title: ChIP_MB_H3k27ac

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with the default configuration
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Macs14

source_name: Medulloblastoma tissue

extract_protocol:
Lysates were clarified from sonicated nuclei and proteine-DNA complexes were isolated with antibody.
Dissociated tissues were fixed for 15 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Sonicated chromatin (~300 µg) was used for immunoprecipitation by incubation with appropriate antibodies (4 mg) overnight at 4°C. Pre-rinsed magnetic protein A/G beads (50 ml) were added to each ChIP reaction and reactions were incubated for 1 hr at 4°C. The beads were then incubated in 200 ml elution buffer at 65°C for 20 min to elute immunoprecipitated materials. The ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2500.

value: H3k27ac (Abcam, ab4729)

value: Medulloblastoma tissue


title: ChIP_MB_Olig2

status: Public on Aug 30 2019

type: SRA

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: antibody

value: Olig2 (Millipore, ab9610)

tag: tissue


title: ChIP_CB_Olig2

source_name: Cerebellum

value: Cerebellum


title: A4573_shARID1A_2

type: RNA

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

hyb_protocol: cRNA was hybridized to the Agilent Human Gene Expression 4x44K v2 Microarray (AMAID: 026652)

scan_protocol: Agilent SureScan (Agilent Technologies Scanner G2505C) microarray scanner was used to measure signal intensity at probe locations with the AgilentHD_GX_1color scan protocol. Feature Extraction software version 2.50

data_processing: Raw intensity values were quantile normalized and background corrected using negative control probes

molecule: total RNA

organism: Homo sapiens

source_name: Total mRNA from A4573, shARID1A

label_protocol: 200 ng of total RNA was used to generate fluorescent cRNA using the Agilent Low Input Quick Amp labeling Kit, One-Color following manufacturer instructions

growth_protocol: Cells were grown in RPMI media supplemented with 10% FBS in 5% CO2

extract_protocol: RNA was extracted with a QIAGEN RNEasy Miniprep kit following manufacturer instructions

treatment_protocol: Cells were lentivirally transduced with shRNA targeting EWS-FLI1 or ARID1A

tag: cell line

tag: genotype/variation


title: 48h-Blood

city: Beijing

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

country: China

institute: Tsinghua University

description: blood feeding

library_source: transcriptomic

data_processing:
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
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.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
Genome_build: NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Supplementary_files_format_and_content: Aaegl3.3
Supplementary_files_format_and_content: Excel files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...

organism: Aedes aegypti

source_name: Midguts

growth_protocol: Aedes Aegypti was reared at 28℃ and 80% humidity.

extract_protocol:
Midguts were dissected from mosquitoes, and 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

treatment_protocol: 7 days old mosquitos were blood fed with or without 250 um ferric ammonium citrate, then treated after 24,48 hours.

tag: strain

value: Rockefeller

tag: tissues

value: Midguts

tag: age

tag: treatment

tag: time point


title: ATAC_Olig2_GFP(-)

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Tophat using default options
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files format and content: wig files were generated by MACS1.4

source_name: medulloblastoma tumor cells

extract_protocol:
Dissociated mouse medulloblastoma tumor cells (∼50,000 cells) were spun down at 500 x g for 5 min at 4C, lysed in cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Afterspinning down at 500 x g for 10 min at 4C, nuclei were resuspended in transposition mix containing 25 μl TD (2x reaction buffer) 2.5 μl TDE1 (Nextera Tn5 Transposase), 22.5 μl Nuclease Free H2O, at 37°C for 30 min. Immediately following transposition, DNA were purified using a Qiagen MinElute PCR Purification Kit. Transposed DNA fragments were subsequently amplified and the amplified library was purified using Qiagen MinElute PCR Purification Kit. Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7–9 total cycles.
Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2500.

value: Postnatal day 20

tag: geneotype

value: hGFAPcre;Pthc/c


title: 24h-Fe

description: blood feeding

value: 250 um ferric ammonium citrate


title: A4573_shEF_1

source_name: Total mRNA from A4573, shEF

value: shEF


title: A4573_shARID1A_1


title: ATAC_Olig2_GFP(+)


title: A4573_WT_2

source_name: Total mRNA from A4573, WT

value: WT


title: HA-DNMT3A_ChIPseq_TKO

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We filtered CpGs with less than 5x coverage, overlapping with SNPs from dbSNPs (build 137) or located within the ENCODE DAC blacklisted regions or Duke excluded regions.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig

source_name: C3H10T1/2 cells

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA Hyper Prep Kit

tag: chip antibody

value: HA (ThermoFisher, #88836)

tag: cell type

value: C3H embryo-derived mesenchymal progenitor cells

tag: genotype

value: sgNsd1/Nsd2/Setd2 #2 cells stably expressing FLAG-HA tagged DNMT3A WT


title: WT_Day7

city: Hong Kong

first: Vincent Ka Fai

last: Cheng

state: -- select --

address: L202 lab block 21 Sassoon road Pokfulam Hong Kong

department: Pharmacology and Pharmacy

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Base calling was performed using Illumina’s RTA (Version 1.12.4.2).
Adapters of RNA-seq reads were trimmed.
The BAM files with coordinate-sorted alignments were imported to Cufflinks 2.2.1 to assemble and quantify the transcripts as fragments per kilobase per million aligned reads (FPKM).
Cuffdiff 2 was employed to perform differential expression analysis.
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: tab-delimited text files include log2 foldchange value

growth_protocol: Cell were maintained in proliferation medium, α‐MEM (Gibco, Thermo Fisher Scientific, Waltham, MA, USA; catalog # 12571) containing 10% v/v fetal bovine serum (FBS), 100 units/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Cell were washed with PBS and RNA was harvested using Trizol reagent.
100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche).

treatment_protocol: 50 µg/ml ascorbic acid and 5 mM β-glycerophosphate were added to the medium for osteogenic differentiation. Medium was changed every 3 days and cells were incubated at 37 °C in a 5% CO2 atmosphere.


title: A4573_shEF_2


title: A4573_WT_1


title: TC32_shARID1A_1

source_name: Total mRNA from TC32, shARID1A


title: Drop_seq

data_processing:
Library strategy: Drop-seq
Illumina Casava software used for basecalling.
Drop-seq mapping and analysis procedure
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expression value of each cell

source_name: medullablastoma tumor cells

extract_protocol:
Tumor tissues were digested by TrypLE added with collagenase type I, and single cell suspension was treated by Red Blood Cell Lysis Buffer, the sequencing followed Drop-seq protocols. Briefly, monodisperse droplets ∼1 nl in size were generated using the microfluidic device, in which barcoded microparticles, suspended in lysis buffer. As soon as droplet generation was complete, droplets were broken with perfluorooctanol in 30 ml of 6× SSC. The addition of a large aqueous volume to the droplets reduces hybridization events after droplet breakage. The beads were then washed and resuspended in a reverse transcriptase mix, followed by a treatment with exonuclease I to remove unextended primers, and PCR amplified.
The amplified cDNA was quantified on a BioAnalyzer High Sensitivity Chip (Agilent). cDNA size selection was performed to reduce reads that end up just giving PolyA tail sequences. The cDNA was then fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina) using custom primers that enabled the specific amplification of only the 3’ ends. The libraries were purified, quantified, and then sequenced on the Illumina Hiseq 2500.

value: Postnatal day 24 to30

value: hGFAPcre;Ptchc/c


title: TC32_shARID1A_2


title: 24h-Blood

description: blood feeding


title: 48h-Fe

description: blood feeding


title: TC32_shEF_1

source_name: Total mRNA from TC32, shEF


title: Sorted cells cultured for 9 passages, biological rep 2

city: Auckland

first: Hilary

last: Sheppard

address: Symonds St

country: New Zealand

institute: Auckland University

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 9 passages in standard tissue culture
Donor 27 passage 9

hyb_protocol: 5 µg of fragmented aRNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: The data was normalise using the RMA function of the R software package affy

label: biotin

source_name: AdMSC ex-vivo then cultured in DMEM+10% FBS for 9 passages

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Primeview Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: cells were grown in DMEM F-12 (Life Technologies) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % Penicillin-Streptomycin 10,000 U/mL (Invitrogen) and 1 × GlutaMAX (Invitrogen)

extract_protocol: RNA was isolated using a miRVANA kit from Ambion following the manufactures instructions (cat # AM1560)

treatment_protocol: cells were isolated using immunomagnetic beads and then grown for 0,3 or 28 days, or for 9 passages in standard tissue culture plates in medium as described above. Some cells were subjected to adipogenic differentiation medium as indicated.

