title: RNA-SEQ, A12-18-11, PCBN35, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-11 from patient PCBN35
processed_counts.txt
processed_TPM.txt
A12-18-11

tag: preoperative psa


title: RNA-SEQ, A12-20-5, PCBN35, prostate tissue

status: Public on Apr 27 2022

type: SRA

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

country: USA

institute: National Cancer Institute

description:
Paired-end RNA-seq for prostate tissue sample A12-20-5 from patient PCBN35
processed_counts.txt
processed_TPM.txt
A12-20-5

library_source: transcriptomic

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.
Assembly: hg19
Supplementary files format and content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

molecule: total RNA

organism: Homo sapiens

source_name: prostate tissue

extract_protocol:
RNA was extracted from OCT prostate tissues using the Qiagen RNeasy kit or from frozen buffy coats using the Macharay-Nagel NucleoSpin RNA Blood  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.
Paired-end

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Blood was drawn into EDTA tubes prior to surgery. Prostate tissues were grossed, accessioned, embedded in OCT, and frozen.

tag: disease state

value: prostate cancer

tag: patient id

tag: gender

value: male

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

value: WHITE

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: BENIGN


title: Normal-7

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: 181205_UNC17-D00216_0591_ACD0YEANXX_AATCCGGA-CTACAGTT_S16_L004

data_processing:
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a1. Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.02 in ‘-quant’ mode, based on the STAR alignments
Raw read counts for all RNAseq samples normalized to fixed upper quartile3
RNAseq normalized gene counts were then log2 transformed (zeros were unchanged) using Cluster 3.0 v1.52
Genes were filtered for those expressed in 70% of samples
Matrix was median centered and column standardized using R studio v1.1.463
Genome_build: hg38
Supplementary_files_format_and_content: txt file. Content: 40n samples logtrans, 70% filtered, median-centered, column standardized

source_name: Paired Normal Tissue

growth_protocol: We obtained 9 flash frozen paired normal and ER+ breast tumor samples, 15 TNBC breast tumor samples, and 7 flash frozen tumor samples from 2 TNBC PDX models (WHIM2 and WHIM30)

extract_protocol:
total RNA extracted using Qiagen Rneasy Mini Kit
mRNAseq libraries were made from total RNA using the Illumina TruSeq mRNA sample preparation kit and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration

treatment_protocol: Untreated

tag: tumor status

value: Normal

tag: tnbc-high tertiles

value: Medium

tag: er-high tertiles

value: High


title: Normal-6

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GGCTTAAG-TCGTGACC_S13_L004

value: Low


title: RNA-SEQ, A12-20-3, PCBN34, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-3 from patient PCBN34
processed_counts.txt
processed_TPM.txt
A12-20-3


title: RNA-SEQ, A12-18-10, PCBN34, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-10 from patient PCBN34
processed_counts.txt
processed_TPM.txt
A12-18-10

source_name: buffy coat


title: RNA-SEQ, A12-20-4, PCBN34, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-4 from patient PCBN34
processed_counts.txt
processed_TPM.txt
A12-20-4

value: TUMOR


title: PBCPRE029

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: Sex

value: F

value: PBC

tag: treatment

value: Pre

tag: tissue

value: serum


title: PBCPRE027

tag: disease state


title: PBCPRE028

value: M


title: RNA-SEQ, A12-20-1, PCBN33, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-1 from patient PCBN33
processed_counts.txt
processed_TPM.txt
A12-20-1

tag: patient id

tag: gender

tag: preoperative psa


title: Normal-5

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TTGGACTC-GGAAGCAG_S14_L004


title: Normal-4

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CCAAGTCT-AAGGATGA_S15_L004


title: RNA-SEQ, A12-20-2, PCBN33, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-20-2 from patient PCBN33
processed_counts.txt
processed_TPM.txt
A12-20-2

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination


title: Normal-3

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CTCTCGTC-TATAACCT_S12_L003


title: PBCPRE024


title: PBCPRE025


title: RNA-SEQ, A12-18-9, PCBN33, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-9 from patient PCBN33
processed_counts.txt
processed_TPM.txt
A12-18-9

tag: patient gleason score

tag: race

tag: pathologic stage


title: Normal-2

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TCTCTACT-CGCGGTTC_S10_L003


title: IECs, WT_4

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent microarray scanner (G2565BA, Agilent)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent)  using default parameters.

organism: Mus musculus

source_name: Intestinal epithelial cells

label_protocol: The miRNAs expression profile was carried out through the Mouse SurePrint G3 miRNA microarray 8x60K (Agilent Technologies) based on Sanger miRBase release 21.0, according to the manufacturer’s instructions. Briefly, 100 ng of total RNA isolated from IECs were firstly dephosphorylated with a calf intestine alkaline phosphatase treatment for 30min at 37◦C before labeling. Samples were diluted with Dimethyl sulfoxide (DMSO), denatured for 10min at 100◦C, and labelled using pCp-Cy3 in T4 RNA ligation buffer.

extract_protocol: Total RNA including miRNAs were extracted using Qiagen miRNeasy mini kit according to the manufacturer's instructions. Total RNA was then eluted in ribonuclease-free water. The RNA concentration was determined with NanoDrop ND-2000 Spectrophotometer (Nanodrop Technologies).

treatment_protocol: At 16 weeks, mice were sacrificed and the colons were collected and digested for IECs isolation after mechanical and enzymatic digestion using gentleMACS™ Dissociator and Lamina Propria Dissociation kit (Miltenyi Biotec) respectively. IECs were selected using anti-CD326 (EpCAM) conjugated microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) for 15 min at 4°C after CD45+ cells depletion. The MACS separation was performed according to the manufacturer’s recommendation.

tag: cell type

value: Intestinal epithelial cells

value: Colon

tag: strain

tag: genotype

value: wild-type

value: control

value: Male


title: Normal-1

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GACCTGAA-TTGGTGAG_S11_L003

tag: tumor status

tag: tnbc-high tertiles

tag: er-high tertiles


title: PBCPRE022

tag: Sex

tag: age

tag: treatment

tag: tissue


title: RNA-SEQ, A12-16-22, PCBN32, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-22 from patient PCBN32
processed_counts.txt
processed_TPM.txt
A12-16-22

tag: disease state

value: prostate cancer

tag: patient id

tag: gender

value: male

tag: preoperative psa

value: WHITE

tag: 5-year disease status

value: remission

tag: sample type


title: RNA-SEQ, A12-18-8, PCBN32, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-8 from patient PCBN32
processed_counts.txt
processed_TPM.txt
A12-18-8

