title: 200669330052_L: mock14_14

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: iScan array scanner

data_processing: Bead-level microarray raw data have been converted to expression values using the lumi R package for quality control, variance stabilization, normalization, and gene annotation

source_name: Primary CD4 positive T-cell

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

growth_protocol: RPMI + 20% FCS + Il-2

extract_protocol: InviTrap Spin Universal RNA Mini Kit

treatment_protocol: for infected samples: 2 ng/p24 per million cells

value: Primary CD4 positive T-cell

tag: donor

tag: day


title: 200669330052_K: mock14_9

status: Public on Jun 14 2021

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment

value: Mock


title: LN6-877AL

type: SRA

city: Palo Alto

first: Nathan

middle: Edward

last: Reticker-Flynn

state: CA

address: 3373 Hillview Ave

department: Pathology

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Raw sequencing reads were filtered and adapters trimmed using Trimmomatic v0.36. Quality was assessed using FastQC v0.11.3.
Transcript abundance was quantified using Salmon v0.7.2 in quasi-mapping mode and using the sequence, GC, and position bias correction parameters.Mitochondrial reads were removed and TPM values were re-normalized following their removal.
Differential expression analysis was performed using DESeq2.
Genome_build: GRCm38 GENCODE release M11
Supplementary_files_format_and_content: tab-delimeted files contain TPM values for each sample generated by Salmon, renormalized after removal of "mt-" transcripts.

organism: Mus musculus

source_name: melanoma

growth_protocol: All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin

extract_protocol:
Cell lines were trypsinized, washed with complete serum, centrifuged, and washed with PBS. Following washing cell pellets were frozen at -80C. After thawing, cells were resuspended in buffer RLT and lysed using QiaShredders. Extraction was performed using the Qiagen RNEasy Plus mini kit according to the manufacturer's protocol.
Library construction was performed by Centrillion Genomic Services using the Illumina TruSeq RNA Sample Prep Kit

tag: strain

tag: generation


title: 200669330052_I: inf14_14

value: HIV-1 infected


title: MeNQ 1500 mg/L, Rep3

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: An Agilent Technologies (Agilent Technologies, Santa Clara, CA, USA) single color custom 8 x 60K microarray format (Amadid #: 063815) was used for all investigations.  A completely randomized design was utilized for microarray hybridizations where each individual D. pulex sample was selected at random (using a random number generator) for hybridization onto individual microarrays.  The Agilent Low Input Hybridization Kit (one color) was used for microarray hybridizations following manufacturer’s recommendations.  A total of 24 microarrays were hybridized which included four replicates for all MeNQ exposures including the control (0 mg/L), 174, 346, 709, 1385, and 2286 mg/L exposure treatments.

scan_protocol: An Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C) was used to scan microarray images at 2 μm resolution.  Data were extracted from microarray images using Agilent Feature Extraction software, version 10.7.3.1.

data_processing: Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX 14.9 (Agilent Technologies).  GeneSpring was also utilized for the expression analysis where a one-way ANOVA was conducted (p = 0.01) including Benjamini-Hochberg multiple-tests corrections.  Post-hoc tests were also conducted where the SNK test was utilized to determine which transcripts had significant differential expression relative to the 0 mg/L control.

organism: Daphnia pulex

source_name: whole animal

label_protocol: The Agilent Low Input Quick Amp Labeling Kit (one color) protocol was followed using 65 ng of total RNA as starting material from each biological sample.

growth_protocol: Daphnia pulex were obtained from in-house cultures (originally purchased from EC Testing) and reared in accordance with guidance in Laird et al. (2015).  REFERENCE:  Laird JG, Kennedy AJ, Melby NL, Gong P.  2015. Development of a Chronic Toxicity Testing Method for Daphnia pulex, US Army, Engineer Research and Development Center Report.  ERDC/EL SR-15-5. pp 1-25.

extract_protocol: The D. pulex samples were flash frozen in liquid nitrogen and stored at -80°C until RNA extractions were conducted.  Frozen samples were homogenized using disposable mortar and pellet pestles for each sample (Kimble Kontes, Vineland, NJ).  Total RNA isolation and on-column DNase digestion was conducted using the Qiagen RNeasy Mini Kit (Qiagen, Germantown, MD) following manufacturer’s recommendations.  RNA quantity was assessed using a NanoDrop One Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA) and final quality was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) where electrophoresis gels were visually inspected for degradation prior to use in downstream applications.

treatment_protocol: MeNQ (CAS Number 4245-76-5) was obtained from a commercial vendor (TCI America, product number M0749).  According to manufacturer specifications, this MeNQ was 98% pure and was hydrated (25% of mass as water) for safety purposes. MeNQ was used as received from the vendor for preparation of exposure solutions. Water used for preparation of stock solutions and for the control exposures was tap water (City of Vicksburg, MS, municipal source) dechlorinated using carbon filtration for all toxicity bioassays. For the D. pulex bioassay, standard synthetic freshwater bioassay medium (moderately hard reconstituted water) was used (USEPA 2002).  Bioassays were conducted at a target temperature of 25 °C for 11 d as this period was required to acquire 3 broods. Exposures were performed in 50 mL beakers with a test solution volume of 40 mL. One test animal was exposed in each beaker, and 10 replicate beakers were tested per treatment. The daily feeding ration mixture consisting of half Raphidocelis subcapitata and half yeast, cereal leaves, and trout chow fish food. Complete water renewals were conducted three times a week on Mondays, Wednesdays and Fridays.  The reproductive output was quantified as the total number of neonates produced in three broods per parental adult that survived to assay completion.  D. pulex were exposed to MeNQ at control (0 mg/L), 174, 346, 709, 1385, and 2286 mg/L (measured concentrations) as juveniles through three-broods of reproduction.   The reproduction assays included 20 animals exposed individually per treatment.  The animals remaining at the termination of the assay were randomly assigned to a set of 4 replicate groups of animals per treatment to serve as treatment replicates in the transcriptomic-expression experimental design (6 treatments x 4 replicates).  REFERENCE:  U.S. Environmental Protection Agency (2002) Methods for measuring the acute toxicity of effluents and receiving waters to freshwater and marine organisms. EPA-821-R-02-012, 5th ed. Office of Water, Washington, DC.

tag: age

value: adult


title: 1479_PK_CD4

city: La Jolla

first: Rekha

last: Dhanwani

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Do not have consent from patient to submit raw data

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Peripheral Blood

growth_protocol: Frozen PBMCs were thawed,stained for T cell surface and memory markers, and sorted in Trizol.

extract_protocol:
100,000 PBMCs, CD4 and CD8 memory T cells were sorted and collected in Trizol in a 1.5 ml tube. Tubes were vortexed, spun and stored at -80C until processed. RNA was extracted using RNA microRNA kit (Qiagen) on a Qiacube.
Purified total RNA was amplified following the smart-seq2 protocol. cDNA was purified using AMPure XP beads, and barcoded Illumina sequencing libraries were generated, loaded and sequenced on the Illumina sequencing platform HiSeq 2500.

treatment_protocol: No treatment

value: CD4 memory

tag: gender

value: M


title: LN6-880AL


title: 1477_PK_CD4


title: LN6-987AL


title: 2457_PK_CD4


title: 1430PK_CD4_Park1


title: LN5-716BR


title: MeNQ 1500 mg/L, Rep2


title: 200669330052_H: inf14_9


title: 1429PK_CD4_Park1


title: LN5-712AL


title: 1423PK_CD4_Park1


title: MeNQ 0 mg/L, Rep4


title: MeNQ 3000 mg/L, Rep3


title: LN5-809CL


title: 200669330052_F: mock13_14


title: 200669330052_G: inf14_7


title: 200669330052_J: mock14_7


title: MeNQ 3000 mg/L, Rep2


title: LN4-521BL


title: MeNQ 187.5 mg/L, Rep2


title: 1416PK_CD4_Park1

value: F


title: MeNQ 750 mg/L, Rep2


title: 200669330052_D: mock13_7


title: 200669330052_E: mock13_9


title: LN4-533BL


title: 200669330052_B: inf13_9


title: MeNQ 750 mg/L, Rep3


title: 200669330052_C: inf13_14


title: MeNQ 750 mg/L, Rep1


title: 1414PK_CD4_Park1


title: MeNQ 0 mg/L, Rep1


title: LN4-473BL


title: MeNQ 187.5 mg/L, Rep1


title: 1413PK_CD4_Park1


title: LN3-377IR


title: LN3-392AL


title: 1421PK_CD4_Park1


title: 1066_PK_CD4


title: ChIP-seq_Crotonate-input

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

country: China

institute: institute of zoology,Chinese academy of sciences

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with default parameters. MACS (v.2.2.7.1) was used to call peaks (-q 0.05) relative to the input sample.
Genome_build: GRCm38
Supplementary_files_format_and_content: bw, Peaks.txt

molecule: genomic DNA

source_name: E13.5 Forebrain

growth_protocol: NSPCs isolated from the E13.5 mice forebrain were cultured with DMEM/F12 medium (Invitrogen) supplemented with 20 ng/ml epidermal growth factor and 20 ng/ml fibroblast growth factor (EGF/FGF, PeproTech), 1% penicillin/streptomycin (Invitrogen), 0.5× B27 (Invitrogen), and 0.5× N2 (Invitrogen).

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 5’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

treatment_protocol: Briefly, NSPCs (passage 2–3) were grown to 50–60% confluence in 10-cm plates, and were treated with water (control group) and 10 mM crotonate (crotonate group) for 24 h.

value: Embryonic Neural Stem/Progenitor Cells (eNSPCs)

value: Crotonate

tag: chip antibody


title: ChIP-seq_Crotonate-H3K27me3

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 4’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

tag: chip antibody vendor

value: PTM Biolab, Hangzhou, China

tag: chip antibody catalog#


title: 1077_PK_CD4


title: ChIP-seq_Crotonate-H3K27ac

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.


title: 3498_CD4


title: ChIP-seq_Crotonate-H3K9cr


title: 3487_CD4


title: ChIP-seq_Crotonate-H3K4me3


title: MeNQ 3000 mg/L, Rep1


title: LN2-225IR


title: MeNQ 1500 mg/L, Rep1


title: 3331_CD4


title: G1 siSTAT rep2

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

description: SAMPLE 11

hyb_protocol: RNA samples were labeled, hybridized to Illumina Human HT12 v4 Beadarrays and scanned at the Cambridge Genomic Center, UK

data_processing: The Bioconductor packages beadarray and lumi were used to perform quality control and preprocessing.

source_name: G1 siSTAT

growth_protocol: human melanoma, patient derived cell lines: WM 902B and T1 (primary melanoma) and WM 239A and G1 (metastatic melanoma). Cells were cultured in RPMI 1640 medium supplemented with 10% FBS (Sigma, Chemical Co., St. Louis, MO) and antibiotics (50 U/ml penicillin and 50 g/ml streptomycin), in a humidified atmosphere of CO2/air (5%/95%) at 37°C. Melanoma cells were passaged weekly, and seeded for experiments at concentration 105 cells/plate

extract_protocol: Total RNA was isolated using The High Pure RNA Isolation Kit (Qiagen). The quality and quantity of total RNA were verified by the Agilent 2100 Bioanalyzer electrophoresis.

treatment_protocol: Cells were transfected with control siRNA or STAT3 siRNA(Santa Cruz Biotechnology, Santa Cruz, CA, USA) at the final concentration of 150 nM using the Cell Line Nucleofector Kit V (Lonza). STAT3 siRNA was a mixture of three different siRNAs specifc for STAT3. Samples were collected 48 h after transfection.

