title: Input replicate 2. BxPC3

tag: cell line

value: BXPC3 PDAC cell line

value: WT


title: 4626

status: Public on Jan 11 2021

type: RNA

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

description: Gene expression data from adults

hyb_protocol: Standard GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: miRNA-4_1 chips were scanned at the Cologne Center for Genomics, Cologne, Germany.

data_processing: Pre-processing, normalization, probe summarization, and data quality control were executed in Expression Console Software (Affymetrix). Robust Multi-array Average (RMA)  normalization and DABG probe-level detection were specified. All other parameters were default.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: blood

label_protocol: 100ng total RNA was labeled using standard GeneChip buffers and reagents (Affymetrix)

growth_protocol: Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.

extract_protocol: Total RNA was isolated in accordance with the PAXgene blood miRNA isolation (QIAGEN) procedure using the QIAcube instrument.

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (approx. 2 hours) while mixing by inversion.

tag: age

tag: gender

value: male

tag: disease state

value: patient

tag: treatment

tag: tissue

value: blood


title: Patient 2 lung

city: Seoul

first: Seung Geun

last: Song

address: 101 Daehak-ro, Jongno-gu

department: Department of Pathology

country: South Korea

institute: Seoul National University College of Medicine

scan_protocol: The nCounter platform

data_processing: Raw data (NanoString RCC file) were imported to nSolver Analysis Software version 4.0. and normalized using positive control and housekeeping genes.

label: nanostring

source_name: primary lung cancer

label_protocol: The nCounter platform

extract_protocol: RNA was extracted from 100 µm thick formalin-fixed paraffin-embedded tissue

tag: organ

value: lung

tag: age at surgery

tag: histology

value: Adenocarcinoma

tag: egfr

value: Mutant

tag: egfr type

tag: Sex

value: Female


title: F5405_ACDiEKO_rep4

city: Albany

first: John

middle: J

last: Schwarz

state: NY

address: 47 New Scotland Ave.

department: Department of Molecular and Cellular Physiology

country: USA

institute: Albany Medical College

hyb_protocol: labeled samples (5.5ug) were hybridized to Clariom D Mouse assay (formally Mouse Transcriptome1.0 Array) (Affymetrix) using standard protocol

scan_protocol: The arrays were scanned on a GCS3000 7G scanner using standard Affymetrix protocols

data_processing: The CEL files were converted to CHP files using Expression Consolev 1.4. Further statistical analysis was done using Affymetrix Transcriptome Console v3.0. RMA data.

organism: Mus musculus

source_name: Cdh5-CreERT2(+); Mef2a f/f; Mef2c f/f; Mef2d f/f mice injected with tamoxifen

label_protocol: 5ng total RNA was converted to fragmented biotinylated cDNA using the standard WT Pico protocol (Affymetrix)

growth_protocol: Mice were housed in specific-pathogen free facility.

extract_protocol: Total RNA was isolated from TRIzol reagent (ThermoFisher) that flushed through the lumen of individaul mouse thoracic aortas according to manufacturer’s protocol with LPA (Sigma-Aldrich) precipitation.

treatment_protocol: Endothelial-specific, inducible combined-deletion of Mef2a, Mef2c and Mef2d was mediated by Cdh5-CreERT2 through 5 daily tamoxifen (dissolved in sunflower seed oil with 10% ethanol) injections (ACDiEKO) in 10 weeks old mice. Tamoxifen injected Cre-negative littermates were used as control. Thoracic aortas from these mice were harvest 14 days after the first injection.

tag: genotype

value: ACDiEKO

value: Thoracic aortic endothelium


title: F5406_ACDiEKO_rep5


title: F5404_ACDiEKO_rep3


title: 4351

description: Gene expression data from adults


title: D339_Biop_Nas1

type: SRA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

library_source: transcriptomic

data_processing:
10xGenomics Cellranger standard analysis.
Genome_build: hg19
Supplementary_files_format_and_content: 10xGenomics Cellranger filtered gene/cellbarcode matrix.

molecule: polyA RNA

source_name: airways

extract_protocol: 10xGenomics 3p single cell rna-seq

value: Nasal epithelium

tag: collection

value: Biopsy


title: 3802

description: Gene expression data from adults


title: 5311

description: Gene expression data from adults


title: F5403_ACDiEKO_rep2


title: 5210

description: Gene expression data from adults

value: female


title: F5364_Cntl_rep3

source_name: Cdh5-CreERT2(-); Mef2a f/f; Mef2c f/f; Mef2d f/f mice injected with tamoxifen

value: control


title: F5363_Cntl_rep3


title: samp_7_17mut

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

data_processing:
Basecalls performed using CASAVA version 1.8
A pseudo-alignment to the zebrafish transcriptome (according to the Ensembl GRCz11 (release 96), with the sequences for unspliced transcripts additionally included) using kallisto v0.43.1
Transcript abundances were summarised using the catchkallisto() function of edgeR
Genome_build: GRCz11 (release 96)
Supplementary_files_format_and_content: Matrix table with raw transcript counts for every gene and every sample

organism: Danio rerio

source_name: sorl1W1818*/+_whole brain

growth_protocol: Fish were raised together in a single tank until 6 months of age.

extract_protocol:
Total RNA was extracted from individual brains using the mirVana miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA).  DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA-free Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). Total RNA was lyophilised in RNAStable (Biomatrica, San Diego, CA, USA) and sent to Novogene (HK) for polyA construction of sequencing libraries.
PE150 PolyA+ library preparaton was performed by Novogene using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

value: Whole brain


title: 4083062

description: Gene expression data from adults


title: samp_9_1W

source_name: wild-type_whole brain

value: wild-type

value: Male


title: samp_6_16W


title: FSK/GDNF3

first: Dusan

last: Matusica

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

institute: FLINDERS UNIVERSITY OF SOUTH AUSTRALIA

data_processing:
Samples were multiplexed and sequenced on the Illumina NextSeq 500 using the stranded paired-end protocol with a read length of 75.
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1 3
The resulting FASTQ files were analysed and quality checked using the FastQC program
The filtered reads were mapped against the Rattus norvegicus genome (Rnor_6) using the STAR alignment algorithm (version 2.5.3a)  with default parameters
Counts of the mapped read to the genes are normalised using RPKM method
Differntial expression analysis carried out using the DESeq2 statistical algorithm and adjusted p-values using Benjamini-Hochberg Procedure
Genome_build: Rnor_6
Supplementary_files_format_and_content: RPKM and Differntial expression files

organism: Rattus norvegicus

source_name: 50B11 cells

growth_protocol: 50B11 cells, were maintained in plated in Neurobasal medium (Life Technologies, Gibco) supplemented with 10% FBS (Life Technologies, Gibco), 1% B27 (Life Technologies), 20mM D-glucose (Life Technologies, Gibco) and 1% glutaMAX™ media supplement (Life Technologies, Gibco).

extract_protocol:
Total RNA was extracted using Trizol and column-based extraction (Zymogen, Direct-Zol RNA kit)
Libraries were genertaed using the illumina TruSeq Staranded Total RNA Preparation Kit with Human/Mouse/Rat Ribosomal RNA depletion as per standard protocol, using 1ug Total RNA input per sample. Libraries were validated using the Labchip GX Touch 24 (Perkin Elmer) and quantified with the Qubit 2.0 (Thermofisher Scientific). Sequencing was performed on a NextSeq 500 using the High Output 150 cycle v2.5 kit.

treatment_protocol: 50B11 cells were plated 1,000,000 cells per T25 flask for. 24 h after plating cells were differentiated by adding forskolin (FSK; Sigma–Aldrich, 10µM) to reduced serum (1%FBS) medium. 17 hrs post-FSK growth factor treatments of (50 ng/ml recombinant mNGF, Peprotech), GDNF (50ng/ml recombinant hGDNF, Peprotech) were performed every 2 days until DIV7 when cells were havrvested for RNAseg.

tag: source tissue

value: E14.5 immortalized dorsal root ganglion neurons

tag: rat strain

value: Sprague Dawley rats

tag: passages

value: forskolin and 50 ng/ml recombinant hGDNF


title: 4081344

description: Gene expression data from adults

value: patient

value: blood


title: D339_Biop_Pro1

value: Lung epithelium


title: 4117485

description: Gene expression data from adults


title: D339_Biop_Int1


title: 3682

description: Gene expression data from adults

value: male


title: F5408_Cntl_rep2

value: Female


title: 3303811

description: Gene expression data from adults


title: D326_Biop_Pro1


title: D326_Brus_Dis1

value: Brushing


title: FSK/GDNF2


title: F5402_ACDiEKO_rep1

value: ACDiEKO

value: Thoracic aortic endothelium


title: samp_8_19W


title: D337_Brus_Dis1


title: D326_Biop_Int1

value: Biopsy


title: Patient 1 lung

value: lung

value: Adenocarcinoma

value: Wild-type


title: samp_5_15mut

value: Whole brain


title: 3549114

description: Gene expression data from adults


title: FSK/GDNF1


title: samp_3_13W

value: wild-type


title: samp_2_12mut


title: D322_Biop_Nas1

value: Nasal epithelium


title: FSK/NGF1

value: E14.5 immortalized dorsal root ganglion neurons

value: Sprague Dawley rats

value: forskolin and 50 ng/ml recombinant mNGF


title: D322_Biop_Pro1


title: FSK/NGF2


title: 3386401

description: Gene expression data from adults

value: sepsis

value: blood


title: FSK/NGF3


title: samp_12_9W


title: undifferentiated 3


title: samp_11_5mut

value: Male


title: 3047641

description: Gene expression data from adults

value: male

value: patient


title: 3618078

description: Gene expression data from adults

value: female


title: samp_4_14W

value: Female


title: D322_Biop_Int1

value: Lung epithelium

value: Biopsy


title: F5407_Cntl_rep1

value: control

value: Thoracic aortic endothelium


title: samp_10_4mut

value: Whole brain


title: undifferentiated 2


title: samp_1_11mut


title: 4107810

description: Gene expression data from adults


title: MCF10Ca1h cells, H3K4me3.GSK484 (S8)

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

library_source: genomic

data_processing:
Peak calling with MACS2. Chipseq.GSK484.vs.CON.4ChIPseq.RNAseq.TSS.4k.matrix.mat.gz is  the MACS2- generated file. It reports MACS2 peaks for all 10 samples.
Genome_build: hg19
Supplementary_files_format_and_content: Chipseq.GSK484.vs.CON.4ChIPseq.RNAseq.TSS.4k.matrix.mat.gz reports peaks

molecule: genomic DNA

source_name: human breast cell lines

growth_protocol: MCF10Ca1h cells were cultured in DMEM/F12 media supplemented with 5% horse serum.

extract_protocol:
ChIPs were done with SimpleChIP Enzymatic chromatin IP kit (Cell Signaling technologies).
Sequencing libraries were prepared using standard Illumina protocols.
Sequencing libraries were run on Illumina NextSeq platform SR 75bp cycle runs of 50M reads/sample

treatment_protocol: Cells were treated with PADI4 inhibitor (GSK484) or control compound (GSK107) for 72 hours.