value: adipose derived mesenchymal stromal cells

tag: donor

value: donor 27


title: Sorted cells cultured for 9 passages, biological rep 1

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 9 passages in standard tissue culture
Donor 24 passage 9

value: donor 24


title: Sorted cells cultured for 9 passages, biological rep 3

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 9 passages in standard tissue culture
Donor 15 passage 9

value: donor 15


title: Sorted cells cultured in adipo medium for 14 days, biological rep 3

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 14 days in adipogenic culture medium
Donor 26 adipo differentiated

source_name: AdMSC ex-vivo then cultured in adipogenic differentiation media for 14 days

value: donor 26


title: TC32_WT_1

source_name: Total mRNA from TC32, WT


title: H3K36me3_ChIPseq_NSD1_2_DKO

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. The bigWig files were generated similarly as ChIP-seq.
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

organism:
Drosophila melanogaster
Mus musculus

source_name: C3H10T1/2 cells & S2 cells (spiked-in)

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma). Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA HTP Library Preparation Kit

value: sgNSD1/2 #1


title: H3K36me2_ChIPseq_mESCs

source_name: Mouse embryonic stem cells & S2 cells (spiked-in)

growth_protocol: Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF.

value: H3K36me2 (Cell Signaling Tech, #2901)

value: ESC line V6.5 1A

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

value: wild-type


title: Sorted cells cultured for 3 days, biological rep 3

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 3 days in standard tissue culture
Donor 26 day 3

source_name: AdMSC ex-vivo then cultured in DMEM+10% FBS for 3 days


title: H3K36me2_ChIPseq_NSD1_2_DKO


title: H3K36me3_ChIPseq_SETD2_KO

value: sgSETD2 #1


title: 10x Genomic Chromium

data_processing:
Illumina Casava software used for basecalling.
10x Genomic Chromium mapping and analysis procedure
Genome_build: mm10

The R2 is biological and R1 is technical including basepair position of the barcode and UMI for 10x fastq files.
Supplementary_files_format_and_content: 10x Genomic Chromium expression files

extract_protocol:
Tumor tissues were digested by TrypLE added with collagenase type I, and single cell suspension was treated by Red Blood Cell Lysis Buffer, the sequencing followed10X genomics chromium protocols.
we followed ChromiumTM Single cell 3’ User Guide. A Single Cell Gel Bead kit (120217), Single cell chip kit (120219) and Single cell library kit (120218) were used along with a 10× GemCode Single Cell Instrument, per the manufacturer's specifications and manuals (document CG00011; revision B). The libraries were purified, quantified, and then sequenced on the Illumina Hiseq 2500.

value: Postnatal day 10


title: TC32_WT_2

value: WT


title: Sorted cells cultured for 28 days, biological rep 3

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 28 days in standard tissue culture
Donor 26 day 28

source_name: AdMSC ex-vivo then cultured in DMEM+10% FBS for 28 days


title: TC32_shEF_2

value: shEF


title: H3K36me2_ChIPseq_SETD2_KO

value: C3H embryo-derived mesenchymal progenitor cells


title: H3K27ac_ChIPseq_Parental

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA HyperPrep Kit


title: Sorted cells cultured in adipo medium for 14 days, biological rep 2

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 14 days in adipogenic culture medium
Donor 27adipo differentiated


title: AS-R_D-3_C: Artesunate resistant Leishmania donovani (test 3)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: In vitro selected artesunate resistant parasite adapted to 50 µM drug pressure (Test sample 3)

hyb_protocol: Labeled cRNA sample were fragmented at 60°C and hybridized on to a Genotypic designed L. donovani Gene expression Microarray 8x15K (AMADID No: 027511) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Leishmania donovani

source_name: Leishmania donovani promastigote

label_protocol: Samples for Gene expression were labeled using the Agilent Quick-Amp labeling Kit (p/n5190-0442). 200 ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasyMini kit columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Leishmania donovani parasites initially isolated from Bone marrow aspirate of antimony sensitive kala azar patient and already cryopreserved in lab was allowed to grow  in vitro as promastigote  in Medium 199 and 10% FCS. This isolate was denoted as WT.

extract_protocol: Total parasite RNA was extracted using Trizol reagent according to manufacturer's instructions.

treatment_protocol: The WT parasite was adapted stepwise to 50 µM artesunate pressure till it attained growth equivalent to its wild type counterpart.

value: Leishmania donovani promastigote

value: K133 AS-R


title: H3K36me3_ChIPseq_TKO

description: According to manufacturer's protocol

source_name: C3H10T1/2 cells & S2 cells

value: sgNsd1/Nsd2/Setd2 #1


title: AS-R_D-3_A: Artesunate resistant Leishmania donovani (test 1)

description: In vitro selected artesunate resistant parasite adapted to 50 µM drug pressure (Test sample 1)


title: Sorted cells cultured for 28 days, biological rep 2

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 28 days in standard tissue culture
Donor 27 day 28

value: adipose derived mesenchymal stromal cells

value: donor 27


title: Freshly sorted cells, biological rep 3

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells
Donor 26 day 0

source_name: AdMSC ex-vivo


title: Freshly sorted cells, biological rep 2

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells
Donor 27 day 0


title: AS-R_D-3_B: Artesunate resistant Leishmania donovani (test 2)

description: In vitro selected artesunate resistant parasite adapted to 50 µM drug pressure (Test sample 2)


title: Sorted cells cultured in adipo medium for 14 days, biological rep 1

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 14 days in adipogenic culture medium
Donor 24 adipo differentiated

value: donor 24


title: Sorted cells cultured for 3 days, biological rep 2

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 3 days in standard tissue culture
Donor 27 day 3


title: Sorted cells cultured for 3 days, biological rep 1

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 3 days in standard tissue culture
Donor 24 day 3


title: H3K4me1_ChIPseq_Parental


title: H3K9me3_ChIPseq_Parental


title: Sorted cells cultured for 28 days, biological rep 1

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells after 28 days in standard tissue culture
Donor 24 day 28


title: H3K27me3_ChIPseq_Parental

value: H3K27me3 (Cell Signaling Tech, #9733)


title: H3K36me3_ChIPseq_Parental


title: ZNFX1-overexpressed in Rig-I-/- cells with poyI:C stimulation

city: Guangzhou

first: Xin

last: Jia

state: Guangdong

address: 135 XinGangXi Road

department: College of Life Sciences

institute: Sun Yat-sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools software were used to map to reference genome.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped(FPKM).
Genome_build: GRCh38_release95
Supplementary_files_format_and_content: files include RPKM values for each Sample

growth_protocol: The A549 cells were purchased from ATCC and  cultured in endotoxin-free DMEM (GIBCO), supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO).

extract_protocol:
The RNA  was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: epithelial

value: ZNFX1-overexpressed in Rig-I-/- cells

value: poyI:C stimulation


title: WT_D-3_B: Artesunate sensitive Leishmania donovani (Control 2)

description: Corresponding wild type artesunate sensitive parasite (Control sample 2)

value: K133 WT


title: H3K36me2_ChIPseq_Parental

value: H3K36me2 (Cell Signaling Tech, #2901)

value: wild-type


title: WT_D-3_A: Artesunate sensitive Leishmania donovani (Control 1)

description: Corresponding wild type artesunate sensitive parasite (Control sample 1)


title: ZNFX1-overexpressed in Rig-I-/- cells

source_name: ZNFX1-overexpressed in Rig-I-/- cells


title: H3K36me2_ChIPseq_SKN_3

organism:
Drosophila melanogaster
Homo sapiens

source_name: SKN-3 cells & S2 cells (spiked-in)

growth_protocol: SKN-3 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
Cells were crosslinked with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and concentrated using Nanosep 10k OMEGA (Pall). Before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing. ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Dynalbeads Protein A (Invitrogen) were washed and then incubated with specific antibodies, and 1.5 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
KAPA HyperPrep Kit

value: Patient-derived head and neck squamous cell carcinoma cell line

value: NSD1 mutant


title: WT_D-3_C: Artesunate sensitive Leishmania donovani (Control 3)

description: Corresponding wild type artesunate sensitive parasite (Control sample 3)