tag: cell line

value: metastatic melanoma

tag: genotype

value: silenced for STAT3


title: 200669330052_A: inf13_7


title: G1 siSTAT rep3

description: SAMPLE 12

scan_protocol: RNA samples were labeled, hybridized to Illumina Human HT12 v4 Beadarrays and scanned at the Cambridge Genomic Center, UK


title: 3035_PK_CD4


title: ChIP-seq_Control-input

value: Control


title: G1 siControl rep2

description: SAMPLE 8

source_name: G1 siControl

label_protocol: RNA samples were labeled, hybridized to Illumina Human HT12 v4 Beadarrays and scanned at the Cambridge Genomic Center, UK

value: control


title: 2933_PK_CD4


title: LN2-189ILR


title: G1 siControl rep1

description: SAMPLE 7


title: G1 siSTAT rep1

description: SAMPLE 10


title: LN1-24IR


title: W239 siSTAT rep3

description: SAMPLE 6

source_name: W239 siSTAT

value: primary melanoma in the vertical growth phase


title: LN2-262IL


title: ChIP-seq_Control-H3K27me3

value: Active Motif


title: LN1-18IL


title: 2885_PK_CD4


title: 2862_CD4


title: W239 siSTAT rep2

description: SAMPLE 5


title: ChIP-seq_Control-H3K27ac

value: Abcam


title: LN3-384IR


title: LN1-16IL


title: 2852_CD4


title: ChIP-seq_Control-H3K4me3


title: 2791_CD4


title: W239 siSTAT rep1

description: SAMPLE 4


title: LN1-15IL


title: Cancer condition medium no lipid_3

city: Epalinges

first: Ping-Chih

last: Ho

state: Vaud

address: Ch. des Boveresses 155

department: Department of Fundamental Oncology

country: Switzerland

institute: University of Lausanne

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Genome_build: Mus musculus GRCm38.p4 genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Bone-marrow derived macrophages (BMDM)

growth_protocol: The bone-marrow derived macrophages obtained from bone marrow of C57BL/6/J mice were cultured 6h days in DMEM with high glucose, 10% fetal bovine serum, and 100 U/ml penicillin and 100 µg/ml streptomycin in presence of 20% L929 condition-medium, in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.
Total RNA was used for library construction via TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: At day 6 BMDM were detached and seeded in 12 well plate (800.000 cells per well). After 6h, BMDM were stimulated with cancer--cell derived CM in presence of lipids (CM)  or in absence of lipids (CM w.o. Lipids)

value: Bone-marrow derived macrophages (BMDM)

value: 7 weeks

tag: tissue

value: bone marrow

tag: growth

value: Cancer condition medium - no lipid


title: W239 siControl rep3

description: SAMPLE 3

source_name: W239 siControl


title: Cancer condition medium no lipid_2


title: 2781_CD4

value: CD4 memory


title: W239 siControl rep2

description: SAMPLE 2


title: Cancer condition medium no lipid_1


title: W239 siControl rep1

description: SAMPLE 1


title: B16-F0 #2


title: B16-F0 #1


title: 2635PK_CD4_Park1


title: Cancer condition medium_3

value: Cancer condition medium


title: 27703 RNA-seq KO Act B cell

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: SuperScript® VILO™ cDNA Synthesis, strand-specific

data_processing:
ChIP-seq and DHS-seq: Sequence reads that passed the Illumina quality filtering were considered for alignment. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (ref. 18). The Pax5 Bio-ChIP-seq data generated with FO B cells stimulated with anti-CD40 plus IL-4 for 2 days were trimmed to 36-mers and aligned as single end sequences, to make them comparable to the already published mature B cell ChIP-seq data (GSM932925-GSM932931). Peaks were called using the MACS program version 1.3.6.1 (ref. 21) with default parameters, a read length of 36 or 76, a mature B cell input14 and a genome size of 2.654.911.517 bp (mm9). For the analysis of DHS data, the read shifting model building was turned off. Peaks were further filtered for P values of < 10-10. ATAC-seq: The sequence data were down-sampled to 20.040.789 reads (corresponding to the sample size of the mature B cell experiment; GSM932925-GSM932931), and peaks were called with MACS_1.3.6.1, using only the first read of each fragment, and the sequencing data of mature B cells (GSM2058441) as input.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.6.1p1 (ref. 28) with the overlap resolution mode set to ‘union’. The datasets were grouped according to genotype and type of stimulation and were analyzed using the R package DESeq2 version 1.8.2 (ref. 29). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Variance stabilizing transformations were computed with the blind option set to ‘FALSE’. Variance stabilized counts were transformed from log2 to log10 scale for the scatterplots shown in Supplementary Figs. 4f, 6a and 8a. The default DESeq2 pair-wise setup (model design formula: “~ genotype”; Wald test) was used for comparison of the RNA-seq data of knockout (Cd23-Cre Pax5fl/–) versus control (Cd23-Cre Pax5fl/+) activated B cells stimulated for 2 days with anti-CD40 and IL4. Untreated and 1-hour anti-IgM-stimulated knockout and control lymph node B (LN B) cells were analyzed, considering the main effects of the genotype (I, II) and time (III, IV) as well as their ‘interaction’ effect, which quantifies if the time effect differs across genotype (model design formula: “~ genotype + time + genotype:time”; Wald tests). If not mentioned otherwise, genes with an adjusted P value < 0.05 and an absolute fold change > 3 as well as a mean TPM (averaged within conditions) > 5 were called as significantly expressed. Immunoglobulin and T cell receptor genes were filtered from the list of significantly expressed genes, but were included in the TPM calculations.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million after extension to 150 base pairs (.density_150.rpm.bw); text tab delim = TPM values in ASCII text format tab delimited

molecule: polyA RNA

source_name: stimulated B cell

extract_protocol: About 1-5 ng of cDNA, (Bio-)ChIP-precipitated DNA or DHS-enriched DNA were used as starting material for generating sequencing libraries with the NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module, as described17. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England BioLabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer's guidelines

value: Cd23-Cre Pax5(F/-)

tag: cell preparation

value: CD43 depleted, 1-hour anti-IgM stimulation

tag: cell sorting strategy

value: CD43 depletion MACS sort


title: ChIP-seq_Control-H3K9cr

value: Embryonic Neural Stem/Progenitor Cells (eNSPCs)

value: PTM Biolab, Hangzhou, China


title: Cancer condition medium_1


title: PB31_41C_rep2

city: Tampa

first: Jenna

last: Oberstaller

state: FL

address: 3720 Spectrum Blvd.

department: Genomics

institute: University of South Florida

data_processing:
RNA-seq reads from each sample were aligned to the P. falciparum reference genome using TopHat (v. 2.1.1). A maximum of one mismatch per read was allowed.
Mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using Cufflinks (v. 2.2.1). The expression level of each gene was normalized as FPKM (fragments per kilobase of exon per million mapped reads).
Filtering low-expressed genes: We defined expressed genes as those having FPKM > 20 for at least one biological replicate at either 37°C or 41°C. Genes not meeting these criteria were filtered out.
Calculating fold-change in response to heat shock: The fold change of normalized gene expression between 41°C and 37°C was calculated for every biological replicate. Fold-change for genes not expressed in both temperatures was set equal to one. We conservatively filtered out genes in the top and bottom 10% of fold-change to remove outliers.
Calculating significance of fold-change: We then fit a Gaussian model to the log2 fold change (log2FC) for every biological replicate using maximum log likelihood estimation to assess the fold-change distribution. The p-value is calculated as the probability of estimated gaussian distribution higher than the observed log2FC (when observed log2FC  the expection of estimated gaussian distribution), or lower than the observed log2FC (when observed log2FC  the expection of estimated gaussian distribution). The false discovery rate (FDR) was calculated for each replicate.
Assigning heat-shock categories: We defined genes for which FDR < 0.1 in both biological replicates as having significant fold-change in response to HS. Genes were assigned HS phenotype-categories based on significance and direction of HS-response.
Genome_build: P. falciparum reference genome (PlasmoDB version 28, RRID:SCR_013331)
Supplementary_files_format_and_content: RNAseq_data_processed.xlsx contains FPKM data, fold-change data, and heat shock classification assigned for all genes with expression above threshold in at least one of the three parasite-lines as measured by RNAseq (FPKM > or = 20 for at least one replicate in at least one temperature-condition).

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

growth_protocol: Parasite cultures were maintained according to standard methods with gassing (5% O2 and 5% CO2, nitrogen balanced) and 5% hematocrit (O+ blood; Interstate Blood Bank) in RPMI 1640 medium (Invitrogen) supplemented with 0.5% Albumax II (Invitrogen), 0.25% sodium bicarbonate, and 0.01 mg/ml gentamicin. Cultures not undergoing heat shock were maintained at 37°C.

extract_protocol:
Parasites were separated from red blood cells via incubation with 0.015% saponin at room temperature for 5 min. Cultures were then pelleted and washed three times in 10 mL room temperature PBS. Samples were stored at − 80 °C in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. At RNA extraction, 200 μl of chloroform was added and samples were vortexed vigorously for 15 seconds, followed by incubation at room temperature for up to 5 minutes. Samples were then spun down at 12000×g (10,800 rpm) at 4 °C for 10 minutes and the supernatant discarded. 1 mL of 75% ethanol was added to the pellet, and samples were spun down at 10000×g (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry. The RNA pellet was then dissolved in 20–50 μl of DEPC-treated water while being incubated at 55 °C for 10–15 min.
0.5 μg–1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit as per kit protocol. Library quantification was measured by qPCR and TapeStation (Agilent Technologies). Sequencing was performed on an Illumina MiSeq using 300-cycle V2 MiSeq reagent kit (Illumina).

treatment_protocol: Cultures of wildtype NF54 and HS-Sensitive mutants LRR5 and DHC were sorbitol-synchronized 3x to highly synchronous rings, then split equally into four T75 flasks each. All parasites were grown at the normal human body temperature (37C) to early ring-stage. Two flasks of each parasite-line were then exposed to febrile temperatures (41C) for 8 hours, while the remaining two flasks were allowed to continue to grow at 37C for 8 hours without exposure to heat-stress. This temperature-cycling was repeated three times to  simulate cyclical malarial fever. After the third round of heat-shock, RNA was harvested simultaneously from both conditions for RNAseq. Parasite staging was verified by Giemsa smear at every time point.

tag: developmental stage

value: ring stage

value: {delta}LRR5 piggyBac mutant

tag: piggybac insertion site

tag: insertion site distance to gene

value: 0 bp

tag: type of insertion

value: exon

tag: disrupted gene id

tag: timepoint

value: 8 hours exposure


title: PB31_37C_rep2

tag: strain

tag: treatment


title: NF54_41C_rep2

value: wildtype


title: PB4_41C_rep2

value: {delta}DHC piggyBac mutant


title: 27702 RNA-seq KO LN B cell

source_name: lymph node mature B cell

value: Ex-vivo, CD43 depleted


title: 2788_CD4

tag: cell type

tag: gender

value: F


title: 1595_PK_CD4


title: B16-F0 #3

tag: generation


title: NF54_37C_rep2


title: 27701 RNA-seq KO Act B cell


title: PB4_37C_rep2


title: Cancer condition medium_2

value: Bone-marrow derived macrophages (BMDM)

tag: age

value: 7 weeks

value: bone marrow


title: PB4_41C_rep1

tag: genotype


title: 1576_PK_CD4

value: CD4 memory

value: M


title: 27700 RNA-seq KO LN B cell

value: Cd23-Cre Pax5(F/-)

value: CD43 depletion MACS sort


title: 1434_PK_CD4


title: PB4_37C_rep1


title: 27699 RNA-seq Act B cell

value: Cd23-Cre Pax5(F/+)

value: CD43 depleted, 1-hour anti-IgM stimulation


title: 1431PK_CD4_Park1


title: 2396PK_CD4_Park1


title: Corneal_Limbus-64y_Right

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

description: single-cell RNA

data_processing:
UMI count matrices were generated using the 10x genomics CellRanger count (3.1.0) pipeline with default parameters.
The count matrices were combined and normalized using Seurat.
The combined matrix was then further filtered to exclude cells not passing the following QC measures: at least 500 genes detected (UMI > 0) and proportion of UMIs derived from mitochondia less than 10%. Genes were also excluded if they were not expressed in at least 5 cells (UMI count > 0).
After filtering, this matrix was used for tSNE projection and graph based clustering. Following cell-embeddings and clustering, the original non-downsampled UMI data was used for all analysis and is provided as the Corneal_Limbus_count_matrix.txt.gz.
Genome_build: Genome_build: GRCh38
Supplementary_files_format_and_content: Corneal_Limbus_count_matrix.txt.gz with UMI counts per gene per cell. Corneal_Limbus_cell_metadata.txt.gz contains information about each cell in the count matrix.