tag: cell line

value: MCF10Ca1h human breast cancer cell line

tag: in vivo timepoint

value: 72 hrs

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys4) (C42D8), Cell Signaling Tech #9751; 1:50


title: undifferentiated 1

value: E14.5 immortalized dorsal root ganglion neurons

value: Sprague Dawley rats


title: MCF10Ca1h cells, H3K27me3.GSK484 (S9)

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb, Cell Signaling Tech #9733; 1:50


title: SARS-CoV-2_Unmod_Rep2

city: New Haven

first: Nicholas

last: Huston

state: Connecticut

address: 260 Whitney Avenue, YSB 308

institute: Yale University

data_processing:
Library strategy: SHAPE-MaP
ShapeMapper
Supplementary_files_format_and_content: ShapeMapper output file for each replicate

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Vero Cells

growth_protocol: Vero cells were cultured in T150 flasks

extract_protocol:
Trizol
cDNA was prepared from modified RNA using gene-specific RT primers, followed by generation of amplicons with gene-specific primers. Nextera-XT kit was used for library construction

treatment_protocol: At 4dpi, each sample was collected and treated with either 200mM NAI (final) or equivalent volume DMSO

tag: strain

value: SARS-CoV-2 isolate USA-WA1/2020 (BEI Resources #NR-52281)

tag: chemical modification

value: dimethyl sulfoxide


title: SARS-CoV-2_Mod_Rep2

value: 2-methylnicotinic acid imidazolide


title: hFUS-R514G mice, ID 1563

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2. (-Q 5)
The RNA-Seq reads were aligned and quantified using Kallisto v.0.44.0 with standard parameters and 100 bootstraps
Sleuth v.0.30.0 was used to quantify abundance
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with gene abundance for all samples

source_name: hippocampus

extract_protocol:
Hippocampus were removed from 12-month old mice and flash frozen under liquid nitrogen. The RNA was harvested using Trizol reagent
RNA-Seq libraries were contructed using the Illumina TruSeq Sample Prep Kit

tag: tissue

value: hippocampus

tag: age

tag: gender

value: F

tag: library preparation

value: Illumina TruSeq RNA Sample Prep Kit


title: hFUS-R514G mice, ID 1561


title: hFUS-R514G mice, ID 1562

value: M


title: MCF10Ca1h cells, IgG.GSK484 (S6)

tag: treatment

value: Normal Rabbit IgG, Cell Signaling Tech #2729; 2ul/IP


title: 3817

description: Gene expression data from adults

value: female

tag: disease state

value: patient

value: blood


title: MCF10Ca1h cells, H3R2/8/17citr.GSK484 (S10)

value: MCF10Ca1h human breast cancer cell line

value: Histone H3 (citrulline R2 + R8 + R17), Abcam ab5103; 1:50


title: 3773892

description: Gene expression data from adults

value: sepsis


title: MCF10Ca1h cells, H3.GSK484 (S7)

value: 72 hrs

value: Histone H3 (D2B12) XP® Rabbit mAb, Cell Signaling Tech #4620; 1:50


title: SARS-CoV-2_Mod_Rep1


title: non-transgenic mice, ID 1554

value: wildtype


title: MCF10Ca1h cells, IgG.GSK484 (IgG)


title: 3787885

description: Gene expression data from adults

value: male


title: non-transgenic mice, ID 1553


title: MCF10Ca1h cells, H3K27me3.CON (S4)

value: CON

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb, Cell Signaling Tech #9733; 1:50


title: FINS_252

city: Carbondale

first: James

middle: Arthur

last: MacLean

state: Illinois

address: 1135 Lincoln Dr, Life Science III, Room 2071

institute: Southern Illinois University

description: DKO Rep 4

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software.
Each sample's fastq file run through trimmomatic 0.36 to first remove any remaining standard Illumina TruSeq SE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove reads shorter than 30 bp (parameters ILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.33/adapters/TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30).  Very few reads were lost to trimming
NCBI's GRCm38.p3 genome was indexed using STAR 2.4.2a with gene models ref_GRCm38.p3_top_level.gff3.gz (NCBI Mus musculus Annotation Release 105) and parameters --sjdbOverhang 99 and --sjdbGTFtagExonParentGene gene. Each sample was then aligned to the genome again using STAR 2.4.2a with gene models ref_GRCm38.p3_top_level.gff3.gz (NCBI Mus musculus Annotation Release 105) and parameter --sjdbGTFtagExonParentGene gene.
Read counts for each gene were generated using featureCounts (from subread v 1.5.2) with parameters -T 4 -s 2 -g gene -t exon -o
Genome_build: NCBI GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files of raw read counts per gene per sample were used directly in edgeR 3.12.0 for statistical analysis and thus are the "normalized" data.

source_name: Whole ovary, eCG, hCG 12 h

growth_protocol: Superovulation of  ~3 wk old  mice was performed using a single 4 IU injection of eCG, followed by a single injection of 5 IU hCG 48 hours after eCG administration.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. DNAse digestion was performed using the accompaning RNAse free DNAse set.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).  Indices (barcodes) were included to be able to differentiate the sequences from each sample.  The adapter sequence used was AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index)

treatment_protocol: Whole ovaries were extirpated from superovulated mice 12 h after the hCG injection, around the normal expected time of ovulation.

tag: Sex

value: Whole ovary

value: Insr-Igf1r double knockout


title: MCF10Ca1h cells, H3K4me3.GSK484 (S3)

value: Tri-Methyl-Histone H3 (Lys4) (C42D8), Cell Signaling Tech #9751; 1:50


title: MCF10Ca1h cells, H3R2/8/17citr.CON (S5)


title: The wild type strain_rep3

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

country: China

institute: Yangzhou University

description:
The transcriptome of the wild type strain
SC2

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Streptococcus suis SC84, complete genome (NC_012924.1).
Supplementary_files_format_and_content: read counts for each strain.
Supplementary_files_format_and_content: fpkm values for each strain.

organism: Streptococcus suis

source_name: the wild type strain of S. suis

growth_protocol: The wild type strain and the ΔtroR mutant were grown at 37 °C in Tryptic Soy Broth supplemented with 10% (vol/vol) newborn bovine serum (TSBS).  Overnight cultures of the strains were diluted 1:100 in fresh medium, and grown to the mid-exponential phase (OD600 = 0.6).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Bacterial cells were collected by centrifugation; the cells were immediately used for RNA extraction.

tag: genotype

value: wild type

tag: medium

value: TSBS

tag: phase

value: mid-exponential phase


title: SARS-CoV-2_Unmod_Rep1

value: SARS-CoV-2 isolate USA-WA1/2020 (BEI Resources #NR-52281)

value: dimethyl sulfoxide


title: The wild type strain_rep2

description:
The transcriptome of the wild type strain
NSC3


title: non-transgenic mice, ID 1552

value: hippocampus

value: M

value: Illumina TruSeq RNA Sample Prep Kit


title: FINS_249

description: DKO Rep 3

value: female


title: 5629

description: Gene expression data from adults

value: patient

value: blood


title: 4205

description: Gene expression data from adults

value: male


title: The wild type strain_rep1

description:
The transcriptome of the wild type strain
NSC2


title: 4840

description: Gene expression data from adults


title: 5785

description: Gene expression data from adults

value: sepsis


title: ΔtroR strain_rep3

description:
The transcriptome of the ΔtroR mutant
Nmts1

source_name: the ΔtroR strain of S. suis


title: ΔtroR strain_rep2

description:
The transcriptome of the ΔtroR mutant
mts3


title: FINS_202

description: DKO Rep 2


title: FINS_201

description: DKO Rep 1


title: 3650

description: Gene expression data from adults


title: 3306810

description: Gene expression data from adults


title: RNAi Ctrl SK-BR-3 cell ribodepleted RNAseq repl5

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
The raw sequencing data were first analyzed using FastQC. Reads of low complexity were first filtered using AfterQC (default parameters). Trimmomatic tool was then used to trim Illumina universal adapter sequences from raw reads using a sliding window of 4 to 15 (ILLUMINACLIP:2:30:10, LEADING:3, TRAILING:3) and filtering reads smaller than 36 bp. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
The remaining reads were mapped on hg19 genome using STAR with ensembl reference transcriptome (version85).
Raw read count were then obtained using HTseq tool and normalised in TPM.
Supplementary_files_format_and_content: read counts in TPM

growth_protocol: SK-BR-3 cells were cultured at 37°C and 5% CO2  in DMEM supplemented with 10% FBS, and  1% penicillin-streptomycin. For RNAi maintenance, cells were kept under selection with 1.5μg/ml puromycin.

extract_protocol:
Total RNA was purified by RNeasy kit from RNAi-depleted FTO (RNAi FTO) and control (RNAi Ctrl) SK-BR-3 cells. Residual DNA removal was performed using the RNase-Free DNase Set. (Ribodepletion was obtained using TruSeq kit [see library construction protocol]).
Library preparation was performed with 1μg of total RNA using TruSeq Stranded Total RNA Library Prep Gold and TruSeq RNA Single Indexes, according to manufacturer’s instructions.

treatment_protocol: Stable knockdown was generated by inserting the target sequence for FTO (GTGAAAGGGTCTAATATAA) or the scramble control (GATCATGTAGATACGCTCA) into the pRetroSuper (pRS) retroviral vector to form short hairpin RNAs for RNAi. Transient co-transfection on HEK293GP packaging cells was used to generate cell-free viral supernatants. Briefly, HEK293GP cells were grown to 50% confluency in a 10 cm dish. Then 5µg of pRS plasmid and 1µg of plasmid encoding the glycoprotein of vesicular stomatitis virus were transfected with 24µl of polyethylene imine in Opti-MEM. After 5h, HEK293GP medium was replaced with complete medium. Forty-eight hours post-transfection, viral supernatants were harvested, sterile filtered, mixed with 8 μg/ml polybrene and incubated with target cells. After 24h, infected cells were selected with 1.5μg/ml puromycin.

tag: cell type

value: breast cancer cell line

tag: RNAi

value: RNAi-Ctrl

tag: replicates

tag: molecule subtype

value: Ribodepleted-RNA


title: FINS_263

description: Control Rep 4

value: Whole ovary

value: wild-type, Pgr-Cre positive


title: 3478

description: Gene expression data from adults


title: nor3

description: nor3 (GSM4653918)

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Streptococcus suis SC84, complete genome (NC_012924.1).
Supplementary_files_format_and_content: read counts for each gene and each sample.
Supplementary_files_format_and_content: fpkm values for each gene and each sample.

source_name: water-treated Streptococcus suis

growth_protocol: Streptococcus suis was grown at 37 °C in Tryptic Soy Broth (TSB) supplemented with 10% (vol/vol) newborn bovine serum.  Overnight culture of the strain was diluted 1:100 in fresh medium, and grown to the mid-exponential phase (OD600 = 0.6).

treatment_protocol: The culture was divided into 2 aliquots, which were supplemented with 1 mM MnSO4 or H2O, respectively. Following 15 min treatment, bacterial cells were collected for RNA extration.

