title: KO-IRAKM-High-2_RNA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed ChIP-seq reads were aligned using bowtie 1.1.2
Aligned ChIP-seq reads that overlapped ENCODE blacklist regions were removed
ChIP-seq reads were extended to 250bp
ChIP-seq samples were normalized to sequencing depth and normalized input was subtracted
ChIP-seq samples were converted to BigWig format
RNA-seq trimmed reads were quantified using Salmon v1.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format
Supplementary_files_format_and_content: Quantified RNA-seq transcripts in text

source_name: Bone-marrow derived monocytes

extract_protocol:
RNA was extracted into a 30-µL volume using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen), following the manufacturer’s instruction. 10,000 cells were used to produce each RNA-seq library, with two replicates for each genotype and experimental condition. The extracted mRNA was then concentrated by ethanol precipitation and resuspended in 4.6 µL of RNase-free water. Next, we used the SMART-seq2 protocol, with minor modifications, to prepare cDNA. 2 µL of oligo-dT primer (100 µM) and 2 µL of dNTP mix (10 mM) were added to 2 ng of mRNA in 4.6 µL of water.  The mRNA solution was denatured at 72 °C for 3 min, then immediately placed on ice. Next, 11.4 µL of reverse transcription mix [1 µL of SuperScript II reverse transcriptase (200 U/µL), 0.5 µL of RNAse inhibitor (40 U/µL), 4 µL of Superscript II first-strand buffer, 1 µL of DTT (100mM), 4 µL of 5 M Betaine, 0.12 µL of 1 M MgCl2, 0.2 µL of TSO (100 M), 0.58 µL of nuclease-free water] was added to the mRNA solution. For the reverse transcription reaction, the solution was incubated at 42 °C for 90 min, followed by 10 cycles of 50 °C for 2 min, 42 °C for 2 min, then inactivation at 70 °C for 15 min. 20 µL of the resulting solution (first-strand mixture) was then mixed with 30 µL of PCR mix [25 µL KAPA HiFi HotStart ReadyMix, 0.5 µL IS PCR primers (10 µM), 0.5 µL Evagreen dye, and 4 µL nuclease-free water] and amplified using the program 98 °C for 1 min, followed by 9-11 cycles of 98 °C 15 s, 67 °C 30 s, 72 °C 6 min. Finally, the cDNA was purified using 50 µL of SPRIselect beads.
RNA-seq libraries were generated with the Nextera XT DNA Library Preparation kit (FC-131-1024, Illumina) and manufacturer’s protocol, using approximately 600 pg of purified cDNA from each sample.

treatment_protocol: Cells were cultured in RPMI complete media (RPMI 1640 with 10% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin) along with M-CSF (10 ng/mL) and either PBS, low-dose LPS (100 pg/mL), or high-dose LPS (1 µg/mL). Fresh LPS was added every two days and the cells were harvested after 5 days.

value: IRAK-M-/-

value: BMDMs

value: high-dose LPS


title: mRNA_LV_PS_9561

status: Public on Mar 18 2021

type: SRA

city: Stanford

first: Hyun Tae

middle: V

last: Hwang

state: CA

address: 300 Pasteur Dr. S242

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
FastQC (v0.11.5) was used to assess read quality.
Reads were mapped to mouse reference genome mm9 using STAR (v2.5.3a) with UCSC gene annotations using default conditions as described in Dobin et al., Bioinformatics, 2013.
Normalized transcript abundances (FPKM) were calculated and differential expression analyses for RNA-Seq were performed using the Cuffdiff program from the Cufflinks v2.2.1 suite using default conditions as described in Trapnell et al., Nature Biotechnology, 2013. The bias detection and correction algorithm was used to significantly improve accuracy of transcript abundance estimates as described in Roberts et al., Genome Biology, 2011. The initial estimation procedure was used to more accurately weight reads mapping to multiple locations in the genome.
Exploration, analysis and visualization of Cuffdiff results were performed using the CummeRbund v2.16.0 R package installed in R v3.3.1 as described in Trapnell et al., Nature Protocols, 2012.
Pathway and gene ontology (GO) analyses were carried out through Advaita Bioinformatics (Ann Arbor, MI).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Heart tissue

growth_protocol: Male FVB mice aged between 10-13 weeks were used.

extract_protocol:
Total RNA from murine right and left ventricles were isolated using miRNeasy Mini Kit (217004; Qiagen, Germantown, MD) following the manufacturer's guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RV failure was induced by pulmonary artery banding. Sham-operated controls were also generated.

tag: tissue

value: Left ventricular free wall

tag: strain

value: FVB

tag: developmental stage

value: Adult

tag: Sex

value: Male

tag: treatment

value: PS


title: Pf-iRBC stimulated-Malian Children [R14]

city: Rockville

first: Rajan

last: Guha

address: 5625 Fishers Lane,Room No:4N07

institute: NIAID/NIH

data_processing:
Quality control using FASTQC
Trimming was performed using cutadapt
Alignment was performed using STAR aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts were generated using featureCounts

molecule: total RNA

organism: Homo sapiens

source_name: Pf-iRBC stimulated-Malian Children

growth_protocol: Monocytes were cultured in complete RPMI (RPMI 1640 plus 10% human AB serum, 1% penicillin/streptomycin), at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Cells were isolated and kept in RNAprotect buffer (Qiagen) at -80 degree before RNA was isolated from the samples. RNA was isolated using RNAeasy kit according to manufacturer’s instruction. Isolated RNA’s were checked for quality and quantified using Agilient Bioanalyzer. RNA’s with RIN values greater than 7 were used for all the analysis.
cDNA was prepared from 10 ng total RNA using the Ovation® RNA Seq System V2 (Tecan) according to manufacturer’s instructions.  This method employs both poly-T and random primers so that both poly-adenylated and non-poly-adenylation messages are included.  The cDNA product was end-repaired using the NEBNext End Repair Module (New England Biolabs). RNA-Seq libraries were prepared using 1 g of end-repaired cDNA using the TruSeq Stranded RNA Kit (Illumina), however due to the method of amplification the libraries are not stranded.  Unique dual-indexed barcode adapters were applied to each library. Libraries were pooled in an equimolar ratio for sequencing.  The pooled libraries were sequenced on one lane of an S4 flow cell on a NovaSeq 6000 using version 1 chemistry to achieve a minimum of 49 million 150 base read pairs.  The data was processed using RTA version 3.4.4 and BWA-0.7.12.

treatment_protocol: Monocytes were stimulated in a ratio of 5 pf-iRBC per monocytes,control monocytes were kept in the same medium without Pf-iRBC.Monocytes were harvested after 24 hrs of incubation and proceed for downstream RNA isolation.

tag: subect status

value: Pf-iRBC stimulated-Malian Children

tag: cell type

value: monocytes


title: 40h_after_UNC0642_removal_H3K9me2

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

library_source: genomic

data_processing:
Adaptor sequences in reads were trimmed using Trim Galore version 0.3.7
Trimmed reads were aligned to the mm10 genome build using bowtie version 0.12.7
Duplicated reads were removed using samtools version 0.1.18
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: mESCs were maintained in DMEM with 1%FCS/10%KSR/LIF on gelatin coated dish. iMEFs were maintained in DMEM with 10% FCS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30seconds off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) or SMARTER ThruPLEX DNA-seq kit (TAKARA) and SMARTer DNA Unique Dual Index Kit (TAKARA) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS).

treatment_protocol: We treated 800 nM 4-OHT for 5 days to Setdb1 conditional KO mESCs to deplete SETDB1. We treated 2uM UNC0642 for 3 days and 5 days to mESCs and iMEFs, respectively to inhibit G9a/GLP catalytic activity.

tag: genotype

value: TT2 mES

value: mouse embryonic stem cells

tag: antibody

value: 6D11 anti-H3K9me2

value: 40h_after_2uM UNC0642 treatment for 3 days


title: mRNA_LV_PS_9553


title: LP01, exosome, non coding small RNA seq

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

data_processing:
1) Getting rid of low quality tag (The criteria for this is listed in the explanation of meaning of each
row in the result table)
2) Getting rid of tag with 5' primer contaminants
3) Getting rid of tag without 3' primer
4) Getting rid of tag without the insert
5) Getting rid of tag with poly A
6) Getting rid of tag shorter than 18nt
7) Summarize the length distribution of the clean tags
After filtering, the remaining tags are called "clean tags" and stored as FASTQ format \[7\] (see FASTQ Format in help page).
Data was processed via miRDeep2.
First, fastq file was mapped to hg38 genome using mapper.pl as
mapper.pl LP01.fq -n -h -g hsa -e -n -i -j -k AGATCGGAAGAGCACACGTCT -l 18 -m -s LP01.fastq.collapsed -p ~/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/genome -t LP01_vs_genome_h38.arf
Then it was processed via miRDeep2.pl as
miRDeep2.pl LP01.fastq.collapsed ~/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/genome.fa LP01_vs_genome_h38.arf   ~/miRBase/mature_human.fa ~/miRBase/mature_chimp.fa ~/miRBase/hairpin_human.fa -t has
Genome_build: hg38
Supplementary_files_format_and_content: csv file reports output from miRDeep2

source_name: exosome

extract_protocol:
Total RNA was extracted by RNeasy mini kit (Qiagen).
1) Filter Small RNA: Separate RNA segment of different size by PAGE gel,select 18-30nt stripe and recycle. 2) Adaptor  ligation: Prepare connection system, blend and centrifuge, connect warmly for a period of time. 3) RT-PCR: Prepare  reverse transcription system, connect warmly for a period on PCR on PCR instrument, then PCR amplification. 4) Purify  PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recylced products in EB solution. Finally,  label to finish the library construction. 5) Library quality testing: Use Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-  TimePCR System to test quality and production of the prepared library.

treatment_protocol: Exosome rich fraction was extracted by Exoquick (System Biosciences).