source_name: Corneal Limbus

extract_protocol: Library generation was performed following the Chromium Single Cell 3' Reagents Kits v3 where we target 10,000 cellls per sample for capture.

treatment_protocol: The dissected tissues were incubated with 5 mg/ml collagenase A (Roche) at 37 °C overnight, and continued to be digested at 37 °C for 10 minutes in TrypLE (Sigma-Aldrich). Then all dissociated limbal cells were resuspended in Ca2+-free buffer (with 1% BSA), filtered to ensure single-cell suspension using a 40um filter membrane, and processed for cell viability test, cell counting and single-cell arresting.

tag: tissue

value: Corneal Limbus


title: Corneal_Limbus-64y_Left

description: single-cell RNA


title: 27698 RNA-seq LN B cell


title: PB31_41C_rep1

value: ring stage

value: {delta}LRR5 piggyBac mutant

value: 0 bp


title: Corneal_Limbus-53y_Right

description: single-cell RNA


title: 1426PK_CD4_Park1


title: PB31_37C_rep1

value: exon

value: 8 hours exposure


title: 1415PK_CD4_Park1


title: G1 siControl rep3

description: SAMPLE 9

tag: cell line

value: metastatic melanoma

value: control


title: NF54_41C_rep1

value: wildtype


title: Corneal_Limbus-53y_Left

description: single-cell RNA


title: 27696 RNA-seq LN B cell

tag: cell preparation

value: Ex-vivo, CD43 depleted


title: Corneal_Limbus-13y_Left

description: single-cell RNA


title: 1422PK_CD4_Park1


title: Corneal_Limbus-95y_Left

description: single-cell RNA


title: 27697 RNA-seq Act B cell

tag: cell sorting strategy


title: DN3_FA_GATA3_ChIP-rep1

status: Public on Jun 13 2021

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm10 mouse assembly.

source_name: BM derived DN3 cells

growth_protocol: For in vitro differentiation of pro-T cells, bone marrow hematopoietic progenitors were used for input.  Bone marrow (BM) was removed from the femurs and tibiae of 2-3 month-old mice.  Suspensions of BM cells were prepared and stained for lineage (Lin) markers using biotin-conjugated lineage antibodies (CD11b (eBioscience; 13-0112-86), CD11c (13-0114-85), Gr-1 (13-5931-86), TER-119 (13-5921-85), NK1.1 (13-5941-85), CD19 (13-0193-85), CD3e (13-0031-082)), then incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec).   Then, hematopoietic progenitors were cultured on OP9-DLL1 monolayers using OP9 medium (α-MEM, 20% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).   On day 7, cultured cells were disaggregated, filtered through 40-m nylon mesh, and re-cultured on new OP9 monolayers with medium containing 5 ng/ml of IL-7 and 5 ng/ml of Flt3L.  In cultures that were continued for longer times, cells were passaged onto fresh OP9-DLL1 monolayers at day 10 and maintained up to day 14 in 1 ng/ml each of IL-7 and Flt3L.

extract_protocol: 5-10M cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by an additional 10 min with addition of formaldehyde up to 1%, or with 1% FA formaldehyde for 10 min. Five ug of anti-GATA3 mAbs (a mixture of 2.5 ug of sc-268, Santa Cruz and, 2.5 ug of MAB26051, R&D systems) were pre-bound to Dynabeads anti-Mouse Ig (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots. Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

value: Cultured on OP9DL1

tag: chip (antibody)

value: GATA3 mAbs (a mixture of 2.5 ug of sc-268 (Santa Cruz) and 2.5 ug of MAB26051 (R&D systems))


title: DN3_FA_GATA3_ChIP-rep2


title: DN3_1percentinput-rep2

growth_protocol: For in vitro differentiation of pro-T cells, bone marrow hematopoietic progenitors were used for input.  Bone marrow (BM) was removed from the femurs and tibiae of 2-3 month-old mice.  Suspensions of BM cells were prepared and stained for lineage (Lin) markers using biotin-conjugated lineage antibodies (CD11b (eBioscience; 13-0112-86), CD11c (13-0114-85), Gr-1 (13-5931-86), TER-119 (13-5921-85), NK1.1 (13-5941-85), CD19 (13-0193-85), CD3e (13-0031-082)), then incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec).   Then, hematopoietic progenitors were cultured on OP9-DLL1 monolayers using OP9 medium (α-MEM, 20% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).   On day 7, cultured cells were disaggregated, filtered through 40-um nylon mesh, and re-cultured on new OP9 monolayers with medium containing 5 ng/ml of IL-7 and 5 ng/ml of Flt3L.  In cultures that were continued for longer times, cells were passaged onto fresh OP9-DLL1 monolayers at day 10 and maintained up to day 14 in 1 ng/ml each of IL-7 and Flt3L.

extract_protocol: 5-10M cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by an additional 10 min with addition of formaldehyde up to 1%.  Five ug of anti-GATA3 mAbs (a mixture of 2.5 ug of sc-268, Santa Cruz and, 2.5 ug of MAB26051, R&D systems) were pre-bound to Dynabeads anti-Mouse Ig (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots.  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB).

value: BM derived DN3

value: none (input)


title: DN3_1percentinput-rep1


title: DN1_1percentinput-rep2

source_name: BM derived DN1 cells

value: BM derived DN1


title: 15-month KIT- oxRRBS rep1

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: KIT- cells from 15-month-old mice

data_processing:
The raw reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and low-quality reads and adapters were removed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using '--rrbs' trimming mode.  Trimmed sequences were mapped to the mouse genome with Bismark (Krueger and Andrews, 2011).
Genome_build: mm9

source_name: Spermatogonial stem cell (SSC)

extract_protocol:
1 million primary cells of each population in two independent experiments were FACS-sorted. Genomic DNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
0.5ug of genomic DNA was digested with MspI followed by end repair, A-tailing, and ligation of adaptors. Adaptor-ligated MspI-digested DNA was size-selected (110-380 bp) and purified. 1/5 the DNA was kept for the generation of the non-oxidized library and remaining DNA was subjected to oxidation.  Both oxidized and non-oxidized DNA samples were bisulfite-treated.  Final library amplification was carried out for 18 cycles, after which the libraries were purified using AMPure XP beads (Agencourt) and sequenced on Illumina platform.
1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Genomic DNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
0.5ug of genomic DNA was digested with MspI followed by end repair, A-tailing, and ligation of adaptors. Adaptor-ligated MspI-digested DNA was size-selected (110-380 bp) and purified. 1/5 the DNA was kept for the generation of the non-oxidized library and remaining DNA was subjected to oxidation.  Both oxidized and non-oxidized DNA samples were bisulfite-treated.  Final library amplification was carried out for 18 cycles, after which the libraries were purified using AMPure XP beads (Agencourt) and sequenced on Illumina platform.
RRBS and oxRRBS.

tag: cell source

value: Oct4-GFP+ germ cells

value: 15 months


title: 6-8-month KIT+ oxRRBS rep2

description: KIT+ cells from 6 to 8-month-old mice

source_name: Spermatogonial progenitor cell

extract_protocol:
1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Genomic DNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
0.5ug of genomic DNA was digested with MspI followed by end repair, A-tailing, and ligation of adaptors. Adaptor-ligated MspI-digested DNA was size-selected (110-380 bp) and purified. 1/5 the DNA was kept for the generation of the non-oxidized library and remaining DNA was subjected to oxidation.  Both oxidized and non-oxidized DNA samples were bisulfite-treated.  Final library amplification was carried out for 18 cycles, after which the libraries were purified using AMPure XP beads (Agencourt) and sequenced on Illumina platform.
1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Genomic DNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
0.5ug of genomic DNA was digested with MspI followed by end repair, A-tailing, and ligation of adaptors. Adaptor-ligated MspI-digested DNA was size-selected (110-380 bp) and purified. 1/5 the DNA was kept for the generation of the non-oxidized library and remaining DNA was subjected to oxidation.  Both oxidized and non-oxidized DNA samples were bisulfite-treated.  Final library amplification was carried out for 18 cycles, after which the libraries were purified using AMPure XP beads (Agencourt) and sequenced on Illumina platform.
RRBS and oxRRBS.

value: 6-8 months


title: DN3_GATA3_ChIP-rep2


title: 15-month KIT+ oxRRBS rep1

description: KIT+ cells from 15-month-old mice


title: DN1_1percentinput-rep1


title: 15-month KIT- oxRRBS rep2

description: KIT- cells from 15-month-old mice


title: DN1_GATA3_ChIP-rep1


title: DN3_GATA3_ChIP-rep1


title: 15-month KIT+ RRBS rep2

description: KIT+ cells from 15-month-old mice


title: DN1_GATA3_ChIP-rep2


title: DN3_FA_1percent_input


title: 6-8-month KIT- oxRRBS rep2

description: KIT- cells from 6 to 8-month-old mice


title: KRAS MEF

city: Shanghai

first: Zhaojuan

last: Yang

address: Wenxuan medical building, Jiaotong University, 800 Dongchuan Road, Shanghai, China

institute: Shanghai Cancer Institute

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to mouse genome (GRCm38.p4) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

source_name: Mouse MEF

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V2 Library Prep Kit for Illumina

value: embryo

value: Kras mutation


title: CON MEF


title: 6-8-month KIT- oxRRBS rep1

description: KIT- cells from 6 to 8-month-old mice


title: SKOV3 shSND1-#2-2

city: Tianjin

first: Lingbiao

last: Xin

address: Qixiangtai RD 22

department: Biochemistry and Molecular Biology

institute: Tianjin Medical University

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: SKOV3 shSND1-#2 stable cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SKOV3 stable cell lines of shSND1-#2 and pLKO-Vector was grown in McCoy's 5A with 10% fetal bovine serum.

