title: shixiehou_naive

city: Kunming

first: Jian

address: Zhiyuan Road,Chenggong

institute: Institute of Primate Translational Medicine, KUST

description: naïve cells

data_processing:
Sequencing data were first processed using the 10X Genomics Cell Ranger pipeline and sequence was aligned using STAR against the Macaca fascicularis reference genome(ensemble release-91).
Subsequently, unique molecular identifiers (UMI) matrices from each sample were merged in R and imported to Seurat.
For pseudotime analysis, the UMI matrix calculated in Seurat was passed into Monocle2,and highly variable genes identified by Seurat were used as ordering genes for trajectory calculation.
After trajectory reconstruction, we used BEAM to identify genes with branch-dependent expression and used plot_multiple_branches_heatmap to visualize the genes along branches.
Genome_build: rheMac8
Supplementary_files_format_and_content: H5, MTX, TSV files were generated using the 10X Genomics Cell Ranger pipeline.

organism: Macaca fascicularis

source_name: embryonic stem cell

growth_protocol: Male (XX) and female (XY) monkey embryonic stem cells (ESCs) were cultured on mitomycin C-inactivated mouse embryonic fibroblasts (MEF). Briefly, ESCs colonies were cultured in Nutrient Mixture F-12(DMEM/F12,Invitrogen) medium containing 20% KOSR (Invitrogen) supplemented with 4 ng/mL bFGF (Chemicon), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen), 1% penicillin-streptomycin-L-glutamate (Invitrogen). For naive state conversion, ESC colonies were dissociated by collagenase IV and reseeded on MEF with naïve conversion medium. The naïve conversion medium comprised ESCs culture medium supplemented with 10 ng/mL human LIF (PeproTech), CHIR99021(3μM) (Tocris), PD0325901 (0.5μM) (R&D Systems), SP600125 (10μM) (Selleck) and SB203580 (10μM) (Selleck).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen).
The scRNA-seq libraries were generated using the Chromium Single Cell 3′Reagent Kit (10X Genomics) . Briefly, a single-cell suspension (500 cells /μL in PBS) was mixed with RT-PCR master mix and loaded together with Single Cell 3′Gel Beads and Partitioning Oil into a Single Cell 3′Chip (10X Genomics) according to the manufacturer’s instructions. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were preamplified and pooled followed by library construction. All libraries were quantified on a 2100 Bioanalyzer (Agilent) and realtime quantitative PCR, and then subjected to 150 bp paired-end sequencing on an Illumina Xten platform (sequenced by Novogene).

treatment_protocol: Monkey PGCLCs differentiation; Immunofluorescence.

value: embryonic stem cell

tag: gender

value: female

value: naive cells


title: shFIP1L1-1_rep2_RNA-seq

status: Public on Dec 31 2021

type: SRA

city: La Jolla

first: Dong-Er

last: Zhang

state: CA

address: 3855 Health Sciences Drive #0815

country: USA

institute: UC San Diego Moores Cancer Center

description:
readcount.txt
FIP1_2

library_source: transcriptomic

data_processing:
RNA-sequencing
First, raw RNA-sequencing reads without adaptors or those containing greater than 10% undetermined bases were removed.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using the DESeq2 software.
3'READS
The libraries were sequenced from 3' to 5' end with respect to the RNA sequence.
Nucleotides corresponding to the 5′ adapter was first removed from raw 3′READS+ reads using cutadapt (version 2.6).
The 5′ random nucleotides and 5′T's in the reads were trimmed before the reads were mapped to the human (hg19) genome using STAR (version 2.7.3a) with the following parameters: "--alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMmultNmax 1 --alignIntronMin 20 --alignIntronMax 1000000". Only reads with a mapping quality score (MAPQ) ≥10 were used for further analysis.
The trimmed 5′T's of each read were then compared to the genomic region downstream from the last aligned position of the read to identify 5′T's that cannot be aligned to the genome. Reads with ≥2 unaligned 5′T's after this process were called polyA site supporting (PASS) reads. Cleavage sites within 24 nt of each other (due to microheterogeneity) were clustered into pAs as previously described (Hoque et al. Nature Methods, 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Both files contain read counts in each analyzed sample. The text file, 'readcount.txt', contains reads per gene as is conventional for RNA-sequencing analysis. The csv file, 'clusters.using.all.reads.csv', contains reads per poly(A) peak for 3'READS analysis.

molecule: total RNA

organism: Homo sapiens

source_name: Kasumi-1 AML Cell Line

growth_protocol: Kasumi-1 cells were maintained in RPMI supplemented with 10% FBS.

extract_protocol:
RNA was extracted using Trizol reagent per the manufacturer's instructions.
RNA-seq: For RNA-sequencing library preparation, the NEBNext® UltraTM RNA Library Prep Kit was used following the manufacturer's instructions.
3'READS: The protocol for 3'READS library preparation is described in detail in (Hoque et al. Nature Methods, 2016).

treatment_protocol: Kasumi-1 cells were transduced with lentivirus containing control shRNAs or shRNAs targeting FIP1L1. Transduced cells were selected with puromycin.

tag: cell line

value: Kasumi-1 AML Cell Line

tag: cell culture conditions

value: RPMI + 10percent FBS

tag: lentiviral shrna for transduction

value: shRNA targeting FIP1L1 #1


title: shFIP1L1-1_rep3_RNA-seq

description:
readcount.txt
FIP1_3


title: A1_3_S6

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

country: Germany

institute: DKFZ

data_processing:
Raw reads data are mapped to mm9 transcriptome with Bowtie1.0.0. Default paramters are used
TPM were generated by RSEM (1.2.15) with default parameters
Cells were filtered basing on the number of genes detected, cells have more than 4500 genes are discarded for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: geneTPM.txt includes TPM values for each Sample

organism: Mus musculus

source_name: neural stem cells

extract_protocol:
Briefly, single cells were lysed in 5 μl lysis buffer and 1 μl of 3’ SMART CDS primer (24 μM) was added and incubated at 72°C for 3 min.
SMARTer Ultra Low Input RNA- High Volume kit was used to prepare amplified cDNA. We added 50 μl of nuclease-free H2O to the amplified cDNA to make a total volume of 60 μl. The cDNA was sheared in a microtube (6x 16mm) with 10% duty cycle, 5% intensity and 200 burst cycle for 5 min in the frequency sweeping mode with Covaris S2 machine. We got the average of 180 bp cDNA fragments after sonication. The illumina sequencing libraries were prepared using NEBNext Ultra DNA library prep kit.

tag: tissue

value: subventricular zone

tag: age

tag: sample type

value: Single cell

tag: cell type

value: neural stem cells (NSCs)

tag: Stage

value: qNSC


title: iBAT SVF_12Weeks_1

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

description: Rabbit.SVF.GeneExpression.FPKM.xls

data_processing:
Sequencing Reads Filtering using SOAPnuke: v1.5.2
Genome Mapping using HISAT2: v2.0.4
Mapping clean reads to reference using Bowtie2: v2.2.5
Gene expression cluster analysis using Cluster v3.0
DEG detection using DEseq2
Genome build: OryCun2.0
FPKM

organism: Oryctolagus cuniculus

source_name: interscapular brown adipose tissue

extract_protocol:
RNA extracted from total or the SVF fraction of BAT
RNA-Seq Quantification Library (Normal Library)

value: interscapular brown adipose tissue

tag: strain

value: New Zealand White

value: 12 weeks

tag: fraction

value: stromal vascular fraction


title: A1_3_S5


title: shFIP1L1-1_rep1_RNA-seq

description:
readcount.txt
FIP1_1


title: shFIP1L1-2_rep1_RNA-seq

description:
readcount.txt
FIP2_1

value: shRNA targeting FIP1L1 #2


title: A1_3_S3

value: aNSC


title: shixiehou_D2EB

country: China

description: cells within EBs

source_name: embryoid body

value: embryoid body

value: day 2 Ebs


title: Control_10dpf_rep3

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

description: Control

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with 2PASS STAR v020201 against  GRCz11 zebrafish reference genome and Ensembl v95 exon-exon junctions
Quantification and normalization with Desq2 v1.22.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Trimed reads in fastq
Supplementary_files_format_and_content: Read count files from RNAstar

organism: Danio rerio

source_name: entire larvae

growth_protocol: Fertilized 3 hpf eggs were collected, counted  and kept in square petri dish with embryo medium (60 mg/L of Instant Ocean© sea salt diluted in ultrapure water) in a thermo-regulated incubator inside a glove box (HTO-contaminated) and in a thermo-regulated  incubator outside the glove box in the same room (control) at 28°C

extract_protocol:
Total RNA extraction with TRIzol/chloroform (Life Technologies), no-DNase I treatment.
Following TruSeq Stranded mRNA Library Prep Kit (Illumina) instructions
Paired end

treatment_protocol: Contamination at 0,4 mGy/h of tritiated water and non-contaminated controls

value: entire larvae

tag: treatment

value: Control

value: AB


title: shControl_rep4_RNA-seq

description:
readcount.txt
CON_4

value: Kasumi-1 AML Cell Line

value: RPMI + 10percent FBS

value: shControl


title: A1_2_S15

value: subventricular zone

value: Single cell


title: shControl_rep2_RNA-seq

description:
readcount.txt
CON_2


title: A1_2_S16

value: neural stem cells (NSCs)

value: qNSC


title: A1_3_S7


title: iBAT SVF_6Weeks_2

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: interscapular brown adipose tissue

value: New Zealand White

value: 6 weeks


title: Control_10dpf_rep2

description: Control


title: iBAT SVF_6Weeks_3

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: stromal vascular fraction


title: shControl_rep3_RNA-seq

description:
readcount.txt
CON_3


title: iBAT SVF_3Weeks_3

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: 3 weeks


title: shixiehou_D4EB

description: cells within EBs

value: embryoid body

value: female

value: day 4 Ebs


title: iBAT SVF_6Weeks_1

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: A1_2_S12


title: shControl_rep1_RNA-seq

description:
readcount.txt
CON_1


title: A1_2_S8


title: Control_7dpf_rep3

description: Control

value: entire larvae

value: Control


title: iBAT SVF_3Weeks_1

description: Rabbit.SVF.GeneExpression.FPKM.xls


title: A1_2_S6

value: aNSC


title: Control_7dpf_rep2

description: Control

value: AB


title: Liang2

city: Beijing

first: Xiangyang

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Life Sciences

institute: Peking University

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.At the same time, Q20, Q30 and GC content the clean data were calculated.
Clean reads were mapped to GRCh38/hg38 of human genome using Hisat v.2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: text files include fpkm values for each Sample

source_name: Primary dermal fibroblasts

growth_protocol: Cells were cultured at 37 ℃ in 5% CO2 in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 100 U ml-1 penicillin, 100 μg ml-1 streptomycin, and 20% fetal bovine serum (FBS, Gibco).