title: 4T_KPhi treated

city: Mar del Plata

first: Mariana

middle: Laura

last: Feldman

state: Buenos Aires

address: Funes 3250 4to nivel

country: Argentina

institute: IIB-CONICET- Univ. Nac. de Mar del Plata

data_processing:
cDNA libraries were generated using the IlluminaTruSeq Small RNA Sample Preparation Kit, according to the manufacture´s protocol (Illumina Inc.)
Purified cDNA libraries were sequenced on an Illumina Hi Seq 2500 following the manufacturer’s instructions
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis, which performs adaptor removal, mapping and alignment of the RNA sequencing reads
Raw reads produced by sequencing were first processed through a data cleaning pipeline to remove low quality reads, contaminating sequences with no 3’ adapter (3ADT), and reads shorter than 15 nt and longer than 32 nt. The clean reads were further filtered to remove reads with less than five counts in each library and were subsequently mapped to reference databases to perform in-depth data analysis
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures were predicted from the flanking 120 nt sequences using the RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi) to detect potential new candidates.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed using a Student’s t test. The significance threshold was set to 0.01 and 0.05 in each test. The sequence reads of the six libraries were normalized to 1 million by the total number of clean small RNA reads in each sample. The log2 ratio formula was as follows: log2 ratio = log2 (miRNA reads in KPhi treated/miRNA reads in control)
Genome_build: miRNA(miRs) database: ftp://mirbase.org/pub/mirbase/CURRENT/; Specific species: stu; Selected species: sly,nta v21.0: Solanum tuberosum (SolTub3.0) GCA_000226075.1; Solanum lycopersicum (SL2.50) GCA_000188115.2  Pre-miRNA(mirs) database: ftp://mirbase.org/pub/mirbase/CURRENT/; Specific species: stu; Selected species: sly,nta v21.0  Genome and mRNA database: https://phytozome.jgi.doe.gov/pz/ portal.html; v4.03
fastq format files were generated as follows: The first file line indicates the sequenced sequence (sequ seq) identification (e.g. 5_18368) composed of the index and the copy number of the sequ seq; the second line presents the sequence; the forth line shows the sequencing quality of the corresponding bases using the average Phred score.  Filtered sequ seqs with lengths between 15 and 32 bases, were grouped by families (unique seqs), and stored in the file [Sample]_mappableReads.fq, and were used to map with the reference database files.
Supplementary_files_format_and_content: Differential expression of miRNAs based on normalized deep-sequencing counts

organism: Solanum tuberosum

growth_protocol: Solanum tuberosum seed tubers (cv. Shepody) were planted in pots containing a pasteurized mixture of soil and vermiculite (3:1, v/v). Pots were maintained under greenhouse conditions (18°C day-night temperature, 16 h of light per day).

extract_protocol:
Total RNAs from each treatment were isolated from  0.1 g of fresh leaf tissue using the RNeasy Plant Mini kit (Qiagen), following the manufacturer’s protocol
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Potassium phosphite (KPhi), 1% (v/v) water solution of the commercial product (Afital Potassium Phosphite, Agro-EMCODI SA) was applied to the foliage at 5 mL per plant (3 L/ha) by using an atomizer (ESAC SA) operating at 200 kPa, 21 days after emergence and leaves were harvested after 72h. Control samples were treated with water.

tag: cultivated variety

value: Shepody

value: 24 days post emergency

value: Potassium phosphite (KPhi)

value: Leaves


title: 6T_KPhi treated


title: Vector-overexpressed in Rig-I-/- cells

source_name: Vector-overexpressed in Rig-I-/- cells

value: Vector-overexpressed in Rig-I-/- cells


title: H3K36me2_ChIPseq_SCC_4

source_name: SCC-4 cells & S2 cells (spiked-in)

growth_protocol: SCC-4 cells were cultured in DMEM:F12 medium (Invitrogen) with 10% fetal bovine serum (Sigma) and 400 ng/ml hydrocortisone (Sigma).


title: ZNFX1

source_name: ZNFX1-overexpressed A549 Cells

extract_protocol:
The RNA of WT or ZNFX1-overexpressed A549 cells was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: H3K36me2_ChIPseq_Fadu

source_name: Fadu cells & S2 cells (spiked-in)

growth_protocol: Fadu cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

value: Fadu

value: NSD1 wild-type


title: 2T_KPhi treated


title: H3K36me2_ChIPseq_Cal27

source_name: Cal 27 cells & S2 cells (spiked-in)

growth_protocol: Cal27 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).


title: 3C_Control

value: water control


title: WT

source_name: Wild Type  A549 Cells

value: wild type


title: Freshly sorted cells, biological rep 1

description:
Gene expression data from ex vivo adipose-derived mesenchymal stromal cells
Donor 24 day 0

value: adipose derived mesenchymal stromal cells

value: donor 24


title: 5C_Control


title: gdT C1

status: Public on Aug 29 2019

city: New Haven

first: Emily

middle: L

last: Goldberg

state: CT

address: 310 Cedar Street

institute: Yale

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
C2

data_processing:
Base-calling: Illumina HiSeq2500 or NextSeq software
Btrim to trim reads; BWA for alignment to GRCm38 and TopHat2 for alignment for cellular gene analysis
Expression quantification was performed using RSEM
DEseq2 was used to calculate differential gene expression
See detailed methods in Goldberg et al., Science Immunology 2019
Genome_build: GRCm38
Supplementary_files_format_and_content: excel spreadsheet of fpkm

molecule: polyA RNA

source_name: sorted gdT

extract_protocol:
Total RNA was extracted with RLT buffer
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: sorted lung gamma delta T cell


title: gdT HFD3

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
H5


title: gdT HFD1

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
H1


title: gdT C2

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
C3


title: gdT KD3

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
K5


title: lung Tcrd KD 2

description:
75bp single-end sequencing
fpkm_lung.xls
H

source_name: Whole lung

value: Mx1 Tcrd-/-

value: whole lung


title: gdT KD2

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
K4


title: lung Tcrd KD 3

description:
75bp single-end sequencing
fpkm_lung.xls
I


title: gdT KD1

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
K2


title: gdT C3

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
C4


title: OX40L-JAG1 Treg_B

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

hyb_protocol: Fluidics protocol FS450_0002, Wash, Stain and Scan Protocol, Affymetrix P/N 702731 Rev.4

scan_protocol: Automated GeneChip Scanner 3000, Wash, Stain and Scan Protocol, Affymetrix P/N 702731 Rev.4

data_processing: Arrays were processed with RMA using oligo from R package.

source_name: OX40L-JAG1 Treg cells

label_protocol: GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for Whole Transcript (WT) Expression Array P/N 703174

growth_protocol: Total splenic  CD4+ cells from 8-week-old Foxp3.eGFP mice on C57BL6 background were used for this study.

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

treatment_protocol: CD4+ cells from Foxp3.eGFP mice containing Foxp3- Teff and Foxp3+ Treg cells were treated with anti-CD3/CD28 monoclonal antibodies (2µg/ml earch) or soluble OX40L (5µg/ml)and JAG1 (1µg/ml) for 3 days to induce TCR-dependent vs TCR-independent Treg proliferation.

value: spleen

value: CD4+Foxp3+ Treg cells


title: Control Teff

source_name: Control Teff cells

value: CD4+Foxp3- Teff cells

value: Untreated


title: a-CD3-CD28 Treg_B

source_name: a-CD3-CD28 Treg cells

value: anti-CD3 + anti-CD28 mAb


title: a-CD3-CD28 Teff_B

source_name: a-CD3-CD28 Teff cells


title: OX40L-JAG1 Teff

source_name: OX40L-JAG1 Teff cells


title: WT_C1

city: St. Louis

first: Qianli

last: Wang

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis School of Medicine

description: gene expression from WT CCR6+ ILC3

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 2.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 2.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G 3000.

data_processing: The data were processed using the AffySTExpressionFileCreator function of GenePattern using default settings that RMA normalize and background correct data, generating a .gct file of gene expression. Log2 transformation was removed because data were analyzed using MultiplotStudio, which automatically log2 transforms data

source_name: small intestine lamina propria

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

extract_protocol: Briefly, small intestines were flushed, opened lengthwise, and subjected to two rounds of gentle agitation of 20 min in HBSS (containing HEPES, BCS, and EDTA) followed by vortexing. The tissues were then rinsed with HBSS prior to digestion with Collagenase IV in complete RPMI-10 for 40 min at 37°C under agitation. Digests were filtered through 100 micron mesh and subjected to density gradient centrifugation using 40% and 70% Percoll. From single cell suspension, CCR6+ ILC3s were purified by sorting live, lymphocyte sized cells that were negative for CD3ε, CD5, CD19, TCRβ, KLRG1, NKp46; positive for CD90.2, CCR6; and intermediate for CD45. RNA was eracted with RNeasy Plus Micro kit from Qiagen following manufacturer's instructions.