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

treatment_protocol: no treatment

tag: genotype/variation

value: SND1 knockdown

value: SKOV3 pLKO-shSND1-#2 stable cell line


title: SKOV3 sh-Vector-3

source_name: SKOV3 pLKO-Vector stable cell line

value: normal

value: SKOV3 pLKO-Vector stable cell line


title: SKOV3 shSND1-#2-3


title: SKOV3 sh-Vector-2


title: NF54_37C_rep1

tag: developmental stage

value: ring stage

tag: piggybac insertion site

tag: insertion site distance to gene

tag: type of insertion

value: 8 hours exposure


title: SKOV3 shSND1-#2-5-1


title: SKOV3 sh-Vector-1


title: 15-month KIT+ oxRRBS rep2

description: KIT+ cells from 15-month-old mice

tag: strain


title: NCI-H1373_RBN012397_300nM_24hr_rep3

city: Cambridge

first: Mario

last: Niepel

state: MA

address: 35 Cambridgepark Dr Suite 300

institute: Ribon Therapeutics, Inc.

data_processing:
Raw transcriptome sequences were analyzed using Salmon v0.11.27.
Using Salmon’s mapping-based mode with a Gencode (release 29) human reference transcriptome index produced transcriptome read counts for each sequenced sample.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were plated at a density of 1.5 × 106 cells/well in 6-well dish and allowed to adhere overnight prior to compound treatment.

extract_protocol:
RNA was isolated using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher Scientific, #AM1839) per manufacturer’s instructions.  RNA concentration was determined using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA).
Paired-end sample libraries consisting of 60 bp with 6 nucleotide indices were prepared for measuring high-throughput 3’ digital gene expression based on a previously published protocol (Massachusetts Institute of Technology, Cambridge, MA) (Soumillon, 2014).

treatment_protocol: Cells were harvested after either 6 or 24 hours of treatment with  RBN012337 (at 3nM, 10nM, or 100nM) or RBN012397 (at 10nM, 30nM, or 300nM) or DMSO.

value: Lung

tag: cell type

value: Non-small cell lung cancer

tag: treatment time

tag: treatment compound

tag: concentration


title: NCI-H1373_RBN012397_30nM_24hr_rep3


title: NCI-H1373_DMSO_24hr_rep3

value: DMSO


title: 15-month KIT- RRBS rep2

description: KIT- cells from 15-month-old mice

tag: age


title: 15-month KIT- RRBS rep1

description: KIT- cells from 15-month-old mice


title: 6-8-month KIT+ RRBS rep1

description: KIT+ cells from 6 to 8-month-old mice


title: 6-8-month KIT- RRBS rep2

description: KIT- cells from 6 to 8-month-old mice


title: NCI-H1373_RBN012397_10nM_24hr_rep3

tag: tissue


title: 15-month KIT+ RRBS rep1

description: KIT+ cells from 15-month-old mice


title: 6-8-month KIT+ RRBS rep2

description: KIT+ cells from 6 to 8-month-old mice


title: NCI-H1373_RBN012337_3nM_24hr_rep3

tag: cell line


title: 6-8-month KIT+ oxRRBS rep1

description: KIT+ cells from 6 to 8-month-old mice


title: NCI-H1373_RBN012337_10nM_24hr_rep3


title: NCI-H1373_RBN012337_100nM_24hr_rep3


title: 15month_KITpos_rep2

description: KIT+ cells from 15-month-old mice

data_processing:
Raw reads were pre-processed with trim-galore for trimming Illumina adaptor sequences.
Counts were assigned to genes defined by the Ensembl (release 67) annotation using RSEM.
Genome_build: mm9
Supplementary_files_format_and_content: Text file with RPKM.

extract_protocol:
1 million primary cells of each population in two independent experiments were FACS-sorted as described above. Total RNA was isolated from each cell fraction using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. RNA yield and purity were evaluated using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific, Waltham, MA). Quality and integrity were determined by RNA 6000 Nano kit with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). The ratio of absorbance at 260 and 280 nm was ≥1.9 and the RNA integrity number (RIN) was >9 for all samples.
Sequencing libraries were prepared with ribosomal RNA (rRNA) depletion using a Ribo-Zero Gold kit (Epicentre) followed by Apollo 324 NGS Library Prep System (WaferGen Biosystems, Fremont, CA, USA).
Sequencing libraries were prepared with ribosomal RNA (rRNA) depletion using a Ribo-Zero Gold kit (Epicentre) followed by Apollo 324 NGS Library Prep System (WaferGen Biosystems, Fremont, CA, USA). The prepared libraries were sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, CA) with 100 base pairs (bp) paired-end RNA-Seq reads.


title: NCI-H1373_DMSO_6hr_rep3


title: 6-8-month KIT- RRBS rep1

description: KIT- cells from 6 to 8-month-old mice


title: 15month_KITpos_rep1

description: KIT+ cells from 15-month-old mice


title: NCI-H1373_RBN012397_300nM_6hr_rep3


title: NCI-H1373_RBN012397_30nM_6hr_rep3


title: 15month_KITneg_rep1

description: KIT- cells from 15-month-old mice


title: NCI-H1373_RBN012397_10nM_6hr_rep3


title: 15month_KITneg_rep2

description: KIT- cells from 15-month-old mice


title: NCI-H1373_RBN012337_100nM_6hr_rep3


title: NCI-H1373_RBN012337_10nM_6hr_rep3


title: 8month_KITneg_rep1

description: KIT- cells from 8-month-old mice

value: 8 months


title: NCI-H1373_RBN012337_3nM_6hr_rep3


title: NCI-H1373_DMSO_24hr_rep2


title: 6day_KITpos_rep2

description: KIT+ cells from 6-day-old mice

value: 6 days


title: NCI-H1373_RBN012397_30nM_24hr_rep2


title: 6day_KITpos_rep1

description: KIT+ cells from 6-day-old mice


title: NCI-H1373_RBN012337_100nM_24hr_rep2


title: 6day_KITneg_rep2

description: KIT- cells from 6-day-old mice


title: NCI-H1373_RBN012397_300nM_24hr_rep2


title: 6day_KITneg_rep1

description: KIT- cells from 6-day-old mice


title: 8-month KIT+ H3K27me3

description: KIT+ cells from 8-month-old mice

data_processing:
Reads were mapped to the mouse genome (mm9 assembly) using Bowtie (Langmead et al., 2009). Mapped reads were filtered for PCR duplicates using MACS2 (Zhang et al., 2008). Peak calling and visualization of tracks were done using EaSeq (Lerdrup et al., 2016).
none provided by the submitter
Genome_build: mm9

extract_protocol:
ChIP experiments and ChIP-Seq libraries were prepared using Diagenode True MicroChIP kit according to the manufacturer's protocol. 0.2 million freshly sorted Oct4-GFP+/KIT- or Oct4-GFP+/KIT+ cells were cross-linked with 1% formaldehyde for 10 minutes. The crosslinking was stopped by incubation with 0.125M glycine at room temperature for 5 minutes. Chromatin was fragmented to 200 to 600 bp by sonication using a Bioruptor sonicator (Diagenode, Liège, Belgium). 1ug antibodies against H3K4me3 or H3K27me3 were used for ChIP. Half of the chromatin was used for each IP, and 10% of the chromatin solution was reserved as input control.
The chromatin immunoprecipitated (ChIPed) DNA was subjected to library preparation using MicroPlex Library Preparation kit (Diagenode, Liège, Belgium). The prepared library was sequenced with single-end 50bp reads using the Illumina HiSeq 2000.


title: NCI-H1373_RBN012397_10nM_24hr_rep2


title: NCI-H1373_RBN012337_10nM_24hr_rep2


title: NCI-H1373_DMSO_6hr_rep2


title: NCI-H1373_RBN012337_3nM_24hr_rep2


title: NCI-H1373_RBN012397_300nM_6hr_rep2


title: 15-month KIT+ H3K4me3

description: KIT+ cells from 15-month-old mice


title: 15-month KIT+ H3K27me3

description: KIT+ cells from 15-month-old mice


title: 8month_KITpos_rep1

description: KIT+ cells from 8-month-old mice


title: 8-month KIT+ H3K4me3

description: KIT+ cells from 8-month-old mice


title: 8-month KIT- H3K4me3

description: KIT- cells from 8-month-old mice


title: 8month_KITneg_rep2

description: KIT- cells from 8-month-old mice


title: 15-month KIT+ input

description: KIT+ cells from 15-month-old mice


title: NCI-H1373_RBN012337_10nM_6hr_rep2


title: 15-month KIT- input

description: KIT- cells from 15-month-old mice


title: NCI-H1373_RBN012337_3nM_6hr_rep2


title: 15-month KIT- H3K4me3

description: KIT- cells from 15-month-old mice


title: NCI-H1373_DMSO_24hr_rep1


title: 15-month KIT- H3K27me3

description: KIT- cells from 15-month-old mice


title: 8-month KIT+ input

description: KIT+ cells from 8-month-old mice


title: 8-month KIT- H3K27me3

description: KIT- cells from 8-month-old mice


title: NCI-H1373_RBN012397_300nM_24hr_rep1


title: NCI-H1373_RBN012337_100nM_24hr_rep1


title: Msp1_Pex19_RPF

city: Salt Lake City

first: Jeff

last: Morgan

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

description: W303 msp1Δpex19Δ

data_processing:
Library strategy: Ribo-Seq
Reads were trimmed of adaptor sequence using cutadapt (v1.8) (5prime adaptor: 5 GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN 3; 3prime adaptor: 5 TCGTANNNNNNTCGGAAGAGCACACGTCTddC 3). Trimmed reads shorter than 10 nucleotides were discarded.
Trimmed reads were aligned to the S. cerevisiae genome (R64-1-1, downloaded from www.yeastgenome.org) using STAR (v2.5) with the parameters “--alignIntronMax 1000 --sjdbOverhang 31 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts” and with “--sjdbGTFfile” supplied with transcript annotations. The transcript annotations included all annotated ORFs, and excluded the first 50 nt of each ORF.
Genome_build: sacCer3 (R64-1-1)
Supplementary_files_format_and_content: Abundance measurements (pseudo-counted reads and TPMs)

organism: Saccharomyces cerevisiae

source_name: saccharomyces cerevisiae cells

growth_protocol: Culture was seeded as a 3 mL starter culture from a fresh YPAD plate and grown overnight. The starter culture was used to seed a 50 mL midi culture, which was grown overnight. The midi culture was used to seed a 500 mL culture at OD600 = 0.1, which was grown for 16 h and harvested at OD600 = 2–2.5

extract_protocol:
All cultures were rapidly harvested by vacuum filtration and flash frozen in liquid nitrogen as described in Weinberg et al., 2016 (GSE53268). Frozen pellets were mechanically lysed using a Spex SamplePrep Freezer/Mill (10 cycles of 2 min on, 2 min off at setting 10). Lysate powder was aliquoted and stored at –80°C.
For RNA-seq samples, total RNA was extracted from lysate powder using TRI Reagent (Ambion) according to the manufacturer’s protocol. rRNA was depleted from 5 μg of total RNA using the Ribo-Zero Gold Yeast rRNA Removal Kit (Illumina) according to the manufacturer’s protocol. For RPF samples, lysate powder was resuspended in a buffer containing cycloheximide and tigecycline in order to arrest translating ribosomes. Monosomes were isolated by treating the lysate with RNase I followed by purification over a 10-50% sucrose gradient. Ribosome-protected fragments were further isolated by Proteinase K/SDS digestion and phenol/chloroform extraction.     Two quantitative spike oligos were added to each library to access gross differences in absolute levels of ribosome-protected fragments between samples (Spike_21: GAUGUAACGAGUUGGAAUGCA/3pp/, Spike_28: CAUCGGUCGAACUUAUGUGAAACAUCAU/3pp/, 2 fmol each spike per sample). RNA-seq samples were fragmented by alkaline hydrolysis and size-selected in the range of 19-40 nt. RPF samples were size-selected in the range of 19-33 nt, and contaminating rRNA sequences were removed via subtractive hybridization. RNA-seq and RPF samples were both ligated to adaptors, reverse-transcribed, and amplified to prepare sequencing libraries as described in Subtelny et al. 2014 (GSE52809). Libraries were sequenced on an Illumina HiSeq 2500 using 60-bp single-end reads.