extract_protocol:
RNA was isolated from cells by TRIzol Reagent (Invitrogen) as recommended by the manual.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: donor age

value: 13 years old

tag: donor gender

value: Male

tag: mutation

tag: disease state

value: Hutchinson-Gilford progeria syndrome


title: Liang3


title: A1_2_S5

value: subventricular zone

value: Single cell

value: neural stem cells (NSCs)


title: iBAT SVF_Day1_2

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: interscapular brown adipose tissue

value: New Zealand White

value: 1 day


title: Control_7dpf_rep1

description: Control


title: iBAT SVF_Day1_1

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: stromal vascular fraction


title: 0,4mGy/h_10dpf_rep3

description: Contaminated with tritium

value: 0,4 mGy/h


title: Control_10dpf_rep1

description: Control


title: Liu3

value: 3 months old

value: Female


title: 0,4mGy/h_10dpf_rep2

description: Contaminated with tritium

value: entire larvae


title: Total iBAT_12Weeks_3

description: Rabbit.Total.iBAT.GeneExpression.FPKM.xls

value: 12 weeks

value: total


title: A1_2_S4

value: qNSC


title: 0,4mGy/h_7dpf_rep3

description: Contaminated with tritium

value: AB


title: iBAT SVF_3Weeks_2

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: 3 weeks


title: A1_2_S1


title: HDF3

value: 4 months old

value: Male

value: No

value: normal


title: Total iBAT_12Weeks_2

value: interscapular brown adipose tissue


title: A1_1_S26

value: subventricular zone

value: Single cell

value: neural stem cells (NSCs)

value: aNSC


title: iBAT SVF_Day1_3

description: Rabbit.SVF.GeneExpression.FPKM.xls

value: New Zealand White

value: 1 day

value: stromal vascular fraction


title: HDF2


title: A1_2_S3


title: 0,4mGy/h_7dpf_rep2

description: Contaminated with tritium

value: entire larvae

value: 0,4 mGy/h


title: 0,4mGy/h_10dpf_rep1

description: Contaminated with tritium


title: Total iBAT_6Weeks_3

value: 6 weeks

value: total


title: Liang1

value: 13 years old

value: Hutchinson-Gilford progeria syndrome


title: 0,4mGy/h_7dpf_rep1

description: Contaminated with tritium

value: AB


title: HDF1

value: 4 months old

value: Male

value: No


title: A1_1_S25

value: subventricular zone

value: qNSC


title: Liu2

value: 3 months old

value: Female


title: A1_2_S2

value: Single cell

value: neural stem cells (NSCs)

value: aNSC


title: Total iBAT_6Weeks_2

value: interscapular brown adipose tissue

value: New Zealand White


title: shG8d_2 [RNA-seq]

city: Shanghai

first: Ping

last: He

address: No. 280, South Chongqing 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase per Million per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo

source_name: MCF10A_SNHG8d knockdown

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

tag: genotype/variaton

value: SNHG8d knockdown


title: shG8d_1 [RNA-seq]


title: Liu1


title: Total iBAT_3Weeks_3

value: 3 weeks

value: total


title: Total iBAT_6Weeks_1

value: 6 weeks


title: shNC_2 [RNA-seq]

source_name: MCF10A_Control; shNC

value: Control; shNC


title: Total iBAT_12Weeks_1

value: 12 weeks


title: M2φ cocultured with control siRNA-transfected and sorafenib-treated Mahlavu cells

city: Taipei City

first: Pei-Yu

last: Wu

address: 128 Academia Road, Section 2, Nankang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

description:
siC-M2φ
processed data files:
normalized_reads.xlsx
clustvisProcessedData.csv

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
Sequencing results were analyzed by QIAGEN's cloud-based QIAseq Targeted RNA Analysis Portal. Reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. After removing 12bp UMI sequence of each read, then mapped to GRCh38 reference genome using the STAR RNA read mapper.
Reads were counted by UMI units and normalized to 'target gene UMIs per average reference genes UMIs' [geNorm (Pre-Defined Reference Genes Only, PubMed ID: 12184808)]
For comparison of samples, normalized reads of genes were analyzed using the ClustVis web tool (PubMed ID: 25969447) by applying vector scaling in centered raws.
Genome_build: GRCh38
Supplementary_files_format_and_content: The xlsx file (normalized_reads.xlsx) includes raw reads, normalization values of all genes read from the 6 samples. The csv file (clustvisProcessedData.csv) summerizes relative expression of genes generated by the ClustVis web tool.

source_name: Monocyte-derived M2 Macrophages obtained from PromoCell company  (C-12915)

growth_protocol: To obtained primary M0 macrophages, whole bloods from Taipei Blood Center of Taiwan Blood Service Foundation were layered by Ficoll–Paque, and the resulted PBMCs were subsequently treated with 150 nM PMA for 24 h, followed by incubatation in the serum-free RPMI medium for additional 72 h. Primary M1 and M2 macrophages were obtained from PromoCell company. All differentiated macrophages were maintained in Macrophage Base Medium DXF (PromoCell) in a humidified atmosphere at 37 °C with 5% CO2.

extract_protocol:
Total RNAs of macrophages were isolated using Trizol according to the manufacturer's instructions (Invitrogen).
RNA libraries were prepared for sequencing using QIAGEN Human Inflammation and Immunity Transcriptome RNA targeted panel (Cat#333002 RHS-005Z).

treatment_protocol: Sub-confluent Mahlavu cells were seeded per well in 6-well plate and transfected with siRNAs for 24 h, followed by treatment with 10 μM sorafenib for 8 h. Primary macrophages were seeded into 0.3 μm Boyden chamber and placed onto aforementioned sorafenib-treate Mahlavu cells for 24 h prior to RNA extraction

value: primary monocytes

tag: cell subtype

value: differented M2 macrophages

tag: cell markers

tag: co-cultured with


title: M2φ cocultured with TIFA siRNA-transfected and sorafenib-treated Mahlavu cells

description:
siT-M2φ
processed data files:
normalized_reads.xlsx
clustvisProcessedData.csv


title: M1φ cocultured with TIFA siRNA-transfected and sorafenib-treated Mahlavu cells

description:
siT-M1φ
processed data files:
normalized_reads.xlsx
clustvisProcessedData.csv

source_name: Monocyte-derived M1 Macrophages obtained from PromoCell company  (C-12914)

value: differented M1 macrophages


title: Total iBAT_3Weeks_2


title: A1_1_S20

value: subventricular zone

value: qNSC


title: shNC_1 [RNA-seq]

tag: cell line


title: M1φ cocultured with control siRNA-transfected and sorafenib-treated Mahlavu cells

description:
siC-M1φ
processed data files:
normalized_reads.xlsx
clustvisProcessedData.csv


title: A1_1_S19

tag: tissue


title: A1_1_S24

tag: age


title: Total iBAT_3Weeks_1


title: M0φ cocultured with TIFA siRNA-transfected and sorafenib-treated Mahlavu cells

description:
siT-M0φ
processed data files:
normalized_reads.xlsx
clustvisProcessedData.csv

source_name: M0 macrophages differentiated from primary PBMCs

value: differented M0 macrophages


title: Total iBAT_Day1_3

value: 1 day


title: A1_1_S17

tag: sample type

value: Single cell

value: neural stem cells (NSCs)


title: Total iBAT_Day1_2

value: interscapular brown adipose tissue


title: A1_1_S23

tag: cell type


title: Midgut WT Rep 1

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

data_processing:
The raw fastq files were aligned to the dm6 genome (Ensembl v97) using STAR v2.7.1a.
The reads were then quantified using RSEM v1.3.1.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: *.genes.results were generated using RSEM v1.3.1 and includes the quantified reads for each sample.

organism: Drosophila melanogaster

source_name: Midgut

growth_protocol: Drosophila melanogaster were maintained at 25°C on food containing 6 g Bacto agar, 114 g glucose, 56 g cornmeal, 25 g Brewer’s yeast and 20 ml of 10% Nipagin in 1L final volume.

extract_protocol:
Flies were dissected in 1 × PBS. RNA was isolated from at least 10 midguts using the Isolate II RNA Mini kit (Bioline, UK).
The extracted RNA was quantified using Nanodrop (Thermo Fisher Scientific). Library preparation was performed using 1µg of total RNA and sequencing was performed using Illumina HiSeq 4000 System (2 × 151 bp read length, 40 million reads per sample) by NovogeneAIT Genomics (Singapore).

treatment_protocol: Transgenic flies were maintained under a white light lamp at all times.

