title: T47D

city: Wuhan

first: Jun

last: Zhou

address: Jiefang Road

institute: Wuhan Union Hospital

data_processing:
original image data file from Illumina Hiseq ™  was transformed into the original sequence  via CASAVA Base Calling
FastQC was used for quality assessment and Trimmomatic was used for  data processing.
HISAT2, RSeQC, BEDTools et al. were also used for analysis.
Transcripts Per Million (TPM) were calculated for assessment of expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: Mean TPM values of gene of each sample were shown in the txt file.

source_name: human breast cancer cells

growth_protocol: All cell lines were maintained at 37°C in a 5% CO2 humidified incubator. Cells were grown in monolayer and the medium was exchanged every 2 days with fresh medium with or without tamoxifen.

extract_protocol:
Total RNA was extracted from cultured cells using RNAiso Plus reagent (TaKaRa, Japan) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Both T47D and T47DR cell lines were cultured in tamoxifen-free medium for more than 7 days before high throughput sequencing.

value: tamoxifen-sensitive


title: T47DR

status: Public on Jun 01 2020

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: tamoxifen-resistant


title: week6_mature_mafko_gd_M1_12

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description: library of 96 Maf KO mature gamma delta T cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Mus musculus

growth_protocol: WT mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany. Maf KO mice were kept in the animal facility of The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, USA. Sox13 KO mice were kept in the animal facility of Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. Rorc KO mice were kept in the animal facility of Institute of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany.

extract_protocol:
Thymocytes were isolated using mechanical dissociation of thymus. Since double negative (DN) thymocytes are rare, we performed the magnetic enrichment for DN thymocytes.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: Maf KO, Sox13 Ko and Rorc KO cells were kept frozen in 90 % fetal bovine serum (FBS) and 10 % Dimethyl sulfoxide (DMSO) -80ºC before performing antibody staining, FACS sorting and single cell RNA sequencing.

tag: strain background

tag: genotype/variation

value: Maf KO

tag: Sex

value: female

tag: age/developemental stage

value: 6-7 weeks

tag: tissue

value: Thymus

value: mature gamma delta T cells


title: Sample 1163_Single mESC cell

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

country: USA

institute: Stanford University

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

source_name: Single mESC cell

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: exp54_3_veh [ve3]

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Alignment using RUM (v 1.09). The reads were aligned to genome (hg19).
Read counts were obtained using summarizeOverlaps from the GenomicFeatures package.
Genome_build: Homo sapiens hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.

source_name: A375_vehicle for 24hrs

growth_protocol: A375 metastatic melanoma cells were grown in DMEM medium supplemented with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent
RNA quality was assessed by spectrophotometry (NanoDrop 8000, Fisher Scientific) and electrophoresis (Bioanalyzer 2100, Agilent Technologies). cDNA libraries were prepared using TruSeq RNA protocol and sequenced on a HiSeq 2000 machine (Illumina, San Diego, CA).

treatment_protocol: Rosiglitazone 5 µM (rgz) and T0070907 2µM (t007) diluted in DMSO vehicle, 1/10000 final DMSO dilution

value: metastatic melanoma

tag: tissue source

value: skin

tag: passages

tag: treated with

value: vehicle for 24hrs


title: exp54_2_veh [ve2]


title: exp54_1_veh [ve1]


title: week6_mature_mafko_gd_16

source_name: library of 96 Maf KO mature gamma delta T cells


title: exp54_3_t007 [tx3]

source_name: A375_2μM T007 for 24hrs

value: 2μM T007 for 24hrs


title: Sample 1162_Single mESC cell


title: week6_mature_mafko_gd_15


title: week6_mature_mafko_gd_M5_1_10


title: HCT116 KMT2C KI2 H3K4me1

city: Uppsala

first: Chatarina

last: Larsson

address: Rudbeck Laboratory

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: Raw data for anti-histone H3K4me1 and input provided

library_source: genomic

data_processing:
ChIP-seq data were aligned using Bowtie 2 (default parameters). BAM files were uploaded into Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Peak calling was performed with MACS peak builder in Seqmonk.
FANTOM5 enhancers were identified by bidirectional transcription using the capped analysis of gene expression technique and obtained from the FANTOM data resource online (http://enhancer.binf.ku.dk/presets/). H3K4me1 signal was quantified by calculating the log2 of the reads per million for each sample relative to input (ChIP/Input).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Data given are the H3K4me1 ChIP-seq peaks identified with MACS using Seqmonk given in BED file format for GRC37/hg19. Supplementary file contains ChIP/Input scores at human enhancers from the FANTOM 5 project for each sample.

molecule: genomic DNA

source_name: Cell culture

growth_protocol: The parental and KMT2C knock-in cell lines were cultured in McCoy’s 5 A medium (Gibco, /Life Technologies, cat. no 26600-080) with 10% heat inactivated FBS.

extract_protocol:
Cells were fixed in 1% paraformaldehyde for 8 minutes. Chromatin was analyzed by ChIP-sequencing the Diagenode iDeal ChIP-seq kit for histones according to the manufacturer’s instructions. Chromatin extracts from one million cells were sonicated to yield 100 to 500 bp fragments using a Bioruptor Pico sonication device (Diagenode) on high power for two rounds of 6 cycles with 30 s on 30 s off at 4 °C. ChIP-seq was performed using 1 microgram of H3K4me1 antibody  (ab8895, Abcam) per ChIP. Cross-links were reversed (4 h at 65 °C) and DNA was purified using the Qiagen MinElute PCR purification kit. Samples were quantified using Qubit (HS dsDNA) and 10 ng of DNA was used for library preparation.
Libraries were prepared for sequencing using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® and sequenced on a HiSeq 2500 System (Illumina).

value: HCT116 ATCC CCL-247

value: KMT2C KI2

tag: chip antibody

value: Anti-Histone H3K4me1

tag: chip antibody source

value: Abcam ab8895


title: exp54_2_r&t [rt2]

source_name: A375_5μM RGZ and 2μM T007 for 24hrs

value: 5μM RGZ and 2μM T007 for 24hrs


title: exp54_2_t007 [tx2]


title: exp54_2_rgz [rg2]

source_name: A375_5μM RGZ for 24hrs

value: 5μM RGZ for 24hrs


title: exp54_1_r&t [rt1]


title: week6_mature_mafko_gd_11

value: Maf KO


title: exp54_1_rgz [rg1]


title: Sample 1158_Single mESC cell


title: Sample 1159_Single mESC cell


title: week6_mature_maf_floxed_gd_M1_15

description: library of 96 Maf floxed mature gamma delta T cells

value: Maf floxed

value: female


title: week6_mature_maf_floxed_gd_M1_16

source_name: library of 96 Maf floxed mature gamma delta T cells

value: 6-7 weeks

value: Thymus


title: Sample 1160_Single mESC cell

value: Differentiated mESC


title: Sample 1157_Single mESC cell

value: day 0


title: exp54_3_r&t [rt3]

value: metastatic melanoma


title: Patient_1_Tumor_rep1

city: New York

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

data_processing:
Reads were adapter and 3'end quality trimmed using cutadapt v1.15 with parameter --quality-base=20
Resultant fastq file was aligned using STAR aligner v2.5.2a, params --runMode alignReads --twopassMode Basic --readFilesCommand zcat --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantTranscriptomeBan "Singleend"
PDX sample were pre-aligned to the mouse mm10 genome before aliging to human to filter out perfect hits from possible stromal cell contamination
Bam files were merged when appropriate using novosort 1.03.09 then quantified using eXpress 1.5.1, counts were then collapsed by gene and summed using effective counts and tpm from output using gencode v 24 backmapped to grch37 for annotation
Genome_build: hg19
Supplementary_files_format_and_content: tsv files with efective read counts and tpms as determined by eXpress quantification.  Counts were filtered by protein_coding and lincRNA only, then collpased and summed on gene name suing the gencode24 backmapped to grch37 reference

source_name: Tumor

extract_protocol:
Illumina non-directional RNA access
A GI pathologist circled areas of high tumor cellularity on H&E sections of the tumor and PDX. RNA was extracted from the same area of an adjacent section using RNeasy FFPE kit (Qiagen, cat # 73504) after treating with Deparaffinization Solution (Qiagen, cat # 19093)
RNA library preparation and sequencing: Exome capture was carried out using the RNA access kit (Illumina, cat # RS-301-2001) for the majority of samples

tag: cell/tissue type

value: pancreatic adenocarcinoma tumor


title: Patient_1_Normal_rep1

source_name: Pancreas

value: adjacent normal pancreas


title: week6_mature_mafko_gd_12

value: mature gamma delta T cells


title: week6_mature_maf_floxed_gd_9


title: HCC_MHCC97L

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Stringtie was used to assemble transcripts from mapped reads. Then expression values were calculated by Cufflinks in both gene and transcript levels.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Hepatocellular Carcinoma cell line MHCC97L

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using RNAseq protocols

value: liver

tag: tissue type

value: cell line


title: Sample 1156_Single mESC cell


title: week6_mature_maf_floxed_gd_14


title: HCC_MHCC97H

source_name: Hepatocellular Carcinoma cell line MHCC97H


title: Sample 1155_Single mESC cell


title: Sample 1161_Single mESC cell


title: week6_mature_maf_floxed_gd_13


title: HCC_HepG2

source_name: Hepatocellular Carcinoma cell line HepG2


title: HCC_Huh7

source_name: Hepatocellular Carcinoma cell line Huh7


title: Sample 1154_Single mESC cell


title: HCC_Hep3B

source_name: Hepatocellular Carcinoma cell line Hep3B


title: HCC_Hep1

source_name: Hepatocellular Carcinoma cell line Hep1


title: HCC_7721

source_name: Hepatocellular Carcinoma cell line 7721


title: week6_mature_maf_floxed_gd_10


title: week6_immature_mafko_gd_M5_6

description: library of 96 Maf KO immature gamma delta T cells

value: immature gamma delta T cells


title: Sample 1153_Single mESC cell

source_name: Single mESC cell


title: week6_immature_mafko_gd_M5_5

source_name: library of 96 Maf KO immature gamma delta T cells


title: Sample 1151_Single mESC cell


title: Sample 1152_Single mESC cell


title: HCC_CR11

source_name: Relapse Hepatocellular Carcinoma sample

tag: patient gender

value: Male

tag: patient age

tag: tumor stage

value: Stage II

value: Relapse tumor


title: HCC_CR10

value: Female

value: Stage III


title: HCC_CR4


title: HCC_MHCCLM3

source_name: Hepatocellular Carcinoma cell line MHCCLM3


title: week6_immature_mafko_gd_M4_4

tag: strain background

value: Maf KO

value: female

tag: cell type


title: Sample 1150_Single mESC cell


title: HCC_CR12

source_name: Primary Hepatocellular Carcinoma sample

value: Stage II-III

value: Primary tumor


title: HCC_CR9


title: Sample 1149_Single mESC cell

value: Differentiated mESC

value: day 0


title: HCC_CR7


title: HCC_CR3


title: week6_immature_mafko_gd_M4_2

tag: genotype/variation

tag: Sex

value: 6-7 weeks

value: Thymus


title: week6_immature_mafko_gd_M4_3

tag: age/developemental stage

tag: tissue


title: exp54_1_t007 [tx1]