title: a-CD3-CD28 Treg


title: Control Treg_B

source_name: Control Treg cells


title: OX40L-JAG1 Teff_B


title: Control Teff_B


title: Control Treg


title: OX40L-JAG1 Treg


title: WT_C2

description: gene expression from WT CCR6+ ILC3


title: KO_C1

description: gene expression from REV-ERBa KO CCR6+ ILC3


title: a-CD3-CD28 Teff


title: KO_C2


title: gdT HFD2

description:
75bp single-end sequencing
fpkm_sorted gdT.xls
H3


title: lung Tcrd KD 1

description:
75bp single-end sequencing
fpkm_lung.xls
G


title: lung KD 1

description:
75bp single-end sequencing
fpkm_lung.xls
D


title: lung KD 3

description:
75bp single-end sequencing
fpkm_lung.xls
F


title: lung Chow 2

description:
75bp single-end sequencing
fpkm_lung.xls
B


title: lung Chow 3

description:
75bp single-end sequencing
fpkm_lung.xls
C


title: lung KD 2

description:
75bp single-end sequencing
fpkm_lung.xls
E


title: cldn15la-GFP(+) f-Dex(+) LREs 3

city: Durham

first: Michel

last: Bagnat

state: NC

address: 333B Nanaline Duke Bldg. Box 3709 Duke University Medical Center

institute: Duke University

data_processing:
HiSeq Control Software used for basecalling
Sequenced reads were trimmed for adapter sequences and low-quality reads using FASTQ Groomer and FASTQ Quality Trimmer, followed by alignment to the GRCz10 reference genome using HISAT2.
The number of reads counted for each gene was calculated using HTSeq.
Genome_build: GRCz10
Supplementary_files_format_and_content: .tabular files containing HT-seq counts for each gene in each sample.

organism: Danio rerio

source_name: cldn15la-GFP(+) f-Dex(+) LREs

extract_protocol:
At 6 dpf (24 hrs post gavage), zebrafish larvae were dissociated using Trypsin/EDTA and collagenase. Then two different intestinal populations were collected using fluorescence-activated cell sorting (FACS). Total RNA was prepared from each population using RNeasy Micro Plus Kit (Qiagen). Quality control was evaluated by Qubit and 2100 Bioanalyzer.
Clonetech ultra low input RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Zebrafish larvae were gavaged with 1-2 nl of 2.5 mg/ml Alexa Fluor 568 Dextran at 5 dpf.

value: EK

value: 6 days post fertilizaton

value: Intestine

value: cldn15la-GFP, Alexa Fluor 568 double-positive lysosome rich enterocytes (LREs)


title: 11.1 mM glucose mIAPP replicate 8 [RNA-9-4]

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq 1.8.4 pipeline.
Low-quality bases (Q score < 10) were removed from the 3 end with Skewer 0.2.2 (Jiang et al., 2014)
Mouse genome cDNA sequences were retrieved from Ensembl version 96 (Cunningham et al., 2019). Reads were mapped to transcripts using Kallisto v0.45.0 (Bray et al., 2016). Transcript counts were aggregated to gene-level counts with the sum function in R. Genes with an average of fewer than 10 reads per sample were omitted from downstream analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq gene level count matrix

source_name: 11.1 mM glucose mIAPP_ex vivo cultured mouse islets

growth_protocol: Islet isolation and culture Transgenic mice expressing wild-type hIAPP that replaced the endogenous mouse IAPP locus were produced by homologous recombination (Hiddinga et al., 2012). These mice, along with their wild-type mIAPP littermates, were bred on a C57BL/6NHsd background (Harlan, Indianapolis, IN, USA) and maintained at the VA Puget Sound Health Care System (VAPSHCS). Islets were isolated from pancreata of a 10-week-old male and female mice by collagenase digestion, purified by gradient separation and handpicked prior to being recovered overnight in RPMI 1640 medium containing 11.1 mmol/l glucose, 10% fetal bovine serum, 1% sodium pyruvate and 1% penicillin/streptomycin. Thereafter, islets were cultured for 48 h in the same RPMI media containing either 11.1 or 16.7 mmol/l glucose (Zraika et al., 2007). The VAPSHCS Institutional Animal Care and Use Committee approved the studies

extract_protocol:
Islets were disrupted by homogenization in PBS and resuspended in 1 ml of TRIzol solution. RNA was extracted using the Directzol RNA mini-prep kit according to the manufacturer’s protocol, with DNase I treatment in the column to remove genomic DNA contamination (Zymo Research, Irvine, CA, USA). RNA was eluted in 30 μl TE buffer, and the quantity and quality of RNA examined on a MultiNA bioanalyzer (Shimadzu, Tokyo, Japan).
A NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA) was used to enrich mRNA from 1 μg of total RNA. The NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® was then used to generate barcoded libraries according to the manufacturer’s protocol, and these libraries were then quantified on the MultiNA bioanalyzer and pooled to equimolar ratios for sequencing.

treatment_protocol: The study design encompassed four different sample groups. Two groups comprised hIAPP islets, cultured either at 11.1 or 16.7 mmol/l glucose, and two groups comprised mIAPP islets cultured under the same two glucose conditions. Eight separate sets of experiments were performed, each comprising the four different sample groups. At the end of each experiment, islets were handpicked, 50 were set aside for histology and the remainder prepared for RNA-seq by washing twice in phosphate-buffered saline (PBS), and resuspending in 100 μl of PBS for storage at −80◦C prior to further processing.

tag: iapp genotype

value: mIAPP

tag: glc conc. in media

tag: tissue/cell type

value: Ex vivo cultured mouse islets


title: 11.1 mM glucose hIAPP replicate 6 [RNA-17-2]

source_name: 11.1 mM glucose hIAPP_ex vivo cultured mouse islets

value: hIAPP


title: 16.7 mM glucose mIAPP replicate 6 [RNA-17-3]

source_name: 16.7 mM glucose mIAPP_ex vivo cultured mouse islets


title: 11.1 mM glucose mIAPP replicate 6 [RNA-17-4]


title: 11.1 mM glucose mIAPP replicate 7 [RNA-18-4]


title: 11.1 mM glucose hIAPP replicate 8 [RNA-9-2]


title: 16.7 mM glucose mIAPP replicate 8 [RNA-9-3]


title: 16.7 mM glucose hIAPP replicate 6 [RNA-17-1]

source_name: 16.7 mM glucose hIAPP_ex vivo cultured mouse islets


title: 16.7 mM glucose hIAPP replicate 7 [RNA-18-1]


title: 11.1 mM glucose hIAPP replicate 7 [RNA-18-2]


title: cldn15la-GFP(+) f-Dex(+) LREs 1

value: wild type

tag: tissue


title: cldn15la-GFP(+) IECs 3

source_name: cldn15la-GFP(+) IECs

value: cldn15la-GFP positive intestinal epithelial cells (IECs)


title: 16.7 mM glucose hIAPP replicate 5 [RNA-16-1]


title: 11.1 mM glucose hIAPP replicate 5 [RNA-16-2]


title: cldn15la-GFP(+) IECs 2


title: 16.7 mM glucose mIAPP replicate 5 [RNA-16-3]


title: cldn15la-GFP(+) f-Dex(+) LREs 2


title: 11.1 mM glucose mIAPP replicate 4 [RNA-15-4]


title: 16.7 mM glucose hIAPP replicate 8 [RNA-9-1]


title: lung Chow 1

description:
75bp single-end sequencing
fpkm_lung.xls
A


title: 16.7 mM glucose mIAPP replicate 7 [RNA-18-3]


title: cldn15la-GFP(+) IECs 1


title: 16.7 mM glucose mIAPP replicate 4 [RNA-15-3]


title: 11.1 mM glucose mIAPP replicate 5 [RNA-16-4]


title: BioGRO_Xrn1

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

hyb_protocol: For BioGRO samples, we followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880), starting from Chapter 5: Hybridization, using the GeneChip® Hybridization, Wash and Stain Kit. For ChIP samples, we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

scan_protocol: For BioGRO samples, we followed the instructions of the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (part # 701880), scanning the array as described in Chapter 7: Scanning. For ChIP samples, we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238), scanning the arrays as described in Chapter 5: Scan.

data_processing:
Raw .CEL images were processed with Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default. BioGRO samples where normalized against a reference genomic DNA hybridized on the same Affymetrix tiling arrays (ArrayExpress E-TABM-590). The ChIP (IP) sample was normalized against its respective Input sample (Input).
The resulting files were obtained with Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default. BioGRO samples where normalized against a reference genomic DNA hybridized on the same Affymetrix tiling arrays (ArrayExpress E-TABM-590). The ChIP (IP) sample was normalized against its respective Input sample (Input).