tag: disease state

value: latent tuberculosis

tag: sample type

value: exosome


title: Pf-iRBC stimulated-Malian Children [R13]


title: Setdb1_KO_UNC_iMEFs_H3K9me2_rep1

source_name: immortalized mouse embryonic fibroblast

value: 3-12#13 Setdb1 KO iMEF

value: immortalized mouse embryonic fibroblast

value: 2uM UNC0642 for 5 days


title: KO-IRAKM-PBS-2_RNA

value: IRAK-M-/-

value: BMDMs

value: PBS


title: mRNA_LV_PS_9552

value: Left ventricular free wall

value: FVB

value: Adult


title: KO-IRAKM-High-1_RNA

value: high-dose LPS


title: Unstimulated Malian Children  [R24]

source_name: Unstimulated Malian Children

value: Unstimulated Malian Children

value: monocytes


title: Setdb1_KO_iMEFs_H3K9me2_rep2


title: 1P11

city: Minneapolis

first: Marc

middle: Kevin

last: Jenkins

state: Minnesota

address: 2101 Sixth St. SE

department: Center for Immunology

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via hisat2 (2.1.0) using the mouse genome (mm10) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

growth_protocol: Not applicable, in vivo samples.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus micro spin column purification kit.
RNA libraries were prepared for sequencing using Takara Pico Mammalian (ribo-depletion) protocols

treatment_protocol: Se infection

tag: age

value: 12 weeks

value: Spleen and lymph nodes

value: LpdAp:I-Ab-specific T cells

value: 30 d after S. enterica infection


title: 32h_after_UNC0642_removal_H3K9me2

value: TT2 mES

value: mouse embryonic stem cells

value: 6D11 anti-H3K9me2

value: 32h_after_2uM UNC0642 treatment for 3 days


title: Unstimulated Malian Children  [R23]


title: mRNA_LV_sham_3

value: Male

value: sham


title: Setdb1_KO_iMEFs_H3K9me2_rep1

value: 3-12#13 Setdb1 KO iMEF

value: immortalized mouse embryonic fibroblast


title: Setdb1_UNC_iMEFs_H3K9me2_rep2

value: WT iMEF

value: 2uM UNC0642 for 5 days


title: KO-TRAM-High-2_RNA

value: TRAM-/-

value: BMDMs

value: high-dose LPS


title: KO-TRAM-High-1_RNA


title: Unstimulated Malian Children  [R22]

value: Unstimulated Malian Children

value: monocytes


title: mRNA_LV_sham_1

value: Left ventricular free wall

value: FVB

value: Adult


title: Setdb1_UNC_iMEFs_H3K9me2_rep1


title: Setdb1_WT_iMEFs_H3K9me2_rep2


title: Unstimulated Malian Children  [R21]


title: mRNA_LV_sham_4


title: KO-TRAM-Low-1_RNA

value: low-dose LPS


title: Setdb1_WT_iMEFs_H3K9me2_rep1

value: 6D11 anti-H3K9me2


title: mRNA_RV_PS_9561

value: Right ventricular free wall

value: PS


title: G9aGlp_DKO_H3K9me2_rep2

value: #248-6 G9a/GLP DKO mES

value: mouse embryonic stem cells


title: mRNA_RV_PS_9552

value: Male


title: KO-IRAKM-PBS-1_RNA

value: IRAK-M-/-

value: PBS


title: ZNI160317_P1_7

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

description: library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. Zebrafish gene models were based on Ensembl release 74 (http://www.ensembl.org) were improved for 3’ UTR annotations as described previously (Junker JP et al. Genome-wide RNA Tomography in the zebrafish embryo. Cell 159: 662-675, 2014)
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: Ensembl release 74
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Danio rerio

source_name: Pronephros

growth_protocol: Tg(wt1b:GFP); Tg(cdh17:GFP) transgenic zebrafish were kept at the Zebrafish Facility of the Renal Division, Medical Center Freiburg

extract_protocol:
Pronephric cells were isolated as previously described Yakulov TA et al., Nat Commun 9: 3660, 2018.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.

tag: line

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros

value: 2 day post fertilization


title: mRNA_RV_PS_9553


title: ZNI160317_P1_5

description: library of 96 cells


title: G9aGlp_DKO_H3K9me2_rep1


title: KO-TRAM-PBS-1_RNA

value: TRAM-/-

value: BMDMs


title: ZNI160317_P1_8

description: library of 96 cells


title: ZNI130317_D3_8

description: library of 96 cells

value: 3 day post fertilization


title: WT-High-2_RNA

value: WT

value: high-dose LPS


title: ZNI160317_P1_6

description: library of 96 cells


title: mRNA_RV_sham_4

value: FVB

value: Adult

value: sham


title: mRNA_LV_sham_2

value: Left ventricular free wall


title: WT-High-1_RNA


title: mRNA_RV_PS_9564

value: Right ventricular free wall

value: PS


title: KO-TRAM-Low-2_RNA

value: low-dose LPS


title: Suv39h_DKO_UNC_H3K9me2

value: ADF157 Suv39h1/2 DKO mES

value: mouse embryonic stem cells

value: 6D11 anti-H3K9me2

value: 2uM UNC0642 for 3 days


title: Suv39h_DKO_3-12_UNC_H3K9me2

value: #4 Setdb1 conditional KO Suv39h1/2 DKO mES


title: mRNA_RV_sham_3

value: Male


title: KO-TRAM-PBS-2_RNA

value: TRAM-/-

value: BMDMs

value: PBS


title: mRNA_RV_sham_2


title: Suv39h_DKO_3-12_H3K9me2


title: ZNI130317_D3_7

description: library of 96 cells

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros

value: 3 day post fertilization


title: ZNI130317_D3_6

description: library of 96 cells


title: WT-Low-1_RNA

value: WT


title: WT-PBS-1_RNA


title: Suv39h_WT_H3K9me2_rep1

value: ADF1-26 WT mES


title: Suv39h_DKO_H3K9me2_rep1


title: ZNC181016_12

description: library of 96 cells

value: 2 day post fertilization


title: WT-PBS-2_RNA


title: ZNC181016_10

description: library of 96 cells


title: Suv39h_UNC_H3K9me2_rep1


title: Setdb1_KO_H3K9me2_rep2

value: #33-6 Setdb1 conditional KO mES

value: 800nM 4-OHT for 5 days


title: mRNA_RV_sham_1

value: Right ventricular free wall

value: FVB

value: Adult

value: sham


title: Setdb1_KO_H3K9me2_rep1

value: mouse embryonic stem cells

value: 6D11 anti-H3K9me2


title: Setdb1_KO_UNC_H3K9me2_rep2

value: 800nM 4-OHT for 2 days then 2uM UNC0642 for 3 days


title: ZNC181016_9

description: library of 96 cells


title: WT-High-2_H3K27ac

extract_protocol:
Samples containing 1M cells were centrifuged at 1600 g for 5 minutes at 4°C. Each sample was washed twice with cold 1 mL PBS and resuspended in 9.375mL of PBS. Then, 0.625 mL of 16% formaldehyde was added and the samples were incubated on a shaker for 5 minutes at room temperature. The samples were then quenched with 0.667 mL of 2M glycine and incubated for 5 minutes at room temperature on a rotator. The cells were then centrifuged at 1600 g for 5 minutes and washed twice with 1 mL cold PBS. The pellet was resuspended in 130 µL of Covaris sonication buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.1% SDS and 1x protease inhibitor cocktail (PIC)) and sonicated with a Covaris S220 sonicator using 75 W peak incident power, 5% duty factor, and 200 cycles per burst for 16 minutes at 4°C. Sonicated samples were centrifuged at 16,100 g for 10 minutes at 4°C before the supernatant containing sheared chromatin was removed to a fresh tube. 2.4 µL of sheared chromatin was then mixed with 46.6 µL of IP buffer (20mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, 1% freshly added PMSF and PIC) to generate a 50µL sample containing chromatin from 20,000 cells for MOWChIP-seq.
Libraries for sequencing were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift-Bio).

value: BMDMs

value: high-dose LPS

tag: chip antibody


title: WT-Low-2_RNA

value: low-dose LPS


title: WT-High-1_H3K27ac


title: E2+P4+PBDE

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger (V2.0.0)'s default settings
Genome_build: mm10
Supplementary_files_format_and_content: text files containing the raw gene expression count

source_name: Mammary gland

extract_protocol:
Mammary glands were digested using a mixture of Collagenase and DNAse I, and processed into a single-cell suspension for loading onto a Chromium Controller (10x Genomics).
Cell number and viability were measured using a TC20 Automated Cell Counter (BioRad). Single-cell RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v2 User Guide (10x Genomics). Approximately 4,000 cells were loaded on a Chromium single cell Controller instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3′ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

treatment_protocol: Special food with PBDEs mixture (BDE-47; 7.1 mg/kg, BDE-100; 0.4 mg/kg, and BDE-153; 0.9 mg/kg) was prepared (Research Diets, Inc, New Brunswick, NJ) and administered per oral to mimic environmental exposure of human to PBDEs via ingestion and diet. The composition was previously determined by us to achieve the relevant exposure with the ratio of the three congeners found in human blood (1 mg/kg/day, 0.056 mg/kg/day, and 0.126 mg/kg/day for BDE-47, -100, -153, respectively). Non-PBDE groups were fed with nutrient-matched special food with DMSO (Research Diets, Inc.). E2 (1 ug/animal) and P4 (0.1 mg/animal) were administered by daily intraperitoneal injection. DMSO was used as vehicle and injected in the control groups. The treatments started 20 weeks after ovariectomy and continued for 1 week.