source_name: A375_2μM T007 for 24hrs

tag: cell line

value: metastatic melanoma

value: skin

value: 2μM T007 for 24hrs


title: HCC_104T

value: liver


title: HCC_CR1

value: Male


title: HCC_CR8


title: Sample 1147_Single mESC cell

tag: day of differentiation


title: HCC_99T

value: Stage II


title: week6_immature_mafko_gd_M4_1

value: immature gamma delta T cells


title: HCC_97T


title: week6_immature_mafko_gd_M3_16


title: Sample 1146_Single mESC cell


title: week6_immature_mafko_gd_M3_15


title: HCC_74T


title: HCC_65T


title: HCC_96T


title: week6_immature_mafko_gd_M3_14


title: Sample 1144_Single mESC cell


title: HCC_CR2

value: Relapse tumor


title: Sample 1145_Single mESC cell


title: HCC_92T


title: Sample 1143_Single mESC cell


title: week6_immature_mafko_gd_M3_13


title: Sample 1148_Single mESC cell


title: HCC_55T


title: HCC_56T

value: Stage III


title: Sample 1142_Single mESC cell


title: HCC_31T


title: week6_immature_mafko_gd_M2_14

value: Maf KO


title: HCC_DR12

source_name: Benign Adjacent liver sample

value: Benign adjacent


title: Sample 1141_Single mESC cell


title: Sample 1140_Single mESC cell


title: HCC_DR11


title: HCC_DR9

value: Female


title: week6_immature_mafko_gd_M1_12

value: female


title: week6_immature_mafko_gd_9


title: HCC_DR10


title: HCC_DR8


title: HCC_59T

value: Stage II-III

value: Primary tumor


title: HCC_DR7


title: Sample 1139_Single mESC cell

value: Differentiated mESC

value: day 0


title: HCC_DR3


title: HCC_DR4


title: Sample 1138_Single mESC cell


title: HCC_DR2


title: week6_immature_mafko_gd_7

value: 6-7 weeks

value: Thymus


title: Sample 1137_Single mESC cell


title: HCC_DR1


title: HCC_104N


title: Sample 1136_Single mESC cell


title: week6_immature_mafko_gd_6


title: HCC_97N


title: Sample 1135_Single mESC cell


title: HCC_96N


title: week6_immature_mafko_gd_12


title: week6_immature_mafko_gd_11


title: Sample 1133_Single mESC cell


title: HCC_74N


title: week6_immature_mafko_gd_10


title: HCC_65N


title: week6_immature_mafko_gd_8


title: HCC_92N


title: Sample 1134_Single mESC cell


title: Sample 1131_Single mESC cell


title: week6_immature_maf_floxed_gd_M1_13

description: library of 96 Maf floxed immature gamma delta T cells

value: Maf floxed


title: HCC_31N

value: liver


title: HCC_56N

value: Male


title: HCC_55N


title: week6_immature_mafko_gd_M2_13


title: ERI2_RNAi.RNAseq.rep2

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq/miRNAseq reads count were calculated using HTSeq 0.6.1p1

growth_protocol: HEK293 cells were cultured in DMEM medium with 10% Fetal bovine serum.

extract_protocol:
Total RNA from frozen cell pellets was prepared using the RNeasy midi kits (Qiagen, Inc.) following manufacturer’s instructions. After elution, RNA samples were concentrated by ethanol precipitation and resuspended in nuclease-free water.
Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.

treatment_protocol: ERI-1, ERI-2 siRNAs and control C2 RNAs were obtained from Dharmacon’s ON-TARGETplusTM siRNA collection and the knockdown was performed using Lipofectamine RNAiMax (Invitrogen) using a two-hit method using 50 nM siRNAs. The second siRNA transfection was performed 48 hrs after the first hit and the cells were cultured for another 72 hrs before harvesting for microarray analysis.

tag: treatment

value: ERI2 RNAi


title: ERI2_RNAi.RNAseq.rep3


title: HCC_99N


title: week6_immature_mafko_gd_5

value: immature gamma delta T cells


title: ERI2_RNAi.RNAseq.rep1


title: HCC_47T

value: Stage II


title: Sample 1129_Single mESC cell


title: Sample 1130_Single mESC cell


title: HCC_47N


title: exp54_3_rgz [rg3]

source_name: A375_5μM RGZ for 24hrs

value: metastatic melanoma

tag: tissue source

value: skin

tag: passages

tag: treated with

value: 5μM RGZ for 24hrs


title: Sample 1132_Single mESC cell


title: Ctrl_RNAi.RNAseq.rep3

value: Control


title: HCC_59N

value: Female

value: Benign adjacent


title: week6_immature_maf_floxed_gd_M1_14

source_name: library of 96 Maf floxed immature gamma delta T cells

value: female


title: e175_mafko_mature_gd_VG3_11

description: library of 96 Maf KO mature gamma5 positive gamma delta T cells

value: Maf KO

value: Embryonic day 17.5


title: Sample 1128_Single mESC cell

value: Differentiated mESC

value: day 0


title: e175_mafko_mature_gd_8

source_name: library of 96 Maf KO mature gamma delta T cells

value: Thymus

value: mature gamma delta T cells


title: Ctrl_RNAi.RNAseq.rep1


title: Ctrl_RNAi.RNAseq.rep2


title: ERI2_RNAi.miRNAseq.rep2


title: Sample 1127_Single mESC cell


title: e175_mafko_mature_gd_7


title: Ctrl_RNAi.miRNAseq.rep3


title: Sample 1126_Single mESC cell


title: ERI2_RNAi.miRNAseq.rep1


title: e175_mafko_mature_gd_VG3_12

source_name: library of 96 Maf KO mature gamma5 positive gamma delta T cells


title: e175_mafko_mature_gd_4


title: Ctrl_RNAi.miRNAseq.rep2


title: Sample 1125_Single mESC cell


title: Sample 1124_Single mESC cell


title: Chip-seq of BRG1 in MCF-7 cells pretreated with a vehicle

city: Amsterdam

first: Koen

last: Flach

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 51 or 65 bp reads), and aligned to the Human Reference Genome (assembly hg19, February 2009). Peak calling over input was performed using MACS peak caller (Zhang et al., 2008) version 1.3.7.1 and  DFilter (Kumar et al., 2013), only considering peaks shared by both peak callers.
The bed files containing the peaks of ERa and p300 (the bedfiles i uploaded) were used to analyse all the other data. We analyzed the binding events of e.g. BRG1 at the peak-locations of ERa and p300. Therefor we didn't perform or required peak-calling on these Chips.
Genome_build: Hg19
Supplementary_files_format_and_content: Bed files contain peaks identified by both peak callers.

growth_protocol: MCF-7were cultured in DMEM medium in the presence of 10% FBS and antibiotics (penicillin, streptavidin).  For hormone deficient conditions, cells were deprived of hormone for 72 hours, by culturing in phenol-red-free DMEM containing 5% charcoal-treated serum, antibiotics and supplemented with L-glutamine, prior to hormone treatment.

extract_protocol:
ChIP experiments were performed as described previously (Zwart et al., 2011).
ChIP DNA was amplified as described (Jansen et al., 2013). Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 51 or 65 bp reads), and aligned to the Human Reference Genome (assembly hg19, February 2009).

treatment_protocol: Hormone treatments consisted of solvent Dimethylsulfoxide (DMSO) or 10nM of estradiol. Additionally cells were pretreated with 100nM of the FEN1 inhibitor prior to hormone treatment. For knockdown experiments 25nM of single or pooled duplexes of siRNA against FEN1 (Dharmacon MU-010344-01) or a non-targeting control pool (Dharmacon, D-001206-14-20) were transfected with Dharmafect according to manufactures protocol.

value: BRG1 control


title: e175_mafko_mature_gd_12


title: Chip-seq of BRG1 in MCF-7 cells pretreated with the FEN1 inhibitor

value: BRG1 fen1 inhibitor


title: Chip-seq of PARP1 in MCF-7 cells pretreated with FEN1 inhibitor after 30 minutes of estradiol stimulation

value: PARP1 30 min E2 FEN1 inhibitor


title: Sample 1123_Single mESC cell


title: e175_mafko_mature_gd_3


title: Chip-seq of XRCC1 in MCF-7 cells after 10 minutes of estradiol stimulation

value: XRCC1 10 min E2


title: e175_mafko_mature_gd_11


title: Sample 1122_Single mESC cell


title: ERI2_RNAi.miRNAseq.rep3

value: ERI2 RNAi


title: Chip-seq of ERα in MCF-7 cells pretreated with FEN1 inhibitor after 10 minutes of estradiol stimulation

value: ERα 10 min E2 FEN1 inhibitor


title: Chip-seq of ERα in MCF-7 cells pretreated with vehicle after 10 minutes of estradiol stimulation

value: ERα 10 min E2 vehicle


title: FAIRE-seq in MCF-7 cells transfected with non-targeting siRNA

value: FAIRE siControl


title: Sample 1121_Single mESC cell


title: FAIRE-seq in MCF-7 cells transfected with siRNA targeting FEN1

value: FAIRE siFEN1


title: e175_mafko_immature_gd_VG3_9

value: immature gamma delta T cells


title: e175_mafko_immature_gd_VG3_10


title: Chip-seq of FOXA1 in MCF-7 cells transfected with siRNA targeting FEN1

value: FOXA1 siFEN1


title: e175_mafko_immature_gd_9

value: Maf KO


title: Ctrl_RNAi.miRNAseq.rep1

value: Control


title: e175_mafko_immature_gd_6

value: Embryonic day 17.5


title: Chip-seq of FOXA1 in MCF-7 cells transfected with non-targeting siRNA

value: FOXA1 siControl


title: Sample 1118_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 1119_Single mESC cell


title: e175_mafko_immature_gd_5

value: Thymus


title: Sample 1117_Single mESC cell


title: Chip-seq of PARP1 in MCF-7 cells pretreated with vehicle after 30 minutes of estradiol stimulation