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Yeast cells grown in YPD to exponential phase.

label_protocol: For BioGRO samples, labeling of nascent RNAs was achieved by incorporating Bio-11-UTP (Ambion) to the nascent chains in vivo by run-on. For ChIP samples, we followed Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

growth_protocol: All yeast strains where grown in standard conditions (YPD medium, 30 ºC). For each sample we used an aliquot of 100 mL cells grown to mid exponetial phase (DO600 = 0.55).

extract_protocol: For BioGRO samples, RNA extraction was done using the “MasterPure Yeast RNA Purification Kit” (Epicentre), following manufacturer’s instructions. Once extracted, genomic DNA was removed digesting with 2 µL of RNase-free DNase I (Roche) for 30 min at 37 °C. The purified RNA was resuspended in 32 µL of water and spectrophotometrically quantified. For ChIP samples, we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

treatment_protocol: For BioGRO samples, cells were collected by centrifugation and frozen in liquid nitrogen. Frozen pellets were transferred immediately to -20 °C. After at least 3 h, cells were thawed on ice and permeabilized with 10 mL of a 0.5% sarkosyl solution. Once permeabilized, cells were treated with RNase A (Roche). RNase trimming was achieved by incubating the cells with 32 µL of RNase A (10 mg/mL) dissolved in 3.2 mL of Sarkosyl 0.5% in agitation for 10 min at 30 °C. In order to remove the RNase, cells were washed three times with 50 mL 0.5% sarkosyl, and then transferred to an eppendorf tube. Cells were resuspended in 115 µL of water plus 5 µL of RNase OUT (Invitrogen) to protect the integrity of nascent RNAs from any residual RNase that might be present. Run-on reactions where performed as described (Jordán-Pla et al., 2014). For ChIP samples we followed the Affymetrix® Chromatin Immunoprecipitation Assay Protocol (PN 702238).

value: xrn1 delta strain - yMC458 (BY4741 derived)


title: 11.1 mM glucose hIAPP replicate 4 [RNA-15-2]


title: 16.7 mM glucose hIAPP replicate 4 [RNA-15-1]


title: 11.1 mM glucose hIAPP replicate 3 [RNA-14-2]


title: 11.1 mM glucose mIAPP replicate 3 [RNA-14-4]


title: 16.7 mM glucose mIAPP replicate 3 [RNA-14-3]


title: WT E16.5 ATAC rep1

city: Shinjuku-ku

first: Haruhiko

last: Siomi

state: Tokyo

address: Shinanomachi 35

department: Department of Molecular Biology

country: Japan

institute: Keio University, School of Medicine

data_processing:
Basecalled performed using Illumina RTA software in sequencer
trim down the base to first 50 bp from 150 bp using seqkit
Reads were alignedto the mm10 genome assembly using bowtie2 with the following settings -N 1 -X 2000 --no-mixed --no-discordant.
only unique reads were extracted
dupicate reads were removed with picard tool
Genome_build: mm10
Supplementary_files_format_and_content: wig

source_name: WT E16.5 ATAC

extract_protocol: Library construction was carried out following the original protocol (Buenrostro et al., 2013, Nature Methods) [PMID:24097267].

value: gonocyte


title: 11.1 mM glucose mIAPP replicate 1 [RNA-10-4]


title: 11.1 mM glucose mIAPP replicate 2 [RNA-13-4]


title: 16.7 mM glucose hIAPP replicate 2 [RNA-13-1]


title: WT E19.5 Hi-C rep2

data_processing:
Basecalled performed using Illumina RTA software in sequencer
Reads were processed using Trimmomatic 0.36 with parameters ‘ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25’
Reads were alignedto the mm10 genome assembly BWA mem 0.7.15 with gap extension penalty and clipping at  5’ and 3’ ends ‘-A 1 -B 4 -E 50 -L 0 -T 25 -t 10’
The unique paired-end reads were used as input to HiCExplorer 1.7.2 (Ramirez et al., 2018) to create Hi-C interaction matrices
interaction maps of 1 Mb resolution by merging 1000 bins of 10 kb resolution was created and then plotted the heatmap using the mode hicPlotMatrix with the parameters ‘--log1p --vMin 1 --vMax 200 --clearMaskedBins’.
Genome_build: mm10
Supplementary_files_format_and_content: matrix file (.h5)

source_name: WT E19.5 Hi-C

extract_protocol:
Hi-C experiments was performed following the published protocol (Rao et al., 2014, Cell) [PMID:25497547]
Libraries were prepared according to NIPPON genetics's instructions accompanying the KAPA Hyper Prep Kit (Part# KK8500). In the adaptor ligation step, the original adaptor reagent was diluted to 200 times. After adapter ligation DNA was PCR amplified with Illumina primers for 16~19 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified with AMPure XP beads(Beckman Coulter). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.


title: mili-/- E17.5 ATAC

source_name: mili-/- E17.5 ATAC


title: WT E16.5 ATAC rep2


title: 16.7 mM glucose mIAPP replicate 2 [RNA-13-3]


title: WT E19.5 Hi-C rep1


title: WT P2 Hi-C rep2

source_name: WT P2 Hi-C


title: WT P2 Hi-C rep1


title: 11.1 mM glucose hIAPP replicate 2 [RNA-13-2]


title: 16.7 mM glucose mIAPP replicate 1 [RNA-10-3]


title: WT E17.5 Hi-C rep1

source_name: WT E17.5 Hi-C


title: BLS type vs. conventional DLBCL

city: Tainan

first: Kung-Chao

last: Chang

address: 138 Sheng-Li Road

department: Department of Pathology

country: Taiwan

institute: National Cheng Kung University Hospital

description: Comparison between BLS vs conventional DLBCL

hyb_protocol: Equal amounts (0.3 µg) of cyanine-labeled samples were hybridized to Agilent 8x60K Microarray chip (Agilent Technologies) according to the manufacturer.

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner, and the scan was quantified using Agilent Feature Extraction software (version 10.5.1.1) and normalized using Rank consistency linear LOWESS with minimum background correction.

data_processing: Agilent Feature Extraction Software (v 108.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: BLS type DLBCL

label_protocol: After RNA isolation, two aliquots of 0.2 µg of RNA were linearly amplified and fluorescently labeled with either Cy3-CTP (DLBCL in effusion) or Cy5-CTP (DLBCL in bone marrow) with the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Lymphoma cells were frozen and thawed before sorted.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: sample type

value: Pooled lymphoma cells of 3 cases from bone marrow

source_name: Conventional DLBCL

value: Pooled lymphoma cells of 2 cases from pleural effusions


title: WT E13.5 Hi-C rep2

source_name: WT E13.5 Hi-C


title: WT E13.5 Hi-C rep1


title: 16.7 mM glucose hIAPP replicate 1 [RNA-10-1]


title: WT P2 nanoCAGE-seq rep3

data_processing:
Basecalled performed using Illumina RTA software in sequencer
Reads were processed in the CAGEscan pipeline (https://gitlab.com/mcfrith/cagescan-pipeline) as described in the following columns.
nanoCAGE tags in the sequenced reads and UMIs were extracted with TagDust2 (ver. 2.31)
Extracted tags originated from the same molecules were assembled into contigs based on UMIs, and aligned to the mm10 genome assembly using LAST
Genome_build: mm10
Supplementary_files_format_and_content: txt

source_name: WT P2 nanoCAGE-seq

extract_protocol:
nanoCAGE-seq experiments was performed following the published protocol (Paulain et al., 2017, Methods Mol. Biol.) [PMID:28349422]
The nanoCAGE libraries were prepared as described previously [PMID:28349422]. Briefly, 70ng of RNA for each sample were used for the first-strand cDNA synthesis with template-switching oligonucleotides and reverse transcription random primers. Purified cDNAs were amplified by PCR. Linkers and unique molecular identifiers (UMIs) were introduced using Nextera library prep kits.


