title: Luciferase_cas9_rep3

status: Public on Mar 20 2021

city: Shanghai

first: Zaijun

last: Ma

address: Qiuyue Road 26

institute: Chinese Academy Science

data_processing:
Sequencing reads were mapped to hg8 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression. Text files include normalized read counts, foldChange, pvalue ('cas9' represents the 'A' group, 'nocas9' represents the 'B' group).

source_name: HEK293T cell

growth_protocol: HEK293T cell line was grown in Dulbecco’s modified Eagle’s Medium (DMEM, Thermo Fisher Scientific ,Waltham, USA) with 10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
HEK293T cells were washed in ice-cold 1× PBS solution, and total RNA was isolated using Trizol according to the manufacturer’s instructions (Life Technologies, MA, USA). DNA was removed using the Ambion TURBO DNA-free Kit (Life Technologies, MA, USA).  cDNA libraries were obtained using the VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina ® (Vazyme Biotech Co., Ltd., Jiangsu, China) from 1μg RNA following the manufacturer’s recommendations.
RNA libraries were prepared according to instructions of VAHTS mRNA-seq library prep kitfor illumina (Vazyme, NR601).

treatment_protocol: HEK293T cells were seeded into 6-well plates one day prior to transfection, and transfected at 70-80% confluency using Polyethylenimine (PEI, Polysciences, Inc.USA) followed by the manufacturer’s protocol. For each well of a 6-well plate, 2 μg DNA and 6 μl PEI were used.

value: Human embryonic kidney


title: Luciferase_no_cas9_rep2

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: tissue

tag: treatment


title: 256740610714_1_2

status: Public on Mar 21 2021

type: RNA

city: Fuzhou

first: Yi

last: Sun

state: Fujian Province

address: Minhou County, Fuzhou, 350122, China Minhou County, Fuzhou, 350122, China

institute: Fujian Medical University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

molecule: total RNA

source_name: Peripheral blood leukocyte, Case

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: Peripheral blood leukocyte

tag: gender

value: Female

tag: age

tag: disease state

value: patient with coronary heart disease


title: Luciferase_no_cas9_rep3


title: UMUC3-c31, Vehicle control_3

city: Los Angeles

first: Dan

last: Theodorescu

state: CA

address: 8700 Beverly Blvd., Davis Building, Rm 3057

country: USA

institute: Cedars Sinai Medical Center

description: Vehicle control

hyb_protocol: These Affymetrix samples were processed and analyzed at the University of Colorado-Anschutz Medical Campus Genomics and Microarray Core Facility.

data_processing: Expression values were normalized and summarized into probesets using robust multichip analysis (RMA) using AffymetrixPowerTools.

label: biotin

source_name: UMUC3-c31 cell line

growth_protocol: Cells were serum starved for 24 hours prior to treatment using charcoal stripped serum (CSS).  After steroid washout, cells were treated with the described compounds for 24 hours prior to total RNA isolation.

extract_protocol: Qiagen RNeasy kit

treatment_protocol: 24 hour treatment with above specified reagents.

tag: group

value: control


title: Luciferase_cas9_rep1


title: 256740610713_1_2

value: Male


title: 6T_no_cas9_rep2


title: 6T_no_cas9_rep3


title: 6T_no_cas9_rep1


title: Luciferase_cas9_rep2


title: 6T_cas9_rep1


title: Luciferase_no_cas9_rep1


title: 256740610713_1_3

source_name: Peripheral blood leukocyte, Control

value: healthy subject


title: 6T_cas9_rep2


title: UMUC3-c31, Vehicle control_1

description: Vehicle control

scan_protocol: These Affymetrix samples were processed and analyzed at the University of Colorado-Anschutz Medical Campus Genomics and Microarray Core Facility.


title: siCtrl- sample-1

city: Hyderabad

first: Bramanandam

last: Manavathi

state: Telangana

address: Dept. of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad

department: Department of Biochemistry

country: India

institute: University of Hyderabad

description: Gene expression data from siCtrl

hyb_protocol: Hybridization cocktail is prepared  including fragmented targets and probe assay comtrol . Nybridized to the probe array during 16 hours incubation period

scan_protocol: Probe array scan controlled by Affymetrix microarray suite or GCOS . Scanning can be processed using Gene chip scanner 2500

data_processing:
The analysis was performed using R/Bioconductor (v 3.12, R 4.0.2). The ReadAffy function of the affy package was used to store the expression values from CEL files. The quality control was done on the log2 transformed expression data. Background correction, quantile normalization, and the RMA (Robust Multichip Average) algorithm were performed using the rma function of the affy package.
The file normalized_data_with_all_controls.txt includes the normalized data for the ERCC controls.

source_name: BeWo Cell line

label_protocol: Invitro Transcription reaction biotin labeled cRNA from the cDNA.One cycle and two cycle labeling assay

growth_protocol: Cell lines were mainitained in DMEM/F12 complete medium containing 10% FBS and 100 µg/mL penicillin and 100 µg/mL streptomycin at 37 ºC in 5% humidified CO2.

extract_protocol: Trizol reagent was used to extract the total RNA from the cells.

treatment_protocol: Cell lines were transfected with either siCtrl and siHPIP using Lipofectamine 2000, and then grown for 48 hr using complete medium.

value: BeWo

tag: cell type

value: Choriocarcinoma

tag: knockdown

value: siCtrl


title: 256740610714_1_1


title: UMUC3-c31, 10nM R1881, 24hrs_3

description: 10nM R1881

label_protocol: These Affymetrix samples were processed and analyzed at the University of Colorado-Anschutz Medical Campus Genomics and Microarray Core Facility.

value: 1881 treated


title: 256740610715_1_2


title: Loucy_ATAC_rep1

city: Beijing

first: Hong

last: Wu

address: Yiheyuan Road 5#

institute: Peking University

description:
ATAC-seq of human: cellline Loucy
Loucy_ATAC_merge.bw

library_source: genomic

data_processing:
RNA-seq reads were aligned to the hg19 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ATAC-seq reads were mapped with Bowtie2 using parameter -X 2000 --no-mixed --no-discordant --no-unal. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 5 kb and 10 kb resolutions with default parameters (except -d 15000,20000) for pooled Hi-C matrices of the healthy T cell controls, ETP and non-ETP samples, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: .validpairs of BL-Hi-C data were generated by HiC-Pro;.hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count and FPKM for each sample

molecule: genomic DNA

source_name: cell line

growth_protocol: Loucy, Jurkat and KE-37 cells were routinly cultured in RPMI-1640 with 10% fetal bovine serum. Maintain cultures at cell concentrations between 3 x 10^5 and 3 x 10^6 viable cells/mL.

extract_protocol:
Leukemia blast cells were prepared by density-gradient centrifugation of bone marrow samples, and CD19-CD14-CD235-CD45+CD7+ cells were further purified by FACS analysis using anti-human antibodies for RNA-seq and Hi-C library preparations. Peripheral blood samples were obtained from four healthy donors under the approval of the ethics committee of Peking University. T cells were purified using the EasySepTM Direct Human T Cell Isolation Kit (StemCell Technology #19661).
Hi-C was performed on one million cells/sample according to the BL-Hi-C protocol (PMID: 29158486 ). RNA libraries were prepared for sequencing using standard Illumina protocols. ATAC  was performed on 50,000 Loucy cells according to the Omni-ATAC protocol  (PMID:28846090) with TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme TD501)

value: cell line


title: Jurkat_RNAseq

description:
RNA-seq of human: cellline Jurkat
TALL_count_FPKM.xls


title: 6T_cas9_rep3


title: 256740610715_1_4


title: Loucy_ATAC_rep2


title: wt_embryo_scRNA_seq_C57BL6 [EXE3_e2-3_E6.5_2]

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description: single-embryo scMARS-seq of mouse embryos from gastrulation stage

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively) and concatenated to the fastq header.
3. Read 1 sequences were mapped to the mm9 genome using bowtie2.
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
5. Header structure of labeled Read 1 fastq files: "ORIGINALHEADER_barcode=similar_oligo-pool_barcode_quality-well_barcode_quality-UMI_quality-pool_barcode-well_barcode-UMI". Concatenated entries are separated by "-"
6. well_barcode (7bp), pool_barcode (4bp) and external_barcode (8bp) of each single cell can be found in metadata.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. Supplementary files contain metadata for each single cell are organized in seven files: One file for wildtype embryo plates from BL6 mice, one file for wildtype embryos from ICR mice, four files for chimera or tetraploid embryos injected with Foxc1/2 DKO or control cells. One file for a mixed plate containing cells from tetraploid control and tetraploid DKO embryos

organism: Mus musculus

source_name: Mouse embryo

growth_protocol: wt embryos were collected from pregnant C57BL/6JRccHsd or Hsd:ICR(CD-1) females, between E6.5-8.25. Blastocyst injections were performed using (C57BL/6xDBA) B6D2F1 (Envigo) host embryos. In brief, 3-4-week old B6D2F1 females were hormone primed by an intraperitoneal (i.p.) injection of pregnant mare serum gonadotropin (PMSG, Vetmarket) followed 46 hr later by an injection of human chorionic gonadotropin (hCG, Sigma). Embryos were harvested at the zygote stage, and cultured in a CO2 incubator until blastocyst stage. On the day of the injection, groups of embryos were placed in drops of M2 medium using a 16-um diameter injection pipet (Biomedical Instruments). Approximately ten cells were injected into the blastocoel of each embryo using a Piezo micromanipulator (Prime Tech). For tetraploid complementation, 2-cell embryos were fused to one cell using a CF150/F instrument (BLS), by 2 DC square pulses of 30V 40ms and 1-2V AC, in 0.3M Manitol solution with BSA. An average of 15 cells were injected to the blastocoel of such embryos. Approximately 20 blastocysts were transferred to each recipient female (CD1 female mice, Envigo); the day of injection was considered as 2.5dpc.

extract_protocol:
single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 2nM poly-dT barcodes, 0.1%triton and RNAse inhibitors.
scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014.

treatment_protocol: Embryos were removed from their implantation sites using fine forceps, in PBS, and Reichert’s membrane and ectoplacental cone removed. Embryos were then washed in fresh PBS and transferred to chilled DMEM (Phenol-red free, Gibco) supplemented with 10% FBS (Biological Industries) for imaging prior to dissociation by Trypsin-A.