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

tag: pathologic stage


title: ER9

description: 181205_UNC17-D00216_0591_ACD0YEANXX_AGTTCAGG-CCAACAGA_S9_L003

source_name: ER Tumor

tag: tumor status

value: ER+

value: LumB

tag: tnbc-high tertiles

value: Medium

tag: er-high tertiles


title: PBCPRE021

tag: Sex

tag: age

tag: treatment


title: IECs, WT_2

tag: cell type

tag: tissue

tag: strain

tag: genotype

tag: disease state


title: IECs, WT_1


title: RNA-SEQ, A12-16-19, PCBN31, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-19 from patient PCBN31
processed_counts.txt
processed_TPM.txt
A12-16-19

tag: patient id

tag: gender

tag: preoperative psa

tag: sample gleason score

tag: 5-year disease status

tag: sample type

value: BENIGN


title: PBCPRE026

value: F

value: PBC


title: IECs, WT_3


title: RNA-SEQ, A12-16-20, PCBN31, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-20 from patient PCBN31
processed_counts.txt
processed_TPM.txt
A12-16-20

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

tag: pathologic stage

value: TUMOR


title: ER8

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TGGATCGA-GTGCGATA_S7_L002

tag: tumor status

value: Normal-like

tag: tnbc-high tertiles

value: Low

tag: er-high tertiles

value: High


title: PBCPRE018

tag: Sex

value: M

tag: age

tag: treatment

value: Pre

tag: tissue

value: serum


title: PBCPRE019

tag: disease state


title: IECs, Winnie_4

tag: cell type

value: Intestinal epithelial cells

value: Colon

tag: strain

tag: genotype

value: Winnie

value: ulcerative colitis mice model

value: Male


title: PBCPRE023


title: RNA-SEQ, A12-18-7, PCBN31, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-7 from patient PCBN31
processed_counts.txt
processed_TPM.txt
A12-18-7

value: prostate cancer

tag: patient id

tag: gender

value: male

tag: preoperative psa

tag: sample gleason score

value: WHITE

tag: 5-year disease status

value: remission

tag: sample type


title: ER6

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GCTTGTCA-GAACATAC_S6_L002

tag: tumor status

value: ER+

value: LumA

value: Medium


title: RNA-SEQ, A12-16-21, PCBN32, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-21 from patient PCBN32
processed_counts.txt
processed_TPM.txt
A12-16-21

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

tag: pathologic stage

value: BENIGN


title: IECs, Winnie_3

tag: tissue

tag: Sex


title: LIP-3

city: Philadelphia

first: George

last: Hajishengallis

state: PA

address: School of Dental Medicine

institute: University of Pennsylvania

data_processing:
Clean reads were mapped to the mouse genome (Ensembl assembly GRCm38) using Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013) with default settings after filtering low-quality, adaptor-polluted and high content of unknown base (N) reads.
Reads count in each gene were calculated by htseq-count package. Subsequently, differential gene expression was analyzed using DEGseq2 (Love et al., 2014) and significantly differentially expressed genes (DEGs) were defined by FDR-adjusted p value < 0.05 in the LIP-subjected group relative to their expression in the control group.
Genome_build: Ensembl assembly GRCm38
Supplementary_files_format_and_content: Reads count in each gene

growth_protocol: C57BL/6 mice were subjected, or not (Non-ligature, NL), to ligature-induced periodontitis (LIP) and BM cells were harvested on day 7. FACS-sorted LSKs were subjected to RNA-sequencing and transcriptome analysis.

extract_protocol:
LSK cells from the BM of LIP-subjected mice or unligated control mice were sorted by flow cytometry. Three mice were pooled for each replicate.  Total RNA was extracted by Trizol (Invitrogen) and DNA was removed by using TURBO DNA-free Kit (Invitrogen).
PolyA-selected mRNA libraries were generated following the manufacturer’s protocols (BGI). Samples were sequenced on BGISEQ platform to generate 100 bp paired-end reads with an average depth of 45.0 M reads per sample.

tag: treatment

value: ligature-induced periodontitis (LIP) for 7 days

value: bone marrow

tag: cell type

value: LSK cells


title: PBCPRE017

value: F

tag: age

tag: disease state

value: PBC

value: Pre

value: serum


title: ER5

description: 181205_UNC17-D00216_0591_ACD0YEANXX_ATCCACTG-AGGTGCGT_S5_L002

tag: tnbc-high tertiles

tag: er-high tertiles


title: RNA-SEQ, A12-16-17, PCBN30, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-17 from patient PCBN30
processed_counts.txt
processed_TPM.txt
A12-16-17

tag: patient id

tag: gender

tag: preoperative psa

tag: sample gleason score


title: IECs, Winnie_2

value: Intestinal epithelial cells

value: Colon

tag: strain

tag: genotype

value: Winnie

value: ulcerative colitis mice model


title: LIP-2


title: PBCPRE016


title: RNA-SEQ, A12-16-18, PCBN30, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-18 from patient PCBN30
processed_counts.txt
processed_TPM.txt
A12-16-18

value: prostate cancer

value: male

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

value: WHITE

tag: 5-year disease status

tag: sample type

value: TUMOR


title: ER7

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CAAGCTAG-ACATAGCG_S8_L002

tag: tumor status

value: ER+

value: LumA

value: Medium


title: ER4

description: 181205_UNC17-D00216_0591_ACD0YEANXX_AAGTCCAA-TATGAGTA_S4_L001

value: Normal-like

value: Low


title: ER3

description: 181205_UNC17-D00216_0591_ACD0YEANXX_GGACTTGG-CGCAGACG_S1_L001


title: IECs, Winnie_1

tag: cell type

tag: tissue

tag: Sex

value: Male


title: RNA-SEQ, A12-18-6, PCBN30, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-6 from patient PCBN30
processed_counts.txt
processed_TPM.txt
A12-18-6

tag: disease state

tag: race

tag: pathologic stage

tag: age

value: remission


title: NL-3

tag: treatment

value: none (control)

value: bone marrow

value: LSK cells


title: LIP-1

value: ligature-induced periodontitis (LIP) for 7 days


title: RNA-SEQ, A12-16-15, PCBN29, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-15 from patient PCBN29
processed_counts.txt
processed_TPM.txt
A12-16-15

tag: patient id

tag: gender

tag: preoperative psa

tag: sample gleason score

value: recurrence

value: BENIGN


title: ER1

description: 181205_UNC17-D00216_0591_ACD0YEANXX_CCGCGGTT-AGCGCTAG_S3_L001

tag: tnbc-high tertiles

tag: er-high tertiles

value: High


title: ER2

description: 181205_UNC17-D00216_0591_ACD0YEANXX_TTATAACC-GATATCGA_S2_L001

value: LumB


title: PBCPRE020

value: M

value: PBC

value: Pre

value: serum


title: RNA-SEQ, A12-16-16, PCBN29, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-16 from patient PCBN29
processed_counts.txt
processed_TPM.txt
A12-16-16