value: midgut

tag: genotype

value: TdTomato


title: Midgut WT Rep 2


title: Midgut WT Rep 3


title: M0φ cocultured with control siRNA-transfected and sorafenib-treated Mahlavu cells

description:
siC-M0φ
processed data files:
normalized_reads.xlsx
clustvisProcessedData.csv


title: Midgut Wg + Aβ-CRY2-mCh Rep 2

description: WgAβ

value: WgA-beta


title: A1_1_S21

tag: Stage

value: aNSC


title: Total iBAT_Day1_1

tag: strain

value: New Zealand White

tag: fraction

value: total


title: Midgut Wg + Aβ-CRY2-mCh Rep 1

description: WgAβ


title: DK21066B_05

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

data_processing:
Basecalls performed using bcl2fastq ver2.17
3' mRNA-Seq reads were aligned to the GRCh38 genome assembly using STAR v2.7.6a
Reads per million (PPM) values were calculated using samtools v1.11 and htseq-count v0.12.4.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pulmonary sarcoidosis

extract_protocol:
Total RNA was extracted with isogen reagent  (Nippon Gene, Tokyo, Japan)  according to the manufacturer's protocol.
Libraries were prepared according to the manufacturer's instructions accompanying the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). Briefly, an oligodT primer containing an Illumina-compatible sequence at its 5’ end is hybridized to the  RNA and reverse transcription is performed. Then, RNA Removal and Second Strand Synthesis were conducted. The libraries were amplified by 12 cycles of polymerase chain reaction (PCR). The purified libraries were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

value: PBMC

tag: diagnosis

value: Pulmonary sarcoidosis

tag: Sex

value: Female

tag: race

value: Asian


title: DK21066B_04

value: Male


title: DK21066B_03


title: DK21066B_02


title: Treatment T47D rep3

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

description: RCF9 treated with T47D

data_processing:
The quality of the raw sequencing reads were assessed with the FastQC v.0.11.2 software. The raw sequencing reads were subjected to trimming process with Trimmomatic v.0.32 software. The surviving paired-end reads were aligned to the Homo sapiens reference genome (Ensembl GRCh38 genome) with HISAT2 v.2.1.0 software. The alignment files were analyzed individually with the StringTie version 1.3.3b software to detect and quantify previously known transcripts. Invidual annotation files generated from transcript assembly process were merged together parsimoniously using StringTie version 1.3.3b. With the merged annotation file.
The expression unit calculated is FPKM, Fragments Per Kilobase Million. Besides, differential expression (DE) analysis was performed according to the given comparison groups . The expression fold change between each comparison group were calculated and log-transformed. Multiple output files were generated by DESeq2 version 1.16.1 and the detail files information are described in the table of result files below. Significant DE genes or transcripts (p-value < 0.05) were extracted for each comparison groups and cancer type.
Genome_build: HG19
Supplementary_files_format_and_content: ID, Gene_id, FPKM of each sample, fold change and P-value of each gene

source_name: PBMC

growth_protocol: The colon cancer cell lines were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

extract_protocol:
PBMCs were collected from Transwell culture six well plates and RNA was harvested using Trizol reagent.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified (by AxyPrep Mag PCR Clean-up (Axygen)) double-stranded cDNA was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer ( Agilent Technologies, Palo Alto, CA, USA ) , and quantified by Qubit 2.0 Fluorometer ( Invitrogen, Carlsbad, CA, USA ).

treatment_protocol: Indirect or co-culture colon cancer cell lines with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The colon cancer cell lines were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.

tag: blood


title: Treatment T47D rep2

description: RCF8 treated with T47D


title: Midgut Wg Rep 3

value: Wg


title: Treatment MCF7 rep3

description: RCF9 treated with MCF7


title: Treatment MCF7 rep2

description: RCF8 treated with MCF7


title: DK21066B_01


title: Midgut Wg Rep 1


title: DK20141B_07


title: Midgut Wg Rep 2


title: Treatment MCF7 rep1

description: RCF7 treated with MCF7


title: DK20141B_04


title: Midgut Aβ-CRY2-mCh exposed to light Rep 3

description: Aβ

value: A-beta


title: Naphthalene_3

type: RNA

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

institute: Kao Corporation

description: Gene expression after 24hr exposure of Naphthalene (30 µM)

hyb_protocol: The labeled samples were hybridized to the SurePrint G3 GE 8×60K Ver 2.0 Microarray (Agilent Technologies, Palo Alto, CA, USA) with rotation at 10 rpm for 17 h at 65°C.

scan_protocol: After hybridization, the microarray chips were washed with the Gene Expression Wash Pack (Agilent Technologies, Palo Alto, CA, USA) and scanned with a DNA microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing: All microarray data were processed using Genespring GX 14.5 (Agilent Technologies, Palo Alto, CA, USA). These data were normalized and modified using quality control flags.

organism: Rattus norvegicus

source_name: hepatocytes

label_protocol: RNA was converted to cDNA and then the labeled cRNA were produced from the cDNA using the Low Input Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA, USA).

growth_protocol: Cryopreserved male Wister rat primary hepatocytes (KaLy-Cell, Plobsheim, France) were used for in vitro assay. The cells were cultured at 37°C with 5% CO2 in the supplied medium (Kurabo, Osaka, Japan).

extract_protocol: After the 24 hours exposure with each chemical, total RNAs were extracted from rat primary hepatocytes using the miRNeasy kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. For elucidating the gene expression profile, 100 ng of RNA in total were used for microarray analysis.

treatment_protocol: After 24 h pre-culture, the cells were exposed to each chemical at 30 µM for 24 h.

value: primary hepatocytes

value: Wister

tag: gender

tag: treatment

value: 24h, Naphthalene, 30 µM


title: Control rep3

description: Female PBMC

value: female


title: DK20141B_01


title: Control rep2

description: Female PBMC


title: Naphthalene_1


title: TreatmentT47D rep1

description: RCF7 treated with T47D


title: scRNA_iBAT SVF_12Weeks

description:
scRNA-Seq
d2.4.6merg-scaled-data.xlsx

data_processing:
Cell Ranger 3.0
Seurat 3.0
Genome build: OryCun2.0
scaled expression of each gene

extract_protocol:
SVF cells isolated from iBAT and dead cell removed
Single cell 5' R2 only; 10X Genomics

value: interscapular brown adipose tissue

value: 12 weeks

value: stromal vascular fraction


title: Midgut Aβ-CRY2-mCh exposed to light Rep 1

description: Aβ

value: midgut


title: Control rep1

description: Female PBMC


title: DK20193B_10

source_name: Healthy control

value: Healthy control


title: DK20193B_11


title: DK20193B_09


title: scRNA_iBAT SVF_3Weeks

description:
scRNA-Seq
d2.4.6merg-scaled-data.xlsx

value: New Zealand White

value: 3 weeks


title: DK20193B_08

value: PBMC


title: scRNA_iBAT SVF_Day1

description:
scRNA-Seq
d2.4.6merg-scaled-data.xlsx

value: 1 day


title: Treatment H292 rep3

description: RCF9 treated with H292

growth_protocol: The lung cancer cell lines (A549 and H292) were grown with DMEM medium (Gibco BRL, USA) supplemented with 10% FBS at 37 ºc 5 % CO2 in culture flask. The cells were harvested at 80% confluence by using 0.05% Trypsin (with 0.5 mM EDTA) and washed by using phosphate buffer saline (PBS). All of this were used for maintaining cells.

treatment_protocol: Indirect or co-culture lung cancer cell lines with PBMCs from healthy were performed in Transwell culture six well plates (Costar, France). The lung cancer cell lines were seeded into plate (106 cells) with DMEM in experiment wells but not in control wells and then incubated overnight at 37 ºc 5 % CO2. The PBMCs from healthy were plated on permanent membrane culture of Transwell (2 × 106 cells) and incubated for 4 hours at 37 ºc 5 % CO2.


title: Treatment H292 rep2

description: RCF8 treated with H292


title: 1-Naphthol_3

description: Gene expression after 24hr exposure of 1-Naphthol (30 µM)

value: 24h, 1-Naphthol, 30 µM


title: Treatment H292 rep1

description: RCF7 treated with H292


title: DK20193B_07

value: Female

value: Asian


title: 1-Naphthol_2

value: Male


title: L. ag. + L. av. feeding, rep2

city: Hangzhou

last: Li

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Basecalls performed using CASAVA version 1.8
Clean data (clean read) is obtained by removing reads containing adapters, reads containing ploy-N, and low-quality reads from the raw data
Use HISAT2 software to quickly and accurately compare Clean Reads with the reference genome to obtain the position information of the Reads on the reference genome
The reads numbers mapped to each gene were count by featureCounts v1.5.0-p3. Then calculate the FPKM of each gene based on the length of the gene, and map the read count to that gene.
Genome_build: Gallus_gallus
Supplementary_files_format_and_content: TXT file includes FPKM of all genes for each sample

organism: Gallus gallus

source_name: intestinal crypt

growth_protocol: HyLine laying hens (Gallus) at the period of laying peak were raised in a commercial chicken farm. The ambient temperature is 21℃. The relative humidity is 60%. Give the laying hens clean food, water and 12 hours of light every day.

extract_protocol:
Isolation of chicken’s intestinal crypt was performed base on the protocol previously published (Li et al., 2018). Briefly, clean duodenum tissues were cut into 2 to 4 mm3 pieces and shaken gently in 2 mM cold EDTA (ethylenediaminetetraacetic acid, pH 7.4) on an orbital shaker (30 min thrice, 4°C). The supernatant was collected and passed through a 70 μm strainer and centrifuged at 25 × g for 2 min. The purified crypt was further used for mRNA transcription assay. Crypt RNA was extracted using TRIzol reagent (Invitrogen) and RNeasy®.
RNA-seq libraries were generated using the TruSeq® RNA-Seq Sample Preparation kit according to the manufacturer's protocol (Illumina Inc., San Diego, CA, USA)

treatment_protocol: Hens were  randomly divided into four groups. One control group (fed the base diet) and three lactobacillus supplement groups, which include (1) L. sa. + L. ag., (2) L. sa. + L. av. and (3) L. ag. + L. av. groups, which were fed with a base diet containing corresponding lactobacillus (10e8 CFUs/hen/day) respectively, and fed for 30 consecutive days.

tag: variety

value: HY-LINE VARIETY BROWN

tag: laying period

value: peak egg production

value: intestinal crypt

tag: feeding

value: L. ag. + L. av. feeding


title: 1,5-Naphthalenediol_3

description: Gene expression after 24hr exposure of 1,5-Naphthalenediol (30 µM)

value: primary hepatocytes

value: Wister

value: 24h, 1,5-Naphthalenediol, 30 µM


title: Treatment A549 rep3

description: RCM9 treated with A549

tag: cell line


title: 1-Naphthol_1


title: DK20193B_06

tag: age


title: Treatment A549 rep2

description: RCM8 treated with A549


title: L. ag. + L. av. feeding, rep1

tag: tissue


title: Treatment A549 rep1

description: RCM7 treated with A549


title: DK20193B_05

tag: cell type


title: L. ag. + L. av. feeding, rep3


title: Midgut Aβ-CRY2-mCh exposed to light Rep 2

description: Aβ

value: midgut

tag: genotype

value: A-beta


title: DK20193B_04

value: Healthy control


title: L. sa. + L. av. feeding, rep2

value: L. sa. + L. av. feeding


title: Control male rep3

description: Male

value: PBMC

value: male


title: DK20193B_03


title: 1,5-Naphthalenediol_1


title: L. sa. + L. av. feeding, rep1


title: 2,7-Naphthalenediol_3

description: Gene expression after 24hr exposure of 2,7-Naphthalenediol (30 µM)

value: 24h, 2,7-Naphthalenediol, 30 µM


title: Control male rep2

description: Male


title: L. sa. + L. ag. feeding, rep2

value: L. sa. + L. ag. feeding


title: 1,5-Naphthalenediol_2


title: Control male rep1

description: Male


title: VC_3

description: Gene expression after 24hr exposure of control (DMSO)

value: 24h, DMSO


title: 2,7-Naphthalenediol_2

value: Male


title: L. sa. + L. ag. feeding, rep1

value: HY-LINE VARIETY BROWN


title: DK20193B_01

value: Asian


title: DK20193B_02


title: VC_2


title: 2,7-Naphthalenediol_1


title: VC_1


title: SF268_OSI3000_D21_R1

city: New York

first: Colin

last: Tang

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the TKOv3 library sequences with bowtie.
Sequenced reads aligned to GRCh38 with salmon. Differential expression analysis was performed with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited .txt file

molecule: genomic DNA

source_name: Glioblastoma

growth_protocol: Cells were cultured in DMEM + 10% FBS

extract_protocol: CRISPR screen sequencing libraries were made with nested PCRs of the sgRNA region.