tag: strain

value: whole embryo

tag: developmental stage


title: chimera_foxc12_dko_scRNA_seq [p12_m3e6_cont]

description: single-embryo scMARS-seq of chimera embryos with injected Foxc1/2 DKO cells

value: BDF1 host blastocyst injected with V6.5 (C57BL/6x129 origin) derived Foxc12 dko mescs


title: chimera_foxc12_dko_scRNA_seq [p6_m2e13_gfp]


title: wt_embryo_scRNA_seq_C57BL6 [EXE3_e1_E6.5_1]


title: wt_embryo_scRNA_seq_C57BL6 [EXE3_e4-e5_E6.5_3]


title: chimera_foxc12_dko_scRNA_seq [p5_m2e13]


title: chimera_foxc12_dko_scRNA_seq [p4_m2e10_cont]


title: chimera_foxc12_dko_scRNA_seq [p3_m2e5_gfp]


title: chimera_foxc12_dko_scRNA_seq [p17_m3e8_regfp]


title: wt_embryo_scRNA_seq_C57BL6 [EXE5_E1-E4_E6.5_1]


title: ChIP_IgG_KE37

description: IgG ChIP-Seq of human: cellline KE-37

data_processing:
RNA-seq reads were aligned to the hg19 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ATAC-seq reads were mapped with Bowtie2 using parameter -X 2000 --no-mixed --no-discordant --no-unal. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIP-seq reads were mapped with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 5 kb and 10 kb resolutions with default parameters (except -d 15000,20000) for pooled Hi-C matrices of the healthy T cell controls, ETP and non-ETP samples, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: .validpairs of BL-Hi-C data were generated by HiC-Pro;.hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count and FPKM for each sample

extract_protocol:
Leukemia blast cells were prepared by density-gradient centrifugation of bone marrow samples, and CD19-CD14-CD235-CD45+CD7+ cells were further purified by FACS analysis using anti-human antibodies for RNA-seq and Hi-C library preparations. Peripheral blood samples were obtained from four healthy donors under the approval of the ethics committee of Peking University. T cells were purified using the EasySepTM Direct Human T Cell Isolation Kit (StemCell Technology #19661).
Hi-C was performed on one million cells/sample according to the BL-Hi-C protocol (PMID: 29158486 ). RNA libraries were prepared for sequencing using standard Illumina protocols. ATAC  was performed on 50,000 Loucy cells according to the Omni-ATAC protocol  (PMID:28846090) with TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme TD501). H3K27ac ChIP of case 077 was performed on 10^5 cells, according to the protocol of Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD 901). H3K27ac ChIP of KE-37 was performed on 10^6 cells, according to the protocol of Zymo-Spin ChIP Kit from Zymo Research for Illumina (Zymo Research,D5209).


title: chimera_foxc12_dko_scRNA_seq [p8_m2e15_gfp]


title: chimera_foxc12_dko_scRNA_seq [p7_m2e15]


title: ChIP_H3K27ac_KE37

description: H3K27ac ChIP-Seq of human: cellline KE-37


title: wt_embryo_scRNA_seq_C57BL6 [EXE5_E6cont-E7_E6.5_3]


title: chimera_foxc12_dko_scRNA_seq [p2_m2e5]


title: wt_embryo_scRNA_seq_C57BL6 [EXE5_E4cont-E6_E6.5_2]


title: chimera_foxc12_dko_scRNA_seq [p11_m3e6]


title: wt_embryo_scRNA_seq_C57BL6 [EXE2_e4_E7.5_3]


title: chimera_foxc12_dko_scRNA_seq [p16_m3e8]


title: wt_embryo_scRNA_seq_C57BL6 [EXE2_e3_E7.5_2]


title: wt_embryo_scRNA_seq_C57BL6 [EXE1_e1-3_E6.25_1]


title: wt_embryo_scRNA_seq_C57BL6 [EXE3_m2e3cont-m3e1-e2_E6.5_5]


title: wt_embryo_scRNA_seq_C57BL6 [EXE_EXP12_E7.5_4]


title: wt_embryo_scRNA_seq_C57BL6 [EXE_EXP12_E7.5_3]


title: wt_embryo_scRNA_seq_C57BL6 [EXE_EXP12_E7.5_2]


title: wt_embryo_scRNA_seq_C57BL6 [EXE3_m2e1-e3_E6.5_4]


title: wt_embryo_scRNA_seq_C57BL6 [EXE_EXP11_E7.5_1]


title: R3_pre

city: Palo Alto

first: Haiyu

last: Zhang

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Sequence reads, after filtering for read quality, were re-filtered by fastx (fastx_artifacts_filter) (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Reads that passed the filter were mapped to the human transcriptome hg19 (refMrna, downloaded from the UCSC genome browser, http://www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches (Guo X, 2013, https://doi.org/10.1186/bcr3586).
Total numbers of sequence reads (read counts) for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix (Guo X, 2013, https://doi.org/10.1186/bcr3586).
Genome_build: Human transcriptome hg19
Supplementary_files_format_and_content: The processed data files are text files. These files can be opened in Microsoft Excel using Text Import Wizard (select: Delimited, Tab, Text for each step to open the file). It contains gene symbol in column A and raw read counts of each gene in column B.

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated using EZNA PX blood RNA kit (Omega bio-tek), and then concentrated using RNA clean & concentrator-5 (ZYMO research).
Alpha- and beta-globin mRNAs were depleted from total RNA samples using GLOBINclear-human globin mRNA removal kit (Life Technologies) according to manufacturer’s instruction. 3SEQ libraries were constructed based on previously published method (Beck AH, 2010, https://doi.org/10.1371/journal.pone.0008768) with modifications. Briefly, after globin mRNA reduction, remaining mRNAs were enriched by poly-A selection using Dynabeads mRNA purification kit (Life Technologies), and heat-fragmented to 100-200 bases. First-strand cDNAs were synthesized using Superscript III reverse transcriptase with Rd2SP-oligodT primer, followed by second-strand cDNA synthesis. Adenine was added to the 3’-end of the double-stranded cDNA and then ligated to the P5-R1SP adapter. The ligated product was amplified by PCR for 15 cycles using primers P5-Rd1SP and P7-index-Rd2SP. Six Illumina indexes, each with six bases, were introduced in the P7 primer. Quality of the library was examined using Agilent DNA 1000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were quantified by Qubit 2.0 fluorometer using Qubit dsDNA BR assay kit (Life technologies). Six samples with different indexes were pooled together and submitted for sequencing at Stanford Center for Genomics and Personalized Medicine. Index associated 36 bp sequences from the P5 primer end, providing the 5’-end sequences of the polyA-containing mRNA fragments, were generated using Illumina HiSeq 2000 system (Illumina, San Diego, CA).
RNA-Seq, specifically, 3’-end sequencing for expression quantification (3SEQ)

treatment_protocol: With informed consent, patients enrolled in this study had been receiving eltrombopag monotherapy (75 mg daily via oral administration) for the management of chronic ITP during the period of blood sample collections.

tag: disease

value: Immune thrombocytopenia, chronic

value: Eltrombopag

tag: treatment time point

value: Pretreatment

tag: response to treatment

value: Response


title: wt_embryo_scRNA_seq_C57BL6 [EXE_EXP10_E7.0_2]


title: ATAC_mouse_NK_WT_ATAC_IL18_2

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
ATAC-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on Tn5-shifted, concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated from BAM files using the bamCoverage function from deepTools (v3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled pileups of reads aligned to the genome.

source_name: splenic NK cells

extract_protocol:
Fresh cells were prepared as previously described (Buenrostro et al., 2013). Briefly, sorted, stimulated cells were washed in cold PBS and lysed. The transposition reaction was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004).
DNA was amplified for 5 cycles. After evaluation by real-time PCR, 8-11 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 36 million paired reads were generated per sample.

treatment_protocol: NK cells were stimulated for 3 hr with 20 ng/ml recombinant mouse IL-12, 10 ng/ml recombinant mouse IL-18, or both.

value: NK cells

tag: genotype

value: WT

tag: condition

tag: replicate


title: chimera_foxc12_dko_scRNA_seq [6D_P01]


title: wt_embryo_scRNA_seq_C57BL6 [EXE_EXP10_E7.0_1]


title: wt_embryo_scRNA_seq_ICR [190710_175]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p2]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p11]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p12]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p16]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p7]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p15]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p3]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p8]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p9]


title: wt_embryo_scRNA_seq_ICR [190710_176]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p1]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p4]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p5]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p10]


title: wt_embryo_scRNA_seq_ICR [190710_172]


title: wt_embryo_scRNA_seq_ICR [190710_168]


title: wt_embryo_scRNA_seq_ICR [190710_167]


title: wt_embryo_scRNA_seq_ICR [190710_173]


title: wt_embryo_scRNA_seq_ICR [190710_169]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p6]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p14]


title: chimera_foxc12_dko_scRNA_seq [6D_P02]


title: wt_embryo_scRNA_seq_ICR [20191217_ICR_e7.5_p13]


title: wt_embryo_scRNA_seq_ICR [190710_166]


title: wt_embryo_scRNA_seq_ICR [190710_114]


title: wt_embryo_scRNA_seq_ICR [190710_164]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P156]


title: wt_embryo_scRNA_seq_ICR [190710_112]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P155]


title: wt_embryo_scRNA_seq_ICR [190710_165]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P151]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P153]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P150]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P102]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P104]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P100]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P105]


title: wt_embryo_scRNA_seq_ICR [190506_P120]


title: wt_embryo_scRNA_seq_ICR [190506_P119]


title: wt_embryo_scRNA_seq_ICR [190506_P125]


title: wt_embryo_scRNA_seq_ICR [190506_P127]


title: wt_embryo_scRNA_seq_ICR [190506_P129]


title: wt_embryo_scRNA_seq_ICR [190506_P126]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P148]


title: wt_embryo_scRNA_seq_ICR [190506_P118]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P101]


title: wt_embryo_scRNA_seq_ICR [190506_P124]


title: wt_embryo_scRNA_seq_ICR [190506_P128]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P152]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P103]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P15]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P16]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P14]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P12]


title: wt_embryo_scRNA_seq_C57BL6 [190527_P146]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P13]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P11]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P09]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P07]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P06]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P04]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P05]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P02]


title: wt_embryo_scRNA_seq_C57BL6 [190311_P02]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P01]


title: wt_embryo_scRNA_seq_C57BL6 [190311_P03]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P14]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P10]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P15]


title: wt_embryo_scRNA_seq_C57BL6 [190304_P02]


title: wt_embryo_scRNA_seq_C57BL6 [190311_P01]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P12]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P16]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P11]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P09]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P10]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P08]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P10]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P09]


title: wt_embryo_scRNA_seq_C57BL6 [190304_P03]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P08]


title: wt_embryo_scRNA_seq_C57BL6 [190313_P03]


title: wt_embryo_scRNA_seq_C57BL6 [190304_P01]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P04]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P03]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P06]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P01]


title: wt_embryo_scRNA_seq_C57BL6 [190214_P05]


title: wt_embryo_scRNA_seq_C57BL6 [190307_P13]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P07]


title: wt_embryo_scRNA_seq_C57BL6 [190214_P02]


title: wt_embryo_scRNA_seq_C57BL6 [190214_P03]


title: wt_embryo_scRNA_seq_C57BL6 [190214_P04]


title: Polyclonal

city: Pittsburgh

first: Khodor

middle: I

last: Abou-Daya

state: PA

address: 200 Lothrop Street

department: Surgery

institute: Starzl Transplantation Institute

data_processing:
Raw fastq files were processed using Partek Flow v9.0.20.0110 (Partek) default setting. Trimming tags, alignment to the mm10 mouse genome using STAR aligner, filtering, barcode and unique molecular identifier counting and deduplication, low-quality cell filtration, and hashtag demultiplexing were applied as recommended in Partek Flow. Multiplets and cells with greater than 3% mitochondrial gene expression were excluded, resulting in a gene expression matrix of 6580 cells by 12,318 genes (OT-I) and 11700 cells by 15,293 genes (Polyclonal).
Data were normalized by log2(counts per million + 1)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files with filtered and normalized mRNA counts for genes detected in sequenced cells that are annotated with sample of origin (HTO)