value: BALB/cj

value: 30 weeks


title: ZNC160317_P1_4

description: library of 96 cells

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros


title: Setdb1_KO_UNC_H3K9me2_rep1


title: Setdb1_UNC_H3K9me2_rep2

value: 2uM UNC642 for 3 days


title: WT-Low-2_H3K27ac

value: WT


title: ZNC160317_P1_1

description: library of 96 cells

value: 2 day post fertilization


title: ZNC160317_P1_3

description: library of 96 cells


title: ZNI130317_D3_5

description: library of 96 cells

value: 3 day post fertilization


title: E2+P4


title: WT-Low-1_H3K27ac


title: ZNC181016_11

description: library of 96 cells


title: Setdb1_WT_H3K9me2_rep2

value: #33-6 Setdb1 conditional KO mES


title: ZNC151116_12

description: library of 96 cells


title: Setdb1_WT_H3K9me2_rep1


title: E2


title: E2+PBDE


title: WT-PBS-2_H3K27ac

value: PBS


title: ZNC151116_11

description: library of 96 cells


title: WT-PBS-1_H3K27ac


title: TT2_H3K9me2_rep1

value: TT2 mES


title: Vehicle

description: Vehicle

value: Vehicle


title: Setdb1_KO_UNC_RNA_rep2

data_processing:
Adaptor sequences in reads were trimmed using Trim Galore version 0.3.7
Trimmed reads were aligned to the mm10 genome and genes/TE using tophat2
Read count each gene and TE were analyzed by TEtranscripts
Genome_build: mm10
Supplementary_files_format_and_content: Text format data of read count

growth_protocol: mESCs were maintained in DMEM with 1%FCS/10%KSR/LIF on gelatin coated dish.

extract_protocol:
mRNA was purified by beads
500 ng of total RNA was used for RNA-seq library construction. RNA-seq library was constructed by KAPA mRNA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit (Roche) according to manufacturer instructions.

treatment_protocol: We treated 800 nM 4-OHT for 5 days to Setdb1 conditional KO mESCs to deplete SETDB1. We treated 2uM UNC0642 for 3 days to mESCs to inhibit G9a/GLP catalytic activity.

value: mouse embryonic stem cells


title: ZNC160317_P1_2

description: library of 96 cells


title: ZNC151116_10

description: library of 96 cells


title: ZNC151116_9

description: library of 96 cells


title: Setdb1_KO_UNC_RNA_rep1

value: 800nM 4-OHT for 2 days then 2uM UNC0642 for 3 days


title: Setdb1_KO_RNA_rep2

value: 800nM 4-OHT for 5 days


title: Setdb1_UNC_H3K9me2_rep1

value: 6D11 anti-H3K9me2


title: ZNC150518_D3_11

description: library of 96 cells


title: Setdb1_KO_RNA_rep1


title: ZNC150518_D3_12

description: library of 96 cells


title: TETTKO rep3

city: Geneva

first: victor

last: YTHIER

state: Geneva

address: Rue Michel-Servet,1

department: GEDEV

country: Switzerland

institute: University of Geneva

description:
abundance measurement
ESC_TETTKO_counts.txt

data_processing:
Bisulfite-Seq
Removing adaptater sequence using flexbar v3.4.0 (-r ${R2} -p ${R1} -b ${adapt} -bt 0.2 -be LEFT -qt 0)
Trimming using trim_galore v0.4.4 (qscore > 20), demultiplexing by barcode (0 missmatch) and UMI tagging (8 nt following barcode) using flexbar (-b ${bc} -bt 0.0 -be LEFT -qt 0  -t trimBC --umi-tags)
Filtering base on barcode-motif-barcode sequence using R v3.6.2 and BioString package v2.54.0 (0 missmatch fixed=FALSE)
Alignment on each reference sequence using bismark v0.20.0 (–non_directional -X 1000 -N 0 -q ref/${motif_name})
Filtering on nonCG conversion (ESC and NP only) (filter_non_conversion -p --percentage_cutoff 2)
UMI deduplication using umitools v0.5.5
Methylation extraction (bismark_methylation_extractor -p --no_overlap --bedGraph --cytosine_report --CX  --genome_folder  ref/${motif_name})
Genome_build: fr1 sequence with particular barcode-motif-barcode into beta globuline locus
Supplementary_files_format_and_content: tab-delimited text files include percentage of methylation for each library per Cell type and treatment …
RNA-Seq
Trimming using Trimmomatic v0.38 (ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Mapping using STAR v2.6.1b (--sjdbOverhang ${49})
Extract feature using featurecounts from Rsubread v1.6.2 (-T 6 -a GRCm38.89.gtf -F GTF -t exon -g gene_id -s 0)
EdgeR use v3.27.0
Genome_build: Ensembl – GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Cell Type

source_name: Embryonic Stem Cell with TET1/2/3 triple knockout

extract_protocol:
cf paper
RNA-seq – Bisulfite-Seq – AmpBis-Seq - Sanger

value: Embryonic Stem Cell with TET triple KO

value: TET1/2/3 triple knockout


title: TETTKO rep1


title: TETTKO rep2


title: Setdb1_UNC_RNA_rep2


title: ZNC150518_D3_10

description: library of 96 cells


title: ZNC150518_D3_9

description: library of 96 cells


title: Setdb1_UNC_RNA_rep1


title: NP rep3

description:
abundance measurement
NP_counts.txt

source_name: Embryonic Stem Cell differenciate into Neuronal Progenitor

value: Neuronal Progenitors

value: wild type


title: Setdb1_WT_RNA_rep2


title: ZNC_Day3_8_cdh17

description: library of 96 cells

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros


title: TCATa

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: TCATa

data_processing:
mapping of reads was done using: bowtie2  --local using Escherichia coli K12 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Escherichia coli K12 | VERSION Date:   2020/06/05 | ASM983288v1 | GenBank assembly accession: GCA_000025145.2
Supplementary_files_format_and_content: Tab delimited text file

organism: Escherichia coli

source_name: Bacterial

growth_protocol: Bacterial cells were grown were grown in MHB II broth at 37 degrees celsius and 200rpm in the dark.

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: Bacterial cells were grown were grown in MHB II broth without (C) and with 3,9 μg/L TMP, 1mg/L TCATa and 5,5 mg/L TCATd respectively. Subsequently, the strains were repeatedly inoculated with increasing concentrations of the respective antimicrobial, either TMP, TCATa or TCATd. The control (C) smaple was repeatedly inocculated without the addition of any compound. After every 8th hour of growth, resistant cultures were complimented with glycerol, snap-frozen in liquid nitrogen and stored at -80 °C until the next step-wise increment. The final resistant cultures were enrichment.

value: CS1562 tolC6::mini-Tn10


title: TCATd

description: TCATd


title: NP rep1

description:
abundance measurement
NP_counts.txt


title: Setdb1_WT_RNA_rep1


title: ESC rep3

description:
abundance measurement
ESC_counts.txt

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell


title: C

description: C


title: Mouse heart , Rhau KO rep2

type: RNA

city: Nanjing

first: Zhongzhou

last: Yang

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

country: China

institute: Nanjing University

description: Gene expression data from Rhau-deletion mouse hearts after Tamoxifen induction.

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

source_name: Mouse heart , Rhau KO

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Mice were housed in groups and had free access to food and water. The experimental animal facility has been accredited by the AAALAC.

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

treatment_protocol: Five successive doses of tamoxifen (Sigma, T5648) were administrated (intraperitoneal injection) to CAAG-ERT2-Cre;Rhau F/F and Rhau F/F mice mice at two months of age.

value: adult

value: CAAG-ERT2-Cre;Rhau F/F

value: hearts


title: ITS_TSC_BMP4_rep2

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg19 genome using Tophat2.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Table of gene names and FPKM values for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Table of gene names and FPKM values for each sample.

source_name: cultured cells

growth_protocol: mESC and iPSCs were grow in 5% matrigel coated 12-well culture plate with ITSC medium composed of 50% RPMI, 25% DMEM F-12, 25% Neurobasal A, 10% FBS, 0.5mM GlutaMAX, 0.1mM 2-mercaptoethanol, 0.5mM sodium pyruvate, 0.25x N2 supplement, 0.5x B27 supplement, plus 12.5 ng/ml FGF4 and 500ng/ml heparin.

extract_protocol:
Pick single clone into 200uL Rnase-free tube with lysis buffer which prepared following the Smart-seq2 protocol (Picelli, 2014)
RNA-seq library was prepared following the Smart-seq2 protocol (Picelli, 2014)

treatment_protocol: Single iPSCs (GFP+) and TSCCs(RFP+) were mixed adequately and then seeded into 5% Matrigel coated 12-well plate. The attached cells were cultured in ITSC medium to induce embryonic body(EB) formation. Two days later, cells were treated for another 24 hours in ITSC medium with or without BMP4. At day 3, single embryoid structure were confirmed carefully in fluorescence microscope. Proper single structure should be composed of two tightly attached colonies with green (iPSC-part) and red (TSC-part) fluorescent individually. Then picked and separated the structure into two individual parts with distinct fluorescent under stereomicroscope. Each part were transfer directly into 200uL RNase-free tube followed with smart-seq protocol. iPSCs or TSCCs only group were treated with the same protocol as described above.


title: Mouse heart , Control rep2

description: Gene expression data from control mouse hearts after Tamoxifen induction.

source_name: Mouse heart , Control

value: Rhau F/F


title: Mouse heart , Control rep1


title: Mouse heart , Rhau KO rep1


title: MCF7-KO

city: Harbin

first: Qiong

last: Wu

address: No.92, Xidazhi Street

institute: Harbin Institute of Technology

data_processing:
Hisat2.1.0 software used for mapping.
Cufflinks2.2.1 uses the results of hisat2 alignment to assemble transcripts.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Cancer cell line

growth_protocol: Cells were cultured in DMEM (GIBCO, USA) containing 10% fetal bovine serum (FBS) with penicillin/streptomycin.

extract_protocol:
Cells from cell culture were used for RNA extraction. RNA was harvested using Trizol reagent.
Vazyme VAHTS mRNA-seq V2 Library Prep Kit for Illumina kit (NR601) is used to construct the sequencing library.