value: PARP1 30 min E2 vehicle


title: e175_mafko_immature_gd_1


title: Sample 1115_Single mESC cell


title: e175_mafko_immature_gd_10


title: Sample 1120_Single mESC cell


title: Sample 1114_Single mESC cell


title: Chip-seq of ERα in MCF-7 cells transfected with siRNA targeting FEN1

value: ERα siFEN1


title: Chip-seq of ERα in MCF-7 cells transfected with non-targeting siRNA

value: ERα siControl


title: Sample 1113_Single mESC cell


title: e175_mafko_gd_panVG2_L4_13

description: library of 96 Maf KO pan gamma4 positive gamma delta T cells

value: pan gamma4 positive gamma delta T cells


title: e175_mafko_gd_panVG2_L3_13

source_name: library of 96 Maf KO pan gamma4 positive gamma delta T cells


title: Sample 1112_Single mESC cell


title: e175_mafko_gd_panVG2_L2_13


title: Sample 1111_Single mESC cell


title: e175_mafko_immature_gd_2


title: Sample 1116_Single mESC cell


title: e175_mafko_gd_panVG2_L1_13


title: Sham Operated;  FVB; 53 Days;   Mouse #5

type: RNA

city: Paris

first: Fabiola

last: Terzi

state: Choisir votre état

address: Inserm U1151 CNRS U8253 Paris University, 160 rue de Vaugirard

country: France

institute: Inserm

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: RNA from whole kidneys from Sham Operated (FVB) 53 days after surgery

label_protocol: standard Affymetrix protocol

extract_protocol: mRNA was extracted from nitrogen-frozen whole kidney using QIAzol Reagent and the miRNeasy Kit (Qiagen) according to the manufacturer’s instructions. Technical quality was checked by visual inspection of density, RNA degradation, and MA plots. All chips were of high technical quality with no irregular degradation pattern and were used for further analysis

tag: strain

value: FVB

tag: surgery

value: Sham Operated

tag: time point

value: 53 Days after surgery


title: Sham Operated;  FVB; 53 Days;   Mouse #3


title: Sample 1110_Single mESC cell


title: e175_maf_floxed_mature_gd_VG3_8

source_name: library of 96 Maf floxed mature gamma delta T cells

value: Maf floxed

value: mature gamma delta T cells


title: Sham Operated;  C57BL/6; 53 Days;   Mouse #6

source_name: RNA from whole kidneys from Sham Operated (C57BL/6) 53 days after surgery


title: Sham Operated;  C57BL/6; 53 Days;   Mouse #5


title: Sham Operated;  FVB; 28 Days;   Mouse #3

source_name: RNA from whole kidneys from Sham Operated (FVB) 28 days after surgery

value: 28 Days after surgery


title: Sham Operated;  FVB; 53 Days;   Mouse #6


title: Sham Operated;  FVB; 28 Days;   Mouse #2


title: Sham Operated;  FVB; 53 Days;   Mouse #1


title: Sham Operated;  FVB; 2 Days;   Mouse #1

source_name: RNA from whole kidneys from Sham Operated (FVB) 2 days after surgery

value: 2 Days after surgery


title: Sham Operated;  FVB; 2 Days;   Mouse #5


title: Sham Operated;  FVB; 28 Days;   Mouse #4


title: e175_maf_floxed_mature_gd_VG3_7


title: Sample 1109_Single mESC cell

source_name: Single mESC cell


title: Sham Operated;  FVB; 2 Days;   Mouse #2


title: Sham Operated;  C57BL/6; 53 Days;   Mouse #3


title: Sham Operated;  FVB; 2 Days;   Mouse #4


title: e175_maf_floxed_mature_gd_VG1_14


title: Sample 1107_Single mESC cell


title: Sham Operated;  FVB; 28 Days;   Mouse #1


title: Sample 1108_Single mESC cell


title: e175_maf_floxed_mature_gd_VG1_13


title: Sham Operated;  C57BL/6; 28 Days;   Mouse #3

source_name: RNA from whole kidneys from Sham Operated (C57BL/6) 28 days after surgery


title: Sham Operated;  C57BL/6; 28 Days;   Mouse #6


title: Sample 1106_Single mESC cell


title: e175_maf_floxed_mature_gd_P3_4


title: Sham Operated;  C57BL/6; 53 Days;   Mouse #1


title: Sample 1105_Single mESC cell


title: Sham Operated;  C57BL/6; 28 Days;   Mouse #5


title: e175_maf_floxed_mature_gd_P3_3


title: Sample 1103_Single mESC cell


title: e175_maf_floxed_mature_gd_7


title: Sham Operated;  C57BL/6; 28 Days;   Mouse #1


title: Sample 1104_Single mESC cell


title: Sample 1102_Single mESC cell


title: e175_maf_floxed_mature_gd_8


title: Sham Operated;  C57BL/6; 2 Days;   Mouse #2

source_name: RNA from whole kidneys from Sham Operated (C57BL/6) 2 days after surgery


title: Nephrectomized;  FVB; 53 Days;   Mouse #8

source_name: RNA from whole kidneys from Nephrectomized (FVB) 53 days after surgery

value: Nephrectomized


title: Sham Operated;  C57BL/6; 2 Days;   Mouse #4


title: Sham Operated;  C57BL/6; 2 Days;   Mouse #1


title: Sham Operated;  C57BL/6; 2 Days;   Mouse #5


title: Sample 1101_Single mESC cell


title: e175_maf_floxed_mature_gd_3

value: Embryonic day 17.5


title: Nephrectomized;  FVB; 53 Days;   Mouse #7


title: Sample 1100_Single mESC cell


title: e175_maf_floxed_immature_gd_VG3_6

value: immature gamma delta T cells


title: Sample 1099_Single mESC cell

value: Differentiated mESC


title: Nephrectomized;  FVB; 28 Days;   Mouse #7

source_name: RNA from whole kidneys from Nephrectomized (FVB) 28 days after surgery


title: e175_maf_floxed_immature_gd_VG3_5


title: e175_maf_floxed_mature_gd_4


title: Nephrectomized;  FVB; 28 Days;   Mouse #2


title: Nephrectomized;  FVB; 53 Days;   Mouse #10

source_name: RNA from whole kidneys from Nephrectomized (FVB) 53 days after surgery0


title: Nephrectomized;  FVB; 2 Days;   Mouse #5

source_name: RNA from whole kidneys from Nephrectomized (FVB) 2 days after surgery


title: Nephrectomized;  FVB; 28 Days;   Mouse #8


title: Nephrectomized;  FVB; 2 Days;   Mouse #4


title: Nephrectomized;  FVB; 28 Days;   Mouse #3


title: Sample 1098_Single mESC cell

value: day 0


title: e175_maf_floxed_immature_gd_VG1_12

value: Thymus


title: e175_maf_floxed_immature_gd_VG1_11


title: Nephrectomized;  FVB; 2 Days;   Mouse #2


title: Nephrectomized;  FVB; 2 Days;   Mouse #1


title: Sample 1096_Single mESC cell


title: Nephrectomized;  C57BL/6; 53 Days;   Mouse #7

source_name: RNA from whole kidneys from Nephrectomized (C57BL/6) 53 days after surgery


title: e175_maf_floxed_immature_gd_P3_2

source_name: library of 96 Maf floxed immature gamma delta T cells


title: Nephrectomized;  FVB; 53 Days;   Mouse #4


title: Sample 1095_Single mESC cell


title: Nephrectomized;  C57BL/6; 53 Days;   Mouse #2


title: Nephrectomized;  C57BL/6; 53 Days;   Mouse #1


title: e175_maf_floxed_immature_gd_P3_1


title: Sample 1094_Single mESC cell


title: RPF (45-140 nts) plasmid

city: Cork

first: John

last: Atkins

address: Western GateWay Building, Western Road, UCC, Cork

department: School of Biochemistry and Cell Biology

country: Ireland

institute: UCC

data_processing:
The adapter sequence at the 5'end of the the reads has being clipped with Cutadapt. Those which mapped to rRNA have being discarded.
Reads were mapped to reference  genomes of E. coli sub-strain MG1655 (accession number NC_000913.2 ) and T4 ( NC_000866.4). The single end reads were mapped with Bowtie with parameters (-m 1) i.e. allowing of no ambigous mapped reads. The  paired-end reads associated with the longer fragments were aligned with Bowtie2 with parameters (-M 10 -I 0 --no-unal --no-discordant --no-mixed –dovetail). Reads less than 45 nucleotides were discarded when processing the “long fragments” fractions.

organism: Escherichia coli

source_name: RPF (45-140 nts) plasmid

growth_protocol: The method for ribosome profiling used was described by Ingolia et al. 2009 and modified for E. coli (Oh et al. 2011). Three 200 ml cultures of E. coli strain MC4100 (OD600 ~ 0.5) were each infected with bacteriophage T4 at a multiplicity of infection (MOI) of 10 and harvested at different time points (2.5, 4 or 5 min) post-infection In parallel, a 200 ml culture (uninfected) was also harvested as a control. In addition, ribosome profiling was also performed on 200 ml cultures of E. coli containing a plasmid-borne cassette with the gp60 sequence. E. coli cells (OD600 ~ 0.5) were induced for 10 min with IPTG.   References  Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. & Weissman, J.S. (2009). Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.    Oh, E., Becker, A.H., Sandikci, A., Huber, D., Chaba, R., Gloge, F., Nichols, R.J., Typas, A., Gross, C.A., Kramer, G. et al. (2011). Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell, 147, 1295-1308.

extract_protocol: Lysates were then loaded onto 10-55% sucrose gradients (gradient buffer: 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris pH 8.0 and 100 µg/ml choramphenicol) and centrifuged at 35,000 rpm for 2.5 hr at 4˚ C. Monosomes fractions were collected and ribosome-protected mRNAs were isolated by acid phenol extraction and isopropanol precipitation. Following dephosphorylation, RNAs (20 µg each) were fractionated on 15% TBE-urea gels and the appropriate size ranges, 30-40 nt or 45-150 nt, were excised. RNAs were eluted from the gel slices.

treatment_protocol: Cells were collected by fast filtration and immediately frozen in liquid nitrogen. Cells were lysed by mechanical disruption while frozen to prevent further translation elongation during sample preparation. Clarified lysates, corresponding to 20 OD260, (in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris pH 8.0, 0.4% Triton X-100, 0.1% NP40, 5 mM CaCl2, 100 units/ml RNase-free DNase, and 100 µg/ml chloramphenicol) were treated with micrococcal nuclease (MNase) (60 units/OD260) for 1 hr at 25˚ C. Nuclease digestion was stopped by the addition of EGTA.