source_name: Polyclonal T cells

extract_protocol:
F1(B6xBalb/c).OVA kidney allografts were harvested 1 or 5 weeks (n = 3 from each time point) after transplantation from B6 recipients that also received 1 x 10^6 effector DsRed+ OT-I cells on day 2. In vivo labelling was done using 3µg of anti-CD45 i.v. 2 min prior to sacrifice. Lin−(CD11c, CD11b, Ter119, CD16/32, B220, F4/80, DX5, NK1.1, Ly6g, CD19) and intravascular CD45+ cells were excluded from sorted cell population. Polyclonal CD45.1+dsRed−Thy1.2+CD5+ T cells and monoclonal CD45.1−dsRed+Thy1.2+CD5+ OT-I cells were sorted separately from each harvested graft. Each sorted polyclonal and OT-I T cell sample  was then labelled with cell hashing antibodies (Totalseq-A, Biolegend) (table S4) for later demultiplexing(64). Polyclonal and OT-I T cell samples were pooled separately and sequenced. scRNAseq was performed using 10X Genomics Single Cell 3′ solution, version 2, according to the manufacturer’s instructions  with 7,000 sorted polyclonal or OT-I T cells loaded for each sample.  mRNA and hashtag oligos cDNA libraries from pooled samples were sequenced on the NextSeq500 Platform (Illumina).
RNA libraries were prepared for sequencing using 10X Genomics Single Cell 3′ solution, version 2

value: Polyclonal T cells

tag: time of harvest

value: 1 or 5 weeks after transplant


title: Polyclonal [HASH]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P05]

tag: tissue


title: OT-I [HASH]

source_name: OT-I cells

value: Monoclonal OVA specific TCR transgenic CD8+ T cells


title: wt_embryo_scRNA_seq_C57BL6 [181209_P04]


title: wt_embryo_scRNA_seq_C57BL6 [181209_P01]


title: wt_embryo_scRNA_seq_C57BL6 [190214_P01]


title: wt_embryo_scRNA_seq_C57BL6 [181209_P03]


title: wt_embryo_scRNA_seq_C57BL6 [190223_P02]


title: M127-Entorhinal Cortex (RRBS)

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

data_processing:
Sequencing quality was assessed using FastQC (version v0.11.7) with all samples characterized by high quality and thus passing QC
Sequences were trimmed using TrimGalore (version 0.4.4_dev), with a quality score of 20 and an error rate of 0.2 used to remove poor quality bases at the ends of reads
Reads with fewer than 20 base pairs after trimming were then removed
Reads were aligned to the mm10  (GRCm38) mouse genome using Bismark v0.19.0 with default parameters, which implements SAMtools 1.8 and Bowtie2 v2.3.4.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix containing methylation values and read depth

source_name: Entorhinal Cortex

growth_protocol: Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.

extract_protocol:
Genomic DNA from all samples was isolated from the entorhinal cortex using the AllPrep DNA/RNA Mini Kit (Qiagen)
RRBS libraries were prepared using the Premium RRBS kit (Diagenode) with some modifications. Libraries were checked using the High Sensitivity D1000 Screentape and 2200 TapeStation System (Agilent Technologies). Final library pools were distributed across thirty-two HiSeq2500 (Illumina) lanes and subjected to 50 bp single-end sequencing.

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent RNA-seq analysis

tag: Sex

value: F

value: Entorhinal Cortex


title: M128-Entorhinal Cortex (RRBS)


title: M125-Entorhinal Cortex (RRBS)


title: M123-Entorhinal Cortex (RRBS)


title: M122-Entorhinal Cortex (RRBS)


title: OT-I


title: M124-Entorhinal Cortex (RRBS)


title: M121-Entorhinal Cortex (RRBS)


title: M117-Entorhinal Cortex (RRBS)


title: M120-Entorhinal Cortex (RRBS)


title: M116-Entorhinal Cortex (RRBS)


title: M115-Entorhinal Cortex (RRBS)


title: M114-Entorhinal Cortex (RRBS)


title: M118-Entorhinal Cortex (RRBS)


title: M112-Entorhinal Cortex (RRBS)


title: Chorionic Villi (Normal) 1

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file containing raw miRNA counts

source_name: Chorionic Villi

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit and TRIzol LS Reagent (for exosomes) or QIAzol (for tissues) following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 1 µg RNA or 100 to 300 ng of exosomal RNA was used as input for library construction.

value: Chorionic Villi

value: Tissue explant

value: normal


title: Chorionic Villi (Normal) exosomes 1

value: Exosomes


title: Chorionic Villi (Gestational diabetes mellitus) 1

value: Gestational diabetes mellitus


title: Chorionic Villi (Gestational diabetes mellitus) exosomes 1


title: Chorionic Villi (Normal) 3


title: Chorionic Villi (Normal) exosomes 3


title: Chorionic Villi (Gestational diabetes mellitus) exosomes 3


title: Chorionic Villi (Gestational diabetes mellitus) 3


title: Chorionic Villi (Normal) exosomes 2


title: Chorionic Villi (Gestational diabetes mellitus) exosomes 2


title: Chorionic Villi (Normal) 2


title: Chorionic Villi (Gestational diabetes mellitus) 2


title: M126-Entorhinal Cortex (RRBS)


title: M119-Entorhinal Cortex (RRBS)


title: M106-Entorhinal Cortex (RRBS)


title: M109-Entorhinal Cortex (RRBS)


title: M105-Entorhinal Cortex (RRBS)


title: M107-Entorhinal Cortex (RRBS)


title: M104-Entorhinal Cortex (RRBS)


title: M102-Entorhinal Cortex (RRBS)


title: M103-Entorhinal Cortex (RRBS)


title: M110-Entorhinal Cortex (RRBS)


title: M113-Entorhinal Cortex (RRBS)


title: M100-Entorhinal Cortex (RRBS)


title: M99-Entorhinal Cortex (RRBS)


title: M101-Entorhinal Cortex (RRBS)


title: M97-Entorhinal Cortex (RRBS)


title: M96-Entorhinal Cortex (RRBS)


title: M87-Entorhinal Cortex (RRBS)


title: M111-Entorhinal Cortex (RRBS)


title: M94-Entorhinal Cortex (RRBS)


title: M86-Entorhinal Cortex (RRBS)


title: M91-Entorhinal Cortex (RRBS)


title: M108-Entorhinal Cortex (RRBS)


title: M85-Entorhinal Cortex (RRBS)


title: M88-Entorhinal Cortex (RRBS)


title: M84-Entorhinal Cortex (RRBS)


title: M90-Entorhinal Cortex (RRBS)


title: M92-Entorhinal Cortex (RRBS)


title: M95-Entorhinal Cortex (RRBS)


title: M98-Entorhinal Cortex (RRBS)


title: M93-Entorhinal Cortex (RRBS)


title: M79-Entorhinal Cortex (RRBS)


title: M78-Entorhinal Cortex (RRBS)


title: M82-Entorhinal Cortex (RRBS)


title: M80-Entorhinal Cortex (RRBS)


title: M83-Entorhinal Cortex (RRBS)


title: M81-Entorhinal Cortex (RRBS)


title: M74-Entorhinal Cortex (RRBS)


title: M76-Entorhinal Cortex (RRBS)


title: M77-Entorhinal Cortex (RRBS)


title: M72-Entorhinal Cortex (RRBS)


title: M73-Entorhinal Cortex (RRBS)


title: M71-Entorhinal Cortex (RRBS)


title: M69-Entorhinal Cortex (RRBS)


title: M70-Entorhinal Cortex (RRBS)


title: M68-Entorhinal Cortex (RRBS)


title: M67-Entorhinal Cortex (RRBS)


title: M65-Entorhinal Cortex (RRBS)


title: M64-Entorhinal Cortex (RRBS)


title: M61-Entorhinal Cortex (RRBS)


title: M62-Entorhinal Cortex (RRBS)


title: M66-Entorhinal Cortex (RRBS)


title: M60-Entorhinal Cortex (RRBS)


title: M58-Entorhinal Cortex (RRBS)


title: head_elavGS/GR100_rep3_1553_I

city: Köln

first: Linda

last: Partridge

address: Joseph-Stelzmann-Straße 9B

department: Biological Mechanisms of Ageing

country: Germany

institute: Max Planck Institute for Biology of Ageing

data_processing:
Quality trimming of raw FastQ files using Trim Galore! (v0.3.7)
Read aligment using Tophat2 (v2.0.14) against Dm6 reference genome.
Multi-mapped reads were filtered using SAMtools
Data analysis was performed using SeqMonk, Deseq2, topGO and org.Dm.eg.db
Genome_build: Dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

extract_protocol:
Female flies were snap frozen. Heads were separated and total RNA was isolated using Trizol and treated with DNase
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female flies were fed for three days with 200µM RU486

tag: treatment

value: head


title: head_elavGS/GR100_rep2_1553_H


title: M59-Entorhinal Cortex (RRBS)


title: M57-Entorhinal Cortex (RRBS)


title: head_elavGS/+_rep3_1553_C

value: elavGS/+

value: control


title: head_elavGS/+_rep1_1553_A


title: M54-Entorhinal Cortex (RRBS)


title: M55-Entorhinal Cortex (RRBS)


title: M52-Entorhinal Cortex (RRBS)


title: RNA_Isl9_High-dose_dex_24hr

city: La Jolla

first: Paola

last: Benaglio

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: University of California San Diego

description:
Raw_gene_counts_matrix.txt
TPM_gene_counts_matrix.txt

data_processing:
ATAC-seq reads were trimmed using Trim Galore with options ‘–paired’ and ‘–quality 10’, then aligned them to the hg19 reference genome using BWA mem with the ‘-M’ flag. Picard was used to mark duplicate reads, and samtools to filer reads with flags ‘-q 30’, ‘-f 3’, ‘-F 3332’. Mitochondrial reads and reads mapping to blacklisted regions were removed.
ATAC-seq read depth signal tracks (bigWig files) were obtained using bamCoverage for each alignment with signal normalization using RPKM.
ATAC-seq enriched regions were defined using Irreproducible Discovery Rate (IDR). For each condition separately, we pooled reads across all assays and randomly split the pooled reads into two ‘pseudo-replicates’. For the pooled and ‘pseudo-replicate’ data we called candidate peaks using MACS2 with the parameters ‘—extsize 150 –keep-dup all –shift -75 –nomodel -p 0.01’. We applied IDR to the ‘pseudo-replicate’ candidate peak calls and obtained the number of peaks at an IDR threshold of .01. We then sorted and filtered the pooled candidate peak calls based on this number. Finally, we merged the resulting peaks across conditions, where if two peaks overlapped, we retained the more significant peak
ATAC-seq alignments for each sample were then supplied as inputs to the R function featureCounts from the Rsubread package to generate a matrix of read counts within each canonical site.
RNA-Seq reads were aligned to the genome using STAR (2.5.3a) with a splice junction database built from the Gencode v19 gene annotation.
RNA-seq raw and TPM gene expression values for each sample were quantified using the RSEM package (1.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain ATAC-seq depth signal for each sample
Supplementary_files_format_and_content: Matrix table with ATAC-seq read counts for eavery peak and every sample
Supplementary_files_format_and_content: Genes abundance tab-delimited text files include expected counts (raw counts), TPM and FPKM values for each sample, quantified using RSEM.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with TPM-normalized gene counts for every gene and every sample

source_name: Pancreatic islets

growth_protocol: Islet samples were enriched using a dithizone stain. Islets were cultured for 24hr at approximately 10mL media/1k islets in 10cm dishes at 37C, 5% CO2 in CMRL 1066 media supplemented with 10% FBS, 1X pen-strep, 8mM glucose, 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, and 250ng/mL Amphotericin B.