treatment_protocol: SC media, Carbon source: 2% glycerol + 2% EtOH

tag: genotype

value: W303 msp1delta pex19delta


title: NCI-H1373_RBN012337_10nM_24hr_rep1


title: NCI-H1373_RBN012397_30nM_6hr_rep2


title: NCI-H1373_RBN012397_10nM_24hr_rep1


title: 8-month KIT- input

description: KIT- cells from 8-month-old mice

value: Oct4-GFP+ germ cells


title: Pex19_RNA

description: W303 pex19Δ

data_processing:
Reads were trimmed of adaptor sequence using cutadapt (v1.8) (5prime adaptor: 5 GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN 3; 3prime adaptor: 5 TCGTANNNNNNTCGGAAGAGCACACGTCTddC 3). Trimmed reads shorter than 10 nucleotides were discarded.
Trimmed reads were aligned to the S. cerevisiae genome (R64-1-1, downloaded from www.yeastgenome.org) using STAR (v2.5) with the parameters “--alignIntronMax 1000 --sjdbOverhang 31 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts” and with “--sjdbGTFfile” supplied with transcript annotations. The transcript annotations included all annotated ORFs, and excluded the first 50 nt of each ORF.
Genome_build: sacCer3 (R64-1-1)
Supplementary_files_format_and_content: Abundance measurements (pseudo-counted reads and TPMs)

value: W303 pex19delta


title: Pex19_RPF

description: W303 pex19Δ


title: Msp1_Pex19_RNA

description: W303 msp1Δpex19Δ


title: NCI-H1373_RBN012397_30nM_24hr_rep1


title: NCI-H1373_RBN012397_10nM_6hr_rep2


title: NCI-H1373_RBN012337_100nM_6hr_rep2


title: WT_RNA


title: WT_RPF


title: Msp1_RNA

description: W303 msp1Δ

value: W303 msp1delta


title: Msp1_RPF

description: W303 msp1Δ


title: NCI-H1373_RBN012397_30nM_6hr_rep1


title: NCI-H1373_RBN012397_300nM_6hr_rep1


title: NCI-H1373_DMSO_6hr_rep1


title: NCI-H1373_RBN012397_10nM_6hr_rep1


title: NCI-H647_DMSO_24hr_rep3


title: NCI-H1373_RBN012337_10nM_6hr_rep1


title: NCI-H1373_RBN012337_100nM_6hr_rep1


title: NCI-H1373_RBN012337_3nM_6hr_rep1


title: 20200922_chan gbm sept 22 2020_MR1_01

city: Calgary

first: Sorana

last: Morrissy

state: Alberta

address: 3310 Hospital Dr NW

country: Canada

institute: Univeristy of Calgary

hyb_protocol: 300 ng of unamplified total RNA was used as same input. Hybridization was performed per manufacturer's protocol using the Nanostring custom gene expression CodeSet and Nanostring Master Kit reagents. RNA was mixed with the Reporter CodeSet, Capture ProbeSet, and Hybridization buffer, then incubated at 65˚C for 24 hours. Hybridized samples were placed in an automated nCounter Prep Station and reagents and consumables from the nCounter Master Kit for further processing of the sample cartridge.

scan_protocol: Cartridges were placed in an automated nCounter Digital Analyzer for digital counting per manufacturer's protocol.

data_processing: Raw counts were background subtracted then normalized using the geometric mean of the samples analyzed using NanoString nSolver. Housekeeping genes and genes not specific to a GBM subtype were removed before NMF. Five outlier genes (CD44, PDGFRA, CHI3L1, MBP, EGFR) and one outlier sample (MP08) were removed as well. In total, 30 genes for 83 patients were passed to NMF.

source_name: recurrent GBM

extract_protocol: 1-2 x 0.6 mm cores were taken from FFPE archival GBM samples and used nucleic acid extraction using the Qiagen Allprep DNA/RNA FFPE kit per manufacturer's protocol

value: recurrent GBM

tag: patient

tag: instance


title: 20200922_chan gbm sept 22 2020_MR2_05


title: NCI-H647_DMSO_6hr_rep3


title: NCI-H647_RBN012337_100nM_6hr_rep3


title: NCI-H647_RBN012397_300nM_6hr_rep3


title: NCI-H647_RBN012337_10nM_24hr_rep3


title: NCI-H647_RBN012337_3nM_24hr_rep3


title: NCI-H647_RBN012337_100nM_24hr_rep3


title: NCI-H647_RBN012397_10nM_6hr_rep3


title: NCI-H647_RBN012397_30nM_6hr_rep3


title: NCI-H647_RBN012397_10nM_24hr_rep3


title: NCI-H647_RBN012337_10nM_6hr_rep3


title: NCI-H647_RBN012397_300nM_24hr_rep3


title: 20200922_chan gbm sept 22 2020_MR3_06


title: 20200922_chan gbm sept 22 2020_UR17_10


title: 20200922_chan gbm sept 22 2020_MR4_07


title: 20200922_chan gbm sept 22 2020_MP31_04

source_name: primary GBM

value: primary GBM


title: 20200922_chan gbm sept 22 2020_MP5_03


title: 20200922_chan gbm sept 22 2020_MR14_08


title: NCI-H647_RBN012337_3nM_6hr_rep3


title: 20200922_chan gbm sept 22 2020_MP16_12


title: 20200922_chan gbm sept 22 2020_MP2_02


title: 20200915_chan gbm sep 15_UR9_09


title: 20200915_chan gbm sep 15_UR8_08


title: 20200915_chan gbm sep 15_UR7_07


title: 20200915_chan gbm sep 15_UR6_06


title: NCI-H647_RBN012397_30nM_24hr_rep3


title: NCI-H647_RBN012397_10nM_24hr_rep2


title: NCI-H647_RBN012397_30nM_24hr_rep2


title: NCI-H647_RBN012337_10nM_24hr_rep2


title: NCI-H647_DMSO_6hr_rep2


title: NCI-H647_DMSO_24hr_rep2


title: NCI-H647_RBN012337_100nM_24hr_rep2


title: NCI-H647_RBN012397_300nM_24hr_rep2


title: NCI-H647_RBN012337_3nM_24hr_rep2


title: 20200915_chan gbm sep 15_UR5_05


title: 20200910_chan gbm sep10_MR15_11


title: 20200922_chan gbm sept 22 2020_UR1_09


title: 20200922_chan gbm sept 22 2020_UR21_11


title: 20200915_chan gbm sep 15_MP14_02


title: 20200915_chan gbm sep 15_UR14_11


title: 20200915_chan gbm sep 15_MR31_04


title: 20200915_chan gbm sep 15_UR12_10


title: 20200910_chan gbm sep10_MR11_10


title: 20200915_chan gbm sep 15_MP4_01


title: NCI-H647_RBN012397_300nM_6hr_rep2


title: NCI-H647_RBN012397_30nM_6hr_rep2


title: Splenic NK cells, MycKO_GH6

city: Cincinnati

first: Yuting

last: Tang

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were aligned to the reference genome using the TopHat aligner
Reads aligning to each known transcript were counted using Bioconductor packages for next-generation sequencing data analysis
The differential expression analysis between different sample types was performed using the negative binomial statistical model of read counts as implemented in the edgeR Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: KO_vs_Ctrl.all.gene.result_uc.txt showing EdgeR results for each Sample

source_name: Splenic NK cells

extract_protocol:
Spleen single cell suspensions were prepared and stained with NK cell markers. CD3-NK1.1+DX5+ live cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Sorted cells were lysed directly in RLT buffer from the RNeasy Micro kit (QIAGEN), and total RNA was extracted according to the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) was used for library preparation, which is dUTP-based stranded library.The library was indexed and amplified under PCR cycle number of 8. After library Bioanalyzer QC analysis and quantification, individually indexed and compatible libraries were proportionally pooled and sequenced using HiSeq 1000 (Illumina, San Diego, CA). Under the sequencing setting of single read 1x51 bp, about 25 million pass filter reads per sample were generated.

value: Splenic NK cells


title: 20200910_chan gbm sep10_MR08_09


title: 20200910_chan gbm sep10_MR07_08


title: 20200910_chan gbm sep10_MR06_07


title: Splenic NK cells, MycKO_GH5


title: 20200910_chan gbm sep10_MP15_06


title: 20200915_chan gbm sep 15_UR15_12


title: 20200915_chan gbm sep 15_MR5_03


title: 20200910_chan gbm sep10_MP11_05


title: NCI-H647_RBN012337_100nM_6hr_rep2


title: NCI-H647_RBN012397_10nM_6hr_rep2


title: 20200910_chan gbm sep10_MP03_12


title: Splenic NK cells, Ctrl_GH3

value: Mycf/f


title: Splenic NK cells, Ctrl_GH1


title: NCI-H647_RBN012337_3nM_6hr_rep2


title: A549-USP12 rep2

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to mouse genome (GRCh38) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

source_name: Human lung cancer

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina

tag: treatment


title: NCI-H647_RBN012337_10nM_6hr_rep2


title: Splenic NK cells, Ctrl_GH2


title: A549-USP12 rep1


title: NCI-H647_DMSO_24hr_rep1


title: 20200910_chan gbm sep10_MP01_01


title: 20200910_chan gbm sep10_MP06_02


title: 20200910_chan gbm sep10_MP07_03


title: 20200910_chan gbm sep10_MP08_04


title: NCI-H647_RBN012397_300nM_24hr_rep1


title: 20200909_chan gbm sept 9 2020_MR44_11


title: 20200909_chan gbm sept 9 2020_MR42_10


title: A549-CON rep2

value: control


title: NCI-H1373_RBN012337_3nM_24hr_rep1


title: NCI-H647_RBN012397_30nM_24hr_rep1


title: 20200909_chan gbm sept 9 2020_MR40_08


title: 20200909_chan gbm sept 9 2020_MR45_12


title: A549-CON rep1


title: NCI-H647_RBN012397_10nM_24hr_rep1


title: 20200909_chan gbm sept 9 2020_MR38_06


title: 20200909_chan gbm sept 9 2020_MP46_03


title: 20200909_chan gbm sept 9 2020_MR16_04


title: 20200909_chan gbm sept 9 2020_MR39_07


title: NCI-H647_RBN012337_3nM_24hr_rep1


title: 20200909_chan gbm sept 9 2020_MP43_02


title: NCI-H647_DMSO_6hr_rep1


title: NCI-H647_RBN012337_10nM_24hr_rep1


title: 20200909_chan gbm sept 9 2020_MP16_01


title: NCI-H647_RBN012337_100nM_24hr_rep1


title: 20200909_chan gbm sept 9 2020_MR41_09


title: NCI-H647_RBN012397_300nM_6hr_rep1


title: 20200904_chan gbm sep 4_MR19_07


title: 20200904_chan gbm sep 4_MR23_11


title: 20200904_chan gbm sep 4_MP22_04


title: 20200904_chan gbm sep 4_MP23_05


title: 20200904_chan gbm sep 4_MP21_03


title: 20200904_chan gbm sep 4_MR20_08


title: 20200909_chan gbm sept 9 2020_MR17_05


title: 20200904_chan gbm sep 4_MR25_12


title: NCI-H647_RBN012397_10nM_6hr_rep1


title: 20200904_chan gbm sep 4_MP25_06


title: 20200904_chan gbm sep 4_MP20_02


title: 20200904_chan gbm sep 4_MP19_01


title: BAT CD45+ cells from AdipoQ-CreERT2 ATGLfl/fl mice

city: Saint-Petersburg

first: Maria

last: Firulyova

address: Kronverksky Pr. 49

department: Department of Computer Technologies

country: Russia

institute: Information Technologies, Mechanics, and Optics University

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v4.0.0)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v4.0.0)
barcode processing, Cell Ranger Single Cell Software Suite (v4.0.0)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v4.0.0)
alignment, Cell Ranger Single Cell Software Suite (v4.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Brown adipose tissue (BAT)

extract_protocol:
Adipose tissues were harvested, shredded with scissors and then incubated for 30 minutes with PBS containing 1.5 mg/ml collagenase A at 37°C. Digested adipose tissues were homogenized using a 1mL syringe with a 20G needle and passed through a 100µm sieve. The resulting suspensions were centrifuged (400g, 5min, 4°C) and stained with anti CD45-APC.Cy7 antibody. Cells were washed and passed again through a 100µm sieve. Unstained cells were acquired to measure autofluorescence. Dapi was added to the cell preparation before acquisition, and CD45+ Dapi- cells were purified using a BD FACS Aria III cell sorter.
Reverse transcription, cDNA synthesis/amplification and library preparation were performed according to the 10x Genomics protocol (Chromium™ Single Cell 3′ Reagent Kit, v3.1 Chemistry).