tag: cell line

value: breast cancer

value: EphA2-SE -/-


title: ZNC_Day3_7

description: library of 96 cells

value: 3 day post fertilization


title: ITS_TSC_BMP4_rep1


title: ZNC_Day3_6_cdh17

description: library of 96 cells


title: MCF7-WT

value: Wild type


title: ITS_iPSC_BMP4_rep2


title: HCT116-KO

value: colon cancer


title: ESC rep1

description:
abundance measurement
ESC_counts.txt


title: ITS_iPSC_BMP4_rep1


title: NP rep2

description:
abundance measurement
NP_counts.txt


title: G3

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

data_processing:
Bases were called using the Real Time Analysis 2 software of the NextSeq 500.
The quality of the reads was verified with FastQC (version 0.11.8)
Reads were trimmed using Trimmomatic (version 0.38) setting following parameters: ILLUMINACLIP:3:30:10, MAXINFO:23:1, SLIDINGWINDOW:5:30, MINLEN:17
STAR (version 2.6.1d) was used for mapping with the following parameters: readFilesCommand zcat, outFilterMultimapNmax 1 and outSAMtype BAM SortedByCoordinate. Afterwards, samtools (version 1.10) was used to merge multiplexed samples
A count table was made using the following R packages: rtracklayer (version 1.44.4) to convert the GTF (Ensembl, version 42)  file into a Granges object, Rsamtools (version 2.0.3) to create a BamFileList object and GenomicAlignments (version 1.20.1) for the summarizeOverlaps function to create the count table. The following options were used for counting: mode = ’Union’, preprocess.reads = invertStrand, singleEnd = TRUE and ignore.strand = FALSE.
To find differentially expressed between galls and uninfected roottips, DESeq2 (version 1.24.0) was used with and FDR cutoff of 0.05. P-values were corrected for multiple testing using the Benjamini-Hochberg correction.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Count table with raw counts.

organism: Oryza sativa Japonica Group

source_name: Gall material

growth_protocol: Oryza sativa L. cv ‘Nipponbare’ (GSOR-100, USDA) seeds were germinated for 7 days at 30 °C on paper cloths that were drenched with tap water. Seedlings were transferred into SAP substrate (sand-absorbent polymer) and grown at 26 °C under a 16 h/8 h light/dark regime.

extract_protocol:
Frozen samples were ground and total RNA was extracted using the ZR Plant RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions. The bead beater step was performed using a speed of 4 m/s for 45 s. All centrifugal steps were performed at 16 000 x g. For DNase treatment 1 µg of total RNA per sample was combined with 3.6 µL DNase I buffer + MgCl2 (B43, ThermoFisher), 1 µL RiboLock RNase Inhibitor (EO0381, Thermo Fisher) and 1 µL DNAse I (EN0521, ThermoFIsher). Afterwards RNase-free water was added until a total volume of 36 µL was reached followed by incubation for 30 minutes at 37 °C. Finally, 4 µL 25 mM EDTA was added before incubating for 10 minutes at 65 °C.
The quality of total RNA of gall and control samples was verified with a RNA 6000 nano chip (Agilent technologies) and the concentraiton was measured with  a Quant-it Ribogreen RNA assay (Life technologies). 1500 ng of RNA was used with the rRNA depletion with Ribo Zero Plant Seed/Root kit (Illumina). Library prep was performed according to manufacturer's instructions. After rRNA depletion, total RNA was purified with RNA clean and concentrator-5 (Zymo Research) and eluted in 10 µL water. Depletion efficiency was checked with Quant-it Ribogreen RNA assay (life technologies). The Truseq stranded total RNA library prep (Illumina) was used for library prep according to manufacturer's instructions. During library prep fragmentation and random priming was performed, followed by first and second strand synthesis, A-tailing and adapter ligation. The cDNA was used for enrichment PCR (13 cycles) and purified with the double AMPure XP cleanup (1:1) (Beckman Coulter). The quality was checked with a High sensitivity DNA chip (Agilent technologies). Quantification of the libraries was done with a qPCR assay according to Illumina protocol to enable equimolar pooling of libraries. Finally, sequencing was performed on a NextSeq 500 using 2% Phix spike-in (single end reads, 76 bp)

treatment_protocol: At two weeks old, ca 200 stage 2 juveniles of Meloidogyne graminicola were used for inoculation per set of three plants. Control plant were mock-inoculated with water. Root tips and galls were collected from control and treated plants respectively, three days post inoculation (3 dpi). Plant materials were immediately frozen in liquid nitrogen and stored at -80 °C. Three biological replicates of control and treated plants were made. Each treated biological replicate consisted of ca 64 plants while each control biological replicate consisted of ca 10 plants.

tag: cultivar

value: Nipponbare

tag: plant age

value: 17 days


title: HCT116-WT


title: ZNC_Day3_8

description: library of 96 cells

tag: tissue


title: ZNC_Day3_5_cdh17

description: library of 96 cells


title: ZNC_Day3_6

description: library of 96 cells


title: ZNC_Day3_5

description: library of 96 cells


title: G1


title: G2


title: TSC_BMP4_rep2

value: TSC


title: TSC_BMP4_rep1


title: ZNC_Day3_7_cdh17

description: library of 96 cells


title: HELA-KO

value: HeLa

value: cervix cancer


title: C3

source_name: Root tip material


title: TMP

description: TMP

tag: strain


title: KC-OSM3

city: Guangzhou

first: Jun

last: Liu

state: Guangdong

address: No.2 Lujing Road

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: epidermal

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

value: Primary Keratinocytes

value: 10 ug/ml OSM


title: ZNC_Day1_4_cdh17

description: library of 96 cells

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros

value: 1 day post fertilization


title: ZNC_Day1_4

description: library of 96 cells


title: C2


title: KC-OSM2


title: ZNC_Day1_3_cdh17

description: library of 96 cells


title: iPS_BMP4_rep2

value: iPS


title: ITS_TSC_rep2

value: control


title: C1


title: LP02, exosome, non coding small RNA seq

value: latent tuberculosis

value: exosome


title: iPS_BMP4_rep1


title: KC-OSM1


title: ITS_TSC_rep1


title: ZNC_Day1_2_cdh17

description: library of 96 cells


title: KC3

value: Non


title: ITS_iPSC_rep2


title: KC1


title: ZNC_Day1_2

description: library of 96 cells


title: ITS_iPSC_rep1


title: ZNC_Day1_3

description: library of 96 cells


title: HELA-WT

value: Wild type


title: KC2


title: ZNC_Day1_1_cdh17

description: library of 96 cells


title: HaCaT-OSM3

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HaCaT cell line treated with OSM

value: HaCaT


title: TSC_rep2


title: TSC_rep1


title: ZNC_Day1_1

description: library of 96 cells


title: HER2:PIK3CA co-culture [CC-4]

city: Baltimore

first: Ian

last: Waters

state: MD

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Following fragmentation and labelling, hybridization was performed using the WT array hybridization protocol for GeneChip instruments in the GeneChip WT PLUS Reagent Kit User Guide

scan_protocol: GeneChips were scanned using  an Affymetrix GeneChip System

data_processing:
Data processing was completed using the Transcriptome Analysis Console (TAC) from Thermo
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

source_name: Co-culture of HER2 L755S and PIK3CA E545K cells in MCF-10A background

label_protocol: Biotinylated cRNA was prepared from 5uG total RNA using the protocol in the GeneChip WT PLUS Reagent Kit User Guide

growth_protocol: HER2 L755S and PIK3CA E545K mutant cells in the MCF-10A background were grown in isolation and in co-culture using physiologic EGF media conditions (see materials and methods). After 7-14 days (when the co-cultures were ~75% HER2 mutant cells by ddPCR), the single and co-cultures were harvested.

extract_protocol: Total RNA was extracted from controls and co-cultures in quadruplicate using the RNeasy and QiaShredder kits (Qiagen)

treatment_protocol: Cells were grown in physiologic EGF conditions and no additional treatment was used.

tag: cell line background

value: Isogenic breast epithelial cell line

tag: genotype/variation

value: HER2:PIK3CA co-culture

tag: culture type

value: Co-culture


title: iPS_rep2

tag: treatment


title: HaCaT-OSM1


title: ZNC_D3_080518_16

description: library of 96 cells

value: 3 day post fertilization


title: ZNC_D3_080518_15

description: library of 96 cells


title: HaCaT2

source_name: HaCaT cell line


title: ZNC_D3_080518_14

description: library of 96 cells


title: HaCaT3


title: ZNC_D3_080518_13

description: library of 96 cells


title: ESC rep2

description:
abundance measurement
ESC_counts.txt

value: Embryonic Stem Cell

value: wild type


title: ZNC_D1CTRL_12

description: library of 96 cells


title: ZNC_D1CTRL_11

description: library of 96 cells


title: GDC-2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using Tophat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The FPKM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HEK293_OTUD5-wild type_GDC0349

extract_protocol:
Total RNA was isolated from OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Cells were treated with 0.1% DMSO or 1μM GDC0349 for 12h.

value: OTUD5-wild type

tag: chemical treatment

value: GDC0349 treatment


title: Rrp6 exo_replicate 1 [s_exo_MTR4_2]

city: New York

first: Christopher

middle: D

last: Lima

state: NY

address: 1275 York Ave RRL301A

department: Structural Biology

institute: Sloan Kettering Institute

description:
BY4741/4743, rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 + pRS413 RRP6 D238N
exo_MTR4_2_IGO_08900_B_5_S5

data_processing:
The output data (FASTQ files) were mapped to the target genome (sacCer3) using the rnaStar aligner version 2.5.0a (Dobin et al., 2012) that maps reads to the genome. The reads were mapped twice using the 2 pass mapping method (Engström et al., 2013). The first mapping pass used a list of known annotated junctions from Ensemble version 94. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done (on the second pass the RemoveNoncanoncial flag was used). After mapping, the output SAM files were post processed using the PICARD tools version 1.124 to add or replace read groups, which in addition sorts the file and converts it to the compressed BAM format. The expression count matrix was then computed from the mapped reads using HTSeq version 0.5.3 (www-huber.embl.de/users/anders/HTSeq) and S. cerevisiae database (R64-1-1.94.gtf). The raw count matrix generated by HTSeq were then processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq), which is used to both normalize the full dataset and to analyze differential expressions between sample groups. The data was clustered in several ways using the normalized counts of all genes that gave a total of 10 counts when summed across all samples. To obtain the normalized BEDGRAPH files, scripts were used to compute the coverage files from RNA-seq BAM files normalized to total unique counts (counts/million) and converted to compressed bedgraph format.
Supplementary_files_format_and_content: Normalized bedgraph files as alignment files
Supplementary_files_format_and_content: Excel file containing scaled gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

source_name: Rrp6 exo

growth_protocol: Individual clones of strains rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 containing pRS413 rrp6 alleles were selected and grown in selective SD-His-Leu-Ura medium overnight at 30 °C. The next day, cells were diluted to an OD600 of 0.2 and grown until they reach mid-log phase and a total of 2-3 OD cells were harvested.