extract_protocol:
RNeasy Mini kit (Qiagen)
Sequence ribodepleted RNA libraries were prepared according to standard illumina protocols.

treatment_protocol: Treated islets had dexamethasone (Sigma) added in the culture media at either 100 ng/mL for 24hr, 4ng/mL for 24hr or 4 ng/mL for 6hr

value: pancreatic islets

tag: source id

tag: study id

value: 100 ng/mL dex, 24hr

tag: donor sex

value: M

tag: donor age

tag: islet purity (%)

tag: islet source

value: Integrated Islet Distribution Program


title: RNA_Isl9_Untreated

value: Untreated


title: M51-Entorhinal Cortex (RRBS)

tag: group


title: M63-Entorhinal Cortex (RRBS)


title: M56-Entorhinal Cortex (RRBS)


title: EMA304_ctrl

first: shan

last: wang

address: Tsinghua university medical building c244

institute: Tsinghua university

description:
Sample 1
EMA304

data_processing:
Illumina Casava1.7 software used for basecalling.
reads were aligned to the mm10 genome assembly using HISAT2 with default configurations
FPKM were caluculated by StringTie with default configurations.
Genome_build: mm10
Supplementary_files_format_and_content: gene FPKM Excel

source_name: intestinal epithelium

growth_protocol: All animal studies were performed in accordance with the relevant guidelines and regulations and with the approval of the Institutional Animal Care and Use Committee of Tsinghua University.

extract_protocol:
For isolation of whole-intestinal epithelial cells, the mouse intestine was cut longitudinally and washed two to three times with ice-cold PBS, then cut into small pieces (3–7 mm long) and incubated for 30 min at 4 °C in PBS containing 30 mM EDTA and 1.5 mM Dithiothreitol on ice, and collecting suspended cells after gentle vortexing.Total RNA was isolated from mouse small intestinal epithelial cells from Ctrl and Myh9-KO mice at day 5 after administered with TAM using TRIzol Reagent (Life Technologies) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.High-throughput sequencing was performed using the Illumina HiSeq 2000. Genes with fold changes of 1.4 were regarded as differentially expressed genes.

treatment_protocol: To induced Myh deletion, we performed daily injection of tamoxifen (TAM) for 5 consecutive days on Control and Myh9-KO mice.

tag: strain

value: intestine

tag: age

value: 8 weeks

value: wild type


title: EMA305_Myh9_KO_5days

description:
Sample 2
EMA305


title: head_elavGS/GR100_rep1_1553_G


title: M50-Entorhinal Cortex (RRBS)

value: F

value: Entorhinal Cortex


title: head_elavGS/+_rep2_1553_B


title: RNA_Isl5_High-dose_dex_24hr


title: RNA_Isl5_Untreated


title: M48-Entorhinal Cortex (RRBS)


title: RNA_Isl8_High-dose_dex_24hr


title: M53-Entorhinal Cortex (RRBS)


title: M49-Entorhinal Cortex (RRBS)


title: M46-Entorhinal Cortex (RRBS)


title: M47-Entorhinal Cortex (RRBS)


title: ATAC_Isl6_High-dose_dex_24hr

extract_protocol:
Islet samples were centrifuged at 500xg for 3’, washed twice in HBSS, and resuspended in nuclei permeabilization buffer. Islets were homogenized using a chilled glass dounce homogenizer and incubated on a tube rotator for 10’ before being filtered through a 30uM filter and centrifuged at 500xg in a 4C microcentrifuge to pellet nuclei.
Nuclei were resuspended in Tagmentation Buffer (Illumina) and counted using a Countess II Automated Cell Counter (Thermo). ~ 50,000 nuclei were transferred to a 0.2mL PCR tube and volume was adjusted to 22.5uL with Tagmentation Buffer. 2.5uL TDE1 (Illumina) was added to each tagmentation reaction and mixed with gentle pipetting. Transposition reactions were incubated at 37C for 30 minutes. Tagmentation reactions were cleaned up using 2X reaction volume of Ampure XP beads (Beckman Coulter) and eluted in 20uL Buffer EB (Qiagen). 10uL tagmented DNA was used in a 25uL PCR reaction using NEBNext High-Fidelity Master Mix (New England Biolabs) and Nextera XT Dual-Indexed primers (Nextera). Final libraries were double size selected using Ampure XP beads and eluted in a final volume of 20uL Buffer EB.


title: ATAC_Isl6_Untreated


title: M45-Entorhinal Cortex (RRBS)


title: RNA_Isl8_Untreated


title: At_GC_3x salt_rep_3_Light

city: Wuerzburg

first: Sohail

middle: Mehmood

last: Karimi

state: Bavaria

address: Julius-von-Sachs-Platz 2,

department: Botany 1

institute: University of Wuerzburg

description: Gene expression after 75+150+200 mM salt treatment

hyb_protocol: following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent Technologies Scanner G2505C US45102963 Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.5.1.1 (Agilent Technologies Germany). Data extraction using protocol GE1_1105_Oct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR). Entities differentially expressed mean an at least 2-fold change in expression level in all transgenic lines compared to wild-type Col-0 plants were further analysed.

organism: Arabidopsis thaliana

source_name: Guard cells

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 100ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Arabidopsis thaliana (accession Columbia-0) plants were grown in pots (7 cm diameter, 200 ml volume) filled with 91 ± 7 g soil (Einheitserde Typ P, Germany). Plants were illuminated for 12 hours (10 A.M. to 10 P.M.) with a light intensity of 80-110 μmol s-1 m-2 using fluorescent lamps (Osram, L58W/77 FLUORA; Munich, Germany) at 22°C in light and 16°C in dark and 60% relative air humidity.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel, Gmbh& co. Germany) according to manufacturer’s protocol from salt (1x and 3x salt) and non-salt treated plants kept in light for four hours after beginning of the light period (from 10 am to 2 pm). Four guard cell samples of each treatment were prepared and hence, a total 12 samples for Arabidopsis and 12 of Thellungiella were used for microarray analysis.

treatment_protocol: Two different salt treatment protocols, a short- and long-term, were applied to 4 to 5 weeks old Arabidopsis plants by soaking the soil pots in salt solutions each time for two hours. In the long-term salt stress experiment plants were treated three times : (i) On day 1 and 2 (75 mM NaCl), (ii) on day 7 and 8 (150 mM NaCl), and (iii) on day 13 and 14 (200 mM NaCl) named as 3x salt. In the short-term salt stress experiment plants were treated with 200mM NaCl on day 13 and 14 (named as 1x salt) while the control group faced tap water (named as (-) salt). All samples were collected at the end of the salt experiments on day 15 to ensure that plants have the same plant age and developmental stage

value: 6-7 weeks


title: ATAC_Isl5_High-dose_dex_24hr


title: At_GC_1x salt_rep_3_Light

description: Gene expression after 200 mM salt treatment


title: At_GC_non salt_rep_4_Light

description: Gene expression after non salt treatment


title: 1a T6 control

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Sequencing data were processed using the Illumina Pipeline Software version 1.84
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3).
Remaining reads were further filtered for low complexity with reaper (v. 15-065)
Reads were aligned against Rattus norvegicus genome (assembly version Rnor 6.0 and annotation Ensembl 87) using STAR (v. 2.5.2b)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1)
Genome_build: Rattus norvegicus (Rnor 6.0)
Supplementary_files_format_and_content: Tab-delimited text files include htseq gene counts for each sample.

organism: Rattus norvegicus

source_name: 3D brain cell aggregates

growth_protocol: Cells were grown 14 days under constant agitatory and medium was replenished every 3 days

extract_protocol:
Total RNAs (RNAeasy Mini kit, QIAGEN) were extracted from aggregates.
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA). Samples were prepared in two batches: 6 hours and 12 hours samples in the first batch, 24 hours samples with two repeated 12 hours controls in the second batch.

treatment_protocol: 120ng/ml sepiaterin or PBS 1x for control samples

value: Sprague Dawley

value: brain

value: embryonic day 15

tag: time point


title: At_GC_1x salt_rep_2_Light


title: M44-Entorhinal Cortex (RRBS)


title: At_GC_non salt_rep_2_Light


title: At_GC_3x salt_rep_2_Light


title: M43-Entorhinal Cortex (RRBS)


title: 11b T12 control


title: 144 T0 control


title: At_GC_non salt_rep_1_Light


title: At_GC_3x salt_rep_1_Light


title: At_GC_non salt_rep_3_Light


title: At_GC_1x salt_rep_1_Light


title: At_GC_3x salt_rep_4_Light


title: 10b T12 control


title: 143 T0 control


title: ATAC_Isl4_High-dose_dex_24hr


title: ATAC_Isl5_Untreated


title: 117 T24 120 ng/ml sepiapterin

value: 120 ng/ml sepiapterin


title: 142 T0 control


title: ATAC_Isl3_Untreated


title: 3a T6 control


title: M42-Entorhinal Cortex (RRBS)


title: 2a T6 control


title: M41-Entorhinal Cortex (RRBS)


title: ATAC_Isl3_High-dose_dex_24hr


title: 114 T24 120 ng/ml sepiapterin


title: ATAC_Isl4_Untreated


title: M40-Entorhinal Cortex (RRBS)


title: 107 T12 120 ng/ml sepiapterin


title: M39-Entorhinal Cortex (RRBS)


title: 106 T12 120 ng/ml sepiapterin


title: 98 T6 120 ng/ml sepiapterin


title: M36-Entorhinal Cortex (RRBS)


title: M37-Entorhinal Cortex (RRBS)


title: 20 T24 control


title: 22 T24 control


title: M38-Entorhinal Cortex (RRBS)


title: 12 T12 control


title: 96 T6 120 ng/ml sepiapterin


title: 19 T24 control


title: M35-Entorhinal Cortex (RRBS)


title: ATAC_Isl2_Untreated


title: ATAC_Isl1_High-dose_dex_24hr

value: University of Alberta


title: 115 T24 120 ng/ml sepiapterin


title: M34-Entorhinal Cortex (RRBS)


title: 11 T12 control

value: control


title: ATAC_Isl1_Untreated

value: pancreatic islets


title: 97 T6 120 ng/ml sepiapterin


title: unkIs7_csgA_1

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

data_processing:
BGISEQ-500 was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using SOAPnuke
Reads are aligned to the reference genome WBcel235 using STAR 2.7.5 with --quantMode GeneCounts to count the number of reads per gene
Differentially expressed genes are discovered by DESeq2 version 1.28.1 in R
Genome_build: WBcel235
Supplementary_files_format_and_content: matrix table with differentially expressed gene
Supplementary_files_format_and_content: gene count list