treatment_protocol: AdipoQ-CreERT2 ATGLfl/fl mice were injected every two days intra-peritoneally with either 10mg/ml Tamoxifen (200uL per mouse in 10% EtoH and sunflower oil) or vehicle, for 1 week. Then, mice were allowed to rest for 2 weeks. Mice were then sacrificed, and tissues were harvested for further investigations.

value: Brown adipose tissue (BAT)

value: Tamoxifen-treated Male AdipoQ-CreERT2 ATGLfl/fl mice

value: 16 week-old


title: BAT CD45+ cells from control mice

value: Vehicle-treated Male AdipoQ-CreERT2 ATGLfl/fl mice


title: 20200902_chan gbm september 2_MR30_12


title: H1944-shUSP12

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Trimmomatic
Clean reads were mapped to human genome (GRCh38) with Hisat2(version:2.0.4)
The mapped fragments of genes were counted by htseq-count(v0.6.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

value: Lung


title: 20200904_chan gbm sep 4_MR21_09


title: NCI-H647_RBN012337_10nM_6hr_rep1

value: Non-small cell lung cancer


title: H1944-shCON


title: 20200902_chan gbm september 2_MR27_09


title: 20200902_chan gbm september 2_MR29_11


title: 20200902_chan gbm september 2_MR18_07


title: 20200902_chan gbm september 2_MP29_05


title: 20200902_chan gbm september 2_MR26_08


title: NCI-H647_RBN012337_3nM_6hr_rep1


title: 20200902_chan gbm september 2_MP30_06


title: Wild_M_Smeg

city: New Delhi

first: Nasreen

middle: Zafar

last: Ehtesham

state: Delhi

address: Safdarjung Hospital campus

country: India

institute: National Institute of Pathology

data_processing:
HQ Reads
Map to Genome reference
Assembly using referebce GTF
Differential gene expression
Annotation-Gene names and funtions, Gene ontology, pathway

organism: Mycolicibacterium smegmatis

source_name: Mycobacterium smegmatis

growth_protocol: In 7H9 broth containing 10% OADC for 36 hrs at 37⁰ C in shaker incubator

extract_protocol:
Total RNA was isolated from the  sample by trizol method. The quality of the total RNA was checked on 1% formaldehyde denature Agarose gel and quantified using Qubit fluorometer.
Isolated RNA from given sample was treated with MICROBExpress Bacterial mRNA Enrichment kit to enrich microbial mRNA from total RNA. The libraries were prepared using TruSeq Stranded RNA Library Preparation Kit and as per its described protocol. The fragmented mRNA was converted into first-strand cDNA, followed by second-strand cDNA generation, A-tailing, adapter ligation and finally ended by limited number of PCR amplification of the adaptor-ligated libraries. Library quantification and qualification was performed using DNA High Sensitivity Assay Kit.

tag: sample type

value: Acid fast Bacilli

tag: phenotye

value: Fast grower

value: wild type


title: 20200902_chan gbm september 2_MP28_04


title: NCI-H647_RBN012337_100nM_6hr_rep1


title: 20200902_chan gbm september 2_MR28_10


title: 20200901_chan gbm sept 1 2020_MR36_11


title: 20200902_chan gbm september 2_MP26_02


title: DBbGlc8_SDA replicate 1

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

description: Replicate 1 of library ∆BbGlc8

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening of differentially expressed genes in paired library of WT_SDA/BbGlc8_SDA. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build:ASM28067v1, Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, FPKM values, log2(fold change), FDR-value and gene discription  for the paired sample.

organism: Beauveria bassiana

growth_protocol: Conidia suspension (100 ul,5X106 conidia ml-1) of WT and ΔBbGlc8 of Beauveria bassiana were inoculated on the SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar), respectively, and incubated at 25 °C for 4 day.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates.

value: ARSEF 2860

tag: time point

value: 3 days

value: mycelia

tag: genotype/variation


title: WT_SDA replicate 1

description: Replicate 1 of library WT

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening of differentially expressed genes in paired library of WT_SDA/BbGlc8_SDA. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build:ASM28067v1,Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, FPKM values, log2(fold change), FDR-value and gene discription  for the paired sample.

source_name: WT

value: Wildtype


title: 20200901_chan gbm sept 1 2020_MR37_12

value: recurrent GBM


title: 20200902_chan gbm september 2_MP18_01

value: primary GBM


title: WT_SDA replicate 2

description: Replicate 2 of library WT


title: 20200902_chan gbm september 2_MP27_03


title: gpi7 mutant cells (gpi7∆/∆)

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.5 and processed by Trim Galore version 0.4.4 to remove adapters and low-quality reads.
Clean reads were aligned to the Candida albicans genome assembly 21 using the STAR version 020201.
Differential expression analysis was performed using edgeR with bcv set to 0.2, differential expression genes (DEGs) were selected according to log2 (fold change) > 1 and FDR < 0.05.
The Gene Ontology enrichment analysis was then carried out with the differentially expressed genes using CGD Gene Ontology Term Finder with default parameters.
Genome_build: C.albicans SC5314 (Assembly 21)

organism: Candida albicans

source_name: cells

growth_protocol: C. albicans cells were grown in YPD medium at 30 C overnight

extract_protocol:
Total RNA was extracted by Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gpi7 knockout


title: 20200901_chan gbm sept 1 2020_MR35_10


title: 20200901_chan gbm sept 1 2020_MR34_09


title: DBbGlc8_SDA replicate 2

description: Replicate 2 of library ∆BbGlc8


title: RvB_M_Smeg

source_name: Mycobacterium tuberculosis

value: Signature protein 2 knock-in


title: wild-type cells (BWP17UH)


title: 20200904_chan gbm sep 4_MR22_10


title: Functional salinomycin liposomes

first: Jingying

address: No. 38·, Xueyuan Road Haidian District

department: School of Pharmaceutical Sciences

institute: Peking University

description: in vivo

hyb_protocol: HOA 7.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent Scanner G2505C 0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: Human tumor tissues

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Briefly, approximately 1×10^7 MDA-MB-435S cells were resuspended in 200 μl of serum-free medium and injected subcutaneously into the right flanks of nude mice.

extract_protocol: RNA extraction by Trizol Reagent (). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: At the 13th, 15th, 17th, 19th and 21th day  after inoculation, physiological saline, free salinomycin (1 mg/kg), salinomycin liposomes (1 mg/kg), and functional salinomycin liposomes (1 mg/kg) were administered to mice via tail vein injection.

value: Functional salinomycin liposomes

tag: gender

value: Female

value: breast


title: 20200901_chan gbm sept 1 2020_MR33_08


title: 20200901_chan gbm sept 1 2020_MP36_05


title: 20200901_chan gbm sept 1 2020_MP35_04


title: 20200901_chan gbm sept 1 2020_MP37_06


title: WT B cells 2 (bulkATAC-seq)

status: Public on Jun 12 2021

city: Stanford

first: Julia

last: Belk

address: 450 Serra Mall

institute: Stanford University

description: Transposed DNA

data_processing:
Adapters were trimmed using fastp
Trimmed reads were aligned to the mm10 genome using hisat2
Aligned reads were deduplicated using picard
Genome coverage was extracted from each BAM file, normalized using reads-in-TSS, and exported as a compressed bigwig file
Genome_build: mm10
Supplementary_files_format_and_content: normalized bigwig genome track files

source_name: Primary B cells

extract_protocol:
B cells were FACS sorted from WT and enhancer KO mice. Nuclei were isolated and then tranposed for ATAC-seq.
Transposed fragments were PCR amplified and indices were added according to the Omni-ATAC protocol.
Paired end dual indexed Nextera libraries

value: WT

value: Primary B cells


title: KO B cells 1 (bulkATAC-seq)

description: Transposed DNA

value: KO


title: 20200901_chan gbm sept 1 2020_MR32_07


title: WT B cells 3 (bulkATAC-seq)

description: Transposed DNA


title: KO B cells 2 (bulkATAC-seq)

description: Transposed DNA


title: Free salinomycin

description: in vivo

value: Free salinomycin


title: suvh2/9_rep2 [Bisulfite-seq]

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
For analysis of whole-genome DNA methylation data, the mapping, duplication filtering, and methylation extracting were all performed using the standard procedure of Bismark (v0.22.3).
The clean reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 and allowing one mismatch.
After duplications were removed, DNA methylation at CG, CHG, and CHH sites were calculated separately.
For the identification of different types of DMRs, the genome was divided in 200-bp bins, and the CG, CHG, and CHH methylation levels in each bin were calculated and compared between the WT and the mutants. Bins that showed differences in DNA methylation levels (CG > 0.4, CHG > 0.2, CHH > 0.1) were recorded and filtered based on Fisher’s exact test and BH method adjusted p values (cutoff = 0.01).
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig format files for each cytosine context (CG, CHG, CHH or CX) with the following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with 16 h of light at 23ºC and 8 h of darkness at 21ºC.

extract_protocol:
Genomic DNA was extracted from 11-day-old Arabidopsis seedlings by CTAB and purified with phenol: chloroform (1:1).
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The 11-day-old seedlings grown on MS plates were harvested and subjected to DNA extraction.

value: seedlings

value: 11 days


title: rrm1_rep3 [Bisulfite-seq]


title: suvh2/9_rep1 [Bisulfite-seq]


title: rrm1_rep4 [Bisulfite-seq]


title: 20200901_chan gbm sept 1 2020_MP32_01


title: rrm1_rep2 [Bisulfite-seq]


title: 20200901_chan gbm sept 1 2020_MP34_03


title: Being treated with salinomycin_24h

description: in vitro

source_name: treated with salinomycin, 24h

growth_protocol: MDA-MB-435S cells were maintained in serum-containing medium consisting of Leibovitz’s L15 medium supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 units/mL streptomycin. MDA-MB-435S stem cells were cultured in serum-free DMEM-Ham’s F12 medium supplemented with 10 ng/mL basic FGF, 20 ng/mL EGF, 5 mg/mL insulin, 0.4% BSA and 0.2% B27, 100 units/mL penicillin, and 100 units/mL streptomycin.

treatment_protocol: MDA-MB-435S stem cells were treated with salinomycin for 24h.