value: prostate cancer

value: male

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

value: WHITE

tag: 5-year disease status

value: TUMOR


title: PBCPRE012

value: F

tag: tissue


title: PBCPRE015

tag: Sex


title: NL-1

tag: strain

value: none (control)

tag: cell type


title: PBCPRE014

tag: disease state


title: PBCPRE011

tag: age


title: PBCPRE013

tag: treatment


title: preNC_bCat_shRNA_rep1

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcriptome mapping was performed with STAR version 2.5.2b to hg19 genome using Gencode V19 release exon/spice-junction annotation.
Differential expression analysis was performed using cufflinks version 2.2.1 using UCSC gene annotation with fr-firststrand library type and the correction of sequencing bias and multiple reads mapping.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

source_name: WA01 ES cells

growth_protocol: Human ESC/iPSC colonies digested with Accutase cell detachment solution (Innovative Cell Technologies) were re-suspended in differentiation medium plus CHIR 99021 (3 µM; #4423 Tocris Bioscience) plated at 20,000 cells per cm2 on Matrigel-coated surfaces. Differentiation medium contained DMEM/F12 medium supplemented with 2% B27 supplement (Life Technologies), 1× Glutamax (Life Technologies) and 0.5% bovine serum albumin (wt/vol) (A9647, Sigma-Aldrich). The ROCK inhibitor Y-27632 (10 µM; Tocris Bioscience) was added for the first two days.

extract_protocol:
Total RNAs were extracted using TRIzol reagent (Life Technologies) according to Manufacturer's instructions. Extracted RNAs were dissolved in H2O and kept at -80oC until ready for library construction.
Libraries were prepared from poly-adenylated (poly-A) mRNAs using a custom kit based on the Illumina’s mRNA-seq kit (Illumina, part # RS-122-2101)

treatment_protocol: shRNA cell lines were generated by infecting wildtype cells with lentiviruses containing constructs that allowed overexpression of either luciferase shRNA or b-catenin shRNAs

value: Pre-neural crest cells

tag: cell line

value: WA01 ES cells

tag: differentiation day

value: day 3

tag: genotype

value: b-catenin shRNA


title: RNA-SEQ, A12-18-5, PCBN29, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-5 from patient PCBN29
processed_counts.txt
processed_TPM.txt
A12-18-5

tag: patient id

tag: gender

tag: preoperative psa

tag: sample gleason score

tag: race

tag: pathologic stage

value: recurrence

tag: sample type


title: RNA-SEQ, A12-16-13, PCBN28, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-13 from patient PCBN28
processed_counts.txt
processed_TPM.txt
A12-16-13

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: 5-year disease status

value: remission

value: BENIGN


title: preNC_Luc_shRNA_rep1

tag: cell type

value: Luciferase shRNA


title: RNA-SEQ, A12-16-14, PCBN28, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-14 from patient PCBN28
processed_counts.txt
processed_TPM.txt
A12-16-14

tag: disease state

tag: age


title: PBCPRE010

tag: Sex

value: PBC

tag: treatment

tag: tissue


title: 24hr_bCat_shRNA_rep1

tag: cell line

tag: differentiation day

value: day 1

tag: genotype


title: UR_PBMC

city: Guangzhou

first: Hongwei

last: Wu

address: Jinan University, No.601, West Huangpu Avenue ,Guangzhou, Guangdong, China

country: China

institute: Jinan University

library_source: genomic

data_processing:
Barcode processing: To improve data quality, a ‘whitelist’ of correct barcode sequences was applied to fix the occasional sequencing error in barcodes obtained from the ‘I2’ index read
Genome alignment: Reference-based analysis was performed using the Cell Ranger ATAC pipeline. BWA-MEM was applied with default parameters to align the trimmed read pairs that were greater than 25 bp to GRCh38
Filteing: We filtered scATAC-seq data using cut-offs of 1,000 unique nuclear fragments per cell and a transcription start site (TSS) enrichment score of 8 to exclude low-quality cells in 10x genomic Cell Ranger ATAC platform
Peak calling: First, the number of transposition events at each base pair along the genome was counted. Next, a smoothed profile of these events with a 401 bp moving window around each base pair and fitting a ZINBA-like mixture model was generated. Then, a signal threshold was set to determine whether a region was a peak signal or noise based on an odds ratio of 1/5. Finally, peaks within 500 bp of each other were merged to produce a position-sorted BED file.
Cell calling and peak-barcode matrix: For each barcode, the mapped high-quality fragments that passed all filters were recorded, and the number of fragments that overlapped any peak regions was used to separate the signal from noise. To capture the signal and noise, a mixture model of two negative binomial distributions was set, and barcodes that corresponded to real cells from the non-cell barcodes were separated by setting an odds ratio of 1000. Subsequently, a raw peak-barcode matrix consisting of the counts of fragment ends within each peak region for each barcode was produced. After filtering to contain only cell barcodes, the matrix was used in subsequent analyses, such as dimensionality reduction, clustering and visualization.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files for barcodes; mtx files for matrix; bed files for peaks

molecule: genomic DNA

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
PBMCs were separated using an equal proportion of Ficoll-Paque Plus. Nuclei suspensions were obtained by adding lysis buffer (10 mM Tris-HCl, 3 mM MgCl2, 10 mM NaCl , 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 1% BSA). The final libraries were constructed via PCR with P5 and P7 primers in Illumina® bridge amplification.
scATAC-seq libraries were generated according to the Chromium Single Cell ATAC protocol (10x GENOMICS)

value: Uremia patients

value: peripheral blood


title: 24hr_Luc_shRNA_rep1


title: RNA-SEQ, A12-18-4, PCBN28, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-4 from patient PCBN28
processed_counts.txt
processed_TPM.txt
A12-18-4

value: prostate cancer

tag: patient id

tag: gender

value: male

tag: preoperative psa

tag: sample gleason score


title: ES_bCat_shRNA_rep1

value: Embryonic stem cells

value: day 0


title: PBCPRE009

value: M

value: Pre

value: serum


title: RNA-SEQ, A12-16-11, PCBN27, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-11 from patient PCBN27
processed_counts.txt
processed_TPM.txt
A12-16-11