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: N2 and UM10 animals were grown on NGM plates fed with either K12 BW25113 or csgA(-) bacteria from egg to L4 stage.

extract_protocol:
the animals were washed with M9 for 3 times and total RNA was extracted using TRIzol.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.

tag: genotype

value: L4 stage


title: ATAC_Isl2_High-dose_dex_24hr

value: 100 ng/mL dex, 24hr


title: M33-Entorhinal Cortex (RRBS)


title: 105 T12 120 ng/ml sepiapterin


title: unkIs7_csgA_2


title: unkIs7_WT_1


title: 10 T12 control


title: M32-Entorhinal Cortex (RRBS)


title: N2_WT_2


title: M31-Entorhinal Cortex (RRBS)


title: M30-Entorhinal Cortex (RRBS)


title: M28-Entorhinal Cortex (RRBS)


title: N2_WT_1


title: M27-Entorhinal Cortex (RRBS)


title: M26-Entorhinal Cortex (RRBS)


title: M29-Entorhinal Cortex (RRBS)


title: M25-Entorhinal Cortex (RRBS)


title: M128-Entorhinal Cortex (array)

type: genomic

hyb_protocol: Standard Illumina protocols

scan_protocol: Illumina HiScan

data_processing: Normalized Average Beta calculated using the SeSame package in R

label: cy3, cy5

label_protocol: DNA methylation was measured using the the Mammalian Methylation Array (HorvathMammalMethylChip4, GEO: GPL28271)

extract_protocol: Genomic DNA from all samples was isolated from the entorhinal cortex using the AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent analysis


title: M127-Entorhinal Cortex (array)


title: M124-Entorhinal Cortex (array)


title: M24-Entorhinal Cortex (RRBS)


title: M125-Entorhinal Cortex (array)


title: M122-Entorhinal Cortex (array)


title: M126-Entorhinal Cortex (array)


title: unkIs7_WT_2


title: M123-Entorhinal Cortex (array)


title: Discovery-MPM-33

city: Torino

first: Luca

last: Bertero

state: TO

address: Via Santena 7

department: Pathology Unit, Dept. Medical Sciences

country: Italy

institute: University of Turin

description: Methylation data from pleural mesothelioma sample

hyb_protocol: Following FFPE restoration bisulphite converted DNA was hybridized to Illumina Infinium Human MethylationEPIC Methylation BeadChip using standard Illumina protocol

scan_protocol: Array BeadChips were scanned on an iScan system

data_processing: DNA methylation data was processed using the minfi Bioconductor R package as previously described (Hovestadt V et al, Acta Neuropathol 2013). Unsupervised hierarchical clustering was performed using the beta-values of the most variably methylated probes as measured by mean absolute deviation. The most variably methylated probes were analyzed (range: 10,000–25,000 probes) using Ward’s minimum variance linkage method and Euclidean distance. Additional analysis of tumor methylation classes was performed using t-distributed stochastic neighbor embedding (t-SNE) (20,000 CpG probes, 5-15 perplexities and 3,000 iterations).

label: Cy5 and Cy3

source_name: primary pleural mesothelioma sample

label_protocol: Illumina standard protocol

extract_protocol: Genomic DNA was extracted and purified from FFPE tissue with the Maxwell 16 FFPE Plus LEV DNA Kit according to manufacturer’s instructions

tag: material type

value: FFPE

tag: gender

value: M

tag: sample type

value: Biopsy

tag: mesothelioma histotype

value: Sarcomatoid MPM


title: M23-Entorhinal Cortex (RRBS)

tag: Sex

tag: tissue


title: M22-Entorhinal Cortex (RRBS)


title: Discovery-MPM-32


title: M112-Entorhinal Cortex (array)


title: Discovery-MPM-24


title: Validation-MPM-8


title: Discovery-MPM-25

value: Resection


title: Discovery-MPM-30


title: Validation-MPM-6


title: M121-Entorhinal Cortex (array)

value: F


title: M110-Entorhinal Cortex (array)

value: Entorhinal Cortex


title: Discovery-MPM-26


title: M20-Entorhinal Cortex (RRBS)


title: Validation-MPM-35


title: M19-Entorhinal Cortex (RRBS)


title: Validation-MPM-4


title: Validation-MPM-3


title: Discovery-MPM-23


title: Discovery-MPM-27


title: M109-Entorhinal Cortex (array)


title: Discovery-MPM-31


title: Discovery-MPM-29


title: M18-Entorhinal Cortex (RRBS)


title: Validation-MPM-10


title: Discovery-MPM-28


title: M102-Entorhinal Cortex (array)


title: M17-Entorhinal Cortex (RRBS)


title: Validation-MPM-9


title: M111-Entorhinal Cortex (array)


title: Discovery-MPM-19

value: Epithelioid MPM


title: Validation-MPM-1


title: Discovery-MPM-22


title: Discovery-MPM-21


title: M16-Entorhinal Cortex (RRBS)


title: M14-Entorhinal Cortex (RRBS)


title: M106-Entorhinal Cortex (array)


title: Validation-MPM-38


title: M15-Entorhinal Cortex (RRBS)


title: M104-Entorhinal Cortex (array)


title: Discovery-MPM-18


title: Discovery-MPM-20


title: Validation-MPM-5


title: Discovery-MPM-17


title: M13-Entorhinal Cortex (RRBS)


title: M12-Entorhinal Cortex (RRBS)


title: Discovery-MPM-14


title: Discovery-MPM-16


title: Validation-MPM-2


title: M21-Entorhinal Cortex (RRBS)


title: M69-Entorhinal Cortex (array)


title: M11-Entorhinal Cortex (RRBS)


title: M107-Entorhinal Cortex (array)


title: Validation-MPM-45


title: M8-Entorhinal Cortex (RRBS)


title: Discovery-MPM-13


title: M73-Entorhinal Cortex (array)


title: M7-Entorhinal Cortex (RRBS)


title: M103-Entorhinal Cortex (array)


title: Validation-MPM-41


title: M101-Entorhinal Cortex (array)


title: Discovery-MPM-15


title: Validation-MPM-44


title: M10-Entorhinal Cortex (RRBS)


title: M6-Entorhinal Cortex (RRBS)


title: M108-Entorhinal Cortex (array)


title: M85-Entorhinal Cortex (array)


title: M4-Entorhinal Cortex (RRBS)


title: Validation-MPM-27


title: M86-Entorhinal Cortex (array)


title: M118-Entorhinal Cortex (array)


title: Wild-type npc2, replicate 3

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
Quality filtering with cutadapt v1.18 with additional parameter -q 20
Alignment with HISAT2 v2.1.0 to the UCSC danRer11 assembly
Reads in feature quantified using featureCounts v1.6.3 using -s 2 (for reverse-stranded library), using the Ensembl GRCz11.94 GTF file, after modifying chromosome names to match those from the UCSC assembly
Genome_build: danRer11
Supplementary_files_format_and_content: counts in exons

organism: Danio rerio

source_name: zebrafish embryos, 30 hpf

extract_protocol:
Total RNA was extracted from zebrafish npc2+/+, Mnpc2+/m and MZnpc2m/m embryos at 30 hpf using Trizol (15596018, ThermoFisher Scientific, Waltham, MA) and RNeasy Mini kit (74104, Qiagen, Hilden, Germany). Mnpc2+/m and MZnpc2m/m embryos were siblings obtained from the same crosses distinguished by their phenotypes while npc2+/+ embryos were from the crosses of npc2+/+ adults which were siblings of Mnpc2+/m and MZnpc2m/m embryos’ parents. Thirty embryos of each genotype were pooled together as one pool for RNA extraction. Three separate pools of each genotype were collected for further analysis. RNA concentration and quality were measured using Nanodrop 2000 (ThermoFisher Scientific, Waltham, MA) and Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA, USA).
RNA-seq libraries were constructed by fragmenting RNA from each sample, reverse transcription of cDNA, and adding adapters for Illumina sequencing (Illumina, San Diego, USA).

value: Wild-type npc2

tag: developmental stage

value: 30 hpf


title: M87-Entorhinal Cortex (array)


title: M5-Entorhinal Cortex (RRBS)


title: Validation-MPM-40


title: M3-Entorhinal Cortex (RRBS)


title: Validation-MPM-21


title: Wild-type npc2, replicate 2


title: Validation-MPM-26


title: Validation-MPM-25


title: M2-Entorhinal Cortex (RRBS)


title: Validation-MPM-24


title: M99-Entorhinal Cortex (array)


title: Validation-MPM-20


title: Validation-MPM-17


title: Homozygous npc2, replicate 3

value: Homozygous npc2 mutation


title: M84-Entorhinal Cortex (array)


title: Validation-MPM-14


title: Validation-MPM-19


title: Wild-type npc2, replicate 1


title: Validation-MPM-18


title: Validation-MPM-7


title: M1-Entorhinal Cortex (RRBS)


title: Homozygous npc2, replicate 2


title: Discovery-MPM-12

value: Biphasic MPM


title: Homozygous npc2, replicate 1


title: Validation-MPM-22


title: M97-Entorhinal Cortex (array)


title: Validation-MPM-23


title: C3H10T1/2 MSCs - OB_rep3

city: guangzhou

first: zhipeng

last: zou

state: guangdong

address: tonghe road

department: Cell Biology

institute: southern medical university

data_processing:
Total RNA quantity and purity were analyzed using a Bioanalyzer 2100 and an RNA 6000 Nano LabChip kit (Agilent), with RNA integrity values of >7.0.
The final cDNA library were created in accordance with the protocol for the TruSeq RNA Sample Preparation v.2
Before assembly, low-quality reads were removed using Trimmomatic software.
Sequencing reads were aligned to the reference genome using the HISAT2 package.
The mapped reads of each sample were assembled and counted using the featureCounts package and a matrix of read counts was generated.
Genome_build: mm10
Supplementary_files_format_and_content: read counts matrix

source_name: C3H10T1/2 MSCs

growth_protocol: C3H10T1/2 cells  were cultured in Modified Eagle’s Medium (MEM) supplemented with 10% FBS, 1% non-essential amino acids, L-glutamine and sodium pyruvate.

extract_protocol:
Total RNA was extracted with Trizol.
Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v.2 (cat. no. RS-122-2001, RS-122-2002) (Illumina)

treatment_protocol: For OB induction, cells were maintained in complete medium supplemented with 50 μM L-ascorbic acid, 10 mM β-glycerophosphate, 10-3 μM dexamethasone, and 1% penicillin-streptomycin for 3 days.