value: treated with salinomycin, 24h

value: breast cancer stem cells


title: Physiological saline

description: in vivo

value: Physiological saline


title: Salinomycin liposomes

description: in vivo

value: Salinomycin liposomes


title: MDA-MB-435S stem cells

description: in vitro

source_name: Serum free culturing, one week

value: Serum free culturing, one week


title: pdp1/2/3_rep2 [Bisulfite-seq]


title: pdp1/2/3;rrm1_rep2 [Bisulfite-seq]


title: rrm1_rep1 [Bisulfite-seq]


title: pdp1/2/3;rrm1_rep1 [Bisulfite-seq]


title: MDA-MB-435S cells

description: in vitro

source_name: serum-containing medium

value: serum-containing medium

value: breast cancer cells


title: WT B cells 1 (bulkATAC-seq)

description: Transposed DNA


title: pdp1/2/3_rep1 [Bisulfite-seq]


title: fve;rrm1_rep1 [Bisulfite-seq]


title: Col-0_rep2 [Bisulfite-seq]

value: wild type


title: fve_rep1 [Bisulfite-seq]


title: Col-0_rep3 [Bisulfite-seq]


title: 20200901_chan gbm sept 1 2020_MP33_02

value: primary GBM


title: Col-0_rep4 [Bisulfite-seq]


title: fve_rep2 [Bisulfite-seq]


title: Col-0_rep1 [Bisulfite-seq]


title: cdMipPs + VPA, rep134

city: Leuven (3000)

first: Maurilio

last: Sampaolesi

address: herestraat, 49

department: Development and regeneration

country: Belgium

institute: KU Leuven

description:
sc3_VPA.rds
S507  AAGGAGTA  N727  CGATCAGT

data_processing:
50 bp single reads were generated.In the Fastq files, tags were trimmed with cutadapt 1.5. The retained tags were aligned to the Ensembl GRC38p7 human reference genome using STAR 2.4.0. Quality control on aligned and counted reads was done with Scater 1.8.4, cells with less than 150,000 reads; less than 2,500 or over 8,500 detected genes; less than 6% mitochondrial DNA and less than 10% of spike-in ERCCs were removed. Read normalization was done with Scran 1.8.4.
Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor packages.The first ten principal components were used to reduce the dimensionality of the data. Afterwards, t-SNE were computed with a perplexity of 5 in the package Seurat v2.1.0. Clustering was performed with SC3 1.8.0 using k = 2-3. Differential expression between clusters was calculated using a likelihood ratio test corrected for multiple testing with a Benjamini-Hochberg False Discovery Rate correction with MAST. Marker genes defined as genes with areas under the receiver operating curve (AUROC) > 0.85 and with P < 0.01 using SC3 1.8.0
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing matrix with read counts normalized by the library size for all samples

source_name: Gibco™ Episomal hiPSC Line  A18945

growth_protocol: one hour prior to differentiation, iPSCs were incubated with RevitaCell™ Supplement (100X, ThermoFisher Scientific). Afterwards, PSCs were seeded single-cell on Corning® Matrigel® Matrix-coated plates (VWR, Leuven, Belgium) at a density of 50,000 cells/cm². The following day, differentiation was induced by Essential 6TM Medium (ThermoFisher Scientific) supplemented with CHIR99021 (8µM, Axon Medchem, Groningen, Nederland) for two days.

extract_protocol:
CdMiPs were sorted single-cell by FACS in 96-well plates in RLT buffer. mRNA was isolated using the genome and transcriptome sequencing protocol CdMiPs were sorted single-cell by FACS in 96-well plates in RLT buffer. mRNA was isolated using the genome and transcriptome sequencing protocol
The libraries were prepared with the Nextera XT library prep and index kit (Illumina). 100pg of cDNA was tagmented by transposase Tn5 and amplified with dual-index primers (i7 and i5, 14 cycles). In total 279 single-cell libraries were pooled together and sequenced single 50bp on a single lane of a HiSeq4000 (Illumina).
SmartSeq2 single cell RNA-Seq

treatment_protocol: Afterwards, cells were cultured in Essential 6TM medium for another two days. Small molecules such as VPA (1mM, Sigma, Saint-Louis, MO, USA) or DAPT (20µM, Tocris, Bristol, UK) were added from day 2-4.

value: VPA

value: mesodermal progenitor cells


title: cdMipPs + VPA, rep128

description:
sc3_VPA.rds
S510  CGTCTAAT  N726  CCTAAGAC


title: cdMipPs + VPA, rep129

description:
sc3_VPA.rds
S511  TCTCTCCG  N726  CCTAAGAC


title: cdMipPs + VPA, rep133

description:
sc3_VPA.rds
S506  ACTGCATA  N727  CGATCAGT


title: cdMipPs + VPA, rep131

description:
sc3_VPA.rds
S503  TATCCTCT  N727  CGATCAGT


title: cdMipPs + VPA, rep132

description:
sc3_VPA.rds
S505  GTAAGGAG  N727  CGATCAGT


title: cdMipPs + VPA, rep130

description:
sc3_VPA.rds
S502  CTCTCTAT  N727  CGATCAGT


title: cdMipPs + VPA, rep126

description:
sc3_VPA.rds
S507  AAGGAGTA  N726  CCTAAGAC


title: cdMipPs + VPA, rep127

description:
sc3_VPA.rds
S508  CTAAGCCT  N726  CCTAAGAC


title: cdMipPs + VPA, rep125

description:
sc3_VPA.rds
S506  ACTGCATA  N726  CCTAAGAC


title: cdMipPs + VPA, rep120

description:
sc3_VPA.rds
S510  CGTCTAAT  N724  ACTGAGCG


title: cdMipPs + VPA, rep123

description:
sc3_VPA.rds
S503  TATCCTCT  N726  CCTAAGAC


title: cdMipPs + VPA, rep121

description:
sc3_VPA.rds
S511  TCTCTCCG  N724  ACTGAGCG


title: cdMipPs + VPA, rep122

description:
sc3_VPA.rds
S502  CTCTCTAT  N726  CCTAAGAC


title: fve;rrm1_rep2 [Bisulfite-seq]


title: cdMipPs + VPA, rep115

description:
sc3_VPA.rds
S503  TATCCTCT  N724  ACTGAGCG


title: cdMipPs + VPA, rep118

description:
sc3_VPA.rds
S507  AAGGAGTA  N724  ACTGAGCG


title: cdMipPs + VPA, rep119

description:
sc3_VPA.rds
S508  CTAAGCCT  N724  ACTGAGCG


title: cdMipPs + VPA, rep117

description:
sc3_VPA.rds
S506  ACTGCATA  N724  ACTGAGCG


title: cdMipPs + VPA, rep116

description:
sc3_VPA.rds
S505  GTAAGGAG  N724  ACTGAGCG


title: cdMipPs + VPA, rep114

description:
sc3_VPA.rds
S502  CTCTCTAT  N724  ACTGAGCG


title: cdMipPs + VPA, rep135

description:
sc3_VPA.rds
S508  CTAAGCCT  N727  CGATCAGT


title: cdMipPs + VPA, rep110

description:
sc3_VPA.rds
S507  AAGGAGTA  N723  TAGCGCTC


title: cdMipPs + VPA, rep109

description:
sc3_VPA.rds
S506  ACTGCATA  N723  TAGCGCTC


title: cdMipPs + VPA, rep112

description:
sc3_VPA.rds
S510  CGTCTAAT  N723  TAGCGCTC


title: cdMipPs + VPA, rep111

description:
sc3_VPA.rds
S508  CTAAGCCT  N723  TAGCGCTC


title: cdMipPs + VPA, rep107

description:
sc3_VPA.rds
S503  TATCCTCT  N723  TAGCGCTC


title: cdMipPs + VPA, rep108

description:
sc3_VPA.rds
S505  GTAAGGAG  N723  TAGCGCTC


title: cdMipPs + VPA, rep124

description:
sc3_VPA.rds
S505  GTAAGGAG  N726  CCTAAGAC


title: cdMipPs + VPA, rep100

description:
sc3_VPA.rds
S505  GTAAGGAG  N722  ATGCGCAG


title: cdMipPs + VPA, rep104

description:
sc3_VPA.rds
S510  CGTCTAAT  N722  ATGCGCAG


title: cdMipPs + VPA, rep105

description:
sc3_VPA.rds
S511  TCTCTCCG  N722  ATGCGCAG


title: cdMipPs + VPA, rep102

description:
sc3_VPA.rds
S507  AAGGAGTA  N722  ATGCGCAG


title: cdMipPs + VPA, rep101

description:
sc3_VPA.rds
S506  ACTGCATA  N722  ATGCGCAG


title: cdMipPs + VPA, rep103

description:
sc3_VPA.rds
S508  CTAAGCCT  N722  ATGCGCAG


title: cdMipPs + VPA, rep99

description:
sc3_VPA.rds
S503  TATCCTCT  N722  ATGCGCAG


title: cdMipPs + VPA, rep94

description:
sc3_VPA.rds
S507  AAGGAGTA  N721  TACGCTGC


title: cdMipPs + VPA, rep97

description:
sc3_VPA.rds
S511  TCTCTCCG  N721  TACGCTGC


title: cdMipPs + VPA, rep96

description:
sc3_VPA.rds
S510  CGTCTAAT  N721  TACGCTGC


title: cdMipPs + VPA, rep95

description:
sc3_VPA.rds
S508  CTAAGCCT  N721  TACGCTGC


title: cdMipPs + VPA, rep113

description:
sc3_VPA.rds
S511  TCTCTCCG  N723  TAGCGCTC


title: cdMipPs + VPA, rep93

description:
sc3_VPA.rds
S506  ACTGCATA  N721  TACGCTGC


title: cdMipPs + VPA, rep89

description:
sc3_VPA.rds
S511  TCTCTCCG  N720  CGGAGCCT


title: cdMipPs + VPA, rep88

description:
sc3_VPA.rds
S510  CGTCTAAT  N720  CGGAGCCT


title: cdMipPs + VPA, rep91

description:
sc3_VPA.rds
S503  TATCCTCT  N721  TACGCTGC


title: cdMipPs + VPA, rep92

description:
sc3_VPA.rds
S505  GTAAGGAG  N721  TACGCTGC


title: cdMipPs + VPA, rep86

description:
sc3_VPA.rds
S507  AAGGAGTA  N720  CGGAGCCT


title: cdMipPs + VPA, rep83

description:
sc3_VPA.rds
S503  TATCCTCT  N720  CGGAGCCT


title: cdMipPs + VPA, rep106

description:
sc3_VPA.rds
S502  CTCTCTAT  N723  TAGCGCTC


title: cdMipPs + VPA, rep82

description:
sc3_VPA.rds
S502  CTCTCTAT  N720  CGGAGCCT


title: cdMipPs + VPA, rep98

description:
sc3_VPA.rds
S502  CTCTCTAT  N722  ATGCGCAG


title: cdMipPs + VPA, rep87

description:
sc3_VPA.rds
S508  CTAAGCCT  N720  CGGAGCCT


title: cdMipPs + VPA, rep79

description:
sc3_VPA.rds
S508  CTAAGCCT  N719  GCGTAGTA


title: cdMipPs + VPA, rep80

description:
sc3_VPA.rds
S510  CGTCTAAT  N719  GCGTAGTA


title: cdMipPs + VPA, rep77

description:
sc3_VPA.rds
S506  ACTGCATA  N719  GCGTAGTA


title: cdMipPs + VPA, rep78

description:
sc3_VPA.rds
S507  AAGGAGTA  N719  GCGTAGTA


title: cdMipPs + VPA, rep81

description:
sc3_VPA.rds
S511  TCTCTCCG  N719  GCGTAGTA


title: cdMipPs + VPA, rep75

description:
sc3_VPA.rds
S503  TATCCTCT  N719  GCGTAGTA


title: cdMipPs + VPA, rep76

description:
sc3_VPA.rds
S505  GTAAGGAG  N719  GCGTAGTA


title: cdMipPs + VPA, rep73

description:
sc3_VPA.rds
S511  TCTCTCCG  N718  GGAGCTAC


title: cdMipPs + VPA, rep74

description:
sc3_VPA.rds
S502  CTCTCTAT  N719  GCGTAGTA


title: cdMipPs + VPA, rep71

description:
sc3_VPA.rds
S508  CTAAGCCT  N718  GGAGCTAC


title: cdMipPs + VPA, rep90

description:
sc3_VPA.rds
S502  CTCTCTAT  N721  TACGCTGC


title: cdMipPs + VPA, rep72

description:
sc3_VPA.rds
S510  CGTCTAAT  N718  GGAGCTAC


title: cdMipPs + VPA, rep70

description:
sc3_VPA.rds
S507  AAGGAGTA  N718  GGAGCTAC


title: cdMipPs + VPA, rep85

description:
sc3_VPA.rds
S506  ACTGCATA  N720  CGGAGCCT


title: cdMipPs + VPA, rep66

description:
sc3_VPA.rds
S502  CTCTCTAT  N718  GGAGCTAC


title: cdMipPs + VPA, rep64

description:
sc3_VPA.rds
S510  CGTCTAAT  N716  ACTCGCTA


title: cdMipPs + VPA, rep63

description:
sc3_VPA.rds
S508  CTAAGCCT  N716  ACTCGCTA


title: cdMipPs + VPA, rep65

description:
sc3_VPA.rds
S511  TCTCTCCG  N716  ACTCGCTA


title: cdMipPs + VPA, rep62

description:
sc3_VPA.rds
S507  AAGGAGTA  N716  ACTCGCTA


title: cdMipPs + VPA, rep69

description:
sc3_VPA.rds
S506  ACTGCATA  N718  GGAGCTAC


title: cdMipPs + VPA, rep61

description:
sc3_VPA.rds
S506  ACTGCATA  N716  ACTCGCTA


title: cdMipPs + VPA, rep67

description:
sc3_VPA.rds
S503  TATCCTCT  N718  GGAGCTAC


title: cdMipPs + VPA, rep84

description:
sc3_VPA.rds
S505  GTAAGGAG  N720  CGGAGCCT


title: cdMipPs + VPA, rep59

description:
sc3_VPA.rds
S503  TATCCTCT  N716  ACTCGCTA


title: NCI-H647_RBN012397_30nM_6hr_rep1

data_processing:
Raw transcriptome sequences were analyzed using Salmon v0.11.27.
Using Salmon’s mapping-based mode with a Gencode (release 29) human reference transcriptome index produced transcriptome read counts for each sequenced sample.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: Lung