extract_protocol:
Cell pellets were washed in sterile nuclease-free water, spun again to remove supernatant and snap-frozen in liquid N2 and saved at -80 °C. Total RNA was isolated from the cell pellets by using MasterPure Yeast RNA Purification kit (Lucigen), resuspended in nuclease-free water and saved at -80 °C.
Total RNA samples extracted from above mentioned yeast strains were subjected to RiboGreen quantification and quality control was assayed by Agilent BioAnalyzer 4. 1 µg of total RNA with an RNA integrity number varying from 6.1 to 8.9 underwent ribosomal depletion with the Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina catalog # MRZY1306). Libraries were prepared using TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to manufacturer’s instructions with 8 cycles of PCR. Samples were barcoded and ran on a HiSeq4000 in a 50bp/50bp paired end run using the HiSeq 3000/4000 SBS Kit (Illumina). On average, 61 million paired reads were generated per sample.

value: BY4741/4743, rrp6{delta} mtr4{delta} + pRS416 MTR4 + pRS415 MTR4 + pRS413 RRP6 D238N

tag: molecule subtype

value: total RNA (ribo depleted)


title: rrp6Δ_replicate2 [s_Empty_MTR4_3]

description:
BY4741/4743, rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 + pRS413 empty
Empty_MTR4_3_IGO_08900_C_1_S7

value: BY4741/4743, rrp6{delta} mtr4{delta} + pRS416 MTR4 + pRS415 MTR4 + pRS413 empty


title: Rrp6 exo_replicate 2 [s_exo_MTR4_3]

description:
BY4741/4743, rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 + pRS413 RRP6 D238N
exo_MTR4_3_IGO_08900_C_5_S11


title: rrp6Δ_replicate1 [s_Empty_MTR4_2]

description:
BY4741/4743, rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 + pRS413 empty
Empty_MTR4_2_IGO_08900_B_1_S1


title: GDC-1


title: iPS_rep1

tag: cell type

value: iPS

value: control


title: ZNC_D1CTRL_10

description: library of 96 cells

source_name: Pronephros

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros

value: 1 day post fertilization


title: HER2:PIK3CA co-culture [CC-1]


title: HER2:PIK3CA co-culture [CC-2]


title: WT RRP6_replicate2 [s_RRP6_MTR4_3]

description:
BY4741/4743, rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 + pRS413 RRP6
RRP6_MTR4_3_IGO_08900_C_3_S9

source_name: WT RRP6

value: BY4741/4743, rrp6{delta} mtr4{delta} + pRS416 MTR4 + pRS415 MTR4 + pRS413 RRP6


title: HER2:PIK3CA co-culture [CC-3]

value: Isogenic breast epithelial cell line


title: ZNC_D1CTRL_9

description: library of 96 cells


title: HaCaT1

value: HaCaT


title: PIK3CA E545K single control [Ex9-1]

source_name: PIK3CA E545K isogenic cell line in MCF-10A background

value: PIK3CA E545K

value: Single control


title: WT-2

source_name: HEK293_OTUD5-wild type_DMSO

value: DMSO treatment


title: HER2 L755S single control [755-3]

source_name: HER2 L755S isogenic cell line in MCF-10A background

value: HER2 L755S


title: PIK3CA E545K single control [Ex9-4]


title: HER2 L755S single control [755-2]


title: ZN_MAX_P2_4

description: library of 96 cells

value: 2 day post fertilization


title: KO-2


title: HER2 L755S single control [755-1]


title: KO-1


title: ZN_MAX_P2_3

description: library of 96 cells


title: ZN_MAX_P2_2

description: library of 96 cells


title: mter-4_3

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Trim low quality reads and apapters. Trimmomatic V0.39 - ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
Remove ribosomal RNA. SortmeRNA
map to the reference genome. HISAT2 V2.1.0.
Count reads on features. htseq-count
Genome_build: C. elegans - WBCEL235
Supplementary_files_format_and_content: HTSeq - count files are tge output from the data pre-processing steps outlined above.

organism: Caenorhabditis elegans

source_name: Young Adult

growth_protocol: Wild-type and mter-4 mutant embryos were grown to young adults on NGM plates seeded with E. coli HB101 at 20C.

extract_protocol:
Frozen pellets of animals were freeze/thawed 5x using liquid nitrogen. Samples were then refrozen and sent to BGI for RNA extraction and DNBseq PE100
BGI performed standard RNA extraction from Trizol
DNBSeq library preparation from BGI for their propriatary sequencing platform.

treatment_protocol: No treatments were done - young adult animals were collected in Trizol and frozen on dry ice.

value: Young adult whole animals

tag: genotype


title: mter-4_2


title: TET_sssi

description:
percentage of methylation per CpG position
TET_sssi

source_name: Embryonic Stem Cell with TET1,2,3 KO


title: ZN_MAX_P2_1

description: library of 96 cells


title: WT-1

value: OTUD5-wild type


title: mter-4_1


title: NP_sssi

description:
percentage of methylation per CpG position
NP_sssi
NP_sssi_merge_mincov0.tab
NP_sssi_pm_mincov10.tab

source_name: Embryonic Stem Cell differenciate into Neuronal Progenitor


title: WT RRP6_replicate1 [s_RRP6_MTR4_2]

description:
BY4741/4743, rrp6Δ mtr4Δ + pRS416 MTR4 + pRS415 MTR4 + pRS413 RRP6
RRP6_MTR4_2_IGO_08900_B_3_S3

value: total RNA (ribo depleted)


title: N2_4


title: NP_untrt

description:
percentage of methylation per CpG position
NP_untrt


title: N2_3


title: ZN_MAX_P1_12

description: library of 96 cells


title: ESC_sssi

description:
percentage of methylation per CpG position
ESC_sssi

source_name: Embryonic Stem Cell


title: CDH17_D3_6

description: library of 96 cells

value: 3 day post fertilization


title: Peripheral whole blood_HVT_rep2

city: shanghai

first: tian

last: chunou

address: 168 changhai road

department: Neurosurgery Department

institute: Changhai Hospital, Second Military Medical University, China

description:
HVT_2
lncRNA expression in human peripheral whole blood of healthy volunteers

hyb_protocol: Each slide was hybridized with Cy3-labeled RNA using Agilent Gene Expression Hybridization Kit(Cat # 5188-5242, Agilent technologies, Santa Clara, CA, US) in hybridization Oven(Cat # G2545A, Agilent technologies, Santa Clara, CA, US) according to the manufacturer’s instructions. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer 1 (Cat # 5188-5325, Agilent technologies, Santa Clara, CA, US) and Gene Expression Wash Buffer 2 (Cat # 5188-5326, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2505C, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7.1.1(Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Genespring Software 13.1(Agilent technologies, Santa Clara, CA, US).

source_name: Peripheral whole blood_HVT

label_protocol: LncRNA molecular in total RNA was labeled by Quick Amp Labeling Kit, One-Color (Cat # 5190-2305, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using PAXgene Blood miRNA Kit (Qiagen 763134, Nordrhein-Westfalen, Germany), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Total RNA was quantified using a NanoDrop ND-2000(Thermo Scientific, Waltham, MA, US) spectrophotometer.

treatment_protocol: 2.5ml peripheral blood of ACI patients and HVTs was collected in PAXgene Blood RNA Tubes (BD 762165, New York, America). Subsequently, the blood-collection tube was rapidly shifted to -80 C refrigerator.

tag: subject status

value: healthy control

tag: gender

value: female

value: Peripheral whole blood


title: N2_2


title: ESC_untrt

description:
percentage of methylation per CpG position
ESC_untrt
ESC_untrt_merge_mincov0.tab
ESC_untrt_pm_mincov10.tab


title: Peripheral whole blood_HVT_rep3

description:
HVT_3
lncRNA expression in human peripheral whole blood of healthy volunteers

value: male

tag: age


title: HER2 L755S single control [755-4]


title: CDH17_D3_5

description: library of 96 cells

tag: line

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

value: pronephros


title: Peripheral whole blood_ACI_rep6

description:
ACI_6
lncRNA expression in human peripheral whole blood of patients with acute cerebral infarction with stroke onset in 6 hours

source_name: Peripheral whole blood_ACI

value: patient with acute cerebral infarction (ACI)

tag: stroke subtype (toast)

value: cerebral infarction

tag: stroke subtype (ocsp)

value: partial anterior circulation infarction


title: Peripheral whole blood_ACI_rep5

description:
ACI_5
lncRNA expression in human peripheral whole blood of patients with acute cerebral infarction with stroke onset in 6 hours


title: Peripheral whole blood_ACI_rep4

description:
ACI_4
lncRNA expression in human peripheral whole blood of patients with acute cerebral infarction with stroke onset in 6 hours

value: posterior circulation infarct


title: Peripheral whole blood_ACI_rep3

description:
ACI_3
lncRNA expression in human peripheral whole blood of patients with acute cerebral infarction with stroke onset in 6 hours

value: total anterior circulation infarction


title: N2_1


title: Peripheral whole blood_HVT_rep1

description:
HVT_1
lncRNA expression in human peripheral whole blood of healthy volunteers


title: Peripheral whole blood_ACI_rep2

description:
ACI_2
lncRNA expression in human peripheral whole blood of patients with acute cerebral infarction with stroke onset in 6 hours


title: Bifidobacterium longum W13R transcriptom sequence 3

status: Public on Mar 17 2021

city: Tianjin

first: Tang

last: jiao

address: Binhai new area

institute: Tianjin University Of Science and Technology

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic)
Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05.
To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05.
Genome_build: Bifidobacterium_W13; https://www.ncbi.nlm.nih.gov/assembly/GCF_004936435.1
Supplementary_files_format_and_content: tab-delimited text files include gene count for each Sample

organism: Bifidobacterium longum

source_name: Bifidobacterium longum W13R total RNA

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0,>10μg) is used to construct sequencing library.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5μg of total RNA. Shortly, rRNA removal by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200-300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, Paired-end libraries were sequenced by Illumina NovaSeq 6000 sequencing (150bp*2.).


