited files representing raw counts or differential analysis with statistial values.

source_name: exosomes from culture supernatant of iPSC-motor neurons

growth_protocol: Human iPSC line, 201B7 was mainained in Stemfit AK02N on the iMatrix-511 coated plate.

extract_protocol:
Culture supernatant of iPSC-derived motor neurons was applied to exoRNeasy spin column and RNA was extracted (QIAGEN). Cellular mRNAs were extracted by miRNeasy which uses same spincolumn with exoRNeasy for RNA isolation (QIAGEN)
Whole cDNA amplification was performed with SMART-seq v4 Ultra Low Input RNA Kit. Illumina library was constructed with Nextera XT DNA Library Prep Kit.

treatment_protocol: 201B7 cells were differentiated to MNP and finally to motor neurons as described in previous reports (Nat Commun. 2015 Mar 25;6:6626.; Mol Brain. 2015 Dec 1;8(1):79.; Stem Cell Rev. 2015 Feb;11(1):194-204.)

tag: rna extraction method

value: exoRNeasy

value: iPSC-derived motor neurons

tag: cell fraction

value: exosomes


title: Exosomal RNA biological replicate_1

description:
Exo_1
Raw_Counts.txt
EdgeR_Results.txt


title: CCMP160 Tmax rep3

tag: strain


title: Exosomal RNA biological replicate_2

description:
Exo_2
Raw_Counts.txt
EdgeR_Results.txt


title: Cellular RNA biological replicate_1

description:
Cell_1
Raw_Counts.txt
EdgeR_Results.txt

source_name: iPSC-derived motor neurons (dd10)

value: miRNeasy

value: whole cell


title: Cellular RNA biological replicate_3

description:
Cell_3
Raw_Counts.txt
EdgeR_Results.txt


title: Med411FH

description: 86 high quality malignant cells

tag: gender

tag: age


title: Med2312FH

description: 68 high quality malignant cells

value: F

value: Subtype V


title: Icb1572

description: 81 high quality malignant cells

value: Subtype III


title: Icb1299

description: 83 high quality malignant cells


title: Med2112FH

description: 72 high quality malignant cells


title: Med211FH

description: 66 high quality malignant cells


title: DMB006

description: 80 high quality malignant cells

value: Group 4

value: Subtype VIII


title: SJ917

description: 333 high quality malignant cells

source_name: Medulloblastoma, diagnostic

value: M+

value: Large Cell/Anaplastic


title: Cellular RNA biological replicate_2

description:
Cell_2
Raw_Counts.txt
EdgeR_Results.txt

tag: cell type


title: SJ723

description: 75 high quality malignant cells

value: Classic


title: SJ970

description: 52 high quality malignant cells

value: M


title: SJ617

description: 400 high quality malignant cells


title: SJ577

description: 493 high quality malignant cells

value: SHH-adult

value: Desmoplastic/Nodular


title: skin healthy control rep2

first: Shengru

last: Zhou

address: No. 197, Rui Jin Er Road

department: Dermatology

institute: Shanghai Jiao Tong University School of Medicine affiliated Rui Jin Hospital

description: control 2

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

data_processing: Then raw data were RMA normalized by Expression Console. Heat maps were generated with R software.

source_name: skin from healthy control

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Human skin samples of 1 cm×1 cm from pemphigus patients and healthy donors were collected and incubated in a buffer containing collagenase IV, hyaluronidase, and DNase-I (Sigma-Aldrich, St. Louis, MO) for digestion at 37°C for 2 hours. After digestion, the samples and were passed through a 70 μm cell strainer (BD Biosciences, San Jose, CA), and single-cell suspensions were obtained. Mononuclear cells were isolated by density separation gradient using LymphoprepTM solution (Axis-shield, Oslo, Norway) and resuspended in RPMI 1640 (Invitrogen, Camarillo, CA) medium supplemented with 5% fetal bovine serum (FBS; Sigma Aldrich, St. Louis, MO).

tag: subject status

value: healthy control

value: mononuclear cells from healthy skin


title: skin healthy control rep1

description: control 1


title: lesion untreated rep3

description: pemphigus 3

source_name: pemphiugs  lesions untreated

value: pemphigus patient

value: mononuclear cells from skin lesion


title: skin healthy control rep3

description: control 3


title: lesion untreated rep1

description: pemphigus 1


title: lesion untreated rep2

description: pemphigus 2


title: SJ625

description: 328 high quality malignant cells

value: Subtype I


title: Med114FH

description: 47 high quality malignant cells

value: Group 3

value: Subtype II


title: SJ516

description: 507 high quality malignant cells

value: F

value: WNT


title: SJ454

description: 293 high quality malignant cells

value: SHH-infant


title: SJ17

description: 334 high quality malignant cells


title: SJ99

description: 338 high quality malignant cells


title: BCH825

description: 330 high quality malignant cells

value: Subtype V


title: MUV39

description: 241 high quality malignant cells

value: Group 4


title: BCH1031

description: 273 high quality malignant cells

value: Subtype VIII

value: Large Cell/Anaplastic


title: MUV19

description: 304 high quality malignant cells

value: M

value: M+

value: Classic


title: MUV37

description: 190 high quality malignant cells

source_name: Medulloblastoma, recurrent


title: BCH1205

description: 326 high quality malignant cells

value: Subtype III


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 8

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg38 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed file contains the raw counts for each gene as estimated by RSEM

source_name: lymph node

extract_protocol:
Cellular RNA was purified using the AllPrep DNA/RNA kit (Qiagen, Ventura CA) as specified by the manufacturer. RNA quality was validated using the Agilent TapeStation, and the High Sensitivity RNA Screentape (Agilent, Santa Clara, CA) and quantity was determined using the Qubit 2·0 Fluorometer (ThermoFisher Scientific, Waltham, MA)
cDNA was generated from 10 ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) according to manufacturer’s directions. Then, 150 pg of the cDNA was used to prepare library for Illumina sequencing using the Nextera XT Library Prep Kit (Illumina, San Diego, CA) according to manufacturer’s directions.

tag: patientid

tag: treatment

tag: tissue

value: lymph node


title: MUV34

description: 294 high quality malignant cells


title: MUV11

description: 431 high quality malignant cells


title: MUV29

description: 314 high quality malignant cells


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 6


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 7


title: BCH807

description: 307 high quality malignant cells


title: MUV27

description: 314 high quality malignant cells


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 4


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 3


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 2


title: SJ217

description: 316 high quality malignant cells


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 1


title: lymph node at baseline from patient 8

value: baseline


title: lymph node at baseline from patient 7


title: SJ129

description: 313 high quality malignant cells


title: MUV41

description: 338 high quality malignant cells

value: Desmoplastic/Nodular


title: MUV44

description: 301 high quality malignant cells


title: lymph node after 24 weeks of TLR9 agonist MGN1703 treatment from patient 5


title: lymph node at baseline from patient 5


title: lymph node at baseline from patient 6


title: lymph node at baseline from patient 1


title: lymph node at baseline from patient 2


title: lymph node at baseline from patient 3