tag: % tumor

tag: race

value: WHITE

tag: pathologic stage

tag: sample type


title: PBCPRE008

value: F


title: NPM1AID_mESC_Auxin_PRC2i_12h_CUTRUN_H3K27me3

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

data_processing:
For CUT&RUN data processing, reads were aligned to the mouse reference genome mm10 using Bowtie2 (v2.4.1) with default parameters. Reads of quality score less than 30 were removed using samtools (v1.9) and PCR duplicates were removed using picard (v2.18.11). Regions in mm10 genome blacklist was removed using bedtools (v2.27.1) and bigwig files were generated using deepTools (v3.2.1) and parameters: --binSize 50 --normalizeUsing RPKM --ignoreDuplicates  --ignoreForNormalization chrX for visualization in IGV. Peaks were called using MACS2 (v2.1.1) with parameters: -f BAMPE -g mm --keep-dup all  --broad  --broad-cutoff 0.1. Heatmaps were performed using the functions computeMatrix followed by plotHeatmap and plotProfile from deepTools (v3.2.1).
Assembly: mm10 and dm6
Supplementary files format and content: Bigwig files generated by deepTools (v3.2.1) are RPKM normalized track files; Broadpeak files generated by MACS2 (v2.1.1) are peak files; featurecount.txt files generated by featureCounts (v1.6.3) are gene counts files.
Library strategy: CUT&RUN

source_name: E14 mESC

growth_protocol: E14 mESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021).

extract_protocol:
The CUT&RUN experiments were performed using the CUTANATM CUT&RUN assay (EpiCypher) under the manufacturer’s instructions. Briefly, the nuclei of cells were isolated using the TMSD buffer. The nuclei were bound by activated Concanavalin A beads, followed by nuclear membrane permeabilization, incubation of primary antibody overnight, and binding of antibody to pA-MNase fusion protein. The MNase was activated by CaCl2 at 4o C for 1 hr. The DNA released into the supernatant were purified and subjected to library preparation and next-generation sequencing.
CUT&RUN released DNA was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments were size-selected using Agencourt AMPure XP beads (0.5X and 0.5X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 100 bp paired-end reads on the Illumina NovaSeq 6000 platform.

tag: cell type

value: mESCs

value: NPM1 degradable mESCs

tag: antibody

value: H3K27me3 (Cell Signaling Technology, Cat# 9733)


title: NPM1AID_mESC_Auxin_12h_CUTRUN_H3K27me3


title: NL-2

tag: strain

value: none (control)

value: bone marrow

value: LSK cells


title: PBCPRE007

tag: Sex

tag: age

tag: disease state

value: PBC


title: RNA-SEQ, A12-16-12, PCBN27, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-12 from patient PCBN27
processed_counts.txt
processed_TPM.txt
A12-16-12

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: 5-year disease status

value: remission

value: TUMOR


title: RNA-SEQ, A12-18-3, PCBN27, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-3 from patient PCBN27
processed_counts.txt
processed_TPM.txt
A12-18-3

value: prostate cancer

tag: patient id

value: male


title: RNA-SEQ, A12-16-9, PCBN26, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-9 from patient PCBN26
processed_counts.txt
processed_TPM.txt
A12-16-9

tag: gender

value: HISPANIC

value: recurrence

value: BENIGN


title: NC_PBMC

value: Healthy controls

tag: tissue

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)


title: NPM1AID_mESC_Control_12h_CUTRUN_IgG

value: mESCs

tag: genotype

value: IgG (Sigma, Cat# I8140)


title: NPM1AID_mESC_NoAuxin_6h_ChIP_H3K27me3

data_processing:
For ChIP-Seq data processing, reads were aligned to the mouse reference genome mm10 and dm6 for spike-in samples, using Bowtie2 (v2.4.1) with default parameters. Reads of quality score less than 30 were removed using samtools (v1.9) and PCR duplicates were removed using picard (v2.18.11). Regions in mm10 genome blacklist was removed using bedtools (v2.27.1) and bigwig files were generated using deepTools (v3.2.1) and parameters: --binSize 50 --normalizeUsing RPKM --ignoreDuplicates  --ignoreForNormalization chrX --extendReads 250 for visualization in IGV. Peaks were called using MACS2 (v2.1.1) with parameters: -g mm --keep-dup all  --broad  --broad-cutoff 0.1. For visualization of ChIP-seq, uniquely aligned reads were normalized using dm6 spike-in. Heatmaps were performed using the functions computeMatrix followed by plotHeatmap and plotProfile from deepTools (v3.2.1).
Assembly: mm10 and dm6
Supplementary files format and content: Bigwig files generated by deepTools (v3.2.1) are RPKM normalized track files; Broadpeak files generated by MACS2 (v2.1.1) are peak files; featurecount.txt files generated by featureCounts (v1.6.3) are gene counts files.

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 15 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina NovaSeq 6000 platform.

value: NPM1 degradable mESCs

value: H3K27me3 (Cell Signaling Technology, Cat# 9733)


title: NPM1AID_mESC_Control_12h_CUTRUN_H3K27me3


title: NPM1AID_mESC_NoAuxin_6h_ChIP_Input

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 15 min and quenched with 0.125 M glycine for 5 min at RT, followed by twice wash with PBS. Cell pellets from above steps were lysed in LB1 buffer (50 mM HEPES, pH 7.5 at 4°C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X; 10 min at 4°C), LB2 buffer (10 mM Tris, pH 8 at 4°C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; 10 min at 4°C), and then resuspended in LB3 buffer  (10 mM Tris, pH 7.5 at 4°C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sheared using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Dynabeads, chromatin was incubated with indicated antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G Dynabeads for 2 hr at 4°C. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked at 65°C overnight, digested with protease K and RNaseA and then purified for library construction.
ChIP input  DNA (10 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Immunoprecipitated DNA (∼1-30 ng) was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 50 bp single-end reads on the Illumina NovaSeq 6000 platform.


title: PBCPRE006

value: F

tag: treatment

value: Pre

value: serum


title: PBCPRE005

value: PBC


title: RNA-SEQ, A12-16-10, PCBN26, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-10 from patient PCBN26
processed_counts.txt
processed_TPM.txt
A12-16-10