value: H2O (control),15 min


title: RNAi Ctrl SK-BR-3 cell ribodepleted RNAseq repl3

tag: cell line


title: RNAi Ctrl SK-BR-3 cell ribodepleted RNAseq repl4


title: 3688590

description: Gene expression data from adults


title: nor1

description: nor1 (GSM4653916)

tag: strain

value: mid-exponential phase


title: FINS_261

description: Control Rep 3


title: MCF10Ca1h cells, H3.CON (S2)

value: MCF10Ca1h human breast cancer cell line

value: CON

tag: in vivo timepoint

value: 72 hrs

tag: chip antibody

value: Histone H3 (D2B12) XP® Rabbit mAb, Cell Signaling Tech #4620; 1:50


title: nor2

description: nor2 (GSM4653917)


title: RNAi Ctrl SK-BR-3 cell ribodepleted RNAseq repl1


title: FINS_259

description: Control Rep 2

tag: tissue


title: RNAi Ctrl SK-BR-3 cell ribodepleted RNAseq repl2


title: ΔtroR strain_rep1

description:
The transcriptome of the ΔtroR mutant
mts1

value: TSBS


title: RNAi FTO SK-BR-3 cell ribodepleted RNAseq repl5

value: RNAi-FTO


title: 3862041

description: Gene expression data from adults

tag: age

tag: gender


title: manganese treatment_rep3

description: The transcriptome of Streptococcus suis following treatment with Mn

source_name: Mn-treated Streptococcus suis

tag: treatment

value: 1 mM Mn, 15 min


title: manganese treatment_rep2


title: 4070142

description: Gene expression data from adults

tag: disease state

value: patient

value: blood


title: manganese treatment_rep1


title: RNAi FTO SK-BR-3 cell ribodepleted RNAseq repl4


title: SCN-DZnep-CT21-3

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

state: CA

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

institute: University of California, Irvine

description:
DZnep infused mice harvested at circadian time (CT) 21 Replicate 3
processed data file:
Gene_Expression_SCN-DZnep.xlsx

data_processing:
Basecalling performed using RTA release 2.7.7
Demultiplexing performed using bcl2fastq release 2.18.0.12
Technical adapters trimmed using Trimmomatic release 0.36
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each sample, one excel file per group, 6 groups total

growth_protocol: Mouse embryonic fibroblasts (MEF) were cultured in DMEM (4.5 g l-1 glucose) supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was isolatedfrom MEF cells at the indicated time points using TRIzol reagent. RNA was extracted from SCN punches using the RNeasy Micro Kit.
From MEF cells libraries were prepared from three biological replicates according to the TruSeq RNA Library Prep Kit v2. From SCN samples, libraries were generated from four biological replicates using the SMARTer Stranded total RNA-seq kit v2, pico input mammalian according to manufacturer’s instructions.

treatment_protocol: Confluent cells were synchronized with 100nM DEX for 1 hour. 3-Deazaneplanocin A (Dznep) was dissolved in DMSO and used at the indicated doses.

value: 10 weeks

value: Suprachiasmatic nucleus

tag: genotype/variation

value: Dznep treated

tag: ct


title: 3791260

description: Gene expression data from adults

value: male


title: SCN-DZnep-CT21-2

description:
DZnep infused mice harvested at circadian time (CT) 21 Replicate 2
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: 4101198

description: Gene expression data from adults


title: 3910077

description: Gene expression data from adults

value: sepsis


title: RNAi FTO SK-BR-3 cell ribodepleted RNAseq repl3

value: breast cancer cell line

value: Ribodepleted-RNA


title: RNAi FTO SK-BR-3 cell ribodepleted RNAseq repl2


title: SCN-DZnep-CT21-1

description:
DZnep infused mice harvested at circadian time (CT) 21 Replicate 1
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: SCN-DZnep-CT21-4

description:
DZnep infused mice harvested at circadian time (CT) 21 Replicate 4
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: SCN-DZnep-CT15-2

description:
DZnep infused mice harvested at circadian time (CT) 15 Replicate 2
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: SCN-DZnep-CT15-4

description:
DZnep infused mice harvested at circadian time (CT) 15 Replicate 4
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: RNAi Ctrl SK-BR-3 cell m6A-RIP Input repl2

data_processing:
The raw sequencing data were first analyzed using FastQC.
Reads were then mapped against the human reference genome (hg19) using STAR algorithm with RefSeq reference transcriptome (download on March 2012).
m6A-enriched regions (peaks) were identified by applying MACS2 peak-calling tool on immunoprecipitated (IP) samples using their input counterpart for estimating background noise (q-value < 0.05). Of note, the expected genome size MACS2 parameter was set as the sum of all transcripts length including exons and introns (counting a single time regions shared by several transcripts) and the summits positions were identified using --call-summits MACS2 option. To avoid identification of extremely large enriched regions, peaks were, then, resized to 100bp from both size of the identified summit.
Genome_build: hg19
Supplementary_files_format_and_content: Peak positions (100bp around both side of the summits) in bed format

source_name: RNAi Ctrl SK-BR-3 cell m6A-RIP Input

growth_protocol: All cells were cultured at 37°C and 5% CO2. SK-BR-3 cells were cultured in DMEM supplemented with 10% FBS,and  1% penicillin-streptomycin. PC-3 cells were cultured in MEM supplemented with 10% FBS and 1% penicillin-streptomycin. For RNAi maintenance, cells were kept under selection with 1.5μg/ml puromycin.

extract_protocol:
(RNA purification) Total RNA was purified with the RNeasy kit from RNAi-depleted FTO (RNAi FTO) and control (RNAi Ctrl) cells. Residual DNA removal was performed using the RNase-Free DNase Set.
(m6A-immunoprecipitation) Total RNA was then fragmented by mixing 90µl of RNA (at 1µg/µl) and 10µl of fragmentation buffer 10x (100mM Tris-HCl and 100mM ZnCl2) in thin-walled 200-μl PCR tubes, which were incubated at 94 °C for 35 seconds in a preheated thermocycler block with the heated lid opened. Then, 10 µl of 0.5M EDTA were added and the tubes were placed on ice. RNA was then subjected to sodium acetate precipitation and resuspended in 300μl of RNase-free water. RNA fragmentation size was assessed by running 0.5µg of RNA on a 2100 Bioanalyzer with an RNA Nano kit. Then, 2-5µg of fragmented RNA were kept at -80°C to later serve as input control. RNA was denatured by heat (70°C for 5 min, then on ice) and the immunoprecipitation mix was prepared as follows: 150µg of fragmented RNA in 755µl, 10µl (400 units) RNasin® Ribonuclease Inhibitors, 10µl 200mM Ribonucleoside Vanadyl Complex (RVC), 200µl IP buffer 5x (50mM Tris-HCl, 750 mM NaCl and 0.5% (vol/vol)), 7.8µl m6A antibody and 17.2µl RNase-free water. The mix was incubated overnight at 4°C on a rotation wheel. The next day, 60 µl of G-protein dynabeads were washed twice with IP buffer 1x supplemented with antiproteases and blocked by incubating the beads in wash buffer supplemented with 0.5 mg/ml BSA for 1h on a rotation wheel. The beads were washed again twice, then added to the immunoprecipitation mix and incubated for 2h at 4°C on a rotation wheel. The beads were washed three times with 1ml of wash buffer supplemented with 10µl of RNasin® and 10µl of RVC, then elution was performed by TriPure extraction and RNA was resuspended in 13µl of RNase-free water.
Retro-transcription of 11µl of immunoprecipitated RNA was completed with the SuperScript II Reverse Transcriptase kit, according to manufacturer’s instructions. Then, second strand synthesis was performed from cDNA with NEBNext mRNA Second Strand Synthesis Module, according to manufacturer’s instructions. Finally, double-stranded DNA was purified using a MinElute PCR purification and quantified by Qubit. Sequencing library was prepared with MicroPlex Library Preparation Kit v2 x12 for both input and IP samples.

tag: tissue/cell line

value: SK-BR-3 breast cancer cell line

value: RNAi-Ctrl


title: RNAi Ctrl SK-BR-3 cell m6A-RIP Input repl1


title: RNAi Ctrl SK-BR-3 cell m6A-RIP IP repl2

source_name: RNAi Ctrl SK-BR-3 cell m6A-RIP IP


title: FINS_167

description: Control Rep 1

tag: Sex

value: female

value: Whole ovary

tag: genotype

value: wild-type, Pgr-Cre positive


title: SCN-DZnep-CT15-1

description:
DZnep infused mice harvested at circadian time (CT) 15 Replicate 1
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: SCN-DZnep-CT09-4

description:
DZnep infused mice harvested at circadian time (CT) 9 Replicate 4
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: SCN-DZnep-CT09-3

description:
DZnep infused mice harvested at circadian time (CT) 9 Replicate 3
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: WN_116_4wk_M

city: St. John's

first: Anne

last: Beemelmanns

address: 0 Marine Drive

department: Ocean Science

country: Canada

institute: Memorial University

data_processing:
raw reads were quality trimmed by the Trim Galore! software (v. 0.4.4) with the following parameters  --nextera, --quality 20, and --phred64
adapters, the number and quality of the reads were checked using MultiQC (v.1.9)
the alignments of the pair-end reads were performed using Bismark (v.0.20.0) with the function “bismark”: --bowtie2, --non-directional, and --score_min 0 + (−0.4 x read length).
methylation calling with bismark_methylation_extractor (v0.19.0) ”: --bedGraph
Supplementary_files_format_and_content: tab-delimited files (sample_name_CpG_report.txt) contain the cytosine methylation report and shows the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per covered CpG (chromosome, base, strand) within the targeted chromosomes [header: <sample name> <chromosome/NCBI-accession_RefSeq> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>]
Genome_build: Salmo salar assembly (ssa) ICSASG_V2;     https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1/

organism: Salmo salar

source_name: liver tissue

growth_protocol: These fish were reared from an aquaculture company’s commercial brood stock (St. John River strain, Canada). This experiment was performed as part of the ‘Mitigating the Impacts of Climate-Related Challenges on Salmon Aquaculture (MICCSA)’ project. A detailed description of the experimental protocol, and the measurements of growth performance, feed conversion ratios and mortalites are published in Gamperl AK, Ajiboye OO, Zanuzzo FS, Sandrelli RM, Peroni E de FC, Beemelmanns A. The impacts of increasing temperature and moderate hypoxia on the production characteristics, cardiac morphology and haematology of Atlantic Salmon (Salmo salar). Aquaculture. 2020;519: 734874. doi:10.1016/j.aquaculture.2019.734874. For this study 48 liver samples were used from the same experimental fish (Fish-ID: #73 - #120) as part of a larger MICCSA project.

extract_protocol:
200 mg of liver tissue was dissected, flash frozen in nitrogen liquid and then stored at -80°C. DNA  was extracted from 10 mg of liver tissue per sample using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA) following the instruction manual. Bisulfite conversion was carried out  from 1 μg of genomic DNA per sample using EZ DNA Methylation-Direct™ Kit (D5020; Zymo Research, Irvine, USA). Illumina Miseq 2500 was used for sequencing the amplicon library.
Library was constructed following the Illumina’s protocol: “16S metagenomic library preparation” using Nextera XT Index Kit V2 set A, FC-131–2001 kit.