treatment_protocol: Inhibitors or DMSO were added to the cultured cells and treated for indicated times.

value: osimertinib 3uM

tag: timepoint

value: 21 days


title: GBM cell line U87_BRU

city: wenzhou

first: Cai

last: Lin

address: nanbaixiang street

department: Neurosurgery

institute: The First Affiliated Hospital of Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.16.1).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: GBM cell line

extract_protocol:
Cells were harvested and RNA was extracted by using Trizol reagent. In total, 3µg of RNA per sample was used as input material for the preparations. Sequencing libraries were generated using the NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA, #E7530L) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.
The library preparations were sequenced on an Illumina platform, and 125bp/150bp paired-end reads were generated.

value: BRU


title: Control female rep3

description: Female

value: female


title: GBM cell line U87_Control

value: control


title: GBM cell line U251_Control


title: SKMG3_NER2000_D14_R2

value: neratinib 2uM

value: 14 days


title: Control female rep2

description: Female


title: basal diet feeding, rep3

value: peak egg production

value: intestinal crypt

value: basal diet feeding


title: Control female rep1

description: Female

value: PBMC


title: basal diet feeding, rep2


title: LN95 cells, siAR-V7_Rep2

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description:
NW20418
LN95_siAR-V7-Ctrl_counts.txt

data_processing:
Raw read sequences from fastq files for each sample were quality trimmed using Trim Galore with a Phred score of 20.
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 using default parameters.
Total aligned reads for each sample at each features were then quantified using featureCounts and a transcript annotation reference for the hg19 genome build (V24).
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads were counted for each feature quantified using featureCounts are provided as text files.
Supplementary_files_format_and_content: counts

source_name: LN95 cells, siAR-V7

growth_protocol: The prostate cancer cell line LN95 was kindly provided by Dr. Jun Luo, Johns Hopkins University. LN95 cells were cultured in phenol red free RPMI 1640 medium containing 10% Charcoal Stripped FBS.

extract_protocol:
Total RNA was extracted, and column purified using an RNAeasy mini kit. (Qiagen). The clean RNA samples having RIN more than 8.0 were used for library preparation in the Genomic and RNA Profiling Core, Baylor College of Medicine.
Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions. cDNA libraries were sequenced on the Illumina NextSeq 500 or NovaSeq 6000 platform in the Genomic and RNA Profiling Core facility, Baylor College of Medicine.

treatment_protocol: For knock-down experiments cells were treated with control siRNA, siRNA targeting exon7 or siRNA targeting cryptic exon of AR-V7 for 48 hours before harvesting. To measure hormone dependent AR FL activity, LN95 cells were treated with vehicle (0.1% ethanol) or 10 nM R1881 (a synthetic androgen) for 24 hours before harvesting.

value: Immortalized prostate cancer cell line


title: basal diet feeding, rep1


title: LN95 cells, siAR-V7_Rep1

description:
NW20413
LN95_siAR-V7-Ctrl_counts.txt


title: LN95 cells, Control for siAR-V7_Rep2

description:
NW20416
LN95_siAR-V7-Ctrl_counts.txt

source_name: LN95 cells, Control

value: Control


title: SKMG3_DMSO_D14_R2

value: vehicle


title: SKMG3_DMSO_D14_R1


title: SF268_NER1500_D21_R2

value: neratinib 1.5uM


title: LN95 cells, siFL_Rep2

description:
NW-19283
LN95_siFL-Ctrl_counts.txt

source_name: LN95 cells, siFL

value: siFL


title: SF268_DMSO_D21_R2


title: SKMG3_NER2000_D14_R1


title: LN95 cells, siFL_Rep1

description:
NW-19275
LN95_siFL-Ctrl_counts.txt


title: SF268_D0_R2

value: untreated

value: 0 hr


title: SF268_D0_R1


title: LN95 cells, Control for siFL_Rep2

description:
NW-19277
LN95_siFL-Ctrl_counts.txt


title: Naphthalene_2

value: primary hepatocytes

tag: strain

value: Wister

value: Male

value: 24h, Naphthalene, 30 µM


title: LN95 cells, Control for siAR-V7_Rep1

description:
NW20410
LN95_siAR-V7-Ctrl_counts.txt


title: LN95 cells, Control for siFL_Rep1

description:
NW-19267
LN95_siFL-Ctrl_counts.txt


title: PC3-sham4h-rep1

first: Wahyu

middle: Wijaya

last: Hadiwikarta

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum

hyb_protocol: 0,6 ug of Cy3 labeled cRNA were hybridized for 17 hr at 65°C on Agilent SurePrint G3 Human GE v3 8x60K Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Agilent Scanner G2505C . The scanned images were analyzed with Feature Extraction Software (Agilent technologies) using default settings.

data_processing: Raw data was processed using R version 4.0.2 and the function read.maimages from the Bioconductor package limma (Ritchie et al., 2015). Raw data was processed to create an EListRaw object. Signal intensities were extracted from this EListRaw object and transformed using log2(x+1) operation for archiving.

label_protocol: The Agilent Low Input Quick Amp Labeling Kit (One-Color) is used to generate single-stranded cRNA from input amounts of 50ng total RNA.

growth_protocol: Experiments were performed with established PC cell lines DU145, PC3 and LNCaP (ATCC), HNSCC cell lines FaDuDD, Cal33 (DSMZ), SAS, and UT-SCC-14 (JCRB), as well as GBM cell lines LN229 and U87MG (ATCC). All cells were cultured according to the manufacturer's recommendations in a humidified incubator supplemented with 5 % CO2 at 37°C. FaDu, Cal33, PC3 and DU145 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sigma-Aldrich) and LNCaP in Roswell Park Memorial Institute (RPMI) 1640 Medium (Sigma-Aldrich) containing 10 % fetal bovine serum (FBS; PAA Laboratories), 1mM L-glutamine (Sigma-Aldrich), 1 % HEPES (1 M; PAA Laboratories), 1 % sodium pyruvate (100 mM; Sigma-Aldrich) and 1 % MEM non-essential amino acids (100x; Sigma-Aldrich). LN229 and U87MG were maintained in Minimum Essential Medium with Earle’s salts (MEM Earle’s; Sigma-Aldrich) containing 10 % FBS, 1 % penicillin/streptomycin (Sigma-Aldrich), and 1 % sodium pyruvate. The U87MG line from ATCC is of unknown origin (Allen et al., 2016). Normal cell line controls included immortalized prostate cell line RWPE-1 (ATCC) cultured in keratinocyte serum free medium (K-SFM, Invitrogen) containing bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF) as well as the keratinocyte cell line HaCaT (CLS) propagated in DMEM media. All cell lines were genotyped using microsatellite polymorphism analysis to validate identity and were tested regularly for mycoplasma contamination. Cells were not further used above passage 20. The irradiated sublines (IR) from established PCa and HNSCC cell lines were irradiated with multiple fractions of 4 Gy irradiation and selected for clones with intrinsic and acquired radioresistance (RR). The molecular and functional characterization of these IR- and RR-sublines has been previously published (Cojoc et al., 2015; Kurth et al., 2015; Peitzsch et al., 2016).

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen) and Qubit RNA assay (Thermo Fischer Scientific) for quantification.

treatment_protocol: Photon irradiation was performed using 200 kV X-rays (Yxlon Y.TU 320; 0.5 mm copper filter) at a dose rate of 1.3 Gy/min at 20 mA. Proton irradiation was performed at the Research Facility of the University Proton Therapy Dresden (UPTD), with 150 MeV protons at a horizontal fixed-beam line with a dose rate of 3 Gy/min. Beam line, setup and dosimetry have been fully described in previous papers (Beyreuther et al., 2018; Suckert et al., 2020). A dedicated beam shaping system consisting of a double-scattering device and a ridge filter provided a laterally extended 10 x 10 cm2 field with a 2 cm spread-out Bragg peak (SOBP) (Helmbrecht et al., 2016). To assure positioning of the cells within the SOBP, resulting in a dose-averaged LET value of 3.7 keV/µm, monolayer culture plates or flasks were placed vertically to the beam axis at a 90° angle, whereas 3D cultures were positioned at a 42° angle. Daily dosimetry with a Markus ionization chamber and Unidos dosimeter (PTW) readout ensured consistent irradiation conditions. The proton beam at UPTD was only available for radiobiological experiments every 3-4 months, causing an increased biological variability between independent repeats. Physical doses of either radiation type ranged from 0 to 8 Gy.

tag: time after dose in days

tag: time after dose in hours


title: PC3-xray4h-rep1


title: UMUC6 - PPARG#3

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the  arrays Clariom D Human

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: ClariomDHuman_Hs_ENTREZG_v22 Brainarray Custom CDF EntrezG version

label: biotin

source_name: UMUC6 - PPARG

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

growth_protocol: UMUC6 cells were grown in DMEM containing 10% SVF

extract_protocol: mRNAs were extracted and purified using RNeasy Mini kits (Qiagen).

treatment_protocol: Cells were transfected with a plasmid encoding PPARG2 isoform or by the emplty backbone plasmid. After 72 h of transient transfection, cells were collected and mRNA extracted. 3 independant experiments were carried out.