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: race

value: TUMOR


title: NPM1AID_mESC_Auxin_12h_RNA_Rep2

data_processing:
For RNA-Seq data processing, reads were aligned to the mouse reference genome mm10 using STAR (v2.6.1d) with parameters: --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 1 --outSAMstrandField intronMotif  --outSAMmapqUnique 60 --twopassMode Basic --outSJfilterReads Unique --outFilterIntronMotifs RemoveNoncanonical. Gene counts were calculated using featureCounts (v1.6.3) with parameters: -p, -s 2, -t exon, and RefSeq mm10 annotation downloaded from GENCODE. The output gene count tables were used as input into DeSeq2 for normalization and differential expression analysis.
Assembly: mm10 and dm6
Supplementary files format and content: Bigwig files generated by deepTools (v3.2.1) are RPKM normalized track files; Broadpeak files generated by MACS2 (v2.1.1) are peak files; featurecount.txt files generated by featureCounts (v1.6.3) are gene counts files.

molecule: polyA RNA

extract_protocol:
Cells were lysed in Tripure isolation reagent (sigma) followed by passing through a 20 gauge needle. RNA was purified by chloroform extraction, and precipitated by isopropyl alcohol. Genomic DNA was removed by RNEasy plus Mini Kit.
PolyA+ RNA was isolated from 5 ug total RNA using Dynabeads Oligo(dT)25, fragmented with Mg2+ contained in the 1st strand buffer at 94°C for 15 min, and reverse transcribed using Superscript III and random hexamers to synthesize the first strand. Single strand cDNA was precipitated and dTTP was removed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I and the E. coli ligase, and then purified by MinElute PCR Purification Kit. Double stranded DNA was end-repaired using End-It Repair Kit, tailed with deoxyadenine using Klenow exo-, and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 200-600 bp were size-selected using Agencourt AMPure XP beads (0.5X and 0.3X), and subjected to PCR amplification using Q5 DNA polymerase. Libraries were size-selected using Agencourt AMPure XP beads (0.75X), quantified by Qubit™ dsDNA HS Assay Kit and quality checked by High Sensitivity D1000 ScreenTape. Libraries were sequenced as 100 bp paired-end reads on the Illumina NovaSeq 6000 platform.

tag: cell type


title: RNA-SEQ, A12-16-7, PCBN25, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-7 from patient PCBN25
processed_counts.txt
processed_TPM.txt
A12-16-7

value: prostate cancer

value: WHITE

tag: pathologic stage

tag: sample type


title: ES_Luc_shRNA_rep1

value: Embryonic stem cells

tag: cell line

value: WA01 ES cells

tag: differentiation day

value: day 0

value: Luciferase shRNA


title: PBCPRE004

tag: Sex

value: M

tag: age

tag: disease state


title: NPM1AID_mESC_Auxin_12h_RNA_Rep1


title: RNA-SEQ, A12-16-8, PCBN25, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-8 from patient PCBN25
processed_counts.txt
processed_TPM.txt
A12-16-8

tag: patient id

value: male

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: 5-year disease status

value: recurrence


title: PBCPRE003

tag: treatment

tag: tissue


title: PBCPRE002


title: PBCPRE001


title: RNA-SEQ, A12-18-1, PCBN25, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-1 from patient PCBN25
processed_counts.txt
processed_TPM.txt
A12-18-1

tag: gender

tag: preoperative psa

tag: sample gleason score


title: AIHPOST023

value: AIH

value: Post


title: AIHPOST027


title: RNA-SEQ, A12-18-2, PCBN26, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-18-2 from patient PCBN26
processed_counts.txt
processed_TPM.txt
A12-18-2

tag: % tumor

tag: race

value: HISPANIC


title: AIHPOST022

value: F


title: NPM1AID_mESC_NoAuxin_12h_RNA_Rep1

tag: cell type

value: mESCs

tag: genotype

value: NPM1 degradable mESCs


title: NPM1AID_mESC_NoAuxin_12h_RNA_Rep2


title: RNA-SEQ, A12-16-5, PCBN24, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-5 from patient PCBN24
processed_counts.txt
processed_TPM.txt
A12-16-5

tag: pathologic stage

value: remission

tag: sample type

value: BENIGN


title: RNA-SEQ, A12-16-6, PCBN24, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-6 from patient PCBN24
processed_counts.txt
processed_TPM.txt
A12-16-6

value: prostate cancer

tag: age

value: TUMOR


title: AIHPOST021

tag: Sex

tag: disease state

value: serum


title: ileum DJB rep3

city: Shanghai

first: Yongjun

last: Liang

address: 2800 Gongwei Road

department: Center for Medical Research and Innovation

institute: Shanghai Pudong Hospital

description: Gene expression after DJB in ileum_rep3

hyb_protocol: After purification with the RNeasy Mini Kit, hybridization was performed using a Gene Expression Hybridization Kit in a Hybridization Oven (Agilent Technology).

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

data_processing: Array images were analyzed and raw data were extracted using the Agilent Feature Extraction software version 11.0.1.1 (Agilent Technology). Quantile normalization and subsequent data processing were performed using the Agilent GeneSpring GX version 12.1 software package (Agilent Technology).

source_name: ileum, DJB

label_protocol: In accordance with the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology), total RNA was amplified and labeled with the RNA Spike-In Kit and Low Input Quick Amp WT Labeling Kit (Agilent Technology).

extract_protocol: Total RNA was extracted from the duodenum with TRIzol reagent (Invitrogen, Grand Island, NY, USA) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany) and RNase-Free DNase Set (Qiagen) according to the manufacturer protocols.

tag: strain

tag: phenotype

value: diabetic

value: DJB

value: ileum


title: RNA-SEQ, A12-17-24, PCBN24, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-24 from patient PCBN24
processed_counts.txt
processed_TPM.txt
A12-17-24

tag: patient id

tag: % tumor-in-normal contamination

tag: patient gleason score

value: WHITE

tag: 5-year disease status


title: Mouse hypothalamus Glp1r-EYFP, sample 3 [S12_L001]

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Sequenced reads were mapped to the primary mouse genome (GRCm39) and GTF file (Ensembl v105) with 3' UTRs for Glp1r and Ghsr extended to include their furthermost 3' UTR in polyA_DB v3. Raw counts generated using CellRanger (v6.1.2).
Gene expression modelling and normalised counts per million were generated using Seurat (v4.1.0).
Assembly: GRCm39
Supplementary files format and content: h5-format file including raw count values for all samples.

source_name: Mouse hypothalamus Glp1r-EYFP

extract_protocol:
Fluorescence-activated cell sorting was performed using a BD Influx Cell Sorter to isolate Glp1rEYFP+ cells. Cells were gated according to cell size (FSC), cell granularity (SSC), FSC pulse-width for singlets, fluorescence at 488 nm/532 nm for EYFP and 647/670 nm for nuclear stain with DraQ5.
Single cell cDNA libraries from purified Glp1rEYFP+ cells were generated using the 10× Genomics Chromium Instrument and single-cell 3’ Reagent kit (V3); R1 = 28 bp, R2 = 91 bp

treatment_protocol: Mice (C57BL/6 background) were sacrificed by cervical dislocation, and tissue from the hypothalamus located ventrally caudal of the optical nerve chiasm (~Bregma -0.3 to -2.92 mm) was dissected into Hibernate-A medium without calcium. The tissue was digested with 20 U/ml Papain for 30 min at 37°C, followed by trituration in Hibernate-A medium containing 0.005% (w/v) DNase 1. The cell suspension was filtered through a 40 μm cell strainer into a fresh tube.