treatment_protocol: Atlantic salmon were exposed to following treatments: (1) Control (CT) constant temperature of 12°C and 100 % air saturation; (2) Warm&Normoxic (WN) incremental temperature increase (1°C per week from 12 - 20°C)  at 100% air saturation; and (3) Warm&Hypoxic (WH) decrease in oxygen content of 70% air saturation over one week, followed by two weeks of acclimation to this oxygen level, and then incremental temperature increase (1°C per week from 12 - 20°C) at 70% air saturation. Liver samples were taken from 8 fish per treatment group (CT, WN, and WH) at 20°C after 3 days and 4 weeks. DNA was extracted from individual liver samples of 8 fish from the 3 treatment groups per exposure time point (n = 8 fish per group/sampling point, N = 48 fish in total). For each treatment group we used 8 biological replicates (4 fish from 2 tank replicates).

value: Liver

value: Warm&Normoxic

tag: FISH-id#

tag: exposure time at 20°c

value: Male

tag: tank replicate

tag: FISH origin

value: aquaculture facilities

tag: life stage

value: Juvenile


title: SCN-DZnep-CT09-2

description:
DZnep infused mice harvested at circadian time (CT) 9 Replicate 2
processed data file:
Gene_Expression_SCN-DZnep.xlsx

tag: strain

value: 10 weeks


title: RNAi FTO SK-BR-3 cell m6A-RIP Input repl2

source_name: RNAi FTO SK-BR-3 cell m6A-RIP Input

tag: RNAi

value: RNAi-FTO

tag: replicates


title: 3866442

description: Gene expression data from adults

source_name: blood

tag: age

value: patient

tag: tissue

value: blood


title: 4063351

description: Gene expression data from adults

tag: gender

value: sepsis

tag: treatment


title: WN_114_4wk_M


title: SCN-DZnep-CT15-3

description:
DZnep infused mice harvested at circadian time (CT) 15 Replicate 3
processed data file:
Gene_Expression_SCN-DZnep.xlsx

value: Suprachiasmatic nucleus

tag: genotype/variation

value: Dznep treated


title: WN_115_4wk_F

value: Female


title: RNAi FTO SK-BR-3 cell m6A-RIP IP repl2

source_name: RNAi FTO SK-BR-3 cell m6A-RIP IP

value: SK-BR-3 breast cancer cell line


title: RNAi Ctrl SK-BR-3 cell m6A-RIP IP repl1

value: RNAi-Ctrl


title: RNAi FTO SK-BR-3 cell m6A-RIP Input repl1


title: SCN-DZnep-CT09-1

description:
DZnep infused mice harvested at circadian time (CT) 9 Replicate 1
processed data file:
Gene_Expression_SCN-DZnep.xlsx

tag: ct


title: 4071636

description: Gene expression data from adults

value: female

tag: disease state


title: WN_113_4wk_M

tag: Sex


title: 4058784

description: Gene expression data from adults


title: 4056506

description: Gene expression data from adults


title: 3768367

description: Gene expression data from adults

value: male

value: noninfectious


title: 3546507

description: Gene expression data from adults


title: 4043961

description: Gene expression data from adults


title: 4092070

description: Gene expression data from adults


title: 4548

description: Gene expression data from adults


title: RNAi FTO SK-BR-3 cell m6A-RIP IP repl1

tag: tissue/cell line


title: RNAi FTO SK-BR-3 cell ribodepleted RNAseq repl1

tag: cell line

tag: cell type

value: breast cancer cell line

tag: molecule subtype

value: Ribodepleted-RNA


title: RNAi Ctrl PC-3 cell m6A-RIP Input

source_name: RNAi Ctrl PC-3 cell m6A-RIP Input

value: PC-3 prostate cancer cell line


title: SCN-DZnep-CT03-3

description:
DZnep infused mice harvested at circadian time (CT) 3 Replicate 3
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: WN_103_4wk_F

value: Liver

value: Warm&Normoxic

tag: FISH-id#

tag: exposure time at 20°c

tag: tank replicate

tag: FISH origin

value: aquaculture facilities

value: Juvenile


title: 4938

description: Gene expression data from adults

value: blood


title: WN_104_4wk_M

value: Male

tag: life stage


title: SCN-DZnep-CT03-2

description:
DZnep infused mice harvested at circadian time (CT) 3 Replicate 2
processed data file:
Gene_Expression_SCN-DZnep.xlsx

tag: strain

tag: age

value: 10 weeks

value: Suprachiasmatic nucleus


title: RNAi Ctrl PC-3 cell m6A-RIP IP

source_name: RNAi Ctrl PC-3 cell m6A-RIP IP

tag: RNAi

tag: replicates


title: RNAi FTO PC-3 cell m6A-RIP Input

source_name: RNAi FTO PC-3 cell m6A-RIP Input

value: RNAi-FTO


title: WN_102_4wk_F

tag: tissue

tag: treatment

value: Female


title: RNAi FTO PC-3 cell m6A-RIP IP

source_name: RNAi FTO PC-3 cell m6A-RIP IP


title: SCN-DZnep-CT03-1

description:
DZnep infused mice harvested at circadian time (CT) 3 Replicate 1
processed data file:
Gene_Expression_SCN-DZnep.xlsx

tag: genotype/variation

value: Dznep treated

tag: ct


title: 5260

description: Gene expression data from adults

tag: gender

value: female

tag: disease state

value: sepsis


title: WN_101_4wk_M

tag: Sex


title: Breast cancer m6A-RIP Input biopsy 3

source_name: Breast cancer m6A-RIP Input biopsy

tag: tissue/cell line

value: breast tumor


title: SCN-DZnep-CT03-4

description:
DZnep infused mice harvested at circadian time (CT) 3 Replicate 4
processed data file:
Gene_Expression_SCN-DZnep.xlsx


title: 4525

description: Gene expression data from adults


title: 4725

description: Gene expression data from adults

value: male

value: patient


title: Breast cancer m6A-RIP Input biopsy 2


title: SCN-Saline-CT21-1

description:
Saline infused mice harvested at circadian time (CT) 21 Replicate 1
processed data file:
Gene_Expression_SCN-Saline.xlsx

value: saline treated


title: 100116

description: Gene expression data from adults


title: 3578493

description: Gene expression data from adults

value: noninfectious


title: WN_92_3d_M

value: Liver

value: Warm&Normoxic

tag: FISH-id#


title: 4625

description: Gene expression data from adults


title: 3211740

description: Gene expression data from adults


title: SCN-Saline-CT21-2

description:
Saline infused mice harvested at circadian time (CT) 21 Replicate 2
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: WN_90_3d_M

tag: exposure time at 20°c

value: aquaculture facilities

value: Juvenile


title: 3428068

description: Gene expression data from adults

value: blood


title: WN_91_3d_F

tag: tank replicate


title: Breast cancer m6A-RIP Input biopsy 1


title: SCN-Saline-CT15-4

description:
Saline infused mice harvested at circadian time (CT) 15 Replicate 4
processed data file:
Gene_Expression_SCN-Saline.xlsx

value: 10 weeks


title: WN_80_3d_F

tag: FISH origin


title: SCN-Saline-CT15-3

description:
Saline infused mice harvested at circadian time (CT) 15 Replicate 3
processed data file:
Gene_Expression_SCN-Saline.xlsx

value: Suprachiasmatic nucleus


title: Breast cancer m6A-RIP IP biopsy 3

source_name: Breast cancer m6A-RIP IP biopsy


title: WN_89_3d_M

value: Male

tag: life stage


title: SCN-Saline-CT15-1

description:
Saline infused mice harvested at circadian time (CT) 15 Replicate 1
processed data file:
Gene_Expression_SCN-Saline.xlsx

tag: strain


title: Breast cancer m6A-RIP IP biopsy 1


title: Breast cancer m6A-RIP IP biopsy 2


title: 5640

city: Minneapolis

first: Qiyuan

last: Han

state: Minnesota

address: 2231 6th St. Se, Tretyakova lab 2-230

institute: University of Minnesota

data_processing:
RNAseq reads were cleaned up of adapter contamination and low-quality bases with Trimmomatic 0.33
Cleaned reads were aligned to the mouse mm10 genome with HISAT2 2.1.0, using an index that was built with known splice sites and known SNPs. Only reads in complete pairs were aligned to the genome.
Fragments that aligned to annotated genes were counted with the “featureCounts” program in the subread package. Raw counts for each gene and each sample were transformed into counts-per-million (CPM) values with the edgeR package.
Differentially expressed genes were identified with a quasi-likelihood test in edgeR, with a 0.05 false discovery rate correction applied.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values in all genes for each sample.

source_name: proximal colon

growth_protocol: 129S6/SvEvTac-Rag2tm1FwIl10-/- (Rag2-/- / Il10-/-) mice were used and housed in an AAALAC-accredited specific pathogen-free barrier facility. Mice were maintained in polycarbonate microisolator caging (Allentown Caging Equipment Inc., Allentown, NJ) and provided pelleted diet (ProLab 3000, Purina Mills, St. Louis, MO) and filtered water ad libitum.

extract_protocol:
Genomic DNA, total RNA were extracted from approximately 10 mg of proximal colon tissue using AllPrep DNA/RNA mini kit (QIAGEN, Hilden, Germany).
RNA-seq libraries were prepared by Clontech Smarter Stranded Total RNA-Seq Kit (Takara Bio Inc, Kusatsu, Japan) according to manufacturer’s instruction.

treatment_protocol: Mice aged 6-7 weeks received two doses every other day of 0.2 mL of 2 x 108 fresh inoculums (infected group) or sterile media (control group).

value: Helicobacter. Hepaticus(strain 3B1, ATCC 51449) infection


title: 4445

description: Gene expression data from adults

data_processing: Pre-processing, normalization, probe summarization, and data quality control were executed in Expression Console Software (Affymetrix). Robust Multi-array Average (RMA)  normalization and DABG probe-level detection were specified. All other parameters were default.