tag: transfection

value: PPARG


title: DU145-proton-rep3


title: DU145-sham-rep3


title: UMUC6 - PPARG#2


title: UMUC6 - PPARG#1


title: UMUC6 - empty#2

source_name: UMUC6 - empty

value: empty


title: media-24-ND3

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: RNA-seq human macrophage, media 24h, donor3

data_processing:
Sequenced reads were aligned to the hg38 genome assembly using Bowtie 2.2.6 and Tophat 2.1.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Genome_build: hg38

growth_protocol: Primary CD14+ monocytes were isolated and plated in 24-well plates at 1 million cells/mL in RPMI + 1% P/S + 1%L-glutamate + 30ng/mL MCSF for 5 days. Media + MCSF was replaced at day 3

extract_protocol:
Total RNA sample integrity was assessed using automated capillary electrophoresis on a Fragment Analyzer (Agilent) using the HS RNA Kit (15NT). For all samples RQN > 8.0, a total RNA amount of > 75 ng was used as input for library preparation using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Sequencing libraries were quantified by real-time PCR using the KAPA Library Quantification Complete kit (Roche) and assessed for size distribution and absence of free adapters and adapter dimers on a Fragment Analyzer.
Sequencing libraries were pooled and sequenced on a HiSeq 3000 System (Illumina) using a HiSeq 3000/4000 PE Cluster Kit and SBS Kit (150 cycles) with run conditions of paired-end reads at 75 bp length.

treatment_protocol: Differentiated macrophages were rested overnight in complete RPMI and then unstimulated or stimulated with 100ng/mL IFNg for 24 hrs

value: Healthy donors

tag: antibody

value: macrophage


title: IFNg-24-ND3

description: RNA-seq human macrophage, IFNg 24h, donor3


title: DU145-xray-rep3


title: DU145-proton4h-rep1


title: UMUC6 - empty#1


title: RNA-seq of A11-64-8

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1009 Pre-treatment
A11-64-8

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

source_name: prostate

extract_protocol:
RNA was extracted from FFPE prostate tissues using the Qiagen RNeasy FFPE kit
Libraries were prepared with the NEBNext Globin and rRNA depletiion library construction kit and the Illumina TruSeq stranded total RNA with ribo-zero globin kit.

treatment_protocol: Patients with prostate cancer received systemic intense neoadjuvant androgen deprivation therapy for six months and then underwent radical prostatectomy. Biopsies acquired prior to treatment , or post-treatment surgical prostatectomy specimens were grossed, accessioned, fixed in formalin, and embedded in paraffin.

tag: treatment status

value: Pre-treatment

value: male

tag: subjectid


title: UMUC6 - empty#3


title: RNA-seq of A11-64-7

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1008 Pre-treatment
A11-64-7

tag: gender


title: RNA-seq of A11-64-9

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1010 Pre-treatment
A11-64-9


title: DU145-sham4h-rep1


title: DU145-xray4h-rep1


title: IFNg-24-ND4

description: RNA-seq human macrophage, IFNg 24h, donor4


title: media-24-ND4

description: RNA-seq human macrophage, media 24h, donor4


title: IFNg-24-ND2

description: RNA-seq human macrophage, IFNg 24h, donor2


title: PC3-proton-rep3


title: RNA-seq of A11-64-6

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1007 Pre-treatment
A11-64-6


title: RNA-seq of A11-64-5

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1005 Pre-treatment
A11-64-5


title: sBAT SVF_Day1_3

institute: University of Minnesota

description: Rabbit.SVF.GeneExpression.FPKM.xls

data_processing:
Sequencing Reads Filtering using SOAPnuke: v1.5.2
Genome Mapping using HISAT2: v2.0.4
Mapping clean reads to reference using Bowtie2: v2.2.5
Gene expression cluster analysis using Cluster v3.0
DEG detection using DEseq2
Genome build: OryCun2.0
FPKM

source_name: subscapular brown adipose tissue

extract_protocol:
RNA extracted from total or the SVF fraction of BAT
RNA-Seq Quantification Library (Normal Library)

value: subscapular brown adipose tissue

value: New Zealand White

value: 1 day

tag: fraction

value: stromal vascular fraction


title: PC3-sham-rep3


title: RNA-seq of A11-64-4

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1004 Pre-treatment
A11-64-4


title: media-24-ND2

description: RNA-seq human macrophage, media 24h, donor2


title: RNA-seq of A11-64-36

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1038 Pre-treatment
A11-64-36


title: PC3-xray-rep3


title: IFNg-24-ND1

description: RNA-seq human macrophage, IFNg 24h, donor1


title: RNA-seq of A11-64-37

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1039 Pre-treatment
A11-64-37


title: RNA-seq of A11-64-34

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1036 Pre-treatment
A11-64-34


title: binglizu 10

city: Zhanjiang

first: You

state: Guandong

address: 57# South Renmin Road

institute: Institute of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China.

description: Disease vs Normal_all_detectable_circRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program. miRanda[6]was used to predict the miRNA target of the circRNA. R was used to generated the figue.
Genome_build: UCSC
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: peripheral blood mononuclear cells

extract_protocol:
Within two hours of admission, a ~10 mL venous blood sample was collected from each study participant in an EDTA-containing tube. LymphoprepTM (Axis-Shield PoCAS, Oslo, Norway) was then used for density gradient centrifugation of blood samples in order to isolate PBMCs.PBMC RNA was isolated with RNAiso Plus (Takara, Japan) based upon provided directions, with a Nanodrop ND2000 instrument (Thermo Scientific Inc., MA, USA) being used to quantify the amount of RNA obtained. In addition, 2% agarose gel electrophoresis was performed to assess RNA integrity and to quantify DNA contamination of samples.
Following enrichment, circRNAs were amplified and labeled. A Total RNA-seq (H/M/R) Library Prep Kit for Illumina® was then used to prepare a strand-specific library from these amplified circRNAs based on provided instructions, after which an Illumina HiSeq™ 3000 instrument was used for library sequencing. Differentially expressed circRNAs were identified using the edgeR package (http://www.rproject.org/), with a subset of these circRNAs being annotated using circBase.

tag: type

value: large-artery atherosclerotic stroke patients

value: blood

tag: developmental stage

value: acute stage


title: binglizu 9


title: media-24-ND1

description: RNA-seq human macrophage, media 24h, donor1


title: binglizu 12


title: RNA-seq of A11-64-32

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1034 Pre-treatment
A11-64-32


title: GBM cell line U251_BRU

tag: treatment

value: BRU


title: PC3-proton4h-rep1

city: Heidelberg

tag: cell line


title: DU145-proton12h-rep1


title: RNA-seq of A11-64-33

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1035 Pre-treatment
A11-64-33


title: DU145-xray12h-rep2


title: RNA-seq of A11-64-31

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1033 Pre-treatment
A11-64-31


title: binglizu 7

tag: tissue


title: binglizu 17


title: S2

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

data_processing:
scRNA reads were aligned and gene level unique molecular identifier (UMI) counts were obtain using the 10X Cell Ranger v3.0.2 'count' program with default parameters and GRCh38. CellRangers' QC report files, details of the code as well as cell labels can be obtained via github.com/abcwcm/Notaras_MolPsy.
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance measurements consist of counts per cell per gene.

molecule: polyA RNA

source_name: brain organoid from Scz donor iPSC

growth_protocol: We adapted the undirected-differentiation organoid system published by Lancaster et al. (Lancaster, M.A., M. Renner, C.-A. Martin, D. Wenzel, L.S. Bicknell, M.E. Hurles, et al., Cerebral organoids model human brain development and microcephaly. Nature, 2013. 501(7467)). First, iPSCs are dissociated with Accutase (Laboratory Disposable Products, CAT#: 25-058-C1) and cultured into three-dimensional embryoid bodies for up to 7 days using custom media (see Lancaster, M.A. & J.A. Knoblich, Generation of cerebral organoids from human pluripotent stem cells. Nature Protocols, 2014. 9(10)) in ultra-low attachment 96 well plates (Corning; CAT#: 3474). Rock inhibitor (1:1000; Stem Cell Tech, CAT#: 72304) and basic fibroblast growth factor (Pepro Tech, CAT#: 100-18B) are included in media for the first 2-4 days of embryoid body culturing to promote stem cell aggregation and survival. Following this, healthy embryoid bodies are isolated and transferred to Nunclon Sphera 24 well plates (Thermo Scientifiic, CAT#: 174930) for neural fate specification, using custom neural induction media (see Lancaster, M.A. & J.A. Knoblich, Generation of cerebral organoids from human pluripotent stem cells. Nature Protocols, 2014. 9(10)). Once neuroepithelium was apparent , successful early ‘organoids’ were embedded in a 30μl Matrigel (Corning, CAT#: 354234) spheroid-droplet and polymerized at 37°C for 20-30min which provided a matrix for subsequent neural expansion. Organoids suspended in matrigel droplets were next cultured in terminal organoid media (see [2]) for 4-6 days without agitation, and then cultured with agitation at 60-70RPM until harvested for experiments. All stages of culturing occurred at 37°C with 5% atmospheric CO2 in a sterile incubator. Cerebral organoids from healthy control and schizophrenia iPSC lines were generated and maintained in parallel, ensuring that idiosyncratic differences in culturing conditions were accounted for between control and schizophrenia organoids. All human iPSC lines were sourced from NIH deposits at the Rutgers University Cell and DNA Repository. All lines have undergone extensive characterization for identity, pluripotency, exogenous reprogramming factor expression, genetic stability and viability. All cases were derived from idiopathic cases, which we define here as schizophrenia cases that maintain unknown disease origins and do not meet a genetic/syndrome-based diagnosis that explains disease (e.g., 22Q11 deletions). A breakdown of idiosyncratic iPSC properties, in the context of organoid generation, maturation, survival and subsequent experiment inclusion details, can be found in Supplementary Table 2 of the linked publication. All iPSC lines were maintained on vitronectin-coated plates and fed with Essential 8 (E8) + E8 supplement media (ThermoFisher, CAT#: A1517001).