title: Monkey sperm - Control 1

city: Los Angeles

first: Dias

last: Brian

address: 4640 West Sunset Boulevard

institute: Children's Hospital Los Angeles

data_processing:
alignment (STAR)
counts stranded reads aligned to MacaM genome (featureCounts)
determine gene coverage by reads (bedtools)
Genome_build: MacaM
Supplementary_files_format_and_content: comma-separated text file, read counts, gene coverage

organism: Macaca mulatta

source_name: sperm cells

extract_protocol:
TRIzol extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PureSperm 40/80 density gradient

tag: group

value: Control


title: Monkey sperm - Control 4


title: Monkey sperm - Control 3


title: Monkey sperm - Maltreated 2

value: Maltreated


title: Bifidobacterium longum W13R transcriptom sequence 1


title: Bifidobacterium longum W13R transcriptom sequence 2


title: Monkey sperm - Maltreated 1


title: Monkey sperm - Control 2


title: PIK3CA E545K single control [Ex9-2]

value: Isogenic breast epithelial cell line

value: PIK3CA E545K

value: Single control


title: Bifidobacterium longum W13 transcriptom sequence 1

source_name: Bifidobacterium longum W13 total RNA


title: Monkey sperm - Maltreated 3


title: Peripheral whole blood_ACI_rep1

description:
ACI_1
lncRNA expression in human peripheral whole blood of patients with acute cerebral infarction with stroke onset in 6 hours

tag: tissue


title: Bifidobacterium longum W13 transcriptom sequence 2

tag: strain


title: Bifidobacterium longum W13 transcriptom sequence 3


title: FluBCR #Vac1

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

description: cDNA of V-D-J region of ig gene

data_processing:
Removing low-quality reads, trimming of adaptor sequence, and connecting read1 and read2 carried out by using tools available on the Galaxy platform (https://usegalaxy.org)
Sequenced reads were analyzed with the IMGT HighV-QUEST (http://www.imgt.org/)
Supplementary_files_format_and_content: V-D-J of Ig

source_name: FluBCR #Vac1

extract_protocol:
Total RNA was isolated from freshly sorted HA binding B cells. cDNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Inc., Shiga, Japan). Ig sequences were amplified by PCR using KOD Fx Neo (Toyobo, Osaka, Japan) and Ig specific primers(ctaatacgactcactgtatcaacgcagagt/ctaatacgactcactatagggc/atctccacacacaggggccagtggataga). cDNA libraries were synthesized using a Nextera DNA Library Prep Kit (Illumina, San Diego, CA) and sequencing data were obtained using the MiSeq system (Illumina).
cDNA libraries were prepared for sequencing using standard Illumina protocols
Nextera XT

value: Lymph node

value: WT


title: FluBCR #Vac2

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #Vac2

value: Spleen


title: FluBCR #Vac3

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #Vac3


title: FluBCR #inf1

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #inf1


title: FluBCR #28Vac

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #28Vac


title: HaCaT-OSM2

source_name: HaCaT cell line treated with OSM

tag: cell line

value: HaCaT

value: 10 ug/ml OSM


title: FluBCR #30Vac

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #30Vac


title: FluBCR #inf2

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #inf2


title: FluBCR #31inf

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #31inf


title: Pond Inlet C3 cDNA

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

institute: National Polar Research Institute

hyb_protocol: Each dried and labelled DNA sample was resuspended in 42 µL of hybridization solution. This solution consisted of 1 x HI-RPM hybridization buffer, 1 x comparative genome hybridization blocking agent, 0.05 µg・µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). The solution was later denatured by remaining at 95 ℃ for 3 min. To remove the bubbles created during the denaturation process, the conditions were maintained at 37 ℃ for 30 min. The hybridizations were carried out at 67 ℃ for 24 h

scan_protocol: The scanned images of the GeoChip hybridizations were obtained and converted by means of the Agilent Feature Extraction 11.5 software (Agilent Technologies, California, USA)

data_processing: The signal intensities, used as a proxy of abundances, were quantified and processed based on previous pipelines48 as follows: (i) removing probes with a signal-to-noise ratio of less than 2.0; (ii) normalizing the signal intensity of each probe by dividing the total signal intensity of a sample and multiplying by a constant

organism: soil metagenome

source_name: Soil

label_protocol: The DNA from each sample (500 ng) was labelled with the fluorescent dye Cy-3 by random priming.

growth_protocol: Samples collected directly from the environment

extract_protocol: Total DNA and RNA were extracted from each soil sample using ZymoBIOMICS DNA & RNA kit. The total RNA extracted were subjected to DNAse I treatment and cDNA was generated from the RNA template using SuperScript IV First-Strand Synthesis System for RT-PCR according to the manufacturer’s instruction.

treatment_protocol: Soil samples were collected using a sterile scoop and placed into a 5 mL sampling tube containing RNAlater Stabilization Solution

tag: source

value: Environmental soil

tag: location

value: High Arctic:Pond Inlet


title: non-primed paw [scRNA-seq]

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description:
acute
scRNA-Seq

data_processing:
Demultiplexing using cellranger mkfastq.
Alignment to precompiled mouse reference and feature counting using cellranger count (v3.0.1) with default parameters.
Genome_build: Precompiled cellranger 3.0.0 mouse reference.
Supplementary_files_format_and_content: *.h5: HDF5 file containing filtered feature barcode matrix.

source_name: collagenase-digested mouse paw

growth_protocol: Mice were housed in cages that were maintained in a room with temperature 22 ± 1°C and relative humidity 50–60% on a 12h light/dark cycle. Water and food were provided ad libitum.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer's instructions.
Library construction followed the 10x Genomics Single Cell Expression Library protocol according to the manufacturer's instructions.

treatment_protocol: Left paw was injected with MSU crystals at day 0 and then again at day 9; right paw was injected with MSU crystals at day 9. RNA was extracted at day 18 from both paws. Left paw, MSU/MSU; right paw, -/MSU, uninjected paw, -/-.

value: synovial tissue CD45-CD3- cells

tag: treatment

value: MSU day 9

tag: time point

value: Day 18

value: BALB/c


title: primed paw [scRNA-seq]

description:
chron
scRNA-Seq

value: MSU days 0 and 9


title: Pond Inlet C3 DNA

type: genomic


title: Pond Inlet A1 cDNA


title: Pond Inlet B9 cDNA


title: Pond Inlet B9 DNA


title: Pond Inlet A8 cDNA


title: FluBCR #29Vac

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #29Vac


title: FluBCR #inf3

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #inf3


title: Pond Inlet B1 cDNA


title: primed paw 1

data_processing:
Adapter trimming using cutadapt v2.5.
Alignment to GRCm38 genome using STAR v2.5.4a.
Determination of raw counts using subread (v1.6.1) featureCounts.
Differential expression analysis using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: rlogcounts.txt: Tab-separated text file containing rlog-normalized count data.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer's instructions.
Profiling of whole-genome transcriptomic patterns was performed with 1000ng high quality total RNA per sample. Libraries of the samples were generated using the Illumina stranded mRNA library kit according to the manufacturer's instructions.

treatment_protocol: Left paw was injected with MSU crystals at day 0 and then again at day 9; right paw was injected with MSU crystals at day 9. RNA was extracted at day 18 from both paws. Left paw, MSU/MSU; right paw, -/MSU. Fibroblasts were cultured for 5 passages.

value: synovial fibroblasts


title: primed paw 3


title: Pond Inlet A1 DNA


title: primed paw 2


title: non-primed paw 3


title: naive paw [scRNA-seq]

description:
naive
scRNA-Seq


title: Pond Inlet B1 DNA


title: non-primed paw 1


title: naive paw 1


title: naive paw 2


title: Pond Inlet A8 DNA


title: naive paw 3


title: FluBCR #27inf

description: cDNA of V-D-J region of ig gene

source_name: FluBCR #27inf


title: Med_4OHT_D7_H3K27ac

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single or paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

growth_protocol: ChIP-seq: Primary brown preadipocytes were isolated from interscapular BAT of newborn Med1f/f;CreER mice) and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid

extract_protocol:
ChIP-seq: Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
ChIP-seq: Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).
ATAC-Seq: 5 × 10^4 freshly collected cells were aliquoted into a new tube and spun down at 500 × g for 5 min at 4 °C. The cell pellet was incubated in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega) on ice for 3 min and was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were collected by centrifugation at 500 × g for 10 min at 4 °C, then resuspended in 50 µl of transposition reaction buffer (25 µl 2x Tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). The reaction was incubated at 37 °C for 30 min with mixing (1000 r.p.m.) and directly subjected to DNA purification using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer’s instructions.
ATAC-Seq: DNA was amplified with PCR using Nextera i7- and i5-index primers for Illumina protocols
RNA-Seq: Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
RNA-Seq: Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.
nascent RNA-Seq: 10^6 cells were labeled with 0.5 mM ethylene uridine for 30 min at 37 °C. After RNA extraction, 1 μg total RNA was depleted of rRNA using the NEBNext rRNA Depletion kit (NEB). To capture nascent RNA, the sample was biotinylated by the Click-iT Nascent RNA Capture Kit (ThermoFisher, C10365) according to the manufacturer’s instructions.
nascent RNA-Seq: Double-stranded cDNAs were synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Library construction was done using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: ChIP-seq: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

tag: strain background

value: 129S4/SvJae - C57BL/6 mixed

tag: genotype/variation

value: Brown adipocytes (differentiated)

tag: stage of adipogenesis

value: Mature adipocytes (D7)