tag: age


title: SCN-Saline-CT21-3

description:
Saline infused mice harvested at circadian time (CT) 21 Replicate 3
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: 5639


title: SCN-Saline-CT15-2

description:
Saline infused mice harvested at circadian time (CT) 15 Replicate 2
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: WN_79_3d_F

value: Female


title: SCN-Saline-CT09-4

description:
Saline infused mice harvested at circadian time (CT) 9 Replicate 4
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: 4393

description: Gene expression data from adults


title: WN_77_3d_M


title: WN_78_3d_F


title: SCN-Saline-CT09-3

description:
Saline infused mice harvested at circadian time (CT) 9 Replicate 3
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: 4829

description: Gene expression data from adults

value: female


title: 4951

description: Gene expression data from adults

value: sepsis


title: 5638


title: SCN-Saline-CT09-2

description:
Saline infused mice harvested at circadian time (CT) 9 Replicate 2
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: WH_119_4wk_F

value: Warm&Hypoxic


title: 5626

value: sterile media

value: male


title: 4736

description: Gene expression data from adults


title: 4737

description: Gene expression data from adults


title: WH_118_4wk_F


title: SCN-Saline-CT09-1

description:
Saline infused mice harvested at circadian time (CT) 9 Replicate 1
processed data file:
Gene_Expression_SCN-Saline.xlsx

value: saline treated


title: SCN-Saline-CT03-3

description:
Saline infused mice harvested at circadian time (CT) 3 Replicate 3
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: WH_120_4wk_M


title: SCN-Saline-CT03-2

description:
Saline infused mice harvested at circadian time (CT) 3 Replicate 2
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: 4368

description: Gene expression data from adults


title: 5624


title: SCN-Saline-CT03-1

description:
Saline infused mice harvested at circadian time (CT) 3 Replicate 1
processed data file:
Gene_Expression_SCN-Saline.xlsx


title: WH_100_4wk_F


title: MEF-Dznep-CT24-3

description:
DZnep treated MEF harvested 24h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_MEF-Dznep.xlsx

value: C57BL/6J background

value: embryo

value: embryonic fibroblast (MEF)

value: Dznep treated


title: 100114

description: Gene expression data from adults

value: patient


title: WH_98_4wk_F

value: Liver

value: aquaculture facilities

value: Juvenile


title: 5625


title: WH_97_4wk_M

value: Male


title: SCN-Saline-CT03-4

description:
Saline infused mice harvested at circadian time (CT) 3 Replicate 4
processed data file:
Gene_Expression_SCN-Saline.xlsx

value: 10 weeks

value: Suprachiasmatic nucleus


title: MEF-Dznep-CT24-2

description:
DZnep treated MEF harvested 24h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_MEF-Dznep.xlsx


title: WH_117_4wk_F

value: Female


title: MEF-Dznep-CT24-1

description:
DZnep treated MEF harvested 24h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_MEF-Dznep.xlsx


title: WH_96_3d_F


title: MEF-Dznep-CT12-3

description:
DZnep treated MEF harvested 12h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_MEF-Dznep.xlsx


title: WH_95_3d_M


title: WH_99_4wk_F


title: WH_94_3d_F


title: MEF-Dznep-CT12-2

description:
DZnep treated MEF harvested 12h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_MEF-Dznep.xlsx


title: 5259

description: Gene expression data from adults

value: female

value: blood


title: WH_93_3d_F

value: Warm&Hypoxic


title: WH_76_3d_M


title: 100110

description: Gene expression data from adults

value: male


title: 3316840

description: Gene expression data from adults

value: noninfectious


title: 4982

description: Gene expression data from adults

value: sepsis


title: 4998

description: Gene expression data from adults


title: WH_75_3d_M


title: MEF-DMSO-CT24-2

description:
DMSO treated MEF harvested 24h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_MEF-DMSO.xlsx

value: C57BL/6J background

value: embryo

value: DMSO treated


title: WH_74_3d_M


title: 4532

description: Gene expression data from adults


title: WH_73_3d_M


title: MEF-DMSO-CT24-3

description:
DMSO treated MEF harvested 24h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_MEF-DMSO.xlsx

value: embryonic fibroblast (MEF)


title: 4923

description: Gene expression data from adults


title: MEF-DMSO-CT24-1

description:
DMSO treated MEF harvested 24h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_MEF-DMSO.xlsx


title: 3140433

description: Gene expression data from adults


title: CT_112_4wk_F

value: Liver

value: Control


title: MEF-Dznep-CT12-1

description:
DZnep treated MEF harvested 12h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_MEF-Dznep.xlsx

value: Dznep treated


title: MEF-DMSO-CT12-3

description:
DMSO treated MEF harvested 12h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_MEF-DMSO.xlsx


title: 4831

description: Gene expression data from adults


title: 3159200

description: Gene expression data from adults


title: 4835

description: Gene expression data from adults


title: MEF-DMSO-CT12-2

description:
DMSO treated MEF harvested 12h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_MEF-DMSO.xlsx


title: 100070 (2)

description: Gene expression data from adults


title: MEF-DMSO-CT12-1

description:
DMSO treated MEF harvested 12h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_MEF-DMSO.xlsx


title: 3699.rep

description: Gene expression data from adults

value: patient


title: CT_110_4wk_M

value: Male

value: aquaculture facilities

value: Juvenile


title: AHCY-KO-MEF-CT32-3

description:
AHCY null MEF harvested 32h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: AHCY null


title: AHCY-KO-MEF-CT32-1

description:
AHCY null MEF harvested 32h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: CT_109_4wk_M


title: CT_111_4wk_F

value: Female


title: CT_108_4wk_M


title: CT_107_4wk_M


title: 3749982

description: Gene expression data from adults

value: blood


title: AHCY-KO-MEF-CT28-2

description:
AHCY null MEF harvested 28h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: CT_105_4wk_M


title: CT_106_4wk_F


title: AHCY-KO-MEF-CT28-1

description:
AHCY null MEF harvested 28h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: CT_87_3d_F


title: AHCY-KO-MEF-CT32-2

description:
AHCY null MEF harvested 32h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: 3261652

description: Gene expression data from adults

value: female


title: 5433

description: Gene expression data from adults


title: 5317

description: Gene expression data from adults

value: male

value: noninfectious


title: AHCY-KO-MEF-CT24-1

description:
AHCY null MEF harvested 24h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: C57BL/6J background


title: AHCY-KO-MEF-CT24-3

description:
AHCY null MEF harvested 24h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: embryo


title: 1001124

description: Gene expression data from adults

value: endotoxemia


title: AHCY-KO-MEF-CT24-2

description:
AHCY null MEF harvested 24h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: embryonic fibroblast (MEF)


title: AHCY-KO-MEF-CT20-3

description:
AHCY null MEF harvested 20h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: AHCY-KO-MEF-CT20-2

description:
AHCY null MEF harvested 20h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: 5442

description: Gene expression data from adults


title: CT_86_3d_F

value: Liver


title: 3317184

description: Gene expression data from adults

value: sepsis


title: 5377

description: Gene expression data from adults


title: CT_88_3d_F

value: Control


title: CT_83_3d_F


title: 5475

description: Gene expression data from adults


title: CT_84_3d_F


title: 3647803

description: Gene expression data from adults


title: AHCY-KO-MEF-CT28-3

description:
AHCY null MEF harvested 28h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: VCaP_FBS_shNEDD9_2_S11

city: Boston

first: Dong

state: MA

address: 100 Morrissey Blvd

department: Biology-CPCT

institute: Umass Boston

data_processing:
Raw reads were processed for quality control using fastqc (v.0.11.5)
Raw reads were trimmed using cutadapt (v. 1.9)
Raw reads were aligned to hg19 (ENCODE GRCh38) using STAR (v2.5.3a)
Gene level read counts was produced by featureCounts from Subread (v1.6.2) package
Genome_build: ENCODE GRCh38.101
Supplementary_files_format_and_content: txt file for gene level read count

growth_protocol: VCaP cells are cultured routinely in 10% FBS containing DMEM and passed every 5-6 days

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
TruSeq® Strnd Total RNA LT (Illumina) was used for RNA-Seq library construction.

treatment_protocol: VCaP cells were insfected with shRNA against non-targeting control (shNTC), or NEDD9 (shNEDD9) in 10% FBS supplemented DMEM.

tag: cell line

value: VCaP

tag: cell type

value: prostate cancer cell line

value: shRNA against NEDD9 (shNEDD9)


title: CT_85_3d_F

tag: tissue

value: aquaculture facilities

value: Juvenile


title: VCaP_FBS_shNEDD9_3_S12


title: AHCY-KO-MEF-CT16-3

description:
AHCY null MEF harvested 16h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: AHCY null


title: CT_82_3d_M

tag: treatment

value: Male


title: VCaP_FBS_shNEDD9_1_S10

tag: genotype/variation


title: 3734523

description: Gene expression data from adults

extract_protocol: Total RNA was isolated in accordance with the PAXgene blood miRNA isolation (QIAGEN) procedure using the QIAcube instrument.

value: female

value: blood


title: 3599379

description: Gene expression data from adults

value: male


title: VCaP_FBS_shNTC_2_S8

value: shRNA against non-targeting control (shNTC)


title: ChIP-seq VP16 HBM HA rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
HA-VP16-rep3.narrowpeak

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample

source_name: Burkitt lymphoma cell line

growth_protocol: Ramos cells were maintained in RPMI 1640 + 10% FBS + penicillin/streptomycin. Cells carrying Cre-ERT2 were additionally maintained in 100 μg/ml hygromycin, and MYC switchable cells (WT, 4A, VP16 HBM) in 150 ng/ml puromycin.

extract_protocol:
For RNA-seq of tumor-derived samples, extraction was performed by Genewiz. Other RNA-seq extractions were performed using TRIzol. For ChIP-seq experiments, cells crosslinked in 1% formaldehyde were subject to sonication, and the resulting sheared chromatin was combined overnight with antibody.
For RNA-seq of tumor-derived or MYC switchable cells (WT, 4A, VP16 HBM), rRNA depletion and library preparation were performed by Genewiz. For RNA-seq of untagged/HCF1N-tagged samples, library preparation was performed by Vanderbilt Technologies for Advanced Genomics (VANTAGE). ChIP-seq libraries were prepared using NEBnext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: See individual samples for relevant treatment protocol

tag: cells

value: Ramos cells

tag: engineered genotype

value: Cre-ERT2, MYC-VP16 HBM

value: 20 nM 4-OHT for 24 hours

tag: antibody

value: HA


title: AHCY-KO-MEF-CT16-1

description:
AHCY null MEF harvested 16h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: C57BL/6J background

value: embryo

value: embryonic fibroblast (MEF)

tag: ct


title: AHCY-KO-MEF-CT12-3

description:
AHCY null MEF harvested 12h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: AHCY-KO-MEF-CT16-2

description:
AHCY null MEF harvested 16h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: ChIP-seq VP16 HBM HA rep2

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
HA-VP16-rep2.narrowpeak


title: VCaP_FBS_shNTC_1_S7

value: VCaP

value: prostate cancer cell line


title: CT_81_3d_M

value: Liver

value: Control

tag: Sex

value: aquaculture facilities


title: ChIP-seq VP16 HBM HA rep1

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
HA-VP16-rep1.narrowpeak


title: 3601304

first: Brendon

address: Msida campus

institute: University of Malta

description: Gene expression data from adults

tag: gender

tag: disease state

value: noninfectious


title: Cal-27-HIPK2-sh-RNA-seq

city: Wuhan

first: Xueqing

address: Luoyu Road

institute: Wuhan University

data_processing:
Adaptors and low quality bases were trimmed from raw sequencing reads using FASTXToolkit (Version 0.0.13), and reads less than 16nt were discarded.
Quality control checks were performed by FastQC.
After data filtering and quality control, reads were aligned to the reference genome GRCh38 by TopHat2 (v2.1.1), allowing up to 4 mismatches.
Reads only unambiguously aligned to unique position were preserved to calculate reads number and RPKM (reads per kilobase and per million) value for each gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all genes in each sample.