tag: polyacrylamide gel size selection

tag: viral infection


title: RPF (30-40 nts) control

source_name: RPF (30-40 nts) control


title: e175_maf_floxed_immature_gd_6

tag: strain background


title: Sample 1097_Single mESC cell


title: Sample 1093_Single mESC cell


title: e175_maf_floxed_immature_gd_5

tag: cell type


title: Nephrectomized;  C57BL/6; 28 Days;   Mouse #5

source_name: RNA from whole kidneys from Nephrectomized (C57BL/6) 28 days after surgery


title: Sample 1092_Single mESC cell


title: Nephrectomized;  C57BL/6; 28 Days;   Mouse #4


title: Nephrectomized;  C57BL/6; 28 Days;   Mouse #3


title: Nephrectomized;  C57BL/6; 28 Days;   Mouse #9


title: Nephrectomized;  C57BL/6; 2 Days;   Mouse #3

source_name: RNA from whole kidneys from Nephrectomized (C57BL/6) 2 days after surgery


title: Nephrectomized;  C57BL/6; 53 Days;   Mouse #4


title: Nephrectomized;  C57BL/6; 2 Days;   Mouse #5


title: Nephrectomized;  C57BL/6; 2 Days;   Mouse #11


title: Nephrectomized;  C57BL/6; 2 Days;   Mouse #9


title: e175_maf_floxed_immature_gd_2

tag: genotype/variation


title: e175_maf_floxed_immature_gd_1


title: e175_maf_floxed_gd_panVG2_L4_14

description: library of 96 Maf floxed pan gamma4 positive gamma delta T cells


title: HUVEC_CECR1_DPM3

city: San Diego

first: Rekha

last: Dhanwani

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: Primary Human Umbilical Vein Endothelial Cells

extract_protocol:
RNA was extracted from 200,000 HUVEC cells using Zymo kit following manufacturers protocol and ~400 ng RNA was used for library construction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Male

tag: passage number


title: Sample 1088_Single mESC cell


title: Sample 1089_Single mESC cell


title: e175_maf_floxed_gd_panVG2_L3_14

source_name: library of 96 Maf floxed pan gamma4 positive gamma delta T cells

tag: age/developemental stage

tag: tissue


title: e175_maf_floxed_gd_panVG2_L2_14


title: HUVEC_CECR1_DPM2

value: Primary Human Umbilical Vein Endothelial Cells


title: e175_maf_floxed_gd_panVG2_L1_14


title: HUVEC_CECR1_DPM1


title: Sample 1087_Single mESC cell

tag: cell line

tag: day of differentiation


title: rorcko_week6_immature_gd_M2_4

description: library of 96 Rorc KO immature gamma delta T cells

value: Rorc KO

tag: Sex

value: female

value: 4-5 weeks


title: HUVEC_CECR13


title: Sample 1086_Single mESC cell


title: Sample 1090_Single mESC cell


title: HUVEC_CECR12


title: Sample 1091_Single mESC cell


title: rorcko_week6_immature_gd_M2_3

source_name: library of 96 Rorc KO immature gamma delta T cells


title: Sample 1085_Single mESC cell


title: Kidney_ischemia reperfusion injury_day 3_rep1

city: Kawasaki City

first: Kohei

last: Matsushita

state: Kanagawa

address: 3-25-26 Tonomachi, Kawasaki-ku

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: We followed protocol of Gene Expression Hybridazation Kit (Agilent)

scan_protocol: We followed protocol of G2565BA microarray scanner (Agilent)

data_processing: Data acquisition and normalization were used Feature Extraction Software

organism: Rattus norvegicus

source_name: Female F344 rat_left kidney_ischemia reperfusion injury_after 3 days

label_protocol: We followed protocol of SureTag DNA labeling Kit (Agilent)

extract_protocol: We followed protocol of RNeasy Micro Kit (Qiagen)

value: F344 rat

tag: age

value: 10 weeks

value: Kidney

tag: operation

value: unilateral ischemia reperfusion injury (left kidney)

tag: sacrifice

value: 3 days after operation


title: HUVEC_CECR11


title: Kidney_sham operation_rep1

source_name: Female F344 rat_left kidney_sham operated_after 7 days

tag: strain

value: Sham operation

value: 7 days after operation


title: Kidney_sham operation_rep2


title: Sample 1084_Single mESC cell

source_name: Single mESC cell


title: rorcko_week6_immature_gd_M2_11


title: HUVEC_control3


title: Sample 1083_Single mESC cell


title: Kidney_ischemia reperfusion injury_day 3_rep4


title: Kidney_sham operation_rep4


title: Kidney_ischemia reperfusion injury_day 7_rep4

source_name: Female F344 rat_left kidney_ischemia reperfusion injury_after 7 days


title: Kidney_sham operation_rep3


title: Kidney_ischemia reperfusion injury_day 3_rep2


title: Sample 1082_Single mESC cell


title: rorcko_week6_immature_gd_M1_8


title: Kidney_ischemia reperfusion injury_day 7_rep1


title: Kidney_ischemia reperfusion injury_day 7_rep3


title: Kidney_ischemia reperfusion injury_day 3_rep3


title: Kidney_ischemia reperfusion injury_day 7_rep2


title: rorcko_week6_immature_gd_M1_7


title: rorcko_week6_immature_gd_M1_12


title: Sample 1081_Single mESC cell


title: QC3

city: Jinan

first: Qi

middle: Wen

last: Tan

state: Shandong

address: Jingshi Road 16369

department: Acupuncture Department

institute: Shandong University of TCM

description: Gene expression of of Quchi group

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: Myocardium，Quchi group

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using standard denaturing agarose gel electrophoresis. RNA quantity and purity were determined by spectrophotometry (NanoDrop ND-1000 spectrophotometer)

treatment_protocol: Rats in Jiaji group（JJ）, Neiguan group（NG）, Yanglingquan group(YL) and Quchi group(QC) were preconditon with 7-day treatment by acupuncturing apupoint respectively , MIRI model was replicated by ligation of the left anterior descending coronary artery in MX group and all acupuncture groups.

value: Myocardium


title: QC4

description: Gene expression of of Quchi group

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)


title: HUVEC_control1


title: Sample 1080_Single mESC cell


title: HUVEC_si_ada2_6


title: Sample 1079_Single mESC cell


title: HUVEC_si_ada2_5


title: sox13wt_week6_mature_gd_M2_4

description: library of 96 Sox13 WT Control mature gamma delta T cells

value: Sox13 WT Control

value: male

value: 5-6 weeks

value: mature gamma delta T cells


title: YL4

description: Gene expression of of Yanglingquan group

source_name: Myocardium，Yanglingquan group


title: HUVEC_si_ada2_4

value: Male


title: sox13wt_week6_mature_gd_M2_3

source_name: library of 96 Sox13 WT Control mature gamma delta T cells

value: Thymus


title: QC2

description: Gene expression of of Quchi group


title: sox13wt_week6_mature_gd_M2_2


title: Sample 1077_Single mESC cell

value: Differentiated mESC

value: day 0


title: QC1

description: Gene expression of of Quchi group


title: Sample 1078_Single mESC cell


title: HUVEC_control2

value: Primary Human Umbilical Vein Endothelial Cells


title: HUVEC_si_control_3


title: sox13wt_week6_mature_gd_M2_1


title: HUVEC_si_control_2


title: HUVEC_si_control_1


title: sox13wt_week6_mature_gd_4


title: Sample 1076_Single mESC cell


title: YL2


title: YL3

value: female


title: YL1


title: Sample 1075_Single mESC cell


title: sox13wt_week6_mature_gd_3


title: Sample 1074_Single mESC cell


title: sox13wt_week6_mature_gd_12


title: Randomly_synthesized_oligos_rep2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

description: Randomly synthesized 10 nt RNA oligos

data_processing:
Firstly, the first 21 nt in the 5' end was trimmed. Then, the 3' adaptor CTCGAGCAGCTGGAAGATCG was removed by Cutadapt. The reads with trimmed length unequal to 10 nt were discarded.
Identical reads were counted by in-house Perl script.
Genome_build: NA
Supplementary_files_format_and_content: The processed files are tab seperated text files, which include the count of all 10 nt random sequences. For each row, there are three values seperated by tabs. The first column is random sequence itself. The second column is the count data. The third column is RPM value, i.e. count data normalized by the total reads per million.

source_name: HEK293, stably expressing H-2Kb

growth_protocol: HEK293 cells and HEK293-Kb cells are cultured in Dulbecco’s Modification of Eagle’s Medium (Corning 10-013-CV) supplemented with 10% fetal bovine serum (Sigma 12306C).

extract_protocol:
Total RNAs from sorted cells are extracted using Trizol reagent (Invitrogen).
Purified total RNAs are suspended in nuclease-free water for reverse transcription.In brief, RNA samples are mixed with 1 μl 10 mM dNTP and 2 pmol reverse primer overlap with 3’end of GFP (oligo 2) and incubated at 65 °C for 5 min, followed by incubation on ice for 5 min. The reverse transcription is carried out by incubating the reaction mixture with 1 × First-Strand Buffer, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III at 50 °C for 60 min followed by heating at 70°C for 15minutes. First-strand cDNA is then used as the template for PCR amplification catalyzed by the Phusion High-Fidelity enzyme (NEB). The PCR is performed in a 20 μL reaction (1× HF buffer, 0.2 mM dNTP, 0.5 μM forward and reverse primers and 0.5 U Phusion polymerase) with barcoded primers (Table S1). PCR is set up based on the following condit 110 ion: 16 cycles of 98 °C, 10 s; 60 °C, 20 s; 72 °C, 10 s followed by 72 °C, 10 min. The PCR products with the expected size 163 base pairs are excised from a 8% polyacrylamide TBE gel (Invitrogen). The DNA products are recovered from DNA gel elution buffer (300 mM NaCl, 1 mM EDTA) followed by quantification using Agilent BioAnalyzer DNA 1000 assay. Equal amounts of barcoded samples were pooled together followed by deep sequencing (Illumina HiSeq).