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: RNA_Med1_flox_pBPA_WT_D20

tag: cell type

value: Primary brown adipocytes (differentiated)

value: Mature adipocytes (D20)


title: RNA_Med1_flox_pWPA_WT_D20

value: Primary white adipocytes (differentiated)


title: RNA_Med1_AdiQ_pBPA_cKO_D20


title: Med_Mock_D7_input


title: Med_Mock_D7_H3K27ac


title: RNA_Med1_8wk_AKO_iWAT

value: Inguinal white adipose tissue


title: Med_4OHT_D7_input


title: RNA_Med1_AdiQ_pWPA_cKO_D20


title: non-primed paw 2

tag: genotype

value: WT


title: RNA_Med1_8wk_WT_iWAT


title: RNA_Med1_8wk_AKO_BAT

value: Brown adipose tissue


title: RNA_Med1_8wk_WT_BAT


title: RNA_TRAP_AdipoQ_ingWAT_12wk_rep2

description:
TRAP_AdipoQ_ingWAT_12wk_rep2_S14_L007
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt

data_processing:
Library strategy: TRAP-seq
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-Seq of factors: Windows (50), Gaps (50), FDR (1e-3)
Single or paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

value: TRAP;Adipoq-Cre

value: White adipocytes (purified)

value: Mature adipocytes

value: anti-GFP (ab290, Abcam)


title: KPp3558-8-Kras-Trp53-Vehi

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: KP.GEMMnodule

data_processing:
mRNA-Seq libraries were aligned to the mouse mm10 using the STAR aligner algorithm. Resulting BAM files were sorted and indexed using Samtools and QC was performed using Picard. Tran-script read counts were determined was performed using Salmon
Gene counts were normalized using upper-quartile normalization, log transformed and median centred to construct the normalized gene matrix
Genome_build: mm10
Supplementary_files_format_and_content: fastqs, raw and normalized data matrix

source_name: activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with p53 conditional knockout

growth_protocol: The genetically engineered mouse model (GEMM) harboring a conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with Lkb1 or p53 conditional knockout (Lkb1fl/fl or Trp53fl/fl) has been previously described. Briefly This KrasLSL-G12D strain carries a Lox-Stop-Lox (LSL) sequence followed by the KrasG12D point mutation allele commonly associated with human cancer. Trp53 exons 2-10 are flanked by loxP sites in this conditional targeted mutation. For Lkb1fl/fl mice, the transcript from the Lkb1 null allele eliminates exons 2–6, resulting in a translational frameshift. All the mice are crossed and confirmed with higher than 90% C57BL/6 genetic background by SNP analysis. CRE recombinase was induced through intranasal inhalation of 1x107 p.f.u. adeno-Cre (University of Iowa adenoviral core). The induced mice were evaluated by MRI imaging to quantify the lung tumor burden, and KP (KrasG12DTrp53fl/fl) and KL (KrasG12DLkb1fl/fl) lung tumor nodules were obtained and tumor cell lines were generated from these nodules ex vivo similar as previously reported.

extract_protocol:
Total RNA was isolated with Qiagen RNeasy Mini Kit from fresh frozen tissue and quality checked by Agilent Bioanalyzer.
mRNA-Seq library made with Illumina TruSeq RNA Library Prep Kit v2 (Cat# RS-122-2001), 0.5ug of total RNAs was used for the construction of libraries according to the manufacturer’s protocol. Unique Dual indexes (TruSeq RNA UD Indexes, Cat# 20022371) were used for each library instead single index. cDNA libraries were sequenced using an Illumina HiSeq2500, producing 2x50bp paired-end reads with multiplexing.

value: Lung Tumor

tag: background strain


title: RNA_TRAP_AdipoQ_BAT_12wk_rep1

description:
TRAP_AdipoQ_BAT_12wk_rep1_S13_L007
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt

value: Brown adipocytes (purified)


title: RNA_TRAP_AdipoQ_BAT_12wk_rep2

description:
TRAP_AdipoQ_BAT_12wk_rep2_S16_L007
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt


title: RNA_TRAP_AdipoQ_ingWAT_12wk_rep1

description:
TRAP_AdipoQ_ingWAT_12wk_rep1_S19_L007
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt


title: RNA_TRAP_AdipoQ_BAT_P0.5_GFP_rep2

description:
TRAP_AdipoQ_BAT_P0.5_GFP_rep2_S2_L001
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt


title: KPp4006-9-Kras-Trp53-Vehi

description: KP.GEMMnodule


title: KP_411-Kras-Trp53-Vehi

description: KP.GEMMnodule


title: KP_414-Kras-Trp53-Vehi

description: KP.GEMMnodule


title: KPp3910-14-Kras-Trp53-Vehi

description: KP.GEMMnodule


title: RNA_TRAP_AdipoQ_BAT_P0.5_GFP_rep1

description:
TRAP_AdipoQ_BAT_P0.5_GFP_rep1_S8_L001
processed data file: TRAP_Adipoq-Cre_BAT_iWAT_RPKM_exon.txt


title: KL5739-Kras-Lkb1-NA

description: KL.GEMMnodule

source_name: conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with Lkb1


title: KL6426-Kras-Lkb1-NA

description: KL.GEMMnodule


title: KL84-Kras-Lkb1-NA

description: KL.GEMMnodule


title: KL80-Kras-Lkb1-NA

description: KL.GEMMnodule


title: d138.Lup.50 [103362-001-199]

city: Zeist

first: Marjolein

last: Meijerink

state: Utrecht

address: Utrechtseweg 48

department: RAPID

institute: TNO

description:
103362-001-199
title format: donor.allergen.dose

data_processing:
Quality filtering and adapter-trimming of the Illumina Nextseq 500 V2 fastq files was performed by Trimmomatic software.
Reads (Single-end, 75bp) of the fastq files were aligned to the reference sequence (Homo_sapiens.GRCh38.primary_assembly.GENCODE) using Tophat 2.0.14 combined with Bowtie 2.1.0. The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package (88-92% of input reads were mapped to the genome).
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count files.
Genome_build: Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample).
Supplementary_files_format_and_content: merged.counts.140samp.tsv.txt includes the mapped read counts per gene for all samples; *.counts.tsv files include the mapped read counts per gene for individual samples.

source_name: PBMCs

growth_protocol: PBMCs were isolated from buffy coats from non-atopic donors from Sanquin (Sanquin Blood Bank, The Netherlands). The PBMCs were washed with PBS/FCS and after centrifugation, the cell pellet was reconstituted in culture medium. Cells were counted and freezing medium was added to prepare a cell suspension of 50 – 150 x 10^6 cells/mL. Cells were stored in a liquid nitrogen tank until further usage.

extract_protocol:
The RNA isolation was performed according to the manufacturer’s protocol. RNA quality was assessed using fragment analysis using the DNF-471-500 standard sensitivity RNA kit from Agilent™. RNA quality number was determined with Prosize 2.0 (Data Analysis software 2.0.0.51).
Strand-specific mRNA-seq libraries for the Illumina platform were generated using Illumina protocols and sequenced at BaseClear BV (Leiden, The Netherlands). Briefly: The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
RNA-seq. Briefly: Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used. Primary data analysis and results: Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.20. The sequencing experiments were performed at the following site(s): GenomeScan B.V., Plesmanlaan 1d, 2333 BZ, Leiden.

treatment_protocol: Frozen PBMCs were thawed in a water bath (37°C), washed in culture medium and plated into sterile 96-well plates (1 x 10^5 cells per well). Allergenic proteins and LPS controls diluted in culture medium were added to the wells and incubated (37°C, 5% CO2) for four hours. The stimulated PBMCs were harvested and RNA isolated.

tag: diagnosis

value: Healthy

value: PBMCs

tag: allergen

value: 2S albumin Lupine


title: d138.Pea.10 [103362-001-188]

description:
103362-001-188
title format: donor.allergen.dose

value: 2S albumin Peanut


title: d138.Lup.10 [103362-001-193]

description:
103362-001-193
title format: donor.allergen.dose


title: d138.Lup.50 [103362-001-197]

description:
103362-001-197
title format: donor.allergen.dose


title: d138.Pea.50 [103362-001-190]

description:
103362-001-190
title format: donor.allergen.dose


title: d138.Lup.10 [103362-001-195]

description:
103362-001-195
title format: donor.allergen.dose


title: d138.Lup.50 [103362-001-200]

description:
103362-001-200
title format: donor.allergen.dose


title: d138.Lup.50 [103362-001-198]

description:
103362-001-198
title format: donor.allergen.dose


title: d138.Pea.50 [103362-001-191]

description:
103362-001-191
title format: donor.allergen.dose


title: d138.Lup.10 [103362-001-196]

description:
103362-001-196
title format: donor.allergen.dose


title: d138.Ctr.0 [103362-001-217]

description:
103362-001-217
title format: donor.allergen.dose

value: Control (no exposure)


title: d138.Ctr.0 [103362-001-219]

description:
103362-001-219
title format: donor.allergen.dose


title: d138.Ctr.0 [103362-001-218]

description:
103362-001-218
title format: donor.allergen.dose


title: d138.Pea.50 [103362-001-192]

description:
103362-001-192
title format: donor.allergen.dose


title: d138.Pea.50 [103362-001-189]

description:
103362-001-189
title format: donor.allergen.dose


title: d138.Lup.10 [103362-001-194]

description:
103362-001-194
title format: donor.allergen.dose


title: d138.Pea.10 [103362-001-185]

description:
103362-001-185
title format: donor.allergen.dose


title: d138.Pea.10 [103362-001-187]

description:
103362-001-187
title format: donor.allergen.dose


title: d138.Pea.10 [103362-001-186]

description:
103362-001-186
title format: donor.allergen.dose


title: KL77-Kras-Lkb1-NA

description: KL.GEMMnodule


title: d138.Ctr.0 [103362-001-220]

description:
103362-001-220
title format: donor.allergen.dose


title: d138.Soy.50 [103362-001-181]

description:
103362-001-181
title format: donor.allergen.dose

value: Soybean 7S globulin


title: d138.Soy.50 [103362-001-184]

description:
103362-001-184
title format: donor.allergen.dose


title: d138.Soy.50 [103362-001-183]

description:
103362-001-183
title format: donor.allergen.dose


title: d138.WB.50 [103362-001-180]

description:
103362-001-180
title format: donor.allergen.dose

value: White Bean 7S globulin


title: d138.WB.50 [103362-001-179]

description:
103362-001-179
title format: donor.allergen.dose


title: PIK3CA E545K single control [Ex9-3]