source_name: oral squamous cell carcinoma

growth_protocol: Cal-27 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA from the tissue specimens was extracted using TRIzol Reagent (Ambion) following the manufacturer's instructions.
RNA-seq libraries were prepared with RNA-seq Library Preparation Kit (Gnomegen) following the manufacturer’s instructions and sequenced on the Illumina Hiseq (150 bp paired-end).

treatment_protocol: For RNA-seq experiments, Cal-27 cells with the stable transduction of shRNA against HIPK2 (GV-248-HIPK2-sh) or control vector (sh-scramble) were grown in regular medium and collected.

tag: source tissue

value: tongue

value: oral squamous cell carcinoma (OSCC) cells

tag: shRNA


title: Cal-27-scramble-RNA-seq

value: sh-scramble


title: AHCY-KO-MEF-CT12-1

description:
AHCY null MEF harvested 12h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-KO.xlsx

value: AHCY null


title: AHCY-KO-MEF-CT20-1

description:
AHCY null MEF harvested 20h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: 100020

city: Msida

description: Gene expression data from adults

growth_protocol: Whole blood was collected in PAXgene blood RNA tubes, mixed by inversion 10X and stored at -80C.

value: male

value: blood


title: AHCY-KO-MEF-CT12-2

description:
AHCY null MEF harvested 12h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-KO.xlsx


title: ChIP-seq 4A HA rep3

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
HA-4A-rep3.narrowpeak

value: Ramos cells

value: Cre-ERT2, MYC-4A

value: 20 nM 4-OHT for 24 hours


title: ChIP-seq 4A HA rep2

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
HA-4A-rep2.narrowpeak

value: HA


title: AHCY-WT-MEF-CT32-3

description:
AHCY WT MEF harvested 32h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-WT.xlsx

value: C57BL/6J background

value: embryo

value: embryonic fibroblast (MEF)

value: WT


title: 100126

description: Gene expression data from adults

value: endotoxemia


title: 3687409

description: Gene expression data from adults

value: female


title: 5479

description: Gene expression data from adults

value: noninfectious


title: 5726

description: Gene expression data from adults

value: sepsis


title: 1 month after second infusion

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: scRNA sequencing with 10X 3' v2 kit

data_processing:
The Cell Ranger Suite (v3.1.0) from 10X genomics with GRCh38 reference genome was used to perform sample de-multiplexing, barcode processing and unique molecular identifier (UMI) counting. Cellranger mkfastq and count funtions were used to quantify the expression values for captured single cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5 or H5) files from 10X Cell Ranger pipeline have been provided.

source_name: BM cells from a patient with MM

extract_protocol:
Bone marrow cells from a patinet with Multiple myeloma collected at various time points during the CAR T cell treatment based on the study protocol.
For all eight samples single-cell library constructions were performed using Chromium Single Cell 3` Reagent kits v2. Each sample was processed individually according to 10X genomics protocols. Poly-A selected transcripts were reverse-transcribed and full-length cDNA along with cell barcode identifiers were PCR-amplified. The constructed libraries then sequenced with Illumina platform using paired end sequencing.

value: Multiple Myeloma

value: Bone Marrow


title: 2 weeks after second infusion

description: scRNA sequencing with 10X 3' v2 kit


title: AHCY-WT-MEF-CT32-2

description:
AHCY WT MEF harvested 32h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: 3717

last: Scicluna

description: Gene expression data from adults


title: AHCY-WT-MEF-CT32-1

description:
AHCY WT MEF harvested 32h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: ChIP-seq WT HA rep3

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
HA-WT-rep3.narrowpeak

value: Cre-ERT2, MYC-WT


title: 3365199

description: Gene expression data from adults


title: 3405860

description: Gene expression data from adults


title: 3186280

description: Gene expression data from adults

value: male


title: AHCY-WT-MEF-CT28-3

description:
AHCY WT MEF harvested 28h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: ChIP-seq WT HA rep1

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
HA-WT-rep1.narrowpeak


title: ChIP-seq WT HA rep2

description:
Cre-ERT2, MYC-WT cells; 24 hours +4-OHT
HA-WT-rep2.narrowpeak


title: 3 months after first infusion

description: scRNA sequencing with 10X 3' v2 kit


title: 3462609

description: Gene expression data from adults

value: blood


title: 5750

description: Gene expression data from adults


title: 1 month after first infusion

description: scRNA sequencing with 10X 3' v2 kit


title: AHCY-WT-MEF-CT28-2

description:
AHCY WT MEF harvested 28h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: AHCY-WT-MEF-CT28-1

description:
AHCY WT MEF harvested 28h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: ChIP-seq parental HA rep3

description: Cre-ERT2 cells; 24 hours +4-OHT

value: Ramos cells


title: ChIP-seq 4A HA rep1

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
HA-4A-rep1.narrowpeak

value: Cre-ERT2, MYC-4A


title: ChIP-seq parental HA rep2

description: Cre-ERT2 cells; 24 hours +4-OHT

value: 20 nM 4-OHT for 24 hours


title: 5235

description: Gene expression data from adults


title: 100024

description: Gene expression data from adults


title: 2 weeks after first infusion

description: scRNA sequencing with 10X 3' v2 kit


title: AHCY-WT-MEF-CT24-1

description:
AHCY WT MEF harvested 24h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: AHCY-WT-MEF-CT24-3

description:
AHCY WT MEF harvested 24h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: ChIP-seq parental HA rep1

description: Cre-ERT2 cells; 24 hours +4-OHT

value: HA


title: GIST intra- tumor tissue from G2 patient

city: Foshan

first: xiaofan

last: Mao

state: China

address: Lingnan Road North 81, Foshan, Guangdong, China

institute: The First People's Hospital of Foshan

description: illumina sequencing of 10X single cell transcriptome

data_processing:
10X Cellranger V3.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 matrix

source_name: gastrointestinal stromal tumor

extract_protocol:
Tumor tissues, obtained from the laparoscopic mass resection surgery, were immediately sent to undergo the process of single cell suspension preparation. Tissues were cut into small pieces, digested in incomplete RPMI-1640 with endotoxin-free collagenaseⅠ (2 mg/mL, Sigma-Aldrich, St Louis, MO, USA) for 1 hour at 37℃. The digested fragments were filtered through a 100 μm cell nylon mesh (BD Bioscience PharMingen) and washed twice in Hanks' balanced salt solution. Five ml erythrocyte lysis solution was added into the cell suspension for 5 minutes, and then PBS was added to stop and wash twice.
10X Chromium Single Cell 5ʹ Library Construction (CG000086 Rev J)

tag: patient

tag: afip risk calssification

value: High

value: Intra- tumor


title: AHCY-WT-MEF-CT20-3

description:
AHCY WT MEF harvested 20h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-WT.xlsx

tag: strain

value: C57BL/6J background

tag: age

value: embryo

value: embryonic fibroblast (MEF)


title: GIST peri- tumor tissue from G2 patient

value: Peri- tumor


title: GIST peri- tumor tissue from G1 patient

value: Low


title: Pre-infusion

description: scRNA sequencing with 10X 3' v2 kit


title: ChIP-seq VP16 HBM HCF1N rep2

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
HCF1N-VP16-rep2.narrowpeak

value: Cre-ERT2, MYC-VP16 HBM


title: ChIP-seq VP16 HBM HCF1N rep3

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
HCF1N-VP16-rep3.narrowpeak


title: ChIP-seq VP16 HBM HCF1N rep1

description:
Cre-ERT2, MYC-VP16 HBM cells; 24 hours +4-OHT
HCF1N-VP16-rep1.narrowpeak


title: AHCY-WT-MEF-CT24-2

description:
AHCY WT MEF harvested 24h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-WT.xlsx

value: WT


title: AHCY-WT-MEF-CT20-2

description:
AHCY WT MEF harvested 20h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: 3344784

description: Gene expression data from adults

value: sepsis


title: ChIP-seq 4A HCF1N rep3

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
HCF1N-4A-rep3.narrowpeak


title: 1001224 (2)

description: Gene expression data from adults

value: endotoxemia


title: GIST intra- tumor tissue from G1 patient


title: AHCY-WT-MEF-CT20-1

description:
AHCY WT MEF harvested 20h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: ChIP-seq 4A HCF1N rep2

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
HCF1N-4A-rep2.narrowpeak


title: AHCY-WT-MEF-CT16-3

description:
AHCY WT MEF harvested 16h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: 3585

description: Gene expression data from adults

value: female


title: 3632

description: Gene expression data from adults

value: male

value: noninfectious

value: blood


title: 3270135

description: Gene expression data from adults


title: ChIP-seq 4A HCF1N rep1

description:
Cre-ERT2, MYC-4A cells; 24 hours +4-OHT
HCF1N-4A-rep1.narrowpeak

value: Ramos cells

value: Cre-ERT2, MYC-4A

value: 20 nM 4-OHT for 24 hours


title: AHCY-WT-MEF-CT16-2

description:
AHCY WT MEF harvested 16h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: RNAseq.HumanSperm.cauda

city: Rochester

first: Xin

last: Li

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

description: Summary.xlsx

data_processing:
LoRDEC (version 0.5.3, parameters -k 17 -s 3 -a 50000) was used to perform error correction on the long reads (LRs) with short reads (SRs) as input.
The corrected LRs were aligned to the mm10 or hg38 reference genome using GMAP (version 2014-12-24, parameters -t 10 -B 5 -A --nofails -f samse -n1). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The SRs were aligned to the mm10 or hg38 reference genome using HISAT2 (version 2.0.4, parameters --ignore-quals --dta --threads 10 --max-intronlen 150000).
Illumina short reads were quantified using Salmon (v0.8.2), and TPM values were summaized in the processed data table. Sperm samples were further normalized to the renilla spikein number.
SpermPacBio1-6 were combined, and TestisPacBio1-5 were combined.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Long reads numbers mapped to each transcript have been summarized into Summary.xlsx table. Transcript TPM values were also summarized in the table.

source_name: sperm

extract_protocol:
Before RNA purification, sperm cells were lysed by 1% SDS and 0.1M DTT, with 10 min incubatin on 37 degree. Sperm RNAs were isolated using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina sequencing uses standard RNAseq library construction protocol.

tag: cell type

value: purfied human sperm from semen


title: AHCY-WT-MEF-CT16-1

description:
AHCY WT MEF harvested 16h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-WT.xlsx

value: C57BL/6J background

tag: tissue


title: AHCY-WT-MEF-CT12-3

description:
AHCY WT MEF harvested 12h after dexamethasone synchronization Replicate 3
processed data file:
Gene_Expression_AHCY-WT.xlsx

value: embryo


title: Mouse Cortex Total RNA-Seq 3

city: Calgary

first: Guang

last: Yang

state: Alberta

address: 3330 Hospital Drive N.W.