value: HEK293, stably expressing H-2Kb

tag: treatment

value: Originally synthesized oligo pool


title: sox13wt_week6_mature_gd_11


title: Sample 1072_Single mESC cell


title: sox13wt_week6_immature_gd_M2_9

description: library of 96 Sox13 WT Control immature gamma delta T cells

value: immature gamma delta T cells


title: sox13wt_week6_immature_gd_M2_8

source_name: library of 96 Sox13 WT Control immature gamma delta T cells


title: Sample 1071_Single mESC cell


title: NG4

description: Gene expression of of Neiguan group

source_name: Myocardium，Neiguan group


title: NG3

description: Gene expression of of Neiguan group


title: NG2

description: Gene expression of of Neiguan group


title: Sample 1069_Single mESC cell


title: Sample 1070_Single mESC cell


title: sox13wt_week6_immature_gd_M2_6


title: NG1

description: Gene expression of of Neiguan group


title: Sample 1068_Single mESC cell


title: Sample 1067_Single mESC cell


title: JJ4

description: Gene expression of of Jiaji  group

source_name: Myocardium，Jiaji  group


title: sox13wt_week6_immature_gd_M2_5


title: sox13wt_week6_immature_gd_M2_11


title: Sample 1066_Single mESC cell


title: sox13wt_week6_immature_gd_M2_12


title: Sample 1065_Single mESC cell


title: Sample 1073_Single mESC cell


title: DZ4

description: Gene expression of sham group

source_name: Myocardium，sham group


title: JJ1

description: Gene expression of of Jiaji  group


title: sox13wt_week6_immature_gd_M2_10


title: sox13wt_week6_immature_gd_M2_7


title: Sample 1064_Single mESC cell


title: Sample 1063_Single mESC cell


title: sox13wt_week6_immature_gd_9


title: JJ3

description: Gene expression of of Jiaji  group


title: Sample 1062_Single mESC cell


title: sox13wt_week6_immature_gd_2


title: sox13wt_week6_immature_gd_1


title: DZ2

description: Gene expression of sham group


title: Sample 1061_Single mESC cell


title: DZ3

description: Gene expression of sham group


title: DZ1

description: Gene expression of sham group


title: MX3

description: Gene expression of IRI in rat myocardium

source_name: Myocardium，IRI group


title: JJ2

description: Gene expression of of Jiaji  group


title: Sample 1059_Single mESC cell


title: sox13ko_week6_mature_gd_M3_19

description: library of 96 Sox13 KO mature gamma delta T cells

value: Sox13 KO


title: MX2


title: Sample 1058_Single mESC cell


title: sox13ko_week6_mature_gd_M3_20

source_name: library of 96 Sox13 KO mature gamma delta T cells


title: sox13ko_week6_mature_gd_M3_18


title: Sample 1057_Single mESC cell


title: sox13ko_week6_mature_gd_M2_4


title: Sample 1055_Single mESC cell


title: sox13ko_week6_mature_gd_M2_3


title: Sample 1054_Single mESC cell


title: Sample 1053_Single mESC cell


title: sox13wt_week6_immature_gd_10


title: Sample 1060_Single mESC cell


title: sox13ko_week6_mature_gd_M2_1


title: Sample 1052_Single mESC cell


title: sox13ko_week6_mature_gd_8


title: Sample 1051_Single mESC cell


title: Sample 1050_Single mESC cell


title: sox13ko_week6_mature_gd_7


title: sox13ko_week6_mature_gd_M3_17


title: Sample 1056_Single mESC cell


title: sox13ko_week6_mature_gd_16


title: sox13ko_week6_mature_gd_M2_2


title: WT adult pancreas at D5, biological rep 2

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

description: Gene expression data from WT pancreas tissue treated with cerulein to induce proliferation

hyb_protocol: Affymetrix hybridization protocol performed by Washington University GTAC Sequencing Core Facility

scan_protocol: Affymetrix scanning and images acquired by Washington University GTAC Sequencing Core Facility

data_processing: Affymetrix chp data generated by Washington University GTAC Sequencing Core Facility

source_name: WT adult pancreas, Cerulein treated, 5 Days

label_protocol: Affymetrix labelling protocol performed by Washington University GTAC Sequencing Core Facility

growth_protocol: Animals housed and maintained according to Washington University Department of Comparative Medicine requirements

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

treatment_protocol: Mice injected with cerulein (100 ug/kg) intraperitoneally to induce pancreatitis (6x daily, every other day, for 5 days).

value: adult pancreas

tag: genotype

value: Wild type

value: 8 weeks


title: IFRD1_KO adult pancreas at D5, biological rep 1

description: Gene expression data from IFRD1 null pancreas tissue treated with cerulein to induce proliferation and observe globel expression changes

source_name: IFRD1 null adult pancreas, Cerulein treated, 5 Days

value: IFRD1 null


title: Sample 1049_Single mESC cell


title: IFRD1_KO adult pancreas at D5, biological rep 2


title: sox13ko_week6_mature_gd_15

value: male


title: sox13ko_week6_immature_gd_M3_9

description: library of 96 Sox13 KO immature gamma delta T cells

value: 5-6 weeks


title: MX1

value: Myocardium


title: Sample 1048_Single mESC cell


title: 3D22_14_Erbium_Glassxfast

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

hyb_protocol: Hybridization cocktails containing 5.5 µg of fragmented, end-labelled cDNA were prepared and applied to GeneChip Human Gene 2.0 ST arrays. Hybridization was performed in 45°C hybridization oven at 60 rpm for 16 hours. Using the GeneChip® Fluidics Station 450 the hybridized GeneChip Human Gene 2.0 ST Arrays were washed and stained (Fluidics Protocol FS450_0001).

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip®Operating Software (GCOS) version 1.4 to produce CEL intensity files.

data_processing:
Data analysis from the exon arrays were processed using GeneSpring GX 14.9 software (Agilent Technologies).
probe group file: GeneChip Human Gene 2.0 ST Array
meta-probeset file: Affymetrix.ExonExprChip.HuGene-2_0-st_na35_hg19_2015-04-15
Expression values of each probe set were determined using the GeneSpring GX 14.9 software (Agilent Technologies). Normalization method: Quantile.

source_name: dermal fibroblasts and keratinocytes

label_protocol: 300µg total RNA from each model were processed using the WT Expression Kit (Ambion)  to generate amplified sense-strand cDNA. Fragmentation and labeling was done using the Affymetrix® GeneChip® WT Terminal Labeling Kit Assay (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Normal primary human keratinocytes and fibroblasts were isolated from biopsies of adult non-keratinized oral mucosa (inside of the cheeks) obtained from volunteers after oral surgery. Normal primary human keratinocytes and fibroblasts were isolated from skin biopsies of adult volunteers. The epidermal sheet was separated from the dermis by incubating the samples for 2 h at 37°C in a dispase-containing solution (5,000 caseinolytic units; BD Biosciences, Franklin Lakes, NY, USA). To generate a single cell suspension, the epidermal part was minced and digested with 10 ml trypsin 0.25% (Lonza, Basel, Switzerland) for 20 min in a 5 % CO2 incubator at 37°C. Digestion was stopped with equal volume of Trypsin Neutralization Solution (TNS) (Lonza). Single cell suspension of NHOK was grown in serum free Keratinocyte Growth Medium (KGM;Lonza) at 37°C in a 5% CO2 incubator. Isolation of the fibroblasts was done by lysis of the dermis in collagenase 1A 100U/ml (Sigma, Taufkirchen, Germany) for 3 h at 37°C in a 5% CO2 incubator. Isolated fibroblasts were grown in DMEM medium high glucose and L-Glutamin (Invitrogen), containing 10 % fetal calf serum (FCS;Biochrom, Berlin, Germany).

extract_protocol: Total RNA was isolated using the Nucleo Spin II RNA Mini Kit, (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions, including on-column digestion of DNA with RNase-free DNase I.

treatment_protocol: In vitro models were irradiated either with an Er:YAG laser (FotonaSmooth™ XS, Fotona LLC, San Clemente, California, USA) using a non-ablative long-pulse mode (5 J/cm2, 200-350 msec, 25% density) or a fractional ablative CO2 laser with energy fluence (CPG scanner, 100 mJ, respectively, 100 Hz, scan pattern 1, scan size 3, density 1) (Lumenis Ultrapulse®, Lumenis Ltd., Yokneam, Israel)  or an ablative fractional erbium:YAG laser with the setting E10% (six pulses, energy per impulse 1.6 J, fluence per impulse 10 J/cm2, and pulse duration of 300 μs) (MCL31 Dermablate, Asclepion Laser Technologies GmbH, Jena, Germany) or a non-ablative fractional Erbium glass laser of the Palomar ICON 1540 Fractional Laser System® with 1540-nm XD Microlens or 1540-nm XF Microlens optic (Palomar Medical Technologies, Burlington, MA, USA). During laser irradiation, culture medium was removed.

value: skin

value: dermal fibroblasts and keratinocytes

value: Er:Glass (non-ablative) treated


title: sox13ko_week6_immature_gd_M3_16

source_name: library of 96 Sox13 KO immature gamma delta T cells

value: Thymus


title: 3D21_15 Kontrolle

value: Er:YAG (ablative) control


title: 3D15_13_Kontrolle

value: CO2 (ablative) control


title: Sample 1047_Single mESC cell

value: Differentiated mESC

value: day 0


title: 3D21_15 E10% Er:YAG

value: Er:YAG (ablative) treated


title: WT adult pancreas at D5, biological rep 1


title: 3D14_15_smooth Er:YAG

source_name: mucosal fibroblasts and keratinocytes

value: mucous membrane

value: mucosal fibroblasts and keratinocytes

value: Er:YAG (non-ablative) treated


title: Sample 1046_Single mESC cell

source_name: Single mESC cell


title: 3D14_15_Kontrolle

value: Er:YAG (non-ablative) control


title: sox13ko_week6_immature_gd_M3_15

value: Sox13 KO

value: immature gamma delta T cells


title: 3D22_14_Kontrolle

value: Er:Glass (non-ablative) control


title: Sample 1045_Single mESC cell


title: 3D15_13_Laser CO2

value: CO2 (ablative) treated


title: SUM159_DAC_72hr_1uM_rep3

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

description: SUM159 Breast cancer cells, 1uM Decitabine, 72 hours

hyb_protocol: Hybridized 16 hours at 45C; Washing FS450_0002

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Transcriptome Analysis Console software (ThermoFisher Scientific) was used to normalize the data and calculate fold changes in expression

label: Biotin

label_protocol: The Centre for Applied Genomics at The Hospital for Sick Children performed Biotin Allonamide Triphosphate Labelling

growth_protocol: SUM159 cells were cultured in F-12 Ham’s Nutrient Mix Medium supplemented with 5% fetal bovine serum (Invitrogen, Gibco), 1X Antibiotic-Antimycotic (Invitrogen, Gibco), 1µM 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid (HEPES; Invitrogen), 0.01µg/mL human insulin (Sigma), 0.05µg/mL hydrocortisone (Invitrogen). Cells were cultured in a humidified 37C incubator with 5% CO.