value: Non-small cell lung cancer


title: cdMipPs + VPA, rep56

description:
sc3_VPA.rds
S521  GAGCCTTA  N715  ATCTCAGG


title: cdMipPs + VPA, rep58

description:
sc3_VPA.rds
S502  CTCTCTAT  N716  ACTCGCTA


title: cdMipPs + VPA, rep57

description:
sc3_VPA.rds
S522  TTATGCGA  N715  ATCTCAGG


title: cdMipPs + VPA, rep55

description:
sc3_VPA.rds
S520  AAGGCTAT  N715  ATCTCAGG


title: cdMipPs + VPA, rep54

description:
sc3_VPA.rds
S518  CTATTAAG  N715  ATCTCAGG


title: cdMipPs + VPA, rep52

description:
sc3_VPA.rds
S516  CCTAGAGT  N715  ATCTCAGG


title: cdMipPs + VPA, rep53

description:
sc3_VPA.rds
S517  GCGTAAGA  N715  ATCTCAGG


title: cdMipPs + VPA, rep48

description:
sc3_VPA.rds
S510  CGTCTAAT  N715  ATCTCAGG


title: cdMipPs + VPA, rep49

description:
sc3_VPA.rds
S511  TCTCTCCG  N715  ATCTCAGG


title: cdMipPs + VPA, rep50

description:
sc3_VPA.rds
S513  TCGACTAG  N715  ATCTCAGG


title: cdMipPs + VPA, rep47

description:
sc3_VPA.rds
S508  CTAAGCCT  N715  ATCTCAGG


title: cdMipPs + VPA, rep51

description:
sc3_VPA.rds
S515  TTCTAGCT  N715  ATCTCAGG


title: cdMipPs + VPA, rep46

description:
sc3_VPA.rds
S507  AAGGAGTA  N715  ATCTCAGG


title: cdMipPs + VPA, rep43

description:
sc3_VPA.rds
S503  TATCCTCT  N715  ATCTCAGG


title: cdMipPs + VPA, rep44

description:
sc3_VPA.rds
S505  GTAAGGAG  N715  ATCTCAGG


title: cdMipPs + VPA, rep45

description:
sc3_VPA.rds
S506  ACTGCATA  N715  ATCTCAGG


title: cdMipPs + VPA, rep42

description:
sc3_VPA.rds
S502  CTCTCTAT  N715  ATCTCAGG


title: cdMipPs + VPA, rep60

description:
sc3_VPA.rds
S505  GTAAGGAG  N716  ACTCGCTA


title: cdMipPs + VPA, rep39

description:
sc3_VPA.rds
S520  AAGGCTAT  N714  GCTCATGA


title: cdMipPs + VPA, rep38

description:
sc3_VPA.rds
S518  CTATTAAG  N714  GCTCATGA


title: cdMipPs + VPA, rep41

description:
sc3_VPA.rds
S522  TTATGCGA  N714  GCTCATGA


title: cdMipPs + VPA, rep35

description:
sc3_VPA.rds
S515  TTCTAGCT  N714  GCTCATGA


title: cdMipPs + VPA, rep36

description:
sc3_VPA.rds
S516  CCTAGAGT  N714  GCTCATGA


title: cdMipPs + VPA, rep33

description:
sc3_VPA.rds
S511  TCTCTCCG  N714  GCTCATGA


title: cdMipPs + VPA, rep34

description:
sc3_VPA.rds
S513  TCGACTAG  N714  GCTCATGA


title: cdMipPs + VPA, rep32

description:
sc3_VPA.rds
S510  CGTCTAAT  N714  GCTCATGA


title: cdMipPs + VPA, rep31

description:
sc3_VPA.rds
S508  CTAAGCCT  N714  GCTCATGA


title: cdMipPs + VPA, rep28

description:
sc3_VPA.rds
S505  GTAAGGAG  N714  GCTCATGA


title: cdMipPs + VPA, rep29

description:
sc3_VPA.rds
S506  ACTGCATA  N714  GCTCATGA


title: cdMipPs + VPA, rep26

description:
sc3_VPA.rds
S502  CTCTCTAT  N714  GCTCATGA


title: cdMipPs + VPA, rep27

description:
sc3_VPA.rds
S503  TATCCTCT  N714  GCTCATGA


title: cdMipPs + VPA, rep24

description:
sc3_VPA.rds
S521  GAGCCTTA  N712  GTAGAGGA


title: cdMipPs + VPA, rep23

description:
sc3_VPA.rds
S520  AAGGCTAT  N712  GTAGAGGA


title: cdMipPs + VPA, rep25

description:
sc3_VPA.rds
S522  TTATGCGA  N712  GTAGAGGA


title: cdMipPs + VPA, rep21

description:
sc3_VPA.rds
S517  GCGTAAGA  N712  GTAGAGGA


title: cdMipPs + VPA, rep22

description:
sc3_VPA.rds
S518  CTATTAAG  N712  GTAGAGGA


title: cdMipPs + VPA, rep17

description:
sc3_VPA.rds
S511  TCTCTCCG  N712  GTAGAGGA


title: cdMipPs + VPA, rep19

description:
sc3_VPA.rds
S515  TTCTAGCT  N712  GTAGAGGA


title: cdMipPs + VPA, rep18

description:
sc3_VPA.rds
S513  TCGACTAG  N712  GTAGAGGA


title: cdMipPs + VPA, rep15

description:
sc3_VPA.rds
S508  CTAAGCCT  N712  GTAGAGGA


title: cdMipPs + VPA, rep40

description:
sc3_VPA.rds
S521  GAGCCTTA  N714  GCTCATGA


title: cdMipPs + VPA, rep14

description:
sc3_VPA.rds
S507  AAGGAGTA  N712  GTAGAGGA


title: cdMipPs + VPA, rep37

description:
sc3_VPA.rds
S517  GCGTAAGA  N714  GCTCATGA


title: cdMipPs + VPA, rep11

description:
sc3_VPA.rds
S503  TATCCTCT  N712  GTAGAGGA


title: cdMipPs + VPA, rep10

description:
sc3_VPA.rds
S502  CTCTCTAT  N712  GTAGAGGA


title: cdMipPs + VPA, rep30

description:
sc3_VPA.rds
S507  AAGGAGTA  N714  GCTCATGA


title: cdMipPs + VPA, rep9

description:
sc3_VPA.rds
S522  TTATGCGA  N711  AAGAGGCA


title: cdMipPs + VPA, rep12

description:
sc3_VPA.rds
S505  GTAAGGAG  N712  GTAGAGGA


title: cdMipPs + VPA, rep7

description:
sc3_VPA.rds
S520  AAGGCTAT  N711  AAGAGGCA


title: cdMipPs + VPA, rep6

description:
sc3_VPA.rds
S518  CTATTAAG  N711  AAGAGGCA


title: cdMipPs + VPA, rep13

description:
sc3_VPA.rds
S506  ACTGCATA  N712  GTAGAGGA


title: cdMipPs + VPA, rep4

description:
sc3_VPA.rds
S516  CCTAGAGT  N711  AAGAGGCA


title: cdMipPs + VPA, rep3

description:
sc3_VPA.rds
S515  TTCTAGCT  N711  AAGAGGCA


title: cdMipPs + VPA, rep5

description:
sc3_VPA.rds
S517  GCGTAAGA  N711  AAGAGGCA


title: cdMipPs + VPA, rep2

description:
sc3_VPA.rds
S513  TCGACTAG  N711  AAGAGGCA


title: cdMipPs, rep135

description:
sc3_UT.rds
S510  CGTCTAAT  N711  AAGAGGCA

value: unVPA


title: cdMipPs + VPA, rep68

description:
sc3_VPA.rds
S505  GTAAGGAG  N718  GGAGCTAC


title: cdMipPs + VPA, rep20

description:
sc3_VPA.rds
S516  CCTAGAGT  N712  GTAGAGGA


title: cdMipPs, rep134

description:
sc3_UT.rds
S508  CTAAGCCT  N711  AAGAGGCA


title: cdMipPs, rep131

description:
sc3_UT.rds
S505  GTAAGGAG  N711  AAGAGGCA


title: cdMipPs, rep130

description:
sc3_UT.rds
S503  TATCCTCT  N711  AAGAGGCA


title: cdMipPs, rep129

description:
sc3_UT.rds
S502  CTCTCTAT  N711  AAGAGGCA


title: cdMipPs + VPA, rep16

description:
sc3_VPA.rds
S510  CGTCTAAT  N712  GTAGAGGA


title: cdMipPs, rep124

description:
sc3_UT.rds
S517  GCGTAAGA  N710  CGAGGCTG


title: cdMipPs + VPA, rep8

description:
sc3_VPA.rds
S521  GAGCCTTA  N711  AAGAGGCA


title: cdMipPs, rep125

description:
sc3_UT.rds
S518  CTATTAAG  N710  CGAGGCTG


title: cdMipPs, rep126

description:
sc3_UT.rds
S520  AAGGCTAT  N710  CGAGGCTG


title: cdMipPs, rep127

description:
sc3_UT.rds
S521  GAGCCTTA  N710  CGAGGCTG


title: cdMipPs, rep128

description:
sc3_UT.rds
S522  TTATGCGA  N710  CGAGGCTG


title: cdMipPs, rep121

description:
sc3_UT.rds
S513  TCGACTAG  N710  CGAGGCTG


title: cdMipPs, rep120

description:
sc3_UT.rds
S511  TCTCTCCG  N710  CGAGGCTG


title: cdMipPs, rep123

description:
sc3_UT.rds
S516  CCTAGAGT  N710  CGAGGCTG


title: cdMipPs, rep115

description:
sc3_UT.rds
S505  GTAAGGAG  N710  CGAGGCTG


title: cdMipPs, rep122

description:
sc3_UT.rds
S515  TTCTAGCT  N710  CGAGGCTG


title: cdMipPs, rep119

description:
sc3_UT.rds
S510  CGTCTAAT  N710  CGAGGCTG


title: cdMipPs, rep117

description:
sc3_UT.rds
S507  AAGGAGTA  N710  CGAGGCTG


title: cdMipPs + VPA, rep1

description:
sc3_VPA.rds
S511  TCTCTCCG  N711  AAGAGGCA


title: cdMipPs, rep116

description:
sc3_UT.rds
S506  ACTGCATA  N710  CGAGGCTG


title: cdMipPs, rep118

description:
sc3_UT.rds
S508  CTAAGCCT  N710  CGAGGCTG


title: cdMipPs, rep112

description:
sc3_UT.rds
S522  TTATGCGA  N707  CTCTCTAC