title: 11.1 mM glucose hIAPP replicate 1 [RNA-10-2]


title: 16.7 mM glucose hIAPP replicate 3 [RNA-14-1]


title: miwi2-/- E17.5 ATAC

source_name: miwi2-/- E17.5 ATAC


title: WT P2 nanoCAGE-seq rep2


title: WT E17.5 Hi-C rep2


title: WT P2 nanoCAGE-seq rep1


title: WT E19.5 nanoCAGE-seq rep3

source_name: WT E19.5 nanoCAGE-seq


title: WT E19.5 nanoCAGE-seq rep2


title: WT E17.5 nanoCAGE-seq rep3

source_name: WT E17.5 nanoCAGE-seq


title: Pooled_Input

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
Raw reads were aligned to the mouse reference (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
ChIP-seq peaks were called for each dataset with matched input using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files are in XLS format

source_name: Skin

extract_protocol:
Snap frozen skin samples from WT and Irf6-/- E16.5 mouse embryos (200 mg, n = 2 of each genotype) were sent to Active Motif for ChIP-Seq.  ChIP was performed with validated antibodies against H3K27me3 (Active Motif 39155), H3K27Ac (Active Motif 39133) or H3K4me3 (Active Motif 39159).  Illumina sequencing libraries were prepared from the ChIP and input DNA using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation using Active Motif’s custom liquid handling robotics pipeline. After the final 15 cycle PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

value: control

value: Skin

tag: background

value: E16.5 days


title: Irf6-KO2_H3K4me3

value: lrf6 knockout

value: Histone H3K4me3 antibody (Active Motif 39159)


title: Irf6-KO2_H3K27me3

value: Histone H3K27me3 antibody(Active Motif 39155)


title: WT E17.5 nanoCAGE-seq rep2

tag: strain


title: WT E17.5 nanoCAGE-seq rep1


title: RNAseq-KSPcre Tfamf/f-12W-2

city: Philadelphia

last: Sheng

institute: University of Pennsylvania

data_processing:
Sequencing reads were firstly assessed sequence quality using FastQC and then trimmed the adaptor and lower quality bases using Trim-galore. RNA-seq reads were aligned to mouse genome using STAR (v2.4.1d) based on GENCODE vM18 annotations. Gene-level expression was estimated on uniquely mapped reads as transcripts per million (TPM) by HTSeq (0.11.0)  by setting '--stranded=reverse'.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include raw reads counts for each Sample.

source_name: Whole kidney

extract_protocol:
Total RNA from whole kidneys were isolated using the RNeasy mini kit (Qiagen).
Only samples with RIN scores above 7 and a minimum total RNA of 100 ng were used for cDNA production. 2*150-bp Strand-specific, poly A+ - selected RNA-seq libraries were generated using the Illumina HiSeq protocol. Bulk strand-specific total-transcriptome RNA-seq libraries were prepared using dUTP during second-strand synthesis with Qiagen Rneasy Kit.

value: kidney

value: post natal day 84

value: KspCre Tfam f/f


title: RNAseq-Tfamf/f-12W-1

value: Tfam f/f


title: RNAseq-Tfamf/f-12W-3


title: Irf6-KO2_H3K27Ac

value: Histone H3K27ac antibody (Active Motif 39133)


title: WT E13.5 nanoCAGE-seq rep3

source_name: WT E13.5 nanoCAGE-seq


title: RNAseq-KSPcre Tfamf/f-12W-1


title: WT E13.5 nanoCAGE-seq rep2


title: Irf6-KO1_H3K4me3


title: Irf6-KO1_H3K27me3


title: RNAseq-KSPcre Tfamf/f-12W-3


title: Irf6-KO1_H3K27Ac


title: WT2_H3K4me3

value: wild type


title: WT P2 H3K27me3 rep1

data_processing:
Basecalled performed using Illumina RTA software in sequencer
adaptor was trimmed with cutadapt tool with the following setting -m 20.
Reads were alignedto the mm10 genome assembly using bowtie with the following setting -m 1.
dupicate reads were removed with picard tool
Genome_build: mm10
Supplementary_files_format_and_content: wig

source_name: WT P2 H3K27me3

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with corresponding anti-body
Libraries were prepared according to QIAGEN's instructions accompanying the QIAseq Ultralow Input Library Kit (Part# 180492). In the adaptor ligation step, the original adaptor reagent was diluted to 100 times. After adapter ligation DNA was PCR amplified with Illumina primers for 13~16 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified with AMPure XP beads(Beckman Coulter). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

value: Merck Millipore (07-449)


title: WT E19.5 H3K27me3 rep2


title: WT2_H3K27me3


title: WT E19.5 H3K27me3 rep1


title: WT E19.5 nanoCAGE-seq rep1


title: RNAseq-Tfamf/f-12W-2


title: WT2_H3K27Ac


title: WT E13.5 H3K27me3 rep1


title: WT1_H3K27Ac


title: WT E17.5 H3K27me3 rep1


title: WT1_H3K27me3


title: WT E19.5 H3K9me3 rep2

source_name: WT E19.5 H3K9me3

value: Active Motif (#39161)


title: WT E13.5 nanoCAGE-seq rep1

value: gonocyte


title: WT P2 H3K9me3 rep1

source_name: WT P2 H3K9me3


title: WT E19.5 H3K9me3 rep1


title: WT E13.5 H3K27me3 rep2


title: WT P2 H3K27me3 rep2


title: PFC P21 scRNA-Seq Sample2

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
Raw sequencing data were processed with cellranger (v.13.1) (Zheng et al., 2017) for sample demultiplexing, cell barcode detection and single-cell expression matrices generation. In brief, the “cellranger  mkfastq” command was used to demultiplex the different samples, extract the UMI barcodes and generate the fastq files. The gene-cell expression matrices were then generated for each sample separately using the “cellranger count” command by aligning the reads to the mm9 genome. In total 15 single-cell gene expression matrices were generated, corresponding to the 6 saline biological replicates (2 in each phase), 6 cocaine biological replicates (2 in each phase) and 3 P21 biological replicates.
the R package Seurat (v2.1.0) 2 was used for data analyses. We merged all the expression matrices of the 12 adult mice samples into a global Seurat object using the “MergeSeurat” function. The gene expression profile of each single cell was then normalized to counts per-million (cpm) and natural log transformed. As an initial quality control, we removed cells that: 1) have a potential mitochondria contamination (>10% of their total transcripts from mitochondrial transcriptome) and cells that most likely represent double-droplets (cells expressing more than the 99th percentile of the number of genes, 4,766 genes ). Previous studies showed that neuronal cells tend to have a higher number of mRNAs (UMI) and genes than non-neuronal cells which was also confirmed in our dataset (Fig. S1B). Hence, we decided to use different filtering criteria for neuronal and non-neuronal cells. Thus, we did an initial clustering analysis in which we grouped cells into broad neuronal and non-neuronal clusters. Then, by exploring the number of expressed gene distribution (Fig. S1B) we decided to select non-neuronal cells expressing ≥800 genes and neuronal cells expressing ≥ 1,500 genes. We also removed all the mitochondria genes and ribosomal genes.
The P21 samples were merged together using the “MergeSeurat” function and filtered using the same criteria as in the adult mice.
expression_matrix.csv was generated then by combining count expression matrices of the adult and P21 filtered cell.
Genome_build: mm9
Supplementary_files_format_and_content:  barcodes.tsv, genes.tsv, matrix.mtx; expression_matrix.csv

source_name: Prefrontal cortex (PFC)

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
For single cell dissociation of Prefrontal cortex (PFC), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing PFC were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the PFC tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation (Figure S1A). The NAc tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion.
The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp).

value: NAc

value: mixed sample (non-demultiplexed)

tag: Sex

value: male

value: 3 weeks


title: PFC P21 scRNA-Seq Sample3

tag: age


title: WT P2 H3K9me3 rep2


title: PFC Adult scRNA-Seq Sample12

value: 8-10 weeks

tag: treatment

value: Saline


title: PFC Adult scRNA-Seq Sample11


title: WT E17.5 H3K9me3 rep2

source_name: WT E17.5 H3K9me3


title: PFC P21 scRNA-Seq Sample1


title: PFC Adult scRNA-Seq Sample9

value: Cocaine


title: PFC Adult scRNA-Seq Sample10


title: WT E17.5 H3K9me3 rep1


title: PFC Adult scRNA-Seq Sample8


title: WT E17.5 H3K27me3 rep2


title: WT E13.5 H3K9me3 rep1

source_name: WT E13.5 H3K9me3


title: WT P2 ATAC rep2

source_name: WT P2 ATAC


title: WT E13.5 H3K9me3 rep2


title: WT1_H3K4me3

value: Skin

value: E16.5 days

value: Histone H3K4me3 antibody (Active Motif 39159)


title: PFC Adult scRNA-Seq Sample7


title: PFC Adult scRNA-Seq Sample6


title: WT P2 ATAC rep1


title: PFC Adult scRNA-Seq Sample5


title: WT E19.5 ATAC rep1

source_name: WT E19.5 ATAC


title: WT E13.5 ATAC rep2

source_name: WT E13.5 ATAC


title: WT E17.5 ATAC rep1

source_name: WT E17.5 ATAC


title: WT E17.5 ATAC rep2


title: SAM24357828 Skin WT

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from kinase dead skin from E16.5

extract_protocol: Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen) and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.