tag: cell type

value: mesenchymal stem cells

tag: treatment

value: induced for osteoblast differentiation for 3 days

tag: cell line

value: C3H10T1/2 MSCs


title: Heterozygous npc2, replicate 3

value: Heterozygous npc2 mutation


title: Validation-MPM-42


title: Validation-MPM-13


title: M83-Entorhinal Cortex (array)


title: Validation-MPM-12


title: Heterozygous npc2, replicate 2


title: M81-Entorhinal Cortex (array)


title: C3H10T1/2 MSCs - OB_rep2


title: Discovery-MPM-11


title: C3H10T1/2 MSCs - OB_rep1


title: Validation-MPM-16


title: Validation-MPM-15


title: C3H10T1/2 MSCs - control_rep3

value: untreated


title: M82-Entorhinal Cortex (array)


title: M80-Entorhinal Cortex (array)


title: Heterozygous npc2, replicate 1


title: HF4-ap

city: New York

first: Jessica

last: White

state: NY

address: 1305 York Ave

institute: Weill Cornell

description:
This Sample includes two lanes of sequence.
mRNA
HF4.ap
norm_counts.csv

data_processing:
The resulting fastq files were pre-processed using fastp (v0.20.1) to remove low quality reads and to trim poly-G and poly-X tails.
Reads were mapped to a reference genome mm10 using STAR (v2.7.0e) with parameters --twopassMode Basic --alignIntronMin 10 --outFilterMultimapNmax 20 --alignSJoverhangMin 8
Read mapping was determined using featureCounts in the Subread package (v1.6.2) with parameters -p -T 2 -s 2 -a
Differential gene expression analysis was performed using R with Bioconductor package limma (v3.42.2) and voom; lane duplicates collapsed by adding counts together.
TMM was used to calcNormFactors and the normalized data reflects the pseudo counts from the estimateCommonDisp function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: norm_counts.csv: Comma-separated text file includes normalized count matrix.

source_name: Inguinal white adipose tissue (iWAT)

extract_protocol:
iWAT were collected into TRIzol and RNA was extracted with RNeasy Lipid Tissue Mini Kit (Qiagen).
Messenger RNA was enriched from the total RNA samples using poly-A selection, and libraries were prepared using the TruSeq Stranded mRNA prep kit (Illumina).

treatment_protocol: Anti-PDGFcc (AF1447 R&D system) antibody was administered to 6-week-old C57BL6/J mice intraperitoneally at 50 mg/kg in 100 µl of PBS every two days for two weeks.

value: Inguinal white adipose tissue

tag: treated with anti-pdgfcc antibody

value: Yes

tag: diet

value: High-fat diet


title: C3H10T1/2 MSCs - control_rep2


title: C3H10T1/2 MSCs - OB_rep4


title: HF4

description:
This Sample includes two lanes of sequence.
mRNA
HF4
norm_counts.csv

value: No


title: C3H10T1/2 MSCs - control_rep1


title: Ctag RAS/DNP53 clone #14 HAsiRNA rep2 (n=1)

city: Montpellier

first: Frederic

middle: Emile

last: Bienvenu

address: 141 rue de la Cardonille

department: Cancer Biology

country: France

institute: CNRS-Institute of Functinal Genomics

description:
#18 MEF RAS Ctag14 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 18

data_processing:
The quality of the data was assessed using FastQC from the Babraham Institute. Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
RNA-seq 100nt reads were aligned to the mouse genome (UCSC mm10) with a set of gene model annotations (genes.gtf downloaded from UCSC on May 23 2014; GeneIDs come from the NCBI: gene2refseq.gz downloaded on September 24 2015), using the splice junction mapper TopHat v2.1.1 (with bowtie 2.2.9). Final read alignments having more than 6 mismatches were discarded. Gene counting was performed using HTSeq-count 0.9.0 (union mode). Since data come from a strand-specific assay, the read has to be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 10 reads (cumulating all the analysed samples) were filtered out.
Differentially expressed genes were identified using the Bioconductor package DESeq2 v1.18.1. Data were normalized using the DESeq2 normalization method. Genes with adjusted p-value less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed. Generalized linear models was used to take into account paired samples; the samples are paired by batch of sequencing.
Genome_build: mm10
Supplementary_files_format_and_content: Text file (tab delimited) with a first column for gene identification. The next columns correspond to the raw counts (non-normalized) for each sample.

source_name: RAS tumor

growth_protocol: 0,5 million cells were implanted subcutaneously into immune compromised mice. Treatment was applied after tumors reached 500 mm3 in size.

extract_protocol:
Animals were sacrificed 30 minutes after the last siRNA injection, tumors were dissected and RNA was extracted using Trizol reagent.
The libraries were prepared with the TruSeq Stranded mRNA sample prep kit from illumina according to the manufacture's instructions. After oligo d(T) purification, mRNA was fragmented by zinc. cDNA was synthesized using random primer. Adapters are then ligated and PCR cycles were performed to enrich the library. The libraries were sequenced on a HiSeq 2500 instrument (from illumina) in a single read 1x100bp. The v3 chemistry was used according to manufacture's instructions.

treatment_protocol: Animals carrying tumors were treated by rectal route with Aonys (MedesisPharma) siRNA formulation (mg/mL) for 5 times per day every other hour.

tag: tumor type

value: Ctag-Cyclin D1 RAS/DNP53-driven tumor

tag: tumor treatment

value: HA-siRNA


title: M96-Entorhinal Cortex (array)

value: F

tag: group

value: Entorhinal Cortex


title: HF3-ap

description:
This Sample includes two lanes of sequence.
mRNA
HF3.ap
norm_counts.csv

tag: strain


title: M95-Entorhinal Cortex (array)


title: Discovery-MPM-9

value: FFPE

tag: age

value: M

value: Resection


title: HF3

description:
This Sample includes two lanes of sequence.
mRNA
HF3
norm_counts.csv


title: Ctag RAS/DNP53 clone #12 HAsiRNA rep2 (n=1)

description:
#17 MEF RAS Ctag12 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 17


title: M94-Entorhinal Cortex (array)


title: HF2-ap

description:
This Sample includes two lanes of sequence.
mRNA
HF2.ap
norm_counts.csv


title: M93-Entorhinal Cortex (array)


title: Ctag RAS/DNP53 clone #12 SCRsiRNA rep2 (n=1)

description:
#16 MEF RAS Ctag12 siScr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 16

value: SCR-siRNA


title: Validation-MPM-11

tag: material type

value: Biopsy

value: Epithelioid MPM


title: HF2

description:
This Sample includes two lanes of sequence.
mRNA
HF2
norm_counts.csv


title: WT RAS/DNP53 clone #18 HAsiRNA rep2 (n=1)

description:
#15 MEF RAS WT18 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 15

value: Untagged-Cyclin D1 RAS/DNP53-driven tumor


title: Discovery-MPM-10

tag: gender

value: Biphasic MPM


title: HF1-ap

description:
This Sample includes two lanes of sequence.
mRNA
HF1.ap
norm_counts.csv


title: N-TAG ERBB2+ clone #24 HAsiRNA rep2 (n=1)

description:
#14 Neu 24 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 14

source_name: ERBB2 tumor

value: Tagged-Cyclin D1 ERBB2-driven tumor


title: Discovery-MPM-6

tag: sample type


title: Discovery-MPM-8

tag: mesothelioma histotype


title: Discovery-MPM-5


title: M68-Entorhinal Cortex (array)

tag: Sex


title: HF1

description:
This Sample includes two lanes of sequence.
mRNA
HF1
norm_counts.csv

tag: tissue

value: Inguinal white adipose tissue


title: Discovery-MPM-7


title: N-TAG ERBB2+ clone #24 SCRsiRNA rep2 (n=1)

description:
#13 Neu 24 siScr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 13


title: N-TAG ERBB2+ clone #18 HAsiRNA rep2 (n=1)

description:
#12 Neu 18 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 12


title: M20-Entorhinal Cortex (array)


title: CD4

description:
This Sample includes two lanes of sequence.
mRNA
CD4
norm_counts.csv

value: Control diet


title: N-TAG ERBB2+ clone #18 SCRsiRNA rep2 (n=1)

description:
#11 Neu 18 siScr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 11


title: M65-Entorhinal Cortex (array)


title: M67-Entorhinal Cortex (array)


title: M18-Entorhinal Cortex (array)


title: Ctag RAS/DNP53 clone #14 HAsiRNA rep1 (n=6)

description:
#9 MEF RAS Ctag14 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 9


title: CD3-ap

description:
This Sample includes two lanes of sequence.
mRNA
CD3.ap
norm_counts.csv

value: Yes


title: M4-Entorhinal Cortex (array)


title: M2-Entorhinal Cortex (array)


title: Validation-MPM-43

description: Methylation data from pleural mesothelioma sample


title: Discovery-MPM-4


title: Ctag RAS/DNP53 clone #14 SCRsiRNA rep1 (n=3)

description:
#8 MEF RAS Ctag14 siScr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 8


title: Discovery-MPM-3


title: CD2-ap

description:
This Sample includes two lanes of sequence.
mRNA
CD2.ap
norm_counts.csv


title: Ntag RAS/DNP53 clone #27 HAsiRNA rep1 (n=6)

description:
#7 MEF Nt27 Si HA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 7

value: Ntag-Cyclin D1 RAS/DNP53-driven tumor


title: CD2

description:
This Sample includes two lanes of sequence.
mRNA
CD2
norm_counts.csv

value: No


title: Validation-MPM-46


title: M61-Entorhinal Cortex (array)


title: M63-Entorhinal Cortex (array)


title: CD1-ap

description:
This Sample includes two lanes of sequence.
mRNA
CD1.ap
norm_counts.csv


title: RNA_Isl12_Low-dose_dex_24hr

description:
Raw_gene_counts_matrix.txt
TPM_gene_counts_matrix.txt

value: pancreatic islets

tag: source id

tag: study id

value: 4 ng/mL dex, 24hr

tag: donor sex

tag: donor age

tag: islet purity (%)

tag: islet source

value: Prodo Labs


title: Discovery-MPM-2

value: FFPE


title: RNA_Isl12_Untreated

tag: treatment

value: Untreated

value: F


title: M66-Entorhinal Cortex (array)

value: Entorhinal Cortex


title: Ntag RAS/DNP53 clone #27 SCRsiRNA rep1 (n=2)

description:
#6 MEF Nt27 Si Scr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 6

tag: tumor type

tag: tumor treatment

value: SCR-siRNA


title: CD1

description:
This Sample includes two lanes of sequence.
mRNA
CD1
norm_counts.csv

tag: strain

tag: treated with anti-pdgfcc antibody

tag: diet


title: Validation-MPM-36

tag: material type

tag: age

tag: gender

value: M

value: Resection


title: M57-Entorhinal Cortex (array)

tag: Sex

tag: group


title: M30-Entorhinal Cortex (array)

tag: tissue


title: N-TAG ERBB2+ clone #24 HAsiRNA rep1 (n=3)

description:
#4 Neu 24 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 4

value: HA-siRNA


title: Validation-MPM-39

tag: sample type

tag: mesothelioma histotype

value: Biphasic MPM


title: WT RAS/DNP53 clone #25 HAsiRNA rep1 (n=6)

description:
#5 MEF RAS WT25 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 5

value: Untagged-Cyclin D1 RAS/DNP53-driven tumor


title: RNA_Isl12_High-dose_dex_24hr

tag: source id

tag: study id

value: 100 ng/mL dex, 24hr

tag: donor sex

tag: donor age


title: CD4-ap

description:
This Sample includes two lanes of sequence.
mRNA
CD4.ap
norm_counts.csv

value: Inguinal white adipose tissue

value: Yes

value: Control diet


title: M49-Entorhinal Cortex (array)


title: chimera_control_scRNA_seq [F4E5_002]

first: Markus

last: Mittnenzweig

address: 234 Herzl St.