department: Department of Medical Genetics

institute: University of Calgary

description: RNA-Seq

data_processing:
Pseudo aligned with the mouse transcriptome (GRCm38 – mm10) using Pachter lab’s Kallisto (version 0.46.1)
Differential expression and quality control was conducted with Pachter lab’s Sleuth (version 0.30.0)
TPM cut-off at ln > 1.52
Genes selected with CELF2 RIP versus total RNA-seq of greater than 1.5 FC and CELF2 RIP versus non-specific RIP greater than 1.5 FC with a FDR of less than 0.05 in both cases
Genome_build: mm10
Supplementary_files_format_and_content: Kallisto Counts

source_name: embryo

extract_protocol:
extracted with phenol/chloroform, subjected to rRNA depletion using the NEBNext rRNA depletion kit (E6350S)
NEBNext Ultra II Directional RNA library prep kit (E7760L)

treatment_protocol: E12.5 cortices were used for RNA-RIP-seq using the EZ-Magna RIP-RNA Immunoprecipitation Kit (Millipore) according to the manufacturer’s instructions with modifications. Cortical tissues were lysed with the cytoplasmic lysis buffer supplemented with the protease and RNase inhibitors (from kit) and 100 U/ml SUPERasine-IN (Ambion), followed by centrifugation to isolated the cytoplasmic content in the supernatant. A portion of the cytoplasmic fraction was directly used for RNA extraction and served as “Input”. The rest of the supernatant was precleared with protein A/G beads and incubated with 5 μg of anti-CELF2 (rabbit, Abcam) or normal rabbit IgG for 3 hours at 4°C. Total RNA from three biological replicates of Input, IgG control and CELF2 immunoprecipitates was isolated.

value: brain cortex


title: PtenS398A/S398A

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

institute: Princess Margaret Cancer Centre, University Health Network

data_processing:
The raw 76-basepair paired-end reads from the sequencer, obtained as compressed FASTQ files with one file per cell, were first quality-checked using FASTQC v0.11.5 and MultiQC v0.8 software packages, and then aligned to the Mus musculus genome assembly version GRCm38 (mm10) from the Genome Reference Consortium using the STAR aligner v2.5.2b. The aligned transcripts were quantified using RSEM v1.3.0. The RSEM quantification output files were then further processed using in-house R scripts to assemble a consolidated gene-by-cell read-count matrix denoting single-cell gene expression, with rows corresponding to genes and columns corresponding to cells.
The assembled matrix of raw count (in which each row is a gene, and each column is a cell), was then fed into the standard workflow of the single-cell data processing R package, Seurat v2.3.4 (run in R v3.5.1). Only genes that were expressed (read count > 0) in at least 3 cells, and only cells that expressed at least 200 genes, were retained for downstream processing. Furthermore, cells expressing more than 7000 genes (potential multiplets), and cells with more than 30% of the reads mapping to mitochondrial genes, were removed from the analysis. The final filtered matrix contained 11908 genes and 206 cells, with 116 Pten+/+ cells and 90 PtenS398A/S398A cells. The filtered matrix was log-normalized using global scaling in Seurat with the scaling factor value set to 10000. To identify highly varying genes, the FindVariableGenes module of Seurat was employed to establish the mean-variance relationship of the normalized counts of each gene across cells. Genes whose log-mean was between 0.1 and 8 and whose dispersion was above 1, were chosen, resulting in a total of 858 highly varying genes.
The log-normalized matrix was then subjected to dimensionality reduction by carrying out principal component analysis (PCA) on the highly varying genes. Upon a visual inspection of the PCA elbow plot, which plots the standard deviations of the principal components (PCs), the top 10 PCs were chosen for further analysis. Clustering was performed on the chosen PCs using the shared nearest neighbor (SNN) modularity optimization algorithm in Seurat, with default parameters (resolution = 0.6). To visualize the clusters in two dimensions, a t-stochastic neighbor embedding (t-SNE) map was computed and plotted using the appropriate modules in Seurat. Cluster-defining canonical marker genes were identified by comparing the gene-by-gene average expression levels within a cluster with the average levels across the rest of the cell population using the Wilcoxon rank sum test.
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM "expected count" matrices
Supplementary_files_format_and_content: Two files in total. These are RSEM "expected count" matrices. One file each for the Pten+/+ and PtenS398A/S398A genotypes, containing counts for 161 Pten+/+ cells and 119 PtenS398A/S398A cells, respectively.

source_name: Long-term hematopoietic stem cells (Lin-Sca1+cKit+CD48-CD150+)

extract_protocol:
Before sorting, a small-sized (5-10 μm) C1 Single-Cell AutoPrep IFC microfluidic chip (Fluidigm) was primed using the script “SMART-Seq v4: Prime Rev B (1771x) for 5-10 μm diameter cells” according to the manufacturer’s instruction. 2.5 μL of Cell Suspension-Viability reagent, prepared  by mixing Cell Suspension buffer (Fluidigm) and LIVE/DEAD Viability/Cytotoxicity Kit for mammalian cells (Thermo Fisher) components at a ratio of 1:1:50 (Ethidium homodimer-1 : Calcein AM : Cell Suspension buffer) was added in the cell loading inlet of the C1 chip. Cells were sorted directly onto the cell loading inlet of the C1 chip, using optimized single-cell sorting parameters on a BD FACSARIA instrument (BD Biosciences). Typically, cells were sorted at an approximate speed of 3500 events/second with low-pressure settings, yielding approximately 1000 LT-HSCs (~0.2% of the total number of events), in a volume of 4.5-5 µL, in around 10 minutes. After sorting, the cell loading inlet of the C1 chip contained approximately 7.5 μL of sorted LT-HSCs at a final concentration of ~130-140 cells/μL and cell buoyancy ratio of ~60-65% (murine primary HSCs : Cell Suspension-Viability reagent). The C1 chip was then processed on a Fluidigm C1 instrument (Fluidigm) using the script “SMART-Seq v4: Cell Load Rev B (1771x) for 5-10 μm diameter cells”. This protocol was designed to capture individual LT-HSC in up to 96 capture chambers in the C1 chip in approximately 30 minutes. The chip was then transferred to an EVOS FL Cell Imaging System (Thermo Fisher), and each cell was imaged under bright-field and fluorescence illumination to visualize the viability stain. C1 reagents (Fluidigm) and SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System (Clontech) were added to the designated wells according to the manufacturers’ instructions. The chip was then returned to the Fluidigm C1 system and the script “SMART-Seq v4: Sample Prep Rev B (1771x), for 5-10 um diameter cells” was executed, which took ~8 h and included single cell lysis, reverse transcription, and full-length cDNA synthesis. After completion of the protocol, the amplified single cell cDNAs were harvested in a total of 8 μL C1 DNA Dilution Reagent (Fluidigm). 1 μL of the diluted cDNA was analyzed using Agilent High Sensitivity DNA Kit on an Agilent BioAnalyzer 2100 (Agilent Technologies, Inc.) and quantified using Quant-iT PicoGreen dsDNA Assay kit (Thermo Fisher) on a SpectraMax M3 Microplate Reader (Molecular Devices). The average size of the single cell cDNA synthesized was between 1300 to 1,700 bp in length and the typical yield was ~400-1200 pg/μL.
Single cell cDNA libraries were constructed using Nextera XT DNA Library Kit (Illumina) according to the modified protocols described in the SMART-Seq V4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs User Manual (Clontech). 100-300 pg of each amplified single cell cDNA was used as the input for Nextera XT library construct, and Illumina N7 and S5 indexes were added (Illumina) for tagmentation followed by PCR amplification using an Applied Biosystems Veriti 96-Well Thermal Cycler (Thermo Fisher). cDNA libraries were pooled and purified with Agencourt AMPure XP beads (Beckman Coulter, Inc.) twice. Final cDNA libraries sizes were validated using the Agilent Bioanalyzer 2100 and quantified by quantitative PCR using KAPA SYBR FAST qPCR kit (Kapa Biosystems, Inc.) on a CFX96 Real-Time system (BioRad).  The libraries were then sequenced on the NextSeq 500 system (Illumina, Inc.) using a pair-end 75 cycle sequencing run to achieve one million reads per cell.

tag: genotype


title: Pten+/+

value: Pten+/+


title: Mouse Cortex Total RNA-Seq 2

description: RNA-Seq


title: NLH_patient_12 (VDJ-seq, TCR)

city: Hong Kong

first: Xin-Yuan

last: Guan

address: L10-56, Laboratory Block, LKS Faculty of Medicine

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

description: T7 TCR

data_processing:
Cell Ranger (version 3.1.0)
The single-cell suspension was converted to uniquely barcoded RNA, TCR and BCR libraries by using the Chromium Single Cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), per manufacturer’s instructions. The libraries were sequenced on a Novaseq 6000, and mapped to the human genome (hg38) using CellRanger (version 3.1.0, 10x Genomics). Gene positions were annotated as per Ensembl build 85 and filtered for biotype (only protein-coding, long intergenic non-coding RNA, antisense, immunoglobulin, T-cell receptor and B-cell receptor).
The raw gene expression matrix generated from each sample were aggregated using CellRanger (version 3.1.0).
Genome_build: hg38
Supplementary_files_format_and_content: clonotypes.csv, contig_annotations.csv

source_name: Nasopharyngeal lymphoid hyperplasia

growth_protocol: not applicable

extract_protocol:
Collagenase Type IV+DNAse
The libraries were constructed using the following kits: Chromium Single Cell 5’ Library & Gel Bead Kit, Chromium Single Cell V(D)J Enrichment Kit, Human T Cell, Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, as per manufacturer’s instructions
Single-cell 5' RNA sequencing+ V(D)J sequencing

treatment_protocol: not applicable

value: Nasopharyngeal lymphoid hyperplasia

tag: site

value: Primary


title: NLH_patient_11 (VDJ-seq, TCR)

description: T5 TCR


title: Mouse Cortex Total RNA-Seq 1

description: RNA-Seq


title: NPC_patient_14 (VDJ-seq, TCR)

description: T215 TCR

source_name: Nasopharyngeal tumor tissue

value: Nasopharyngeal tumor tissue


title: 4917

description: Gene expression data from adults

source_name: blood

treatment_protocol: PAXgene blood RNA tubes were left at room temperaturee to defrost (approx. 2 hours) while mixing by inversion.