extract_protocol:
Organoids were dissociated using Accutase, serially filtered to remove debris, and were subjected to high-throughput FACS (Aria II flow cytometer, Becton Dickson). This procedure allowed us to isolate only live cells in a defined concentration (2000 live cells/uL) that could be standardized between lines for microfluidic device loading. Cell viability was confirmed using Countess-II (Invitrogen, Thermofisher, CAT: AMQAX1000). Next, cells were prepared for 10X Genomics Chromium library preparation according to manufacturer instructions (Single-Cell 3' Library, Gel Bead and Chromium CHIP kit, 10X Genomics).
Barcoded emulsions were broken, amplified and libraries prepared using the 10X Chromium kits. cDNA was examined on a Fragment Analyzer running PROSize v.3/0 3.0.1.6.
Single-Cell 3'

tag: disease state

value: Scz

tag: donor


title: RNA-seq of A11-64-3

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1003 Pre-treatment
A11-64-3


title: S1


title: RNA-seq of A11-64-30

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1032 Pre-treatment
A11-64-30


title: DU145-xray12h-rep1


title: U87MG-proton-rep2


title: U87MG-xray-rep2


title: U87MG-sham-rep2


title: LN229-proton-rep2


title: RNA-seq of A11-64-29

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1031 Pre-treatment
A11-64-29


title: C4

source_name: brain organoid from healthy control donor iPSC

value: healthy


title: 1336007

value: healthy control group


title: S3


title: duizhao15


title: RNA-seq of A11-64-28

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1030 Pre-treatment
A11-64-28


title: 1335685


title: C2


title: LN229-sham-rep2


title: C9_diff_day5_4_MIP24

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description:
MeDIP_seq_RNA_seq_H3K27M_Day_5_vs_Day_0.xlsx
MeDIP_seq_RNA_seq_H3K27M_vs_WT_Day_5.xlsx

data_processing:
Illumina Casava1.8 software was used for basecalling
Sequence reads were mapped to the hg19UCSC genome using the associated bowtie2 index provided by Illumina iGenomes
MEDIPS software (PMID: 24227674) was used to map MBD-seq peaks and perform differential abundance calculations
Genome_build: hg19
Supplementary_files_format_and_content: excel table of MeDIP and RNAseq abundance

source_name: H1 ESC

growth_protocol: H1 human embryonic stem cell (hESC) lines were grown under feeder-free conditions on Matrigel (Corning) in Essential 8™ Flex Medium (A2858501, ThermoFisher Scientific) and regularly passaged as aggregates with ReLeSR (STEMCELL Technologies, Cat# 05872). PSC colonies (especially the H3K27M mutant colonies) showing increased differentiation were carefully cleaned up manually scratching the colonies with a pipette tip under the microscope and maintained over time.  Experiments adhered to protocols approved by the Washington University hESC Research Oversight Committee (#12-002). As this work was designated “nonhuman subjects research” by Washington University’s Institutional Review Board, informed consent was not required. Cells were regularly checked for Mycoplasma contamination (Mycoalert Mycoplasma Detection Kit, Lonza, Cat# LT07-118). The H3F3a-K28M-Puro clonal cell lines (mutant clone 1 and clone 9)  were generated from H1 embryonic stem cell (H1ESC) line (obtained from WiCell) by the Genome Engineering and iPSC Center (GEiC), Washington University in St. Louis. Prior to transfection the cells were treated with 10 µmol Rock (Y-27632) inhibitor for at least 1 hr. Approximately 1.5 × 106 H1ESC cells were resuspended in P3 primary buffer and electroporated using a 4D-Nucleofector (Lonza) with 1 μg of H3F3a-K28M-KI-Puromyocin donor plasmid (GeneArt), 1 μg gRNA SM928.H3F3a.g37 targets 5’- atgctggtaggtaagtaagg agg-3’  and 1.2 μg Cas9 vectors. Nucleofected cells were plated in media containing Rock inhibitor for 24hrs post nucleofection and then returned to regular E8-Flex media. Following nucleofection, cells were screened with PCR using primer sets specific to the 5' and 3' junctions of the donor plasmid and the target gene. After confirmation of donor plasmid KI in the nucleofected pool the cells were treated with 0.2 µg/ml of Puromycin for 72 hrs. Surviving cells were then passaged and treated with 0.5 µg/ml of Puromycin for 72 hrs and Sanger sequencing was used to confirm the homozygous KI of the K28M mutation in the 5' junction PCR product of the subclones. Karyotyping of H3F3a-K28M line was performed by Cell Line Genetics.

extract_protocol:
Genomic DNA was isolated from the harvested cells using the PureLink™ Genomic DNA Mini Kit (ThermoFisher Scientific, K182002) and about 3 µg DNA (except for two samples which were of 1µg) was fragmented to 100- to 500-bp fragments in a water bath sonicator (Bioruptor Pico, Diagenode) using 30 sec on/off cycles for 10 min. MBD2 enrichment was performed with the MethylMiner™ Methylated DNA Enrichment Kit (ThermoFisher Scientific, Cat# ME10025). Approximately 1-2 μg of fragmented genomic DNA was incubated with human MBD2-biotin Protein coupled to paramagnetic Dynabeads® M-280 Streptavidin for methylated CpG enrichment  according to the manufacturer’s protocol and the methylated CpG fragments were finally eluted twice with high salt (2000 mM NaCl) elution buffer . The enriched DNA was purified and concentrated by ethanol precipitation and the DNA concentration was measured with Quant-iT™ dsDNA HS (High Sensitivity) Assay (ThermoFisher Scientific, Cat # Q32854).
Enrichment of methylated DNA with the MBD2 pulldown was confirmed by qPCR of the methylated positive control region of BRD1 and the unmethylated negative control region of CoQ3 (Taiwo et al., Nat. Protocols, 2012 and oligo sequences provided in the table below).  Enriched DNA was then sent to GTAC sequencing core for the library preparation and sequencing. (From GTAC) MeDIP DNA was run on Agilent bioanalyzer high sensitivity chips to assay size range. 10ng of DNA as determined by Qubit was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs and underwent amplification for 15 cycles with primers incorporating p5 and p7 sequences and a unique index tag for multiplexing.
The resulting libraries were sequenced using the Illumina HiSeq3000 as paired reads extending 150 bases.

treatment_protocol: For hESC Differentiation into Early Cortical Neural Progenitor Cells (NPCs), hESCs were dissociated with Accutase to single cells, counted and 1.5-3.5 (mostly it was 3.5 million )million cells per well were seeded into each well (with 300 microwells each) of anti-adherent AggreWell™800 Plates ((Stem Cell Technologies, Cat# 34815) the cell number is within the manufacturer’s recommended range for each well of the AggreWell 800 plate)) to produce uniform size embryoid bodies (EBs) (~11,666 cells/EB). AggreWell plates were prerinsed with warm neural induction medium (NIM) before plating the single cell suspension of H1 hESCs (WT and H3K27M mutant) and the plates were spun at 100 × g for 3 min to capture the cells into the microwells and were incubated at 37 °C with 5% CO2 in NIM medium for 2 days for the EB formation. The NIM medium was based on published protocols (Chambers et al., Nat. Biotech., 2009, Surmacz et al., Stem Cells, 2013, Mark Tomishima, Stem Book, 2012) and consisted of Neurobasal-A (Life Technologies), 1x B27 supplement without vitamin A (LifeTechnologies, 12587010), 10 μM SB-431542 (Tocris Biosciences), 100 nM LDN-193189 (Stemgent), and 10 μM Y-27632 (Tocris Biosciences). On day 2, EBs were removed from the AggreWell 800 plates and seeded onto poly-L-ornithine (20μg/mL) and laminin (10μg/mL)-coated plates to grow them into neural rossettes. Medium was replenished every other day and the NPCs of telencephalic character were isolated on day 5 using Accutase (Gibco, A1110501).

tag: genotype

value: Mutant C9

tag: differentiation

value: differentiated

tag: time

value: Day 5

tag: cell type

value: differentiated neural EB derivatives

tag: replicate


title: C1


title: C9_diff_day5_3_MIP23


title: RNA-seq of A11-64-26

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1028 Pre-treatment
A11-64-26

value: Pre-treatment


title: C3


title: C9_diff_day5_2_MIP22


title: s_PDX_WDLS0010__s_normalfat

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Library strategy: shallow WGS
For the sequenced cell lines (LPS141, PDX_WDLS0010) the seqCNA pipeline was used. Reads were mapped with BWA and then copy number was called using the seqCNA package. All code available at: https://github.com/soccin/seqCNA
For the sequenced tumor sample (WD5816_SCL_1) the pipeline used was from the published methods of: Baslan, et. Al; Nature Protocols 2012. [PMID: 22555242]
Genome_build: HG19
Supplementary_files_format_and_content: IGV Segmentation files (SEG)

source_name: PDX tumor derived from Dedifferentiated liposarcoma (DDLS) WD5816

growth_protocol: Cell lines were grown in a 1:1 mixture of DMEM high glucose and F12 media with 10% fetal bovine serum, 100 units/mL penicillin plus 100 µg/mL streptomycin (complete medium) and maintained at 37 °C in 5% CO2

extract_protocol: genomic DNA was extracted suing DNeasy Blood (Qiagen)  and Tissue kits

treatment_protocol: not treated

value: DDLS PDX

value: dedifferentiated liposarcoma


title: Cal33-xray-rep2

tag: time after dose in days

tag: time after dose in hours


title: RNA-seq of A11-64-25

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1027 Pre-treatment
A11-64-25

tag: treatment status

value: male

tag: subjectid


title: C9_diff_day5_1_MIP21


title: Cal33-sham-rep2


title: s_CL_LPS141__s_CL_L090310

source_name: Dedifferentiated liposarcoma (DDLS) cell line

value: DDLS Cell Line


title: LN229-xray-rep2


title: RNA-seq of A11-64-23

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1025 Pre-treatment
A11-64-23

tag: gender


title: DU145-proton12h-rep2


title: FaDu-xray-rep2

source_name: FaDu

value: FaDu


title: C1_diff_day5_3_MIP19

value: Mutant C1


title: RNA-seq of A11-64-24

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1026 Pre-treatment
A11-64-24


title: LN95 cells, R1881_rep1

description:
NW_15133
LN95_R1881-Eth_counts.txt

source_name: LN95 cells, R1881

value: Immortalized prostate cancer cell line


title: C1_diff_day5_2_MIP18


title: LN95 cells, R1881_rep2

description:
NW_15139
LN95_R1881-Eth_counts.txt


title: RNA-seq of A11-64-21

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1023 Pre-treatment
A11-64-21


title: RNA-seq of A11-64-27

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1029 Pre-treatment
A11-64-27


title: Cal33-proton-rep2


title: FaDu-proton-rep2


title: duizhao 6

tag: type

value: blood


title: FaDu-sham-rep2


title: PC3-proton-rep2


title: C1_diff_day5_4_MIP20


title: RNA-seq of A11-64-35

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1037 Pre-treatment
A11-64-35


title: PC3-xray-rep2


title: LN95 cells, Eth_rep2

description:
NW_15136
LN95_R1881-Eth_counts.txt

source_name: LN95 cells, Eth

value: untreated


title: C1_diff_day5_1_MIP17


title: RNA-seq of A11-64-2

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1002 Pre-treatment
A11-64-2


title: RNA-seq of A11-64-22

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1024 Pre-treatment
A11-64-22