extract_protocol: Cells were collected in Trizol (Invitrogen) and RNA was purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions

treatment_protocol: SUM159 cells were treated with 1µM 5'-deoxy-azacytidine (Sigma) for 72 hours with media refreshed daily

value: SUM159 Breast cancer cells

value: DAC


title: sox13ko_week6_immature_gd_M3_14

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

institute: University Medical Center Freiburg

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

extract_protocol:
Thymocytes were isolated using mechanical dissociation of thymus. Since double negative (DN) thymocytes are rare, we performed the magnetic enrichment for DN thymocytes.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: male

value: 5-6 weeks


title: SUM159_NT_72hr_1uM_rep3

description: SUM159 Breast cancer cells, NT media, 72 hours

value: NT


title: MX4

value: Myocardium


title: Sample 1044_Single mESC cell

city: Stanford

first: Alina

address: 318 Campus drive

institute: Stanford University

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

value: Differentiated mESC


title: MCF10A-YAP A

city: amsterdam

first: LI

last: LI

address: hamontstraat, 378

data_processing:
Reads were adaptor-trimmed using cutadapt
Gene counts were quantified using Salmon with an index based on GENCODE human v31 annotation
Supplementary_files_format_and_content: Plain-text, tab-separated, Salmon quant.sf file with gene abundances

molecule: polyA RNA

source_name: MCF10A cells

growth_protocol: MCF10A cells were cultured in DMEM/F12 medium (Gibco), supplemented with 1% penicillin/streptomycin (Gibco), 5% horse serum, EGF 10 ng/ml(Sigma), insulin 10μg/ml (Sigma), hydrocortisone 0.5μg /ml (Sigma).

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen), following the  manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen)
Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the  manufacturer's instructions.

treatment_protocol: MCF10A cells were transduced with the indicated vectors. After the antibiotic selection was completed, cells were kept in cell culture until they reach 70-80% confluency. Total RNA was extracted using Trizol Reagent (Invitrogen) and following the manufacturers protocol.

tag: condition

value: MCF10A cells transduced with YAP-overexpression vector


title: MCF10A-YAP B


title: Sample 1043_Single mESC cell

last: Isakova

value: day 0


title: sox13ko_week6_immature_gd_M3_13

tag: strain background

value: Thymus


title: Sample 1042_Single mESC cell


title: sox13ko_week6_immature_gd_M3_12

tag: cell type


title: MCF10A-TRAM2 C

value: MCF10A cells transduced with TRAM2-overexpression vector


title: Sample 1041_Single mESC cell


title: MCF10A-TRAM2 B


title: sox13ko_week6_immature_gd_M3_10

tag: genotype/variation


title: sox13ko_week6_immature_gd_M3_11


title: SUM159_DAC_72hr_1uM_rep2

source_name: SUM159 Breast cancer cells, 1uM Decitabine, 72 hours


title: MCF10A-control D

value: MCF10A cells transduced with empty vector


title: sox13ko_week6_immature_gd_M2_8


title: Sample 1040_Single mESC cell


title: sox13ko_week6_immature_gd_M2_7


title: Sample 1038_Single mESC cell


title: Sample 1039_Single mESC cell


title: SUM159_DAC_72hr_1uM_rep1


title: MCF10A-control C


title: MCF10A-TRAM2 A


title: SUM159_NT_72hr_1uM_rep2

source_name: SUM159 Breast cancer cells, NT media, 72 hours


title: SUM159_NT_72hr_1uM_rep1


title: sox13ko_week6_immature_gd_M2_6


title: MCF10A-control B


title: Sample 1037_Single mESC cell


title: MCF10A-TRAM2 D


title: sox13ko_week6_immature_gd_M2_5


title: Sample 1036_Single mESC cell


title: sox13ko_week6_immature_gd_M2_16


title: sox13ko_week6_immature_gd_M2_15


title: MCF10A-control A


title: Sample 1035_Single mESC cell


title: shLAMB3_2

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic ( 0.36 ), then mapped to GR38p7 whole genome using Hisat2 ( 2.0.5 ) with parameters ( --rna-strandness RF --fr  )
FPKM value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count (  0.9.1 )
Genome_build: GR38p7

source_name: LoVo cells

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cells


title: shLAMB3_1


title: sox13ko_week6_immature_gd_M2_13

value: Sox13 KO


title: pLKO.1-2


title: MCF10A-YAP  TRAM2-KO2 B

description: 5781_8_MCF10A-YAP_TRAM2_KO2-B_GTCCGCA_S23

source_name: MCF10A-YAP  TRAM2-KO2

growth_protocol: MCF10A-YAP cells were cultured in DMEM/F12 medium (Gibco), supplemented with 1% penicillin/streptomycin (Gibco), 5% horse serum, EGF 10 ng/ml(Sigma), insulin 10μg/ml (Sigma), hydrocortisone 0.5μg /ml (Sigma).

treatment_protocol: MCF10A-YAP cells were transduced with the indicated vectors. After the antibiotic selection was completed, cells were kept in cell culture until they reach 70-80% confluency. Total RNA was extracted using Trizol Reagent (Invitrogen) and following the manufacturers protocol.

tag: cell line background

value: sgRNA targeting TRAM2


title: MCF10A-YAP  TRAM2-KO2 C

description: 5781_9_MCF10A-YAP_TRAM2_KO2-C_GTGAAAC_S24


title: pLKO.1-1


title: MCF10A-YAP  TRAM2-KO2 A

description: 5781_7_MCF10A-YAP_TRAM2_KO2-A_CCGTCCC_S22


title: sox13ko_week6_immature_gd_dup_6

value: immature gamma delta T cells


title: MCF10A-YAP  TRAM2-KO1 C

description: 5781_6_MCF10A-YAP_TRAM2_KO1-C_ATGTCAG_S21

source_name: MCF10A-YAP  TRAM2-KO1


title: Selective RPF [IP-3E-80S]

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

description:
ribosome profiling
ribosome footprints protected from ribosomes interacted with eIF3E isolated from  total lysate

data_processing:
Library strategy: Ribo-seq
Adapter sequences were trimmed from raw data using cutadapt 1.18 with parameters (-m 25 -M 35 --match-read-wildcards). Reads without adapter sequence were discarded.
Low-quality reads with Phred quality scores lower than 25 (>75% of bases) were removed using the fastx_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/).
Then sequence reads originating from rRNAs were identified and discarded by aligning the reads to human rRNA sequences downloaded from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) using Bowtie 1.1.2 with no mismatch allowed.
The remaining reads were mapped to the genome hg38 using STAR 2.5 with the following parameters: --runThreadN 8 --outFilterType Normal --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outSAMattributes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: The counts files were generated from alignment files by HTSeq-count in intersection-strict mode.

source_name: MCF10-A cell lines

growth_protocol: MCF-10a cells were cultured in DMEM/F12 medium with 0.5mg/mL hydrocortisone, 10µg/mL insulin, 20ng/mL EGF, 5% serum, 1X Pen/Strep, and incubate in 37℃ with 5% CO2.

extract_protocol:
The RNA were extracted with TRIzol reagent(thermo ambion, REF,15596018) and its standard protocol.
After clarification, 5 OD260 units of lysates were treated with 450 units of RNaseI (Ambion) for 45 min at RT. RPFs were isolated with Sephacryl S400 (GE, MicroSpin S-400 HR, 27514001). mRNAs and RPFs were isolated with TRIzol reagent(thermo ambion, REF,15596018). The rRNA removal for total mRNAs and RPFs was accomplished using Ribo-zero Gold (rRNA removal reagent(Human/Mouse/Rat)(illumina, REF, RZG1224) & Core kit(illumina, REF, MRZ11124C). For RPF, the extracted RNA was size-selected from 15% denaturing PAGE gels, cutting between 26-34 nt. An oligonucleotide adaptor was ligated to the 3’ end of footprints. Followed by reverse transcription, circularization and PCR amplification.

treatment_protocol: The cells were treated with 20nM si-control or si-eIF3e for 72h.

value: epithelial

value: Selective RPF


title: MCF10A-YAP  TRAM2-KO1 B

description: 5781_5_MCF10A-YAP_TRAM2_KO1-B_AGTTCCG_S20


title: sox13ko_week6_immature_gd_6


title: Sample 1032_Single mESC cell


title: MCF10A-YAP  TRAM2-KO1 A

description: 5781_4_MCF10A-YAP_TRAM2_KO1-A_AGTCAAC_S19


title: sox13ko_week6_immature_gd_14


title: Selective RPF

description:
Ribosome footprint
ribosome profiling

source_name: MCF10-A cell line

value: Selective RPF (eIF3B-bound ribosomes protected footprints)


title: MCF10A-YAP  control C

source_name: MCF10A-YAP  control

value: control non-targeting sgRNA


title: Total RPF

description:
Ribosome footprint
ribosome profiling

value: Total RPF (all the ribosome protected footprints from the 80S ribosomes isolated from total cell lysate)


title: Sample 1034_Single mESC cell


title: sox13ko_week6_immature_gd_13

value: male

value: 5-6 weeks


title: MCF10A-YAP  control B


title: Sample 1028_Single mESC cell

value: Differentiated mESC


title: si_ctrl_3_TL

description:
total RNA
mRNA_counts.xlsx

data_processing:
Adapter sequences were trimmed from raw data using cutadapt 1.18 with parameters (-m 25 -M 35 --match-read-wildcards). Reads without adapter sequence were discarded.
Low-quality reads with Phred quality scores lower than 25 (>75% of bases) were removed using the fastx_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/).
Then sequence reads originating from rRNAs were identified and discarded by aligning the reads to human rRNA sequences downloaded from GenBank (https://www.ncbi.nlm.nih.gov/genbank/) using Bowtie 1.1.2 with no mismatch allowed.
The remaining reads were mapped to the genome hg38 using STAR 2.5 with the following parameters: --runThreadN 8 --outFilterType Normal --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outSAMattributes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: The counts files were generated from alignment files by HTSeq-count in intersection-strict mode.