tag: strain background

tag: tissue

value: Hypothalamus


title: ileum DJB rep2

description: Gene expression after DJB in ileum_rep2

tag: gender

value: male

tag: treatment


title: ileum sham rep4

description: Gene expression after sham in ileum_rep4

source_name: ileum, sham

value: control


title: ileum sham rep3

description: Gene expression after sham in ileum_rep3


title: RNA-SEQ, A12-16-3, PCBN23, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-3 from patient PCBN23
processed_counts.txt
processed_TPM.txt
A12-16-3

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: race

value: recurrence


title: AIHPOST020

tag: age

value: AIH

value: Post


title: ileum sham rep1

description: Gene expression after sham in ileum_rep1


title: ileum sham rep2

description: Gene expression after sham in ileum_rep2


title: RNA-SEQ, A12-16-4, PCBN23, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-4 from patient PCBN23
processed_counts.txt
processed_TPM.txt
A12-16-4

tag: pathologic stage

tag: sample type


title: ileum DJB rep1

description: Gene expression after DJB in ileum_rep1

tag: strain


title: ileum DJB rep4

description: Gene expression after DJB in ileum_rep4

tag: phenotype


title: RNA-SEQ, A12-17-23, PCBN23, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-23 from patient PCBN23
processed_counts.txt
processed_TPM.txt
A12-17-23

tag: disease state

tag: patient id


title: Mouse hypothalamus Glp1r-EYFP, sample 1 [S10_L001]

tag: genotype


title: AOM/DSS-5FU/I-d1_2

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
dual index
3927_AS6_d1_2

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Chen et al., 2021), resulting in the processed data table.
MGI-Seq: Biological read: read1 - 3' end.  Technical read: read2 -UMI/cell barcode - the oligo barcodes are inDrop which is positioned exactly as in (Klein et al., 2015)
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020). Biological read: read2 - 3' end
Assembly: Mouse: GRCm38.85
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: colon

growth_protocol: primary cells

extract_protocol:
Mouse pithelial cell suspensions were generated accroding to protocol in (Vega et al., 2022). Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015. Chen et al., 2021.
CEL-Seq linear amplification of using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on BGI MGI-Seq (for single index) 100 read 1, 50 read2

tag: prep

value: inDrop scRNA-seq

value: WT

tag: cell type

value: AOM/DSS tumors - normal dissociation


title: WT fibroblast

description:
dual index
7396_AS3_fibro

value: fibroblast dissociation

value: untreated


title: Adjacent normal tissue_B541155

city: Yinchuan

first: Yuan

middle: li

last: Liu

state: Ningxia

address: Guangdong Medical University, 1 Xincheng Avenue, Songshan Lake Science and Technology Industrial Park, Dongguan City, Guangdong Province

institute: Clinical Laboratory and Diagnosis Center of Ningxia Hui Autonomous Region People's Hospital

description: Total RNA from each sample was treated with Rnase R to enrich circular RNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar),and incubated for 17 hours at 65℃ in an Agilent Hybridization.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: Adjacent normal tissue

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

tag: tissue

value: intestine

value: circular RNA


title: AIHPOST018

tag: Sex

value: F

value: serum


title: AIHPOST016

tag: treatment


title: AIHPOST019


title: Adjacent normal tissue_B629380


title: Mouse hypothalamus Glp1r-EYFP, sample 2 [S11_L001]

tag: strain background


title: AOM/DSS-5FU/I-d6

description:
dual index
4240_AS2_d6


title: RNA-SEQ, A12-17-22, PCBN22, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-22 from patient PCBN22
processed_counts.txt
processed_TPM.txt
A12-17-22

value: prostate cancer

tag: gender

tag: preoperative psa

tag: sample gleason score

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: 5-year disease status


title: AIHPOST015

tag: age


title: Mouse hypothalamus Gipr-EYFP, sample 2 [S2_L001]

data_processing:
Sequenced reads were mapped to the primary mouse genome (GRCm39) and GTF file (Ensembl v105) with 3' UTRs for Glp1r and Ghsr extended to include their furthermost 3' UTR in polyA_DB v3. Raw counts were generated using CellRanger (v6.1.2).
Gene expression modelling and normalised counts per million were generated using Seurat (v4.1.0).
Assembly: GRCm39
Supplementary files format and content: h5-format file including raw count values for all samples.

source_name: Mouse hypothalamus Gipr-EYFP

extract_protocol:
Fluorescence-activated cell sorting was performed using a BD Influx Cell Sorter to isolate GiprEYFP+ cells. Cells were gated according to cell size (FSC), cell granularity (SSC), FSC pulse-width for singlets, fluorescence at 488 nm/532 nm for EYFP and 647/670 nm for nuclear stain with DraQ5.
Single cell cDNA libraries from purified GiprEYFP+ cells were generated using the 10× Genomics Chromium Instrument and single-cell 3’ Reagent kit (V3); R1 = 28 bp, R2 = 91 bp

value: Gipr+


title: Mouse hypothalamus Glp1r-EYFP, sample 4 [S9_L001]

value: Hypothalamus


title: Mouse hypothalamus Gipr-EYFP, sample 1 [S1_L001]


title: Adjacent normal tissue_B633270

tag: sample type


title: AIHPOST014

tag: disease state


title: RNA-SEQ, A12-16-1, PCBN22, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-1 from patient PCBN22
processed_counts.txt
processed_TPM.txt
A12-16-1

tag: patient id

value: male

tag: % tumor

tag: race

value: WHITE

tag: pathologic stage

value: BENIGN


title: RNA-SEQ, A12-16-2, PCBN22, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-16-2 from patient PCBN22
processed_counts.txt
processed_TPM.txt
A12-16-2

value: recurrence

value: TUMOR


title: Mouse hypothalamus Gipr-EYFP, sample 4 [S4_L001]

tag: genotype

tag: tissue


title: Colorectal cancer tissue_B541155

source_name: Colorectal cancer tissue


title: RNA-SEQ, A12-15-21, PCBN20, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-21 from patient PCBN20
processed_counts.txt
processed_TPM.txt
A12-15-21

value: remission


title: Colorectal cancer tissue_B629380


title: Mouse hypothalamus Rxfp4-EYFP, sample 23 [S20_L007]

data_processing:
Sequenced reads were mapped to the primary mouse genome (GRCm39) and GTF file (Ensembl v105) with 3' UTRs for Glp1r and Ghsr extended to include their furthermost 3' UTR in polyA_DB v3. Raw counts generated using CellRanger (v6.1.2).
Gene expression modelling and normalised counts per million were generated using Seurat (v4.1.0).
Assembly: GRCm39
Supplementary files format and content: Separate h5-format files including raw count values for samples 1 to 12 (rep1) and 13 to 24 (rep2).