institute: Weizmann Institute of Science

description: single-embryo scMARS-seq of chimera embryos with injected control cells

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively) and concatenated to the fastq header.
3. Read 1 sequences were mapped to the mm9 genome using bowtie2.
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
5. Header structure of labeled Read 1 fastq files: "ORIGINALHEADER_barcode=similar_oligo-pool_barcode_quality-well_barcode_quality-UMI_quality-pool_barcode-well_barcode-UMI". Concatenated entries are separated by "-"
6. well_barcode (7bp), pool_barcode (4bp) and external_barcode (8bp) of each single cell can be found in metadata.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. Supplementary files contain metadata for each single cell are organized in seven files: One file for wildtype embryo plates from BL6 mice, one file for wildtype embryos from ICR mice, four files for chimera or tetraploid embryos injected with Foxc1/2 DKO or control cells. One file for a mixed plate containing cells from tetraploid control and tetraploid DKO embryos

source_name: Mouse embryo

extract_protocol:
single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 2nM poly-dT barcodes, 0.1%triton and RNAse inhibitors.
scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014.

value: BDF1 host blastocyst injected with V6.5 (C57BL/6x129 origin) derived control mescs

value: whole embryo

tag: developmental stage


title: N-TAG ERBB2+ clone #24 SCRsiRNA rep1 (n=3)

description:
#3 Neu 24 siScr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 3

tag: tumor type

value: Tagged-Cyclin D1 ERBB2-driven tumor

tag: tumor treatment


title: RNA_Isl12_Low-dose_dex_6hr

value: pancreatic islets

tag: treatment

value: 4 ng/mL dex, 6hr

tag: islet purity (%)

tag: islet source

value: Prodo Labs


title: Validation-MPM-33

tag: material type

value: FFPE

tag: age

value: F

value: Biopsy


title: N-TAG ERBB2+ clone #18 HAsiRNA rep1 (n=3)

description:
#2 Neu 18 siHA
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 2

tag: strain


title: N-TAG ERBB2+ clone #18 SCRsiRNA rep1 (n=3)

description:
#1 Neu 18 siScr
Raw_Counts_RNA-Seq_Bienvenu_invivo.txt
Sample 1

value: SCR-siRNA


title: chimera_control_scRNA_seq [F4E4_002]


title: RNA_Isl11_Untreated

value: Untreated

value: M


title: Ctag-Cyclin D1 clone #14 Leptomycin B (n=4)

description:
Cells treated with LMB O/N
I2: Ctag 14 + LMB
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 28

data_processing:
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
RNA-seq reads were aligned to the mouse genome (UCSC mm10) with a set of gene model annotations (genes.gtf downloaded from UCSC on May 23 2014; GeneIDs come from the NCBI: gene2refseq.gz downloaded on September 24 2015), using the splice junction mapper TopHat 2.0.13 [1] (with bowtie 2.2.3 [2]). Final read alignments having more than 3 mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode) [3]. Since data come from a strand-specific assay, the read has to be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 20 reads (cumulating all the analysed samples) were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: Text file (tab delimited) with a first column for gene identification. The next columns correspond to the raw counts (non-normalized) for each sample.

source_name: RAS cancer cell line

growth_protocol: Cells were seeded in the morning into 6-well plates at 80% confluency the day before the RNAs were collected. In the evening cells were treated or not.

extract_protocol:
Cells were harvested in the morning of the day after siRNA transfection or treatment and total RNAs was extracted using Trizol reagent.
The libraries were prepared with the TruSeq Stranded mRNA sample prep kit from illumina according to the manufacture's instructions. After oligo d(T) purification, mRNA was fragmented by zinc. cDNA was synthesized using random primer. Adapters are then ligated and PCR cycles were performed to enrich the library. The libraries were sequenced on a HiSeq 2500 instrument (from illumina) in a single read 1x100bp. The v3 chemistry was used according to manufacture's instructions.

treatment_protocol: The evening of the seeding day, cells were transfected over night using Lipofectamin (RNAiMAX) or treated with Leptomycin B at 20ng/mL.

tag: cell line

value: RAS cancer cell line

tag: cell type

value: transformed MEFs

value: Treated with Leptomycin B


title: chimera_control_scRNA_seq [F4E5_001]

tag: tissue


title: chimera_control_scRNA_seq [F4E4_001]


title: RNA_Isl11_High-dose_dex_24hr

value: 100 ng/mL dex, 24hr


title: chimera_control_scRNA_seq [F4E2_002]


title: M59-Entorhinal Cortex (array)

tag: Sex

tag: group

value: Entorhinal Cortex


title: Ctag-Cyclin D1 clone #14 Untreated (n=4)

description:
Cells untreated
I1: Ctag 14 Non traité
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 27

value: no treatment


title: RNA_Isl11_Low-dose_dex_6hr

tag: source id

tag: study id


title: RNA_Isl11_Low-dose_dex_24hr

value: 4 ng/mL dex, 24hr

tag: donor sex

tag: donor age


title: Validation-MPM-32

description: Methylation data from pleural mesothelioma sample

tag: gender

tag: sample type

tag: mesothelioma histotype

value: Biphasic MPM


title: Validation-MPM-34


title: Validation-MPM-37

value: Resection


title: M47-Entorhinal Cortex (array)


title: M58-Entorhinal Cortex (array)


title: M62-Entorhinal Cortex (array)


title: Validation-MPM-31


title: Ctag-Cyclin D1 clone #12 Leptomycin B (n=4)

description:
Cells treated with LMB O/N
H2 du 23/03: Ctag 12 + LMB
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 26

tag: treatment


title: M60-Entorhinal Cortex (array)


title: Discovery-MPM-1


title: RNA_Isl10_Untreated

value: pancreatic islets

tag: islet purity (%)

tag: islet source

value: Integrated Islet Distribution Program


title: Ctag-Cyclin D1 clone #12 Untreated (n=4)

description:
Cells untreated
H1 du 23/03: Ctag 12 Non Traité
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 25


title: RNA_Isl10_Low-dose_dex_24hr


title: Untagged-Cyclin D1 clone #18 + FLAG-mCherry-HA/PURO FLAG-siRNA REP2 (n=3)

description:
Cells treated with siRNA O/N
H1: tag-mcherry2 + F3
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 24

value: FLAG-RNAi


title: Validation-MPM-29

tag: material type

value: FFPE

tag: age

value: F


title: Validation-MPM-30

value: Biopsy


title: RNA_Isl10_High-dose_dex_24hr


title: tetraploid_foxc12_dko_scRNA_seq [3011f7e2_p17]

description: single-embryo scMARS-seq of tetraploid embryos with injected Foxc1/2 DKO cells

tag: strain

value: BDF1 4N host blastocyst injected with V6.5 (C57BL/6x129 origin) derived Foxc12 dko mescs

value: whole embryo

tag: developmental stage


title: RNA_Isl10_Low-dose_dex_6hr

description:
Raw_gene_counts_matrix.txt
TPM_gene_counts_matrix.txt

tag: tissue

value: 4 ng/mL dex, 6hr


title: tetraploid_foxc12_dko_scRNA_seq [3011f7e2_p16]


title: chimera_control_scRNA_seq [F4E1_001]

value: BDF1 host blastocyst injected with V6.5 (C57BL/6x129 origin) derived control mescs


title: ATAC_Isl12_Untreated

value: Untreated

value: Prodo Labs


title: ATAC_Isl12_Low-dose_dex_6hr


title: CD3

description:
This Sample includes two lanes of sequence.
mRNA
CD3
norm_counts.csv

value: Inguinal white adipose tissue

tag: treated with anti-pdgfcc antibody

value: No

tag: diet

value: Control diet


title: ATAC_Isl11_Untreated

tag: source id

value: M


title: ATAC_Isl11_Low-dose_dex_6hr

tag: study id


title: chimera_control_scRNA_seq [F4E2_001]


title: ATAC_Isl10_Untreated

tag: donor sex


title: ATAC_Isl10_Low-dose_dex_6hr

tag: donor age


title: Untagged-Cyclin D1 clone #18 + FLAG-mCherry-HA/PURO HA-siRNA REP1 (n=3)

description:
Cells treated with siRNA O/N
D1: Tag-mCherry1 + HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 20

tag: cell line

value: RAS cancer cell line

tag: cell type

value: transformed MEFs

value: HA-RNAi


title: Untagged-Cyclin D1 clone #18 HA-siRNA (n=3)

description:
Cells treated with siRNA O/N
F3: WT 18 + HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 18


title: Untagged-Cyclin D1 clone #18 + FLAG-mCherry-HA/PURO HA-siRNA REP2 (n=4)

description:
Cells treated with siRNA O/N
H2: tag-mcherry2 + HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 22


title: Untagged-Cyclin D1 clone #18 FLAG-siRNA (n=4)

description:
Cells treated with siRNA O/N
F2: WT 18 + F3
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 17

value: FLAG-RNAi


title: Untagged-Cyclin D1 clone #18 + mCherry/PURO FLAG-siRNA REP2 (n=4)

description:
Cells treated with siRNA O/N
G1: mcherry2 + F3
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 23


title: Untagged-Cyclin D1 clone #18 + mCherry/PURO HA-siRNA REP1 (n=3)

description:
Cells treated with siRNA O/N
C1: mCherry1 + HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 19


title: Untagged-Cyclin D1 clone #18 + mCherry/PURO HA-siRNA REP2 (n=4)

description:
Cells treated with siRNA O/N
G2: mcherry2 + HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 21


title: tetraploid_control_scRNA_seq [3011f6e5_p12]

description: single-embryo scMARS-seq of tetraploid embryos with injected control cells

value: BDF1 4N host blastocyst injected with V6.5 (C57BL/6x129 origin) derived control mescs


title: tetraploid_control_scRNA_seq [3011f6e2_p10]


title: tetraploid_control_scRNA_seq [3011f6e6_p15]


title: tetraploid_control_scRNA_seq [3011f6e2_p11]


title: Ishikawa

city: Fukushima

first: Hideki

last: Chiba

address: 1 Hikarigaoka

country: Japan

institute: Fukushima Medical University

description:
No treatment
Ishikawa_RNAseq.txt

data_processing:
RNA sequencing and mapping were performed by TaKaRa Bio Inc. For mapping, the index trimmed singleend 100 bp reads were aligned to the human reference genome (GRCh38 v90) to generate bam files.
The mapped bam files were imported to SeqMonk software (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) as single ended RNA-Seq data.
Quantification was performed by using the default RNA-Seq quantitation pipeline.
P-value was calculated from the intensity difference and representative genes of showing significant change (P<0.05)
Genome_build: GRCh38 v90
Supplementary_files_format_and_content: Matrix table with gene expression ratio for every gene

source_name: Ishikawa

growth_protocol: Roswell Park Memorial Institute 1640 medium supplimented with 10% Fetal bovine serum and 1% penicillin streptomycin

extract_protocol:
Total RNA isolaton was performed using TRIzol reagent (Thermo Fisher) followed by manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CLDN6 lentiviral vector was generated by transfecting HEK293T cells with 10 μg of the CSII plasmids containing the target genes, 5 μg of packaging plasmids psPAX2 (Addgene, #12260) and pCMV-VSV-G (Addgene, #8454) using PEI Max. Culture media containing recombinant lentiviruses were collected 72 h after transfection. The lentiviral vectors were added to cell culture medium after filtration.