value: Control siRNA


title: Sample 1027_Single mESC cell

value: day 0


title: Sample 1033_Single mESC cell


title: sox13ko_week6_immature_gd_M2_14

value: Thymus


title: Sample 1031_Single mESC cell


title: week6_cd122pos_gd_11

description: library of 96 WT CD122 positive gamma delta T cells

value: wild type

value: female

value: CD122 positive gamma delta T cells


title: Sample 1030_Single mESC cell


title: Sample 1025_Single mESC cell


title: week6_cd122pos_gd_9

source_name: library of 96 WT CD122 positive gamma delta T cells


title: si_3e_3_TL

description:
total RNA
mRNA_counts.xlsx

value: eIF3e siRNA


title: si_3e_2_TL

description:
total RNA
mRNA_counts.xlsx


title: week6_immature_gamma1_delta63_gd_3

description: library of 96 WT immature variable chain gamma1 delta6.3 positive gamma delta T cells


title: Sample 1026_Single mESC cell


title: Sample 1029_Single mESC cell


title: si_3e_1_TL

description:
total RNA
mRNA_counts.xlsx


title: Sample 1022_Single mESC cell


title: Sample 1021_Single mESC cell


title: Sample 1020_Single mESC cell


title: week6_immature_gamma1_gd_2

description: library of 96 WT immature variable chain gamma1 positive gamma delta T cells


title: Sample 1023_Single mESC cell


title: week6_immature_gamma1_gd_3

source_name: library of 96 WT immature variable chain gamma1 positive gamma delta T cells


title: si_ctrl_1_80S

description:
Ribosome footprint
ribosome profiling
RPF_counts.xlsx


title: week6_cd122pos_gd_10


title: week6_immature_gamma1_gd_1

value: immature variable chain gamma1 positive gamma delta T cells


title: Sample 1019_Single mESC cell


title: MCF10A-YAP  control A


title: week6_immature_gamma1_gd_4


title: si_ctrl_1_TL

description:
total RNA
mRNA_counts.xlsx


title: si_ctrl_2_TL

description:
total RNA
mRNA_counts.xlsx


title: Sample 1024_Single mESC cell


title: week6_cd122pos_gd_12


title: si_3e_3_80S


title: week6_immature_gamma2_gd_1

description: library of 96 WT immature variable chain gamma4 positive gamma delta T cells


title: Sample 1018_Single mESC cell


title: si_3e_2_80S


title: week6_immature_gamma2_gd_2_1

source_name: library of 96 WT immature variable chain gamma4 positive gamma delta T cells


title: week6_immature_gamma1_delta63_gd_4

source_name: library of 96 WT immature variable chain gamma1 delta6.3 positive gamma delta T cells


title: week6_immature_gamma2_gd_2_2

value: immature variable chain gamma4 positive gamma delta T cells


title: Sample 1017_Single mESC cell


title: si_ctrl_3_80S

value: epithelial


title: Sample 1016_Single mESC cell


title: Sample 1015_Single mESC cell


title: si_ctrl_2_80S


title: KYSE180shIRF1-AS

first: Jianbing

last: Huang

state: State...

address: No. 17 Pan-jia-yuan South Lane, Chaoyang District, 100021 Beijing, China

institute: Cancer Institute and Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences

data_processing:
TopHat was used to map reads to the reference genome
and HTSeq was used to count the read numbers mapped of each gene
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: ESCC cell line

growth_protocol: Human ESCC cell lines KYSE30, KYSE180 and KYSE450 were cultured at 37 ℃ in an atmosphere of 5% CO2 in RMPI 1640 (Hyclone) supplemented with 10% FBS (Gibco), penicillin, and streptomycin (Thermo Fisher).

extract_protocol:
Total RNA from each sample was extracted with Trizol (Thermo Fisher), quality control for total RNA was assessed using NanoPhotometer® spectrophotometer, Qubit® 2.0 Fluorometer, and Agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the treatment with IFN-β, ESCC cell lines were treated with IFN-β at 1000 IU/ml or PBS for 72 h. For knockdown of IRF1-AS, the recombined plasmid and the packing plasmid mixture (Invitrogen) were co-transfected into HEK 293T cells using Lipofectamine 3000 (Invitrogen). The supernatant containing lentivirus was collected and used to infect ESCC cell lines; For overexpression of IRF1-AS, plasmid vectors PCDNA3.1 were transfected into ESCC cancer cells using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.

value: ESCC cell line

value: IRF1-AS knockdown

tag: passages


title: Sample 1013_Single mESC cell


title: week6_immature_gamma2_gd_2_4

tag: age/developemental stage


title: week6_immature_gamma2_gd_2_3

tag: tissue


title: week6_immature_gamma2_gd_3


title: KYSE30shIRF1-AS

tag: cell line


title: KYSE180shControl

value: Vector control


title: KYSE30shControl


title: week6_immature_gamma2_gd_2


title: KYSE450beta

value: IFN-β treated


title: Sample 1014_Single mESC cell

tag: day of differentiation


title: Sample 1011_Single mESC cell


title: week6_immature_gamma2_gd_4

tag: Sex


title: KYSE180beta


title: KYSE450

value: Untreated control


title: Sample 1012_Single mESC cell


title: week6_mature_gamma1_delta63_gd_7

description: library of 96 WT mature variable chain gamma1 delta6.3 positive gamma delta T cells

value: 5-6 weeks


title: Sample 1009_Single mESC cell

value: Differentiated mESC


title: week6_mature_gamma1_delta63_gd_8

source_name: library of 96 WT mature variable chain gamma1 delta6.3 positive gamma delta T cells


title: si_3e_1_80S


title: week6_mature_gamma1_gd_5

description: library of 96 WT mature variable chain gamma1 positive gamma delta T cells


title: KYSE180


title: week6_mature_gamma1_gd_6

source_name: library of 96 WT mature variable chain gamma1 positive gamma delta T cells


title: Sample 1007_Single mESC cell

source_name: Single mESC cell


title: Sample 1010_Single mESC cell


title: Sample 1006_Single mESC cell


title: KYSE30beta


title: KYSE30


title: week6_mature_gamma2_gd_10

description: library of 96 WT mature variable chain gamma4 positive gamma delta T cells


title: Sample 1004_Single mESC cell


title: week6_mature_gamma2_gd_9

source_name: library of 96 WT mature variable chain gamma4 positive gamma delta T cells


title: Sample 1005_Single mESC cell


title: Sample 1003_Single mESC cell


title: Sample 1008_Single mESC cell


title: Sample 1001_Single mESC cell


title: AVAglio_GSM2225633

city: South San Francisco

first: Radia

last: Johnson

address: 1 DNA Way

country: United Kingdom

institute: Genentech

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

data_processing:
Blanks were not available for the AVAglio dataset, as a result background correction was implemented using global negative control probes. Sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) using the NanoStringQCPro package on Bioconductor.

label: Nucleotide/fluorophore barcode

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

tag: age

value: Female

tag: corticosteroids

value: Off

tag: surgical status

value: Partial resection

value: Bevacizumab

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade V

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing


title: AVAglio_GSM2225632

scan_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

tag: treatment

value: Placebo

value: Grade IV


title: Sample 998_Single mESC cell

value: day 0


title: AVAglio_GSM2225628

label_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

value: Proliferative

value: Classical

value: Methylated


title: AVAglio_GSM2225631

value: Male

value: Mesenchymal

value: Non-methylated


title: AVAglio_GSM2225630

value: On


title: Sample 999_Single mESC cell

value: Differentiated mESC


title: Sample 997_Single mESC cell


title: Sample 996_Single mESC cell


title: AVAglio_GSM2225625

value: Off


title: AVAglio_GSM2225627

value: Total resection

value: Grade III


title: Sample 995_Single mESC cell


title: AVAglio_GSM2225623


title: AVAglio_GSM2225624

value: Female

value: Partial resection

value: Bevacizumab


title: AVAglio_GSM2225622

value: Placebo


title: Sample 994_Single mESC cell


title: AVAglio_GSM2225626


title: Sample 1002_Single mESC cell


title: Sample 993_Single mESC cell


title: Sample 992_Single mESC cell


title: Sample 1000_Single mESC cell


title: AVAglio_GSM2225621

value: Proneural

value: Grade IV

value: Missing


title: Sample 991_Single mESC cell

value: day 0


title: Sample 990_Single mESC cell


title: Sample 989_Single mESC cell


title: Sample 987_Single mESC cell


title: AVAglio_GSM2225616

value: Unclassified


title: AVAglio_GSM2225618

value: Male


title: AVAglio_GSM2225619

value: Mesenchymal


title: AVAglio_GSM2225620

value: Classical

value: Methylated


title: AVAglio_GSM2225615

value: On

value: Grade V

value: Non-methylated


title: Sample 986_Single mESC cell

value: Differentiated mESC


title: AVAglio_GSM2225614


title: AVAglio_GSM2225613

value: Off


title: AVAglio_GSM2225612

value: Female

value: Partial resection


title: Sample 988_Single mESC cell


title: Sample 985_Single mESC cell


title: AVAglio_GSM2225610

value: Total resection

value: Bevacizumab


title: AVAglio_GSM2225611

value: Grade IV


title: Sample 983_Single mESC cell


title: AVAglio_GSM2225609

value: Placebo

value: Proneural


title: Sample 982_Single mESC cell

value: day 0


title: AVAglio_GSM2225608

value: Male


title: Sample 984_Single mESC cell


title: D80CP4

type: genomic

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

hyb_protocol: DNA methylation profiling was performed at the GenomeScan (GenomeScan B.V., Leiden, The Netherlands). Genomic DNA was bisulfite-converted using the EZ DNA Methylation Gold Kit (Zymo Research) and used for microarray-based DNA methylation analysis, on the HumanMethylation850 BeadChip (Illumina, Inc.), according to the manufacturer’s instructions.