source_name: Hypothalamus

extract_protocol:
Fluorescence-activated cell sorting was performed using a BD Influx Cell Sorter to isolate GiprEYFP+ cells. Cells were gated according to cell size (FSC), cell granularity (SSC), FSC pulse-width for singlets, fluorescence at 488 nm/532 nm for EYFP and 647/670 nm for nuclear stain with DraQ5.
Single cell cDNA libraries from purified GiprEYFP+ cells were generated using the 10× Genomics Chromium Instrument and single-cell 3’ Reagent kit (V2).

tag: cell population


title: RNA-SEQ, A12-15-24, PCBN21, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-24 from patient PCBN21
processed_counts.txt
processed_TPM.txt
A12-15-24

source_name: prostate tissue

extract_protocol:
RNA was extracted from OCT prostate tissues using the Qiagen RNeasy kit or from frozen buffy coats using the Macharay-Nagel NucleoSpin RNA Blood  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.
Paired-end


title: Mouse hypothalamus Gipr-EYFP, sample 3 [S3_L001]

tag: strain background


title: Colorectal cancer tissue_B633270


title: Mouse hypothalamus Rxfp4-EYFP, sample 24 [S20_L008]


title: AIHPOST010

tag: Sex

value: AIH

tag: treatment

value: Post


title: Mouse hypothalamus Gipr-EYFP, sample 21 [S19_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 21


title: Mouse hypothalamus Rxfp4-EYFP, sample 22 [S20_L006]


title: AIHPOST011

value: M


title: RNA-SEQ, A12-15-22, PCBN20, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-22 from patient PCBN20
processed_counts.txt
processed_TPM.txt
A12-15-22

tag: gender

tag: preoperative psa

tag: sample gleason score


title: RNA-SEQ, A12-15-19, PCBN19, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-19 from patient PCBN19
processed_counts.txt
processed_TPM.txt
A12-15-19

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: 5-year disease status


title: AIHPOST009

tag: age

tag: disease state


title: AIHPOST007


title: AIHPOST008


title: AIHPOST012


title: RNA-SEQ, A12-17-21, PCBN21, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-21 from patient PCBN21
processed_counts.txt
processed_TPM.txt
A12-17-21

tag: patient id

tag: % tumor

tag: sample type


title: RNA-SEQ, A12-15-20, PCBN19, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-20 from patient PCBN19
processed_counts.txt
processed_TPM.txt
A12-15-20

tag: race

tag: pathologic stage


title: Mouse hypothalamus Gipr-EYFP, sample 19 [S19_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 19

tag: tissue

tag: cell population


title: AIHPOST005

tag: Sex


title: AIHPOST004

tag: treatment


title: Mouse hypothalamus Gipr-EYFP, sample 17 [S18_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 17


title: Mouse hypothalamus Gipr-EYFP, sample 18 [S18_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 18


title: RNA-SEQ, A12-17-19, PCBN19, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-19 from patient PCBN19
processed_counts.txt
processed_TPM.txt
A12-17-19

tag: gender


title: RNA-SEQ, A12-15-17, PCBN18, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-17 from patient PCBN18
processed_counts.txt
processed_TPM.txt
A12-15-17

tag: preoperative psa


title: AIHPOST006


title: AIHPOST001


title: HEK_WT-4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: HEK cells, non-transfected

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build GRCh38.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

extract_protocol:
Cells were frozen until RNA extraction was performed. RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HEK 293

tag: genotype

value: WT


title: HEK_WT-3

description: HEK cells, non-transfected


title: RNA-SEQ, A12-17-20, PCBN20, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-20 from patient PCBN20
processed_counts.txt
processed_TPM.txt
A12-17-20

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.
Assembly: hg19
Supplementary files format and content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

tag: sample gleason score

tag: % tumor-in-normal contamination

tag: patient gleason score


title: Mouse hypothalamus Gipr-EYFP, sample 16 [S18_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 16


title: Mouse hypothalamus Gipr-EYFP, sample 15 [S17_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 15


title: HEK_WT-1

description: HEK cells, non-transfected


title: RNA-SEQ, A12-15-18, PCBN18, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-18 from patient PCBN18
processed_counts.txt
processed_TPM.txt
A12-15-18

tag: disease state

tag: age

tag: 5-year disease status


title: HEK_WT-2

description: HEK cells, non-transfected


title: EBO4_MUT-249

description: HEK cells stably transfected with MRPS5 V336Y

value: MRPS5 V336Y


title: RNA-SEQ, A12-17-18, PCBN18, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-18 from patient PCBN18
processed_counts.txt
processed_TPM.txt
A12-17-18

tag: patient id

tag: % tumor

tag: sample type


title: AIHPRE028

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: F

value: Pre

tag: tissue


title: RNA-SEQ, A12-15-15, PCBN17, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-15 from patient PCBN17
processed_counts.txt
processed_TPM.txt
A12-15-15

value: prostate cancer

tag: race

tag: pathologic stage


title: Mouse hypothalamus Gipr-EYFP, sample 14 [S17_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 14

tag: cell population

value: Gipr+


title: AIHPRE026

tag: Sex

tag: treatment

value: serum


title: Mouse hypothalamus Gipr-EYFP, sample 13 [S17_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 13

value: Hypothalamus


title: AIHPRE027


title: AIHPRE025


title: EBO4_MUT-246

tag: cell line


title: Mouse hypothalamus Gipr-EYFP, sample 11 [S12_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 11


title: RNA-SEQ, A12-15-13, PCBN16, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-13 from patient PCBN16
processed_counts.txt
processed_TPM.txt
A12-15-13

tag: gender

value: male

tag: preoperative psa

value: WHITE


title: RNA-SEQ, A12-17-17, PCBN17, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-17 from patient PCBN17
processed_counts.txt
processed_TPM.txt
A12-17-17

tag: sample gleason score

tag: % tumor-in-normal contamination


title: Mouse hypothalamus Gipr-EYFP, sample 10 [S12_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 10