source_name: PIK3CA E545K isogenic cell line in MCF-10A background

tag: cell line background

value: Isogenic breast epithelial cell line

value: PIK3CA E545K

tag: culture type

value: Single control


title: d137.Lup.50 [103362-001-156]

description:
103362-001-156
title format: donor.allergen.dose


title: d137.Lup.10 [103362-001-150]

description:
103362-001-150
title format: donor.allergen.dose


title: d138.Soy.50 [103362-001-182]

description:
103362-001-182
title format: donor.allergen.dose


title: d138.WB.50 [103362-001-177]

description:
103362-001-177
title format: donor.allergen.dose


title: d137.Ctr.0 [103362-001-175]

description:
103362-001-175
title format: donor.allergen.dose


title: d138.WB.50 [103362-001-178]

description:
103362-001-178
title format: donor.allergen.dose


title: d137.Lup.10 [103362-001-151]

description:
103362-001-151
title format: donor.allergen.dose


title: d137.Lup.10 [103362-001-152]

description:
103362-001-152
title format: donor.allergen.dose


title: d137.Ctr.0 [103362-001-173]

description:
103362-001-173
title format: donor.allergen.dose


title: d137.Pea.50 [103362-001-147]

description:
103362-001-147
title format: donor.allergen.dose


title: d137.Pea.10 [103362-001-142]

description:
103362-001-142
title format: donor.allergen.dose


title: d137.Pea.10 [103362-001-144]

description:
103362-001-144
title format: donor.allergen.dose


title: d137.Pea.50 [103362-001-146]

description:
103362-001-146
title format: donor.allergen.dose


title: d137.Soy.50 [103362-001-137]

description:
103362-001-137
title format: donor.allergen.dose


title: d137.Ctr.0 [103362-001-174]

description:
103362-001-174
title format: donor.allergen.dose


title: d137.Pea.10 [103362-001-143]

description:
103362-001-143
title format: donor.allergen.dose


title: d137.Pea.10 [103362-001-141]

description:
103362-001-141
title format: donor.allergen.dose


title: d137.Ctr.0 [103362-001-176]

description:
103362-001-176
title format: donor.allergen.dose


title: d137.Pea.50 [103362-001-145]

description:
103362-001-145
title format: donor.allergen.dose


title: d137.Soy.50 [103362-001-140]

description:
103362-001-140
title format: donor.allergen.dose


title: d137.Lup.10 [103362-001-149]

description:
103362-001-149
title format: donor.allergen.dose


title: d137.Lup.50 [103362-001-155]

description:
103362-001-155
title format: donor.allergen.dose


title: d137.Soy.50 [103362-001-138]

description:
103362-001-138
title format: donor.allergen.dose


title: d137.WB.50 [103362-001-136]

description:
103362-001-136
title format: donor.allergen.dose


title: d137.Lup.50 [103362-001-154]

description:
103362-001-154
title format: donor.allergen.dose


title: d137.Lup.50 [103362-001-153]

description:
103362-001-153
title format: donor.allergen.dose


title: ZN_MAX_P1_11

city: Freiburg im Breisgau

first: Toma

last: Yakulov

address: Hugstetter Str. 55

institute: University Freiburg Medical Center

description: library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. Zebrafish gene models were based on Ensembl release 74 (http://www.ensembl.org) were improved for 3’ UTR annotations as described previously (Junker JP et al. Genome-wide RNA Tomography in the zebrafish embryo. Cell 159: 662-675, 2014)
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: Ensembl release 74
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Pronephros

extract_protocol:
Pronephric cells were isolated as previously described Yakulov TA et al., Nat Commun 9: 3660, 2018.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: The idolation of pronephric cells was followed by FACS sorting and single cell RNA sequencing.

tag: line

value: Tg(wt1b:GFP); Tg(cdh17:GFP)

tag: tissue

value: pronephros

tag: age

value: 2 day post fertilization


title: d137.WB.50 [103362-001-134]

description:
103362-001-134
title format: donor.allergen.dose


title: d136.Ctr.0 [103362-001-132]

description:
103362-001-132
title format: donor.allergen.dose


title: d137.Pea.50 [103362-001-148]

description:
103362-001-148
title format: donor.allergen.dose


title: d137.Soy.50 [103362-001-139]

description:
103362-001-139
title format: donor.allergen.dose


title: d137.WB.50 [103362-001-133]

description:
103362-001-133
title format: donor.allergen.dose


title: d137.WB.50 [103362-001-135]

description:
103362-001-135
title format: donor.allergen.dose


title: d136.Ctr.0 [103362-001-129]

description:
103362-001-129
title format: donor.allergen.dose


title: d136.Lup.50 [103362-001-111]

description:
103362-001-111
title format: donor.allergen.dose


title: d136.Pea.50 [103362-001-103]

description:
103362-001-103
title format: donor.allergen.dose


title: d136.Ctr.0 [103362-001-131]

description:
103362-001-131
title format: donor.allergen.dose


title: d136.Pea.50 [103362-001-104]

description:
103362-001-104
title format: donor.allergen.dose


title: d136.Lup.10 [103362-001-106]

description:
103362-001-106
title format: donor.allergen.dose


title: d136.Ctr.0 [103362-001-130]

description:
103362-001-130
title format: donor.allergen.dose


title: d136.Lup.50 [103362-001-110]

description:
103362-001-110
title format: donor.allergen.dose


title: d136.Lup.50 [103362-001-109]

description:
103362-001-109
title format: donor.allergen.dose


title: d136.Lup.10 [103362-001-107]

description:
103362-001-107
title format: donor.allergen.dose


title: d136.Pea.50 [103362-001-102]

description:
103362-001-102
title format: donor.allergen.dose


title: d136.Lup.10 [103362-001-105]

description:
103362-001-105
title format: donor.allergen.dose


title: d136.Pea.50 [103362-001-101]

description:
103362-001-101
title format: donor.allergen.dose


title: d136.Lup.50 [103362-001-112]

description:
103362-001-112
title format: donor.allergen.dose


title: d136.Lup.10 [103362-001-108]

description:
103362-001-108
title format: donor.allergen.dose


title: d136.Pea.10 [103362-001-099]

description:
103362-001-099
title format: donor.allergen.dose


title: d136.Pea.10 [103362-001-097]

description:
103362-001-097
title format: donor.allergen.dose


title: d136.Pea.10 [103362-001-098]

description:
103362-001-098
title format: donor.allergen.dose


title: d136.Soy.50 [103362-001-094]

description:
103362-001-094
title format: donor.allergen.dose


title: d136.Soy.50 [103362-001-096]

description:
103362-001-096
title format: donor.allergen.dose


title: d136.Soy.50 [103362-001-095]

description:
103362-001-095
title format: donor.allergen.dose


title: d136.Soy.50 [103362-001-093]

description:
103362-001-093
title format: donor.allergen.dose


title: d136.WB.50 [103362-001-090]

description:
103362-001-090
title format: donor.allergen.dose


title: d136.WB.50 [103362-001-089]

description:
103362-001-089
title format: donor.allergen.dose


title: d134.Ctr.0 [103362-001-087]

description:
103362-001-087
title format: donor.allergen.dose


title: d134.Ctr.0 [103362-001-088]

description:
103362-001-088
title format: donor.allergen.dose


title: d136.WB.50 [103362-001-092]

description:
103362-001-092
title format: donor.allergen.dose


title: d136.WB.50 [103362-001-091]

description:
103362-001-091
title format: donor.allergen.dose


title: d134.Lup.50 [103362-001-084]

description:
103362-001-084
title format: donor.allergen.dose


title: d134.Lup.50 [103362-001-081]

description:
103362-001-081
title format: donor.allergen.dose


title: d134.Ctr.0 [103362-001-085]

description:
103362-001-085
title format: donor.allergen.dose


title: d134.Pea.50 [103362-001-075]

description:
103362-001-075
title format: donor.allergen.dose


title: d134.Lup.50 [103362-001-082]

description:
103362-001-082
title format: donor.allergen.dose


title: d134.Lup.10 [103362-001-077]

description:
103362-001-077
title format: donor.allergen.dose


title: d134.Lup.10 [103362-001-080]

description:
103362-001-080
title format: donor.allergen.dose


title: d134.Lup.10 [103362-001-078]

description:
103362-001-078
title format: donor.allergen.dose


title: d136.Pea.10 [103362-001-100]

description:
103362-001-100
title format: donor.allergen.dose


title: d134.Pea.10 [103362-001-072]

description:
103362-001-072
title format: donor.allergen.dose


title: d134.Pea.10 [103362-001-070]

description:
103362-001-070
title format: donor.allergen.dose


title: d134.Pea.10 [103362-001-071]

description:
103362-001-071
title format: donor.allergen.dose


title: d134.Soy.50 [103362-001-049]

description:
103362-001-049
title format: donor.allergen.dose


title: d134.Lup.10 [103362-001-079]

description:
103362-001-079
title format: donor.allergen.dose


title: d134.WB.50 [103362-001-048]

description:
103362-001-048
title format: donor.allergen.dose


title: d134.Soy.50 [103362-001-052]

description:
103362-001-052
title format: donor.allergen.dose


title: d134.Soy.50 [103362-001-050]

description:
103362-001-050
title format: donor.allergen.dose


title: d134.WB.50 [103362-001-047]

description:
103362-001-047
title format: donor.allergen.dose


title: d134.Pea.10 [103362-001-069]

description:
103362-001-069
title format: donor.allergen.dose


title: d134.WB.50 [103362-001-046]

description:
103362-001-046
title format: donor.allergen.dose


title: d134.Pea.50 [103362-001-074]

description:
103362-001-074
title format: donor.allergen.dose


title: d134.WB.50 [103362-001-045]

description:
103362-001-045
title format: donor.allergen.dose


title: d133.Ctr.0 [103362-001-044]

description:
103362-001-044
title format: donor.allergen.dose


title: d134.Pea.50 [103362-001-076]

description:
103362-001-076
title format: donor.allergen.dose


title: d133.Ctr.0 [103362-001-043]

description:
103362-001-043
title format: donor.allergen.dose


title: d133.Ctr.0 [103362-001-042]

description:
103362-001-042
title format: donor.allergen.dose