title: RNA-seq of A11-64-20

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1022 Pre-treatment
A11-64-20


title: wt_diff_day5_4_MIP16

description:
MeDIP_seq_RNA_seq_WT_Day_5_vs_Day_0.xlsx
MeDIP_seq_RNA_seq_H3K27M_vs_WT_Day_5.xlsx

value: Wild-type (control)


title: Sample_039

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
Sequence data were converted to FASTQ files
analyzed using CLC Genomics  Workbench (v.12.02) and UMIs were extracted
Reads were mapped to MiRNA database  miRbase v22 and human genome GRCh38 versions 97
Differential expression analysis was  performed via the Bioconductor Package DESeq2,
Genome_build: MiRNA database  miRbase v22 and human genome GRCh38 versions 97
Supplementary_files_format_and_content: .csv count file

source_name: UAMS Breast Cancer Patient

extract_protocol:
Blood samples (10ml) were collected in EDTA collection tubes and plasma was isolated  within next 2 hours by centrifugation at 2000 Xg for 20 min. Plasma was stored at -80oC until  analysis. Total RNA, including miRNA was isolated from 1 ml frozen plasma samples using  exoRNeasy Serum/Plasma Maxi Kit (Qiagen, Valencia, CA, USA) [31]. Briefly, pre-filtered  plasma (0.8 μm syringe filter) was mixed 1:1 with 2x binding buffer (XBP) and added to the  exoEasy membrane affinity column to bind the EVs to the membrane. After centrifugation, the  flow-through was discarded, and wash buffer (XWP) was added to the column to wash off nonspecifically  retained material. After another centrifugation and discarding of the flow-through,  the vesicles were lysed by adding QIAzol to the spin column, and the lysate was collected by  centrifugation. The miRNeasy Serum/Plasma Spike-In Control (Qiagen, Valencia, CA, USA)  was added. Following addition of chloroform, thorough mixing, and centrifugation to separate  organic and aqueous phases, the aqueous phase was recovered and mixed with ethanol. The  sample-ethanol mixture was added to Rneasy MinElute spin column and centrifuged. The  column was washed once with buffer RWT, and then twice with buffer RPE followed by elution  of RNA with water. The purity and concentrations of total RNA of the plasma samples were  measured with NanoDrop ND-1000.
3’ and 5’ adapters are ligated to mature miRNAs. The ligated miRNAs are then  reverse transcribed to cDNA using a reverse transcription (RT) primer with unique molecular  indices (UMI). After library amplification, a cleanup of the miRNA library is performed using a  streamlined magnetic bead-based method and quality control (QC).

value: plasma

tag: patient diagnosis

value: breast cancer

tag: molecule subtype

value: exosomal miRNA


title: RNA-seq of A11-64-19

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1021 Pre-treatment
A11-64-19


title: Sample_040


title: wt_diff_day5_3_MIP15

value: differentiated


title: wt_diff_day5_2_MIP14

value: Day 5


title: varbin50k.WD5816_SCL_1.bulk.dd

source_name: Dedifferentiated liposarcoma (DDLS) original patient's tumor that gave rise to the PDX WD0010

value: DDLS Tumor


title: RNA-seq of A11-64-18

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1020 Pre-treatment
A11-64-18

value: Pre-treatment


title: wt_diff_day5_1_MIP13

value: differentiated neural EB derivatives


title: RNA-seq of A11-64-17

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1019 Pre-treatment
A11-64-17


title: LN95 cells, Eth_rep1

description:
NW_15131
LN95_R1881-Eth_counts.txt

tag: cell line

tag: treatment


title: Sample_037

tag: tissue


title: Sample_038


title: C9_undiff_day0_1_MIP12

description: MeDIP_seq_RNA_seq_H3K27M_Day_5_vs_Day_0.xlsx

value: Mutant C9

value: undifferentiated

value: Day 0

value: undifferentiated H1 hESCs


title: PC3-sham-rep2


title: DU145-proton-rep2


title: RNA-seq of A11-64-16

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1018 Pre-treatment
A11-64-16

value: male


title: Sample_036


title: C9_undiff_day0_1_MIP11


title: DU145-xray-rep2


title: U87MG-proton-rep1


title: DU145-sham-rep2


title: RNA-seq of A11-64-15

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1017 Pre-treatment
A11-64-15


title: U87MG-xray-rep1


title: U87MG-sham-rep1


title: Sample_035


title: C9_undiff_day0_1_MIP10


title: Sample_034


title: RNA-seq of A11-64-14

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1016 Pre-treatment
A11-64-14


title: C9_undiff_day0_1_MIP9


title: C1_undiff_day0_4_MIP8

value: Mutant C1


title: RNA-seq of A11-64-10

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1011 Pre-treatment
A11-64-10


title: Sample_033


title: RNA-seq of A11-64-13

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1015 Pre-treatment
A11-64-13


title: Sample_032


title: C1_undiff_day0_3_MIP7


title: Sample_031


title: Sample_030


title: RNA-seq of A11-64-1

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1001 Pre-treatment
A11-64-1


title: RNA-seq of A11-64-11

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1012 Pre-treatment
A11-64-11


title: RNA-seq of A11-64-12

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1013 Pre-treatment
A11-64-12


title: C1_undiff_day0_1_MIP5


title: wt_undiff_day0_4_MIP4

description: MeDIP_seq_RNA_seq_WT_Day_5_vs_Day_0.xlsx


title: RNA-seq of A11-120-9

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1010 Post-treatment
A11-120-9

value: Post-treatment


title: C1_undiff_day0_2_MIP6


title: Sample_028


title: RNA-seq of A11-120-8

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1009 Post-treatment
A11-120-8


title: Sample_027


title: wt_undiff_day0_2_MIP2


title: wt_undiff_day0_3_MIP3


title: RNA-seq of A11-120-7

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1008 Post-treatment
A11-120-7


title: RNA-seq of A11-120-6

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1007 Post-treatment
A11-120-6


title: Sample_026


title: Sample_029


title: Sample_025


title: RNA-seq of A11-120-5

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1005 Post-treatment
A11-120-5


title: LN229-proton-rep1


title: wt_undiff_day0_1_MIP1


title: LN229-sham-rep1


title: Sample_024


title: Cal33-sham-rep1


title: wt_undiff_day0_4_SPOND4

description: Replicate 4

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the hg38UCSC genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene in the hg38UCSC gene annotation

extract_protocol:
High quality RNA from H1 hESC and their differentiated derivatives was isolated with RNeasy Plus Mini kit (Qiagen, cat # 74134) using QIAshredder (Qiagen, cat # 79654) and on-column digestion of genomic DNA following manufacturer’s recommendations. The kit captures RNA molecules higher than 200 nucleotide length effectively removing smaller RNAs such as 5.8S rRNA, 5S rRNA and tRNAs. For RNA-Seq, RNA was initially quantified by NanoDropND-1000 spectrophotometer (Thermo Scientific) and the concentration/quality of total RNA was further confirmed on Agilent Bioanalyzer2100. Only samples that had RNA integrity number (RIN) > 8 were used for RNA-Seq studies.
RNA-seq library preparation and Illumina sequencing were performed by the Genome Technology Access Center (GTAC) at Washington University School of Medicine. Total RNA was enriched for polyA-tailed mRNA and mRNA fragmentation, first- and second-strand cDNA synthesis, and addition of indexed adapters was carried out as previously described [S. J. Matkovich, G. W. Dorn, 2nd, Deep sequencing of cardiac microRNA-mRNA interactomes in clinical and experimental cardiomyopathy. Methods Mol. Biol. 1299, 27-49 (2015)].
non-strand-specific, single-end RNA-SeqSingle-end, 50 nt reads were obtained on an Illumina HiSeq 3000 instrument and the sequencing reads were mapped to the human genome (hg19 UCSC) using HISAT2 [M. Pertea, D. Kim, G. M. Pertea, J. T. Leek, S. L. Salzberg, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650-1667 (2016)]. The mean number of transcriptome-aligned reads per heart was 17.2 million.  Read quantitation on a per-gene basis was performed with HTSeq [S. Anders, P. T. Pyl, W. Huber, HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015)]. Detectable RNAs were assessed as those present at or above 1 read per million (18 reads) in at least 2 of 4 samples from any treatment group, resulting in 16,083 RNAs for downstream analyses.  Calculation of fold-change and FDR for differentially expressed RNAs used the R/Bioconductor packages limma and edgeR/voom [C. W. Law, M. Alhamdoosh, S. Su, G. K. Smyth, M. E. Ritchie, RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Res 5, 1408 (2016)]. Partek Genomics Suite v6.6 (Partek, St. Louis, MO) was used for inter-sample quality control by principal components analysis and for heat map construction. To visualize differentially expressed mRNAs, normalized read counts from edgeR were subjected to unsupervised hierarchical clustering with Euclidean distance and average linkage using Partek Genomics Suite v6.6. Unless otherwise specified, standardized heatmaps are shown in which map colors represent the extent of deviation from the row average. For clarity of presentation and to enable comparison with other studies, individual gene expression levels in column graphs are rendered as FPKM (Fragments Per Kilobase of exon per Million reads mapped to the transcriptome), calculated from Tophat-aligned read counts using Cufflinks 2.1.1 [C. Trapnell et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012)].

tag: group

tag: time point


title: LN229-xray-rep1


title: wt_undiff_day0_3_SPOND3

description: Replicate 3

tag: genotype


title: Cal33-xray-rep1


title: Cal33-proton-rep1


title: Sample_023


title: FaDu-xray-rep1

value: FaDu


title: RNA-seq of A11-120-4

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1004 Post-treatment
A11-120-4


title: FaDu-proton-rep1


title: RNA-seq of A11-120-36

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1039 Post-treatment
A11-120-36


title: RNA-seq of A11-120-35

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1038 Post-treatment
A11-120-35


title: Sample_022


title: RNA-seq of A11-120-34

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1037 Post-treatment
A11-120-34


title: Sample_021


title: wt_undiff_day0_2_SPOND2

description: Replicate 2

value: Wild-type (control)


title: PC3-xray-rep1


title: wt_diff_day5_4_SPOND18

description: Replicate 4


title: PC3-proton-rep1


title: PC3-sham-rep1


title: Patient_8_post_G207

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description:
108_post
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

hyb_protocol: 150ng DNase-treated RNA was used as input for PanCancer immune gene expressional panel from NanoString Technologies. Hybridization with reporter CodeSet and capture ProbeSet was performed according to manufacturer's protocol for 16 hours at 65 degrees C. Hybridized samples were then processed on the nCounter MAX/FLEX prep station using high sensitivity setting.