tag: genotype/variation

value: WT


title: PFC Adult scRNA-Seq Sample1

value: Maintenance


title: Vector-overexpressed in Rig-I-/- cells with poyI:C stimulation

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools software were used to map to reference genome.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped(FPKM).
Genome_build: GRCh38_release95
Supplementary_files_format_and_content: files include RPKM values for each Sample

extract_protocol:
The RNA  was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell line

value: epithelial

value: Vector-overexpressed in Rig-I-/- cells

value: poyI:C stimulation


title: PFC Adult scRNA-Seq Sample2


title: 1C_Control

data_processing:
cDNA libraries were generated using the IlluminaTruSeq Small RNA Sample Preparation Kit, according to the manufacture´s protocol (Illumina Inc.)
Purified cDNA libraries were sequenced on an Illumina Hi Seq 2500 following the manufacturer’s instructions
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis, which performs adaptor removal, mapping and alignment of the RNA sequencing reads
Raw reads produced by sequencing were first processed through a data cleaning pipeline to remove low quality reads, contaminating sequences with no 3’ adapter (3ADT), and reads shorter than 15 nt and longer than 32 nt. The clean reads were further filtered to remove reads with less than five counts in each library and were subsequently mapped to reference databases to perform in-depth data analysis
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures were predicted from the flanking 120 nt sequences using the RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi) to detect potential new candidates.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed using a Student’s t test. The significance threshold was set to 0.01 and 0.05 in each test. The sequence reads of the six libraries were normalized to 1 million by the total number of clean small RNA reads in each sample. The log2 ratio formula was as follows: log2 ratio = log2 (miRNA reads in KPhi treated/miRNA reads in control)
Genome_build: miRNA(miRs) database: ftp://mirbase.org/pub/mirbase/CURRENT/; Specific species: stu; Selected species: sly,nta v21.0: Solanum tuberosum (SolTub3.0) GCA_000226075.1; Solanum lycopersicum (SL2.50) GCA_000188115.2  Pre-miRNA(mirs) database: ftp://mirbase.org/pub/mirbase/CURRENT/; Specific species: stu; Selected species: sly,nta v21.0  Genome and mRNA database: https://phytozome.jgi.doe.gov/pz/ portal.html; v4.03
fastq format files were generated as follows: The first file line indicates the sequenced sequence (sequ seq) identification (e.g. 5_18368) composed of the index and the copy number of the sequ seq; the second line presents the sequence; the forth line shows the sequencing quality of the corresponding bases using the average Phred score.  Filtered sequ seqs with lengths between 15 and 32 bases, were grouped by families (unique seqs), and stored in the file [Sample]_mappableReads.fq, and were used to map with the reference database files.
Supplementary_files_format_and_content: Differential expression of miRNAs based on normalized deep-sequencing counts

extract_protocol:
Total RNAs from each treatment were isolated from  0.1 g of fresh leaf tissue using the RNeasy Plant Mini kit (Qiagen), following the manufacturer’s protocol
Libraries were prepared for sequencing using standard Illumina protocols

value: Shepody

value: 24 days post emergency

value: water control

value: Leaves


title: SAM24357831 Skin Irf6_KO


title: SAM24357832 Skin Irf6_KO


title: PFC Adult scRNA-Seq Sample3

value: NAc

value: mixed sample (non-demultiplexed)

value: male


title: SAM24357829 Skin WT


title: SAM24357830 Skin Irf6_KO


title: SAM24325576 Hyperplasia Epidermal Ripk4KD

source_name: RNA from kinase dead skin from E15.5

value: Hyperplasia Epidermal


title: SAM24325569 Hyperplasia Epidermal Irf6KO


title: WT E19.5 ATAC rep2

value: gonocyte


title: E2_r7_3

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0194

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: nanus_anchored_Vs2
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

organism: Acrobeloides nanus

source_name: embryo

extract_protocol:
Egg shells were removed from a A. nanus embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.

tag: developmental stage

value: stage E2

value: embryonic cell


title: E2_r6_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0193

tag: cell type


title: PFC Adult scRNA-Seq Sample4

value: 8-10 weeks

value: Cocaine


title: E2_r5_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0192


title: WT E13.5 ATAC rep1


title: E2_r4_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0191


title: SAM24331835 Hyperplasia Epidermal Irf6.S413A.S424A


title: SAM24331834 Hyperplasia Epidermal Irf6.S413A.S424A


title: E2_r3_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0190


title: SAM24325577 Hyperplasia Epidermal Ripk4KD


title: SAM24331832 Hyperplasia Epidermal Irf6.S413A.S424A


title: E2_r1_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0188


title: SAM24325566 Hyperplasia Epidermal Irf6KO


title: mGLUTag 16h2

city: Toronto

first: Patricia

middle: Lee

last: Brubaker

state: ON

address: Rm 3366 MSB 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description: replicate 2

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data were normalized first using log2, then using NormalizeBetweenArrays in R

source_name: mGLUTag

label_protocol: standard Illumina protocol

growth_protocol: Reported in Gil-Lozano et al. Diabetes 2014;63:3674-3685 | DOI: 10.2337/db13-1501

extract_protocol: none provided by the submitter

tag: time


title: 5_c_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0187

value: 5 cell


title: mGLUTag 4h1

description: replicate 1


title: mGLUTag 4h3

description: replicate 3


title: E2_r2_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0189


title: mGLUTag 4h2

description: replicate 2


title: mGLUTag 16h1

description: replicate 1


title: SAM24325578 Hyperplasia Epidermal Ripk4KD


title: 5_p4_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0186


title: SAM24325570 Hyperplasia Epidermal Irf6KO


title: SAM24357827 Skin WT

value: Skin

value: WT


title: SAM24325575 Hyperplasia Epidermal Ripk4KD


title: 4_AB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0185

value: 4 cell


title: SAM24331831 Normal WT

value: Normal


title: SAM24325574 Hyperplasia Epidermal Ripk4KD


title: SAM24331836 Hyperplasia Epidermal Irf6.S413A.S424A


title: mGLUTag 16h3

description: replicate 3


title: SAM24325572 Normal WT


title: 15_15

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0180

value: 15 cell


title: 4_p4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0181


title: 4_c_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0182


title: SAM24325565 Normal WT


title: 15_14

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0179


title: SAM24325564 Normal WT


title: SAM24331833 Hyperplasia Epidermal Irf6.S413A.S424A


title: 15_12

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0177


title: 15_13

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0178


title: SAM24331829 Normal WT


title: SAM24325567 Hyperplasia Epidermal Irf6KO


title: SAM24325573 Normal WT


title: SAM24331830 Normal WT


title: 15_10

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0175


title: 15_9

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0174


title: SAM24325571 Normal WT


title: 4_p4_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0183


title: SAM24325563 Normal WT


title: 15_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0171


title: 15_8

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0173


title: Dam_organoids_R1

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Dam seq from FACS sorted after transfection
Tet1DamID_broadpeak_FDR2.bed and Tet1DamID_broadpeak_FDR2.bed and TET1Dam_peaks.xlsx

data_processing:
Library strategy: DamID-seq
DamID sequencing data from the replicates were mapped to GRCM38/mm10 and processed using the damidseq_pipeline script (Marshall et al., Bionformatics, 2015). Details are available in Methods. Bed files are provided.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPMs (tsv), peaks (bed), coverage (bedgraph), peaks (xlsx), calls (bed)

source_name: FACS sorted after transfection of liver organoids

growth_protocol: see Material and Methods

extract_protocol:
DNA extraction (see methods)
DamID-sequencing

value: Adult healthy liver

tag: gender

value: Male


title: 15_7

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0172


title: Dam_organoids_R2


title: Dam_organoids_R3


title: 15_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0170


title: 15_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0169


title: TET1-Dam_organoids_R3


title: TET1-Dam_organoids_R2


title: TET1-Dam_organoids_R1


title: 15_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0168


title: 15_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0167


title: H3K4me3 ChIP-seq

description:
H3K4me3 ChIP-seq in cells tissue culture
H3K4me3_broadpeak_FDR2.bed and H3K4me3_peaks.xlsx