value: sepsis

tag: treatment


title: 3620

description: Gene expression data from adults


title: AHCY-WT-MEF-CT12-1

description:
AHCY WT MEF harvested 12h after dexamethasone synchronization Replicate 1
processed data file:
Gene_Expression_AHCY-WT.xlsx

value: embryonic fibroblast (MEF)

tag: genotype/variation

value: WT


title: 3351972

description: Gene expression data from adults

value: female


title: NPC_patient_10 (VDJ-seq, TCR)

description: T8 TCR


title: 3547

description: Gene expression data from adults

value: male

value: noninfectious


title: 3769

description: Gene expression data from adults

value: blood


title: 3586270

description: Gene expression data from adults


title: Mouse Cortex IgG RIP 3

description: RIP-Seq


title: NLH_patient_13 (VDJ-seq, TCR)

description: T9 TCR


title: TestisPacBio5

description: Summary.xlsx

value: cauda sperm

value: adult


title: NPC_patient_9 (VDJ-seq, TCR)

description: T6 TCR


title: Mouse Cortex IgG RIP 2

description: RIP-Seq


title: TestisPacBio4

description: Summary.xlsx


title: NPC_patient_8 (VDJ-seq, TCR)

description: T147 TCR


title: Mouse Cortex IgG RIP 1

description: RIP-Seq


title: Mouse Cortex CELF2 RIP 3

description: RIP-Seq


title: TestisPacBio3

description: Summary.xlsx


title: AHCY-WT-MEF-CT12-2

description:
AHCY WT MEF harvested 12h after dexamethasone synchronization Replicate 2
processed data file:
Gene_Expression_AHCY-WT.xlsx


title: TestisPacBio2

description: Summary.xlsx


title: 3530376

description: Gene expression data from adults

value: patient


title: NPC_patient_7 (VDJ-seq, TCR)

description: T4 TCR


title: 3253688

description: Gene expression data from adults


title: Mouse Cortex CELF2 RIP 2

description: RIP-Seq


title: NPC_patient_6 (VDJ-seq, TCR)

description: T11 TCR


title: NLH_patient_13 (VDJ-seq, BCR)

description: T9 BCR


title: NPC_patient_4 (VDJ-seq, TCR)

description: T2 TCR


title: 3284876

description: Gene expression data from adults


title: 3287179

description: Gene expression data from adults


title: Mouse Cortex CELF2 RIP 1

description: RIP-Seq


title: SpermPacBio6

description: Summary.xlsx


title: NLH_patient_12 (VDJ-seq, BCR)

description: T7 BCR


title: P1 Control female fl/fl Msi1 fl/fl Msi2

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

description: virgin, diestrous female

data_processing:
Demultiplexed fastq files were analyzed with the 10x Genomics Cell Ranger 3.1.0 count function for sequence alignment and gene counting
The UCSC mm10 reference mouse transcriptome was amended by annotating chromosome 11: 50,948,572-50,949,192 in the gene transfer file (gtf) as an artificial single exon gene on the negative strand named “Prop1L” as described by Cheung et al A custom reference was then compiled using the cellranger mkref command, and the custom reference was used for Cell Ranger/STAR alignment instead of the original UCSC mm10 transcriptome.
Seurat was used to pre-process the raw counts generated by cellranger count to filter cells with low quality cells, cell doublets, and cells with high percentage of mitochondrial genes
Filtered cells that have unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less than the 25th percentile minus 1.5 time the IQR. Additionally, filtered cells with mitochondrial counts falling outside the same range with respect to mitochondrial gene percentage
Counts were normalized using the LogNormalize method, which normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result using the natural log.
The 2000 highest variable features were selected. The data was then scaled by a linear transformation and PCA performed on the scaled data. A JackStraw procedure was implemented to determine the significant PCA components that have a strong enrichment of low p-value features
A graph-based clustering approach was then applied to embed cells in a graph structure with edges drawn between cells with similar feature expression patterns, and then attempt to partition this graph into highly interconnected ‘quasi-cliques’ or ‘communities’. To this end, we employed Uniform Manifold Approximation and Projection (UMAP) (41), a non-linear dimensional reduction technique to visualize and explore the results using Seurat.
Seurat FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections and cell types assigned
Differential expression analysis was performed using MAST, a GLM-framework that treats cellular detection rate as a covariate
Genome_build: The UCSC mm10 reference mouse transcriptome was amended by annotating chromosome 11: 50,948,572-50,949,192 in the gene transfer file (gtf) as an artificial single exon gene on the negative strand named “Prop1L” as described by Cheung et al A custom reference was then compiled using the cellranger mkref command, and the custom reference was used for Cell Ranger/STAR alignment instead of the original UCSC mm10 transcriptome.

source_name: pituitary

growth_protocol: Growth in low adherant culture for 7 days

extract_protocol:
Pituitaries from 8-week old control diestrous FVB females (n = 6) were collected and individually dispersed as previously described (14).  Following mechanical dispersion, cells were pelleted and washed once with DMEM.  Cells were pelleted again and fixed with methanol according to the 10x Genomics methanol fixation protocol.
Single cell 3’ library generation was performed using a 10X Genomics Chromium Controller and the v3 reagent kit (10x Genomics) according to the manufacturer’s protocol.  Cell suspensions were loaded on to the middle four channels of a Chromium Single Cell A Chip according to the manufacturer’s instructions, aiming for 10,000 cells per channel.  Following generation of single-cell gel bead-in-emulsions (GEM), reverse transcription, fragmentation and cDNA amplification, library preparations and bar coding were performed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit v2 as per manufacturer’s instructions
200pM of each library was pooled for sequencing on the Illumina NextSeq 500 platform using a high output flow cell (100 cycles) to generate approximately 25 million 75 base reads per sample.

treatment_protocol: Pituispheres were prepared from dispersed whole female pituitaries (REF). After growth in low adherent culture for 7 days, pituispheres were fixed and dual labeled for Sox2 and Musashi1 or Sox2 and Musashi2.

value: pituitary

value: 8-week old

value: FVB


title: P2 Control female fl/fl Msi1 fl/fl Msi2

description: virgin, diestrous female


title: SpermPacBio5

description: Summary.xlsx


title: SpermPacBio4

description: Summary.xlsx


title: 3311112

description: Gene expression data from adults


title: 3528466

description: Gene expression data from adults


title: hv177

description: Gene expression data from adults

value: healthy


title: NLH_patient_11 (VDJ-seq, BCR)

description: T5 BCR

value: Nasopharyngeal lymphoid hyperplasia


title: SpermPacBio3

description: Summary.xlsx


title: NPC_patient_14 (VDJ-seq, BCR)

description: T215 BCR

value: Primary


title: TestisPacBio1

description: Summary.xlsx


title: SpermPacBio2

description: Summary.xlsx


title: 3021476

description: Gene expression data from adults


title: d4_PY_4

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.5.3a.
2) Gene read coverages were computed with featureCounts v1.5.2 using ENSEMBL mouse annotation release 92 (GRCm38.92)
3) Differential expression analysis was performed using edgeR v3.22.0 with "y ~ 0 + group + Experiment" design while filtering low read counts less than 2 CPM in at least 5 samples
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts

source_name: Mesenchymal C3H/10T1/2 cells

growth_protocol: Cell were differntiated by targeted over-expression of endogenous Pparγ (transfection with plasmids containing Pparγ-targeted guide RNA) and treated with 5uM Rosiglitazone on day 0 (48 hrs after tranfection) to promote adipogenesis.

extract_protocol:
Cells were lysed with RLT/β-Me and mRNA extracted using Rneasy spin columns (Quiagen) with DNAse treaamnet. mRNA concentrations were determined with nano-drop and RNA quality/integrity assessed using RNA 6000 Nano (Aligent Technology) chips.
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold

treatment_protocol: Transfection conditions: EV (Empty Vector plasmid, Control), P (Pparγ gRNA-plasmid only), PY (Pparγ gRNA-plasmid and Ybx1 gRNA-plasmid). All transfections were performed using 250ng of plasmid DNA total. Treatment conditions: all cells received 5uM Rosiglitazone 48hrs post-transfection.

tag: group

tag: transfection

tag: day of differentiation

tag: experiment


title: NPC_patient_10 (VDJ-seq, BCR)

description: T8 BCR

value: Nasopharyngeal tumor tissue


title: d4_PY_5

value: Pparγ gRNA-plasmid and Ybx1 gRNA-plasmid


title: hv199

description: Gene expression data from adults

tag: gender

tag: disease state


title: hv213

description: Gene expression data from adults


title: hv181

description: Gene expression data from adults


title: hv209

description: Gene expression data from adults


title: SpermPacBio1

description: Summary.xlsx


title: NPC_patient_9 (VDJ-seq, BCR)

description: T6 BCR


title: d4_PY_6


title: RNA-seq tumor delta264 rep3

description:
Tumor-derived Cre-ERT2, MYC-delta264 cells; 48 hours post 4-OHT treatment
RNA-seq-Tumor-count.txt

tag: cells

value: Ramos cells

tag: engineered genotype

value: Tumor-derived MYC-delta264

value: 48 hours post 4-OHT treatment


title: RNA-seq tumor delta264 rep4


title: hv189

description: Gene expression data from adults

value: female


title: NPC_patient_7 (VDJ-seq, BCR)

description: T4 BCR


title: d4_PY_1


title: d2_PY_5


title: RNA-seq tumor delta264 rep2


title: hv185

description: Gene expression data from adults

value: male


title: RNA-seq tumor delta264 rep1


title: NPC_patient_6 (VDJ-seq, BCR)

description: T11 BCR


title: hv207

description: Gene expression data from adults

value: blood


title: NPC_patient_4 (VDJ-seq, BCR)

description: T2 BCR


title: RNA-seq FKBPFV-HCF-1N dTAG rep3

description:
FKBPFV-HCF-1N cells; 3 hours +dTAG-47
RNA-seq-FKBPFV-HCF-1N-count.txt

value: 500 nM dTAG-47 for 3 hours


title: hv235

description: Gene expression data from adults


title: d2_PY_4


title: d2_PY_3


title: d4_PY_3


title: hv205

description: Gene expression data from adults


title: d2_PY_2


title: RNA-seq tumor 4A2 rep3

description:
Tumor-derived Cre-ERT2, MYC-4A2 cells; 48 hours post 4-OHT treatment
RNA-seq-Tumor-count.txt

value: Tumor-derived MYC-4A2


title: RNA-seq tumor 4A2 rep2


title: NPC_patient_8 (VDJ-seq, BCR)

description: T147 BCR


title: d4_PY_2


title: RNA-seq FKBPFV-HCF-1N dTAG rep1


title: hv191

description: Gene expression data from adults


title: d0_PY_6


title: d2_PY_1


title: RNA-seq tumor 4A2 rep1


title: RNA-seq FKBPFV-HCF-1N DMSO rep3

description:
FKBPFV-HCF-1N cells; 3 hours +DMSO
RNA-seq-FKBPFV-HCF-1N-count.txt

value: DMSO for 3 hours


title: RNA-seq tumor 4A1 rep4

description:
Tumor-derived Cre-ERT2, MYC-4A1 cells; 48 hours post 4-OHT treatment
RNA-seq-Tumor-count.txt

value: Tumor-derived MYC-4A1


title: VCaP_FBS_shNTC_3_S9

tag: cell line

value: VCaP

value: prostate cancer cell line

value: shRNA against non-targeting control (shNTC)


title: hv195

description: Gene expression data from adults

value: healthy


title: RNA-seq FKBPFV-HCF-1N DMSO rep1


title: RNA-seq tumor 4A2 rep4


title: RNA-seq tumor 4A1 rep3


title: d0_PY_5

tag: strain


title: hv182

description: Gene expression data from adults

tag: age


title: RNA-seq FKBPFV-HCF-1N dTAG rep2


title: hv198

description: Gene expression data from adults


title: d0_PY_4


title: RNA-seq untagged dTAG rep3

description:
untagged, wild-type cells; 3 hours +dTAG-47
RNA-seq-untagged-count.txt


title: RNA-seq tumor 4A1 rep2


title: hv215

description: Gene expression data from adults


title: RNA-seq tumor 4A1 rep1


title: hv186

description: Gene expression data from adults


title: d0_PY_3


title: d0_PY_2