scan_protocol: Cartridges were scanned on nCounter digital analyzer at Max setting (555 fields of view).

data_processing: Digital counts were normalized using a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within that sample lane. All normalization techniques were applied in nSolver software according to manufacturer's protocol. The 'NS_CANCERIMMUNE_V1.1.G207.csv' is an excel template which contains individual RCC data files produced by the nCounter digital analyzer into a single spreadsheet.

source_name: glioblastoma tumor

extract_protocol: RNA was extracted from formalin-fixed paraffin-embedded tumor tissue blocks using Covaris truXTRAC FFPE total nucleic acid kit per manufacturer’s instructions. RNA was DNase-treated using Zymo RNA clean/concentrator protocol.

treatment_protocol: Human recurrent glioblastoma tumors resected before (pre-G207) and after (post-G207) treatment with the oncolytic herpes simplex virus G207.

tag: individual

value: brain tumor

tag: diagnosis

value: glioblastoma

tag: glioblastoma subtype

value: Proneural/Neural

tag: brain location

value: right frontal

tag: g207 treatment

value: post-G207 inoculation

tag: age (years)

tag: Sex

tag: survival post g207 (days)


title: FaDu-sham-rep1

tag: time after dose in days

tag: time after dose in hours


title: wt_diff_day5_3_SPOND17

description: Replicate 3

value: differentiated

value: Day 5


title: DU145-proton-rep1


title: Sample_019

value: plasma

tag: patient diagnosis

value: breast cancer

tag: molecule subtype

value: exosomal miRNA


title: DU145-xray-rep1

tag: cell line


title: Sample_020

tag: tissue


title: RNA-seq of A11-120-33

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1036 Post-treatment
A11-120-33

tag: treatment status

tag: gender

tag: subjectid


title: RNA-seq of A11-120-32

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1035 Post-treatment
A11-120-32


title: Sample_018


title: Patient_7_post_G207

description:
107_post
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

tag: individual

value: Mesenchymal

value: female


title: RNA-seq of A11-120-31

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1034 Post-treatment
A11-120-31

value: male


title: Sample_017


title: wt_undiff_day0_1_SPOND1

description: Replicate 1

tag: genotype

tag: group

value: undifferentiated

tag: time point

value: Day 0


title: wt_diff_day5_2_SPOND16

description: Replicate 2


title: DU145-sham-rep1


title: Patient_6_post_G207

description:
106_post
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

tag: diagnosis

tag: glioblastoma subtype

tag: brain location

value: right frontoparietal

tag: g207 treatment


title: Patient_6_pre_G207

description:
106_pre
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

value: pre-G207 inoculation

tag: age (years)

tag: Sex

tag: survival post g207 (days)


title: Sample_016

tag: patient diagnosis

tag: molecule subtype


title: C9_undiff_day0_4_SPOND14

description: Replicate 4

value: Mutant C9


title: Patient_5_post_G207

description:
105_post
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

tag: tissue

value: brain tumor

value: glioblastoma


title: wt_diff_day5_1_SPOND15

description: Replicate 1

value: Wild-type (control)


title: RNA-seq of A11-120-30

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1033 Post-treatment
A11-120-30

tag: treatment status

value: Post-treatment


title: RNA-seq of A11-120-3

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1003 Post-treatment
A11-120-3

tag: gender


title: C9_undiff_day0_3_SPOND13

description: Replicate 3


title: Patient_5_pre_G207

description:
105_pre
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

value: right frontal


title: RNA-seq of A11-120-29

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1032 Post-treatment
A11-120-29

tag: subjectid


title: C9_undiff_day0_2_SPOND12

description: Replicate 2


title: RNA-seq of A11-120-28

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1031 Post-treatment
A11-120-28


title: C9_undiff_day0_1_SPOND11

description: Replicate 1


title: C9_diff_day5_4_SPOND27

description: Replicate 4

value: differentiated

value: Day 5


title: Sample_014

value: plasma

value: breast cancer


title: Sample_013

value: exosomal miRNA


title: RNA-seq of A11-120-27

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1030 Post-treatment
A11-120-27


title: Sample_012


title: RNA-seq of A11-120-26

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1029 Post-treatment
A11-120-26


title: Patient_3_pre_G207

description:
103_pre
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

tag: individual

value: Classical/Proneural

value: left frontoparietal

value: female


title: Sample_011


title: Patient_1_post_G207

description:
101_post
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

value: Mesenchymal

value: left frontal

value: post-G207 inoculation

value: male


title: C9_diff_day5_3_SPOND26

description: Replicate 3

tag: genotype

value: Mutant C9


title: Sample_015


title: Patient_1_pre_G207

description:
101_pre
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

value: brain tumor

value: glioblastoma

value: pre-G207 inoculation


title: Sample_010


title: C1_undiff_day0_4_SPOND8

description: Replicate 4

value: Mutant C1

tag: group

value: undifferentiated

value: Day 0


title: C9_diff_day5_1_SPOND24

description: Replicate 1

value: differentiated

tag: time point

value: Day 5


title: RNA-seq of A11-120-25

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1028 Post-treatment
A11-120-25

value: Post-treatment


title: Sample_008

value: plasma

value: breast cancer

value: exosomal miRNA


title: Sample_009


title: RNA-seq of A11-120-23

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1026 Post-treatment
A11-120-23


title: RNA-seq of A11-120-24

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1027 Post-treatment
A11-120-24


title: C1_undiff_day0_3_SPOND7

description: Replicate 3


title: RNA-seq of A11-120-22

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1025 Post-treatment
A11-120-22


title: Patient_3_post_G207

description:
103_post
We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel.
Raw data file: NS_CANCERIMMUNE_V1.1.G207.csv

tag: diagnosis

value: Classical/Proneural

value: left frontoparietal

value: female


title: C1_undiff_day0_2_SPOND6

description: Replicate 2


title: Sample_006


title: C9_diff_day5_2_SPOND25

description: Replicate 2


title: C1_undiff_day0_1_SPOND5

description: Replicate 1


title: RNA-seq of A11-120-21

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1024 Post-treatment
A11-120-21

value: male


title: RNA-seq of A11-120-20

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1023 Post-treatment
A11-120-20


title: C1_diff_day5_4_SPOND22

description: Replicate 4


title: Sample_005


title: RNA-seq of A11-120-2

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1002 Post-treatment
A11-120-2


title: Hippocampus_db/db_DMDD_rep2

city: Nanning

first: Lihui

last: Wang

address: No. 22 Shuangyong Road

institute: Guangxi Medical University

description: gene expression in 14 weeks db/db_DMDD mice hippocampus

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: hippocampus, db/db mice

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and Rnase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: After behavioral tests, microarray analysis was performed on the hippocampal tissues of 3 db/db_vehicle and 3 db/db_DMDD mice at the age of  14 weeks.

value: hippocampus

tag: age

value: 14 weeks

tag: mice

value: db/db


title: Hippocampus_db/db_DMDD_rep3


title: C1_diff_day5_3_SPOND21

description: Replicate 3


title: Sample_004


title: RNA-seq of A11-120-19

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1022 Post-treatment
A11-120-19


title: Sample_003


title: Hippocampus_db/db_DMDD_rep1


title: Sample_002


title: C1_diff_day5_2_SPOND20

description: Replicate 2


title: Sample_001


title: Sample_007


title: RNA-seq of A11-120-18

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1020 Post-treatment
A11-120-18


title: PDPN3

city: Shanghai

first: Han

last: Zhou

address: No.639 Zhizaoju Road

institute: Ninth People Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Barcode data quality analysis. Cellbarcodes with lower sequencing qualitywere filtered out to ensure the accuracy of subsequent analysis.
FastQC for quality evaluation, fastp for trimming, STAR aligner (2.5.3a) for alignment, featureCounts (1.6.2) for transcript counting.
The cells with genes ＞2500 or ＜200 and the cells that have >5% mitochondrial genes were filtered out. Gene expressions of each cell were normalized by total expression, multiplied by a scale factor of 10,000, and log-transformed.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every single cell in the specific samples

source_name: Dorsal root ganglion

extract_protocol:
The single-cell suspensions of DRG tissue were loaded onto microfluidic devices. Then, millions of beads with unique cell-barcodes and unique molecular identifiers (UMIs) were loaded similar to cells. Only one bead was loaded in each microwell. Following lysis, mRNA were captured onto the beads for the construction of sequencing libraries.
single-cell RNA libraries were prepared for sequencing using standard Illumina protocols accompanying the GEXSCOPE Single-Cell RNA Library Kit (Singleron, China)
single-cell RNA seq

treatment_protocol: Diabetic rats were induced by injected streptozotocin (STZ) on Day 0. We grouped diabetic rats according to the 50% paw withdrawal threshold (PWT) on Day 28. Rats with PWT ≤ 8 g were selected into the PDPN group and rats with PWT ≥ 15g were selected into the DM group. Rats in normal group (N group) were injected vehicle on Day 0.

tag: strain

value: Sprague Dawley

value: Dorsal root ganglion

tag: treatment

value: streptozotocin

tag: disease state

value: PDPN


title: RNA-seq of A11-120-17

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1019 Post-treatment
A11-120-17


title: PDPN1


title: PDPN2


title: DM2

value: DM


title: PDPN4

extract_protocol:
The single-cell suspensions of DRG tissue were loaded onto microfluidic devices. Then, millions of beads with unique cell-barcodes and unique molecular identifiers (UMIs) were loaded similar to cells. Only one bead was loaded in each microwell. Following lysis, mRNA were captured onto the beads for the construction of sequencing libraries.
single-cell RNA libraries were prepared for sequencing using standard Illumina protocols accompanying the GEXSCOPE Single-Cell RNA Library Kit (Singleron, China)

value: Rattus norregicus


title: DM1


title: Hippocampus_db/db_vehicle_rep2

description: gene expression in 14 weeks db/db_vehicle mice hippocampus


title: RNA-seq of A11-120-16

description:
RNA-seq of bulk prostate tissue from case 15-c-0124_1018 Post-treatment
A11-120-16

value: Post-treatment


title: Hippocampus_db/db_vehicle_rep1