data_processing:
ChIP-seq reads were mapped to GRCM38 with bowtie2 (v2.2.9). Peak-calling was done using MACS2 (v2.1.0). Details available in Methods. Bed files are provided.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPMs (tsv), peaks (bed), coverage (bedgraph), peaks (xlsx), calls (bed)

extract_protocol:
chromatin extraction (see methods)
ThruPLEX DNA-seq kit (Rubicon Genomics)

value: Female


title: 13_d_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0165

value: 13 cell


title: 15_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0166


title: Input signals liver organoids (ChIP)

description:
Input for ChIP in cells in tissue culture
H3K4me3_broadpeak_FDR2.bed and H3K4me3_peaks.xlsx

source_name: liver organoids


title: 15_11

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0176


title: 13_c_1_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0163


title: 13_c_2_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0164


title: Epcam+_day3_DDC_RNA_R2

description:
RNA profile from cells in DDC damaged tissue
TPM_RNAseq_vivo.txt.gz

data_processing:
RNA-seq reads were mapped and quantified (TPM) and mapped to GRCm38.  Details are available in the Methods. TPM are provided.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPMs (tsv), peaks (bed), coverage (bedgraph), peaks (xlsx), calls (bed)

source_name: FACS sorted cells from adult liver

extract_protocol:
Total RNA extracted using Arcturus Pico Pure (Applied Biosystems) according to manufacture's instructions
SmartSeq2 followed by NexteraXT tagmentation (according to protocols published in PMID 24385147)

value: Adult DDC damaged liver


title: 13_E_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0161


title: Epcam+_day5_DDC_RNA_R1


title: 13_AB4_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0162


title: Comma_posterior_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0159

value: gastrula


title: Epcam+_day3_DDC_RNA_R1


title: 13_P4_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0160


title: Epcam+_undamaged_RNA_R1

description:
RNA profile from cells in undamaged tissue
TPM_RNAseq_vivo.txt.gz


title: organoids_RNA_R3

description:
RNA profile from cells cultured in matrigel in organoid medium for 6 days
TPM_RNAseq_vitro.txt.gz


title: Comma_posterior_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0158


title: Comma_posterior_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0157


title: organoids_RNA_R2

description:
RNA profile fromcells cultured in matrigel in organoid medium for 6 days
TPM_RNAseq_vitro.txt.gz


title: E _13_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0156


title: organoids_RNA_R1

extract_protocol:
Total RNA extracted using RNAeasy micro kit (Qiagen) according to manufacture's instructions
SmartSeq2 followed by NexteraXT tagmentation (according to protocols published in PMID 24385147)


title: E _12_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0155


title: E _11_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0154


title: EpCAM+_24h_RNA_R3

description:
RNA profile from cells cultured in matrigel in organoid medium for 24h
TPM_RNAseq_vitro.txt.gz


title: EpCAM+_48h_RNA_R2

description:
RNA profile from cells cultured in matrigel in organoid medium for 48hrs
TPM_RNAseq_vitro.txt.gz


title: Epcam+_day5_DDC_RNA_R2


title: Comma_anterior_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0151


title: Comma_anterior_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0152


title: E _10_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0150


title: Epcam+_undamaged_RNA_R2


title: EpCAM+_24h_RNA_R1


title: E _8_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0148


title: EpCAM+_24h_RNA_R2

extract_protocol:
Total RNA extracted using Arcturus Pico Pure (Applied Biosystems) according to manifacture's instructions
SmartSeq2 followed by NexteraXT tagmentation (according to protocols published in PMID 24385147)


title: E _9_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0149


title: Comma_middle_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0147


title: EpCAM+_12h_RNA_R2

description:
RNA profile from cells cultured in matrigel in organoid medium for 12h
TPM_RNAseq_vitro.txt.gz


title: Comma_middle_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0145


title: EpCAM+_12h_RNA_R1


title: Comma_middle_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0146


title: EpCAM+_48h_RNA_R3


title: E _7_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0144


title: EpCAM+_48h_RNA_R1


title: Comma_anterior_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0153


title: EpCAM+ 0h_RNA_R1

description:
RNA profile from cells cultured in matrigel in organoid medium for 10 min
TPM_RNAseq_vitro.txt.gz


title: EpCAM+ 0h_RNA_R2


title: E _6_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0143


title: E _5_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0142


title: Mst1Gal3 rep5

description: rRNA depleted RNA

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.19.1.403 pipeline was used to generate the sequence data.
FastX Toolkit was used to trim low quality bases from the 5’ end of reads using a minimum phred threshold of 20 and minimum length of 18 using (Hannon 2009).
Reads were mapped with STAR (Dobin et al, 2013) to the mouse genome downloaded from Ensembl (GRCm38).
FeatureCounts (Liao et al, 2014) was used to count reads mapped to gene exons on the correct strand with a minimum mapping quality of 20 using Ensembl genome annotation (Mus musculus.GRCm38.85.gtf).
Genes with fewer than 10 reads per sample on average were excluded from downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-wise raw read counts of gene expression

source_name: Mst1Gal3, left ventricle

growth_protocol: Standard mouse housing conditions

extract_protocol:
Left ventricle RNA was isolated from Trizol homogenates using the Direct-zol™ RNA MiniPrep Kit (Zymo Research).
RNA quality was assessed by Multi-NA bioanalyzer (Shimadzu Japan). 200 ng of total RNA underwent ribosomal RNA depletion using the NEBNext® rRNA Depletion Kit followed by library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

tag: background strain

tag: genotype

value: Mst-1 overexpressing and Gal-3 knock out

value: Left ventricle


title: EpCAM+ 0h_RNA_R3


title: VE_middle_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0139

value: embryonic cell


title: Mst1Gal3 rep3

description: rRNA depleted RNA


title: VE_middle_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0140


title: Mst1Gal3 rep4

description: rRNA depleted RNA


title: EpCAM+_12h_RNA_R3


title: EpCAM+_12h_RNA_R4


title: Mst1Gal3 rep2

description: rRNA depleted RNA


title: E _3_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0138


title: E _2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0137


title: VE_ant_pharynx_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0136


title: Gal3Ko rep8

description: rRNA depleted RNA

source_name: Gal3Ko, left ventricle

value: Gal-3 knock out


title: VE_ant_pharynx_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0135


title: Gal3Ko rep7

description: rRNA depleted RNA


title: E _1_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0134


title: Gal3Ko rep6

description: rRNA depleted RNA


title: Gal3Ko rep5

description: rRNA depleted RNA


title: 4_C_a

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0133

value: c4 cell


title: Gal3Ko rep4

description: rRNA depleted RNA


title: Gal3Ko rep3

description: rRNA depleted RNA


title: 4_P3_a

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0132


title: Gal3Ko rep2

description: rRNA depleted RNA


title: E8_ant_Pharynx_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0130

value: stage E8


title: E _4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0141


title: E8_ant_mesoderm_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0131


title: E8_ant_mesoderm_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0129


title: MstTg rep7

description: rRNA depleted RNA

source_name: MstTg, left ventricle

value: Mst-1 overexpressing


title: Gal3Ko rep1

description: rRNA depleted RNA


title: E8_post_Abp_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0128


title: MstTg rep6

description: rRNA depleted RNA


title: E8_post_E_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0125


title: MstTg rep4

description: rRNA depleted RNA


title: Mst1Gal3 rep1

description: rRNA depleted RNA


title: E8_post_Abp_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0127


title: E2 _ 6_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0124

value: stage E2


title: E8_post_E_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0126


title: E2 _ 5_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0123


title: MstTg rep3

description: rRNA depleted RNA


title: MstTg rep1

description: rRNA depleted RNA


title: MstTg rep2

description: rRNA depleted RNA


title: E2 _ 4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0122


title: E2 _ 3_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0121


title: E2 _ 2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0120


title: wt rep6

description: rRNA depleted RNA

source_name: wt, left ventricle

value: Wild type


title: wt rep5

description: rRNA depleted RNA


title: wt rep4

description: rRNA depleted RNA


title: wt rep3

description: rRNA depleted RNA


title: wt rep2

description: rRNA depleted RNA


title: E2 _1_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0119