value: Ishikawa

tag: disease state

value: Endometrial adenocarcinoma

tag: genotype/variation

value: WT


title: tetraploid_control_scRNA_seq [3011f6e6_p14]

city: Rehovot

value: whole embryo


title: M45-Entorhinal Cortex (array)

tag: Sex

value: F

tag: group

value: Entorhinal Cortex


title: tetraploid_control_scRNA_seq [3011f6e5_p13]


title: tetraploid_control_scRNA_seq [3011f5e2_p08]


title: tetraploid_control_scRNA_seq [3011f5e2_p09]


title: Ishikawa:CLDN6_Rep1

description:
Transient overexpression of CLDN6 in Ishikawa
Ishikawa_RNAseq.txt


title: Untagged-Cyclin D1 clone #18 SCR-siRNA (n=3)

description:
Cells treated with siRNA O/N
F1: WT 18 + SCR
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 16

tag: treatment

value: SCR-RNAi


title: Untagged-Cyclin D1 clone #25 SCR-siRNA (n=3)

description:
Cells treated with siRNA O/N
B1: WT 25 + SCR
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 13


title: Untagged-Cyclin D1 clone #25 FLAG-siRNA (n=4)

description:
Cells treated with siRNA O/N
B2: WT 25 + F3
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 14


title: tetraploid_foxc12_dko_scRNA_seq [3011f4e5_p07]

value: BDF1 4N host blastocyst injected with V6.5 (C57BL/6x129 origin) derived Foxc12 dko mescs


title: Untagged-Cyclin D1 clone #25 HA-siRNA (n=4)

description:
Cells treated with siRNA O/N
B3: WT 25 + HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 15


title: Ctag-Cyclin D1 clone #14 Life-siRNA (n=4)

description:
Cells treated with siRNA O/N
E6: CTAG 14 Life
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 12

value: Life Technologies Cyclin D1-RNAi


title: M42-Entorhinal Cortex (array)


title: M41-Entorhinal Cortex (array)


title: M50-Entorhinal Cortex (array)


title: M46-Entorhinal Cortex (array)


title: M44-Entorhinal Cortex (array)


title: M35-Entorhinal Cortex (array)


title: Ishikawa:CLDN6_Rep2


title: M40-Entorhinal Cortex (array)


title: M39-Entorhinal Cortex (array)


title: M36-Entorhinal Cortex (array)


title: tetraploid_foxc12_dko_scRNA_seq [3011f4e5_p06]

description: single-embryo scMARS-seq of tetraploid embryos with injected Foxc1/2 DKO cells


title: Ctag-Cyclin D1 clone #14 Nature-siRNA (n=4)

description:
Cells treated with siRNA O/N
E5: CTAG 14 Nature
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 11

value: Published Nature Cyclin D1-RNAi


title: CD44 negative pediatric posterior fossa ependymoma_5

city: tianjin

first: chang

last: shu

address: 94 weijin road

institute: Tianjin HuanHu hospital,School of medicine,Nankai university

description: microRNA expression analysis.

hyb_protocol: Labeled cRNA was hybridezed using miRNA complete Labeling and Hyb Kit（24×） according to the manufacturer protocol.

scan_protocol: microRNA microarrys were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantile normalized for every comparison using only the relevant samples for the respective comparison

source_name: frozen tumor tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Only samples with more than 80% tumor cells were selected for RNA extraction. Total RNA from frozen tumor samples was extracted using the mirVana miRNA Isolation kit (Ambion) according to the manufacturer’s protocol. RNA concentration and quality were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). And quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male


title: Ctag-Cyclin D1 clone #14 Qiagen-siRNA (n=4)

description:
Cells treated with siRNA O/N
E4: CTAG 14 Qiagen
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 10

tag: strain

value: Qiagen Cyclin D1-RNAi


title: tetraploid_foxc12_dko_scRNA_seq [3011f4e2_p04]

tag: developmental stage


title: CD44 negative pediatric posterior fossa ependymoma_6

description: microRNA expression analysis.

tag: tissue


title: M48-Entorhinal Cortex (array)

source_name: Entorhinal Cortex


title: tetraploid_foxc12_dko_scRNA_seq [3011f4e2_p05]


title: M38-Entorhinal Cortex (array)


title: M37-Entorhinal Cortex (array)


title: tetraploid_foxc12_dko_scRNA_seq [3011f4e2_p03]


title: M23-Entorhinal Cortex (array)


title: mixed_plate_control_and_foxc12_dko_scRNA_seq [3011f2e2_p02]

description: mixed plate wih cells from control and dko embryo

value: plate including 2 4N injected embryos as above, one embryo injected with foxc12 dko cells. And another with control mescs


title: CD44 negative pediatric posterior fossa ependymoma_3

description: microRNA expression analysis.


title: CD44 negative pediatric posterior fossa ependymoma_4

description: microRNA expression analysis.

value: female


title: tetraploid_foxc12_dko_scRNA_seq [3011f2e1_p01]


title: CD44 negative pediatric posterior fossa ependymoma_1

description: microRNA expression analysis.


title: Ctag-Cyclin D1 clone #14 FLAG-siRNA (n=4)

description:
Cells treated with siRNA O/N
E2: CTAG 14 F3
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 8

value: RAS cancer cell line

value: transformed MEFs


title: CD44 negative pediatric posterior fossa ependymoma_2

description: microRNA expression analysis.


title: Ctag-Cyclin D1 clone #12 Life-siRNA (n=3)

description:
Cells treated with siRNA O/N
A6: CTAG 12 + Life
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 6


title: Roquin-1 san:san macrophage derived exosomes2

city: Shanghai

first: Lei

address: 639 Zhizaoju Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medi-cine

data_processing:
The original image data obtained by Illumina sequencing is transformed into sequence data by Base Calling, namely the FASTQ format, to obtain the most original sequencing data file.
The original FASTQ data contains low-quality reads with joints. In order to ensure the accuracy of subsequent bioanalysis, quality control (QC) should be carried out on raw reads to obtain high-quality sequencing results (clean reads), and subsequent bioanalysis should be carried out based on clean reads. The quality control steps are as follows: 1) Removal of the 3 'joint sequence in reads, and removal of reads without inserted fragments due to reasons such as joint self-connection; 2) Cut the bases with low sequencing quality at the 3 'end (< 20); 3) Removal of reads containing unknown base N; 4) Removal of excessively short reads(<18nt); 5) Removal of excessively long reads(>32nt);
For the clean reads obtained, the reads with the same sequence were combined to obtain unique sequences, which were used to calculate the types and abundance of small RNA in the samples, and the types and distribution of common small RNA sequences and their own unique small RNA sequences among the samples.
The software was used to analyze and statistically the distribution of all clean reads measured by sequencing, and the preference information of miRNA could be obtained, so as to understand the processing and mechanism of miRNA, and at the same time, it could indirectly reflect the sample quality, database construction and accuracy of sequencing experiments.
Using the latest Rfam (12.1, http://Rfam.sanger.ac.uk/) database to annotation of measured small RNA, removal of the miRNA sequences, such as rRNA, snRNA, tRNA, ribozyme etc, but also compared to the types and number of miRNA sequences on the statistics.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

source_name: Roquin-1 san:san Bone marrow derived macrophage supernatant

extract_protocol: miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: sample type

tag: genotype

value: Roquin-1 san:san


title: Ctag-Cyclin D1 clone #12 Nature-siRNA (n=4)

description:
Cells treated with siRNA O/N
A5: CTAG 12 + Nature
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 5


title: Ctag-Cyclin D1 clone #12 Qiagen-siRNA (n=4)

description:
Cells treated with siRNA O/N
A4: CTAG 12 + Qiagen
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 4


title: Roquin-1 san:san macrophage derived exosomes3

value: Bone marrow derived macrophage supernatant


title: Ctag-Cyclin D1 clone #14 HA-siRNA (n=4)

description:
Cells treated with siRNA O/N
E3: CTAG 14 HA5
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 9

value: HA-RNAi


title: Roquin-1 san:san macrophage derived exosomes1


title: CD44 positive pediatric posterior fossa ependymoma_6

description: microRNA expression analysis.


title: CD44 positive pediatric posterior fossa ependymoma_5

description: microRNA expression analysis.


title: M21-Entorhinal Cortex (array)

first: Emma

address: RILD Barrack Rd

institute: University of Exeter


title: WT macrophage derived exosome3

source_name: WT Bone marrow derived macrophages supernatant

value: Bone marrow-derived macrophage supernatant

value: WT


title: CD44 positive pediatric posterior fossa ependymoma_4

description: microRNA expression analysis.


title: Ctag-Cyclin D1 clone #14 SCR-siRNA (n=4)

description:
Cells treated with siRNA O/N
E1: CTAG 14 SCR
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 7


title: CD44 positive pediatric posterior fossa ependymoma_3

description: microRNA expression analysis.


title: M7-Entorhinal Cortex (array)

value: F


title: WT macrophage derived exosome2


title: CD44 positive pediatric posterior fossa ependymoma_2

description: microRNA expression analysis.


title: Ctag-Cyclin D1 clone #12 FLAG-siRNA (n=4)

description:
Cells treated with siRNA O/N
A2: CTAG 12 + F3
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 2

value: FLAG-RNAi


title: M17-Entorhinal Cortex (array)

value: Entorhinal Cortex


title: M5-Entorhinal Cortex (array)


title: WT macrophage derived exosome1


title: Ctag-Cyclin D1 clone #12 SCR-siRNA (n=4)

description:
Cells treated with siRNA O/N
A1: CTAG 12 + SCR
Raw_Counts_RNA-Seq_Bienvenu_invitro.txt
Sample 1

value: SCR-RNAi


title: M16-Entorhinal Cortex (array)


title: chimera_control_scRNA_seq [F4E1_002]

description: single-embryo scMARS-seq of chimera embryos with injected control cells

value: BDF1 host blastocyst injected with V6.5 (C57BL/6x129 origin) derived control mescs

value: whole embryo