scan_protocol: Beadchip images were scanned on the iScan system

data_processing:
Illumina Infinium MethylationEPIC fluorescent data (>850,000 CpG sites) were imported and transformed to methylated (M) and unmethylated (U) signal by minfi package. CpG probes were quality checked and filtered using the following criteria: (i) probes that failed in at least 5% samples were removed, (ii) probes with bead count < 3 in at least 5% of samples were removed, (iii) probes targeting SNP sites were removed, and (iv) probes that align to multiple locations were removed as described in Nordlund et al. (5). We further removed the probes for the sex chromosomes. One sample (moDC differentiation sample from donor 4 on day 2) did not pass the quality check and was removed from the subsequent analysis (therefore not included in the records). Approximately 558,000 CpG sites remained after the quality checks. The intra-array data normalization for the bias introduced by two types of Infinium probes was performed by Beta-mixture quantile normalization (BMIQ) method in ChAMP (version 2.6.0) package (6). DNA methylation level of each CpG was depicted by the ratio of methylated (M) signal relative to the sum of both methylated and unmethylated (U) signal β= M/(M+U +100).
The signal_intensities.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: Day8_CXCL4-moDC_24h stimulation_donor4

label_protocol: Standard Illumina Protocol

growth_protocol: PBMCs were isolated from heparinized venous blood using Ficoll PaqueTM Plus (GE Healthcare) density gradient. Monocytes were purified with anti-CD14 magnetic beads-based positive separation using an autoMACS Pro Separator assisted cell sorting (Miltenyi Biotec), according to the manufacture’s protocol. Monocyte purity was above 95% for all the samples (data not shown). For the differentiation of monocyte-derived dendritic cells (moDCs), monocytes were cultured at a density of 1x106 cells/ml in culture medium: RPMI 1640 with GlutaMAX (Life Technologies) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS; Biowest) and 1% (v/v) antibiotics (penicillin and streptomycin) (Life Technologies). In order to generate moDCs, GM-CSF (800 U/ml; R&D) and IL-4 (500 U/ml; R&D) were added. For the experiments where we investigated the effects of CXCL4, we added 10 µg/ml of recombinant human CXCL4 (PeproTech) on day 0 and day 3. Medium and cytokines were refreshed on day 3. Differentiated moDCs were obtained after 6 days from monocytes cultured at 37oC in the presence of 5% CO2. After differentiation, cells were washed, plated at a density of 0.5x106 cells/ml and left overnight (O/N) in new culture medium. Cells were stimulated with 25 µg/ml of polyinosinic-polycytidylic acid (polyI:C; InvivoGen) for 4 hours or 24 hours, or kept unstimulated, as shown in the Fig. 1A.

extract_protocol: Cells were lysed in RLTplus buffer (Qiagen) containing 1% (v/v) beta-mercaptoethanol (Sigma). DNA were extracted using the Allprep Universal Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: For the experiments where we investigated the effects of CXCL4, we added 10 µg/ml of recombinant human CXCL4 (PeproTech) on day 0 and day 3. Medium and cytokines were refreshed on day 3.  After differentiation, cells were washed, plated at a density of 0.5 million cells/ml and left overnight (O/N) in new culture medium. Cells were stimulated with 25 µg/ml of polyinosinic-polycytidylic acid (polyI:C; InvivoGen) for 4 hours or 24 hours, or kept unstimulated.

tag: donor id

value: M

tag: cell type

value: monocytes

tag: cell subtype

value: Day8_CXCL4-moDC_24h stimulation


title: Sample 981_Single mESC cell

tag: cell line

tag: day of differentiation


title: AVAglio_GSM2225607

tag: age

tag: Sex

value: On

value: Proliferative

value: Methylated


title: D80MP5

source_name: Day8_moDC_24h stimulation_donor5

value: Day8_moDC_24h stimulation


title: D80MP4

source_name: Day8_moDC_24h stimulation_donor4


title: D80CP3

source_name: Day8_CXCL4-moDC_24h stimulation_donor3

value: F


title: D80MP1

source_name: Day8_moDC_24h stimulation_donor1


title: D80CP5

source_name: Day8_CXCL4-moDC_24h stimulation_donor5


title: Sample 979_Single mESC cell

value: Differentiated mESC


title: AVAglio_GSM2225606

value: Female

tag: corticosteroids

value: Off

tag: surgical status

value: Unclassified

value: Mesenchymal

value: Non-methylated


title: D80CP1

source_name: Day8_CXCL4-moDC_24h stimulation_donor1


title: D80MP2

source_name: Day8_moDC_24h stimulation_donor2


title: D80MP3

source_name: Day8_moDC_24h stimulation_donor3


title: AVAglio_GSM2225604

value: Partial resection

value: Bevacizumab

tag: phillips subtype

value: Proneural

tag: tcga subtype

value: Grade V


title: Sample 978_Single mESC cell

value: day 0


title: D74CP4

source_name: Day7_CXCL4-moDC_4h stimulation_donor4

value: M

value: monocytes

value: Day7_CXCL4-moDC_4h stimulation


title: D80CP2

source_name: Day8_CXCL4-moDC_24h stimulation_donor2

value: Day8_CXCL4-moDC_24h stimulation


title: AVAglio_GSM2225603

value: Male

value: On

value: Placebo

value: Proliferative

tag: kps

tag: mmse

value: Grade IV


title: D74CP2

source_name: Day7_CXCL4-moDC_4h stimulation_donor2

value: F


title: D74CP5

source_name: Day7_CXCL4-moDC_4h stimulation_donor5


title: D74MP2

source_name: Day7_moDC_4h stimulation_donor2

value: Day7_moDC_4h stimulation


title: D74CP1

source_name: Day7_CXCL4-moDC_4h stimulation_donor1


title: Sample 976_Single mESC cell

source_name: Single mESC cell

value: Differentiated mESC


title: D74MP3

source_name: Day7_moDC_4h stimulation_donor3


title: Sample 975_Single mESC cell


title: AVAglio_GSM2225601

value: Off

value: Total resection

value: Unclassified

value: Classical

tag: rpa

value: Grade III

tag: os (diagnosis)

value: Non-methylated


title: AVAglio_GSM2225605

value: Partial resection

value: Bevacizumab

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: Sample 974_Single mESC cell

value: day 0


title: Sample 980_Single mESC cell


title: AVAglio_GSM2225602

value: Male

tag: treatment

value: Proneural

value: Mesenchymal


title: D74MP4

source_name: Day7_moDC_4h stimulation_donor4

tag: donor id

value: M

tag: cell type

value: monocytes


title: D74MP5

source_name: Day7_moDC_4h stimulation_donor5

tag: cell subtype


title: AVAglio_GSM2225600

value: Biopsy

value: Placebo


title: Sample 973_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation


title: CRPC_15-023AA1_BONE [re-analysis]

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
15-023AA1_BONE
CRPC bone metastasis
15-023AA1_BONE

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.X
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC bone metastasis

extract_protocol:
Total RNA was isolated from 138 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 72 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50-71 bp paired end reads.

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: bone

tag: patient

tag: molecular phenotype


title: D74CP3

source_name: Day7_CXCL4-moDC_4h stimulation_donor3

tag: age

tag: Sex

value: F

value: Day7_CXCL4-moDC_4h stimulation


title: Sample 977_Single mESC cell


title: D70M_5


title: Sample 972_Single mESC cell


title: D70M_4


title: AVAglio_GSM2225599

tag: corticosteroids

value: Off

tag: surgical status

tag: phillips subtype

tag: tcga subtype

value: Unclassified

tag: kps

tag: mmse

value: Grade IV

value: Non-methylated


title: AVAglio_GSM2225598

value: Female

value: Total resection

tag: treatment

value: Bevacizumab

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing


title: D74MP1

source_name: Day7_moDC_4h stimulation_donor1

tag: donor id

tag: cell type

value: monocytes

tag: cell subtype

value: Day7_moDC_4h stimulation


title: AVAglio_GSM2225597

value: On

value: Partial resection

value: Mesenchymal

value: Classical

value: Methylated


title: Sample 971_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 970_Single mESC cell


title: Sample 968_Single mESC cell


title: AVAglio_GSM2225595

tag: age

tag: Sex

value: Male

value: Off

value: Placebo

value: Proneural

value: Grade V


title: D70M_1

value: F


title: AVAglio_GSM2225596

value: Female

tag: corticosteroids

tag: surgical status

value: Total resection

value: Bevacizumab

value: Grade IV


title: AVAglio_GSM2225593

tag: phillips subtype

tag: tcga subtype

value: Non-methylated


title: Sample 969_Single mESC cell


title: D70C_5

value: M

value: monocytes


title: Sample 967_Single mESC cell


title: AVAglio_GSM2225594

tag: kps

tag: mmse


title: Sample 965_Single mESC cell


title: AVAglio_GSM2225591

tag: treatment

value: Mesenchymal

tag: rpa

value: Missing


title: Sample 964_Single mESC cell

value: Differentiated mESC


title: AVAglio_GSM2225592

value: On

value: Biopsy

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Sample 966_Single mESC cell

value: day 0


title: AVAglio_GSM2225590

value: Male

value: Off

value: Placebo

value: Unclassified

tag: mgmt status


title: D70M_2

tag: donor id

value: F

tag: cell type


title: Sample 963_Single mESC cell

tag: cell line


title: D60M_5

tag: cell subtype

value: Day6_differentiation without CXCL4


title: AVAglio_GSM2225589

tag: age

value: Female

value: Total resection

value: Bevacizumab

value: Grade V


title: D70M_3

tag: Sex

value: monocytes


title: Sample 962_Single mESC cell

tag: day of differentiation


title: AVAglio_GSM2225588

tag: corticosteroids

tag: surgical status

value: Mesenchymal

value: Grade III


title: CRPC_14-053FF3_BONE

description:
14-053FF3_BONE
CRPC bone metastasis
14-053FF3_BONE

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: bone

tag: patient

tag: molecular phenotype


title: D70C_3


title: D70C_2


title: D70C_1


title: Sample 960_Single mESC cell

value: Differentiated mESC

value: day 0


title: D70C_4

value: M


title: Sample 961_Single mESC cell


title: CRPC_14-053AA3_BONE [re-analysis]

description:
14-053AA3_BONE
CRPC bone metastasis
14-053AA3_BONE


title: AVAglio_GSM2225587

value: On

value: Partial resection

tag: treatment

value: Placebo

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

value: Grade IV

value: Non-methylated


title: AVAglio_GSM2225584

value: Male

value: Off

value: Bevacizumab

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Missing


title: AVAglio_GSM2225586

tag: age

tag: Sex

value: Proneural


title: Sample 957_Single mESC cell

tag: cell line

tag: day of differentiation


title: Sample 959_Single mESC cell


title: Sample 958_Single mESC cell


title: D60M_4

tag: donor id

tag: cell type

value: monocytes

tag: cell subtype

value: Day6_differentiation without CXCL4


title: Sample 956_Single mESC cell

value: Differentiated mESC


title: D60M_1

value: F


title: AVAglio_GSM2225582

tag: corticosteroids

tag: surgical status

value: Grade V

value: Methylated


title: Sample 955_Single mESC cell

value: day 0


title: AVAglio_GSM2225583

value: Total resection

tag: treatment

value: Placebo

tag: phillips subtype


title: AVAglio_GSM2225581

value: Mesenchymal

tag: tcga subtype

tag: kps

value: Grade III


title: D60C_2

source_name: Day6_differentiation with CXCL4_donor6

value: Day6_differentiation with CXCL4


title: AVAglio_GSM2225580

value: Female

value: Partial resection

tag: mmse

tag: rpa

value: Non-methylated


title: Sample 954_Single mESC cell


title: D60M_3


title: D60C_5

source_name: Day6_differentiation with CXCL4_donor5

value: M