title: EBO4_MUT-244

tag: genotype


title: RNA-SEQ, A12-15-14, PCBN16, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-14 from patient PCBN16
processed_counts.txt
processed_TPM.txt
A12-15-14

tag: disease state

tag: patient gleason score

tag: age


title: EBO4_MUT-245


title: RNA-SEQ, A12-17-16, PCBN16, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-16 from patient PCBN16
processed_counts.txt
processed_TPM.txt
A12-17-16

tag: patient id

tag: % tumor

tag: 5-year disease status


title: Mouse hypothalamus Gipr-EYFP, sample 9 [S11_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 9

tag: tissue


title: AIHPRE022


title: EBO1_MUT-307

description: HEK cells stably transfected with MRPS5 G313R

value: MRPS5 G313R


title: AIHPRE023


title: RNA-SEQ, A12-15-16, PCBN17, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-16 from patient PCBN17
processed_counts.txt
processed_TPM.txt
A12-15-16

tag: race

tag: pathologic stage

tag: sample type

value: TUMOR


title: AIHPRE024

tag: Sex

tag: treatment


title: AIHPRE021


title: EBO1_MUT-306

tag: cell line


title: RNA-SEQ, A12-15-12, PCBN15, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-12 from patient PCBN15
processed_counts.txt
processed_TPM.txt
A12-15-12

tag: gender

tag: preoperative psa

value: recurrence


title: Mouse hypothalamus Gipr-EYFP, sample 12 [S12_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 12

tag: cell population


title: AIHPRE020

value: AIH


title: Mouse hypothalamus Gipr-EYFP, sample 7 [S11_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 7


title: RNA-SEQ, A12-15-11, PCBN15, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-11 from patient PCBN15
processed_counts.txt
processed_TPM.txt
A12-15-11

tag: sample gleason score

tag: % tumor-in-normal contamination

value: BENIGN


title: Mouse hypothalamus Gipr-EYFP, sample 6 [S10_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 6


title: Mouse hypothalamus Gipr-EYFP, sample 5 [S10_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 5


title: EBO4_MUT-243

tag: genotype


title: Mouse hypothalamus Gipr-EYFP, sample 8 [S11_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 8


title: AIHPOST003

value: M

tag: age

tag: disease state

value: Post


title: Mouse hypothalamus Gipr-EYFP, sample 3 [S9_L008]

description: Mouse hypothalamus Gipr-EYFP, sample 3


title: EBO1_MUT-240

value: HEK 293


title: EBO1_MUT-239


title: EBO1_MUT-304


title: EBO1_4_WT-260

description: HEK cells stably transfected with MRPS5 WT

value: MRPS5 WT


title: Mouse hypothalamus Gipr-EYFP, sample 2 [S9_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 2


title: Mouse hypothalamus Gipr-EYFP, sample 1 [S9_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 1


title: EBO1_4_WT-238


title: EBO1_MUT-305


title: RNA-SEQ, A12-17-15, PCBN15, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-15 from patient PCBN15
processed_counts.txt
processed_TPM.txt
A12-17-15

tag: patient id

tag: % tumor

tag: patient gleason score


title: RNA-SEQ, A12-17-14, PCBN14, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-14 from patient PCBN14
processed_counts.txt
processed_TPM.txt
A12-17-14

tag: race

tag: 5-year disease status


title: RNA-SEQ, A12-15-10, PCBN14, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-10 from patient PCBN14
processed_counts.txt
processed_TPM.txt
A12-15-10

tag: pathologic stage

tag: sample type


title: RNA-SEQ, A12-15-9, PCBN14, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-9 from patient PCBN14
processed_counts.txt
processed_TPM.txt
A12-15-9


title: RNA-SEQ, A12-15-7, PCBN13, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-7 from patient PCBN13
processed_counts.txt
processed_TPM.txt
A12-15-7

value: remission


title: RNA-SEQ, A12-15-8, PCBN13, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-8 from patient PCBN13
processed_counts.txt
processed_TPM.txt
A12-15-8


title: Mouse hypothalamus Gipr-EYFP, sample 4 [S10_L006]

description: Mouse hypothalamus Gipr-EYFP, sample 4

tag: tissue


title: RNA-SEQ, A12-17-13, PCBN13, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-13 from patient PCBN13
processed_counts.txt
processed_TPM.txt
A12-17-13


title: EBO1_4_WT-237

tag: cell line


title: EBO1_4_WT-236


title: RNA-SEQ, A12-15-5, PCBN12, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-5 from patient PCBN12
processed_counts.txt
processed_TPM.txt
A12-15-5

tag: gender


title: EBO4_MUT-247

description: HEK cells stably transfected with MRPS5 V336Y

value: MRPS5 V336Y


title: Mouse hypothalamus Gipr-EYFP, sample 20 [S19_L007]

description: Mouse hypothalamus Gipr-EYFP, sample 20


title: HFF cells_G3-YSD2

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed RNA after G3-YSD transfection

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the human genome (hg19) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Genome_build: hg19 (human)
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: HFF cells

growth_protocol: Cells were were cultured in Dulbecco's modified Eagle's medium (DMEM) plus 10% fetal bovine serum (FBS) (Gibco), supplemented with 1% penicillin-streptomycin (Invitrogen).These cells were maintained in a humidified 5% CO2 incubator at 37˚C

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq4000 by a 2X150 bp run.

treatment_protocol: Transfection experiments were conducted in human HFF cells Total RNA was prepared 6 hours after transfection. The RNA with polyA tails were isolated, ligated to the adapters, amplified, and sequenced following the standard RNAseq preparation protocol (Illumina, USA) with no modifications. The transfection experiments were conducted in duplicates.

value: Human Foreskin Fibroblast cell line

tag: treatment

value: G3-YSD transfection


title: L_LSK

description: Mouse LSK cells

data_processing:
Cell Ranger 3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/ overview/ welcome) was used to process raw paired-end sequencing data. Briefly, Cell Ranger mkfastq pipeline was used to demultiplex sample index reads to generate FASTQ files for each sequencing library, and then raw reads were aligned to the UCSC mouse reference genome (mm10) using STAR aligner with default parameters.
Data filtering, normalization, scaling, and Principal component analysis (PCA) were performed using the R package Seurat version 4.0.3 and dimensionality reduction and clustering were further done by Uniform Manifold Approximation and Projection (UMAP) analysis.
Low-quality cells and possible cell doublets were filtered out using the following criteria: (i) number of detected genes between 200 and 2500, and (ii) percentage of UMIs derived from mitochondrial genes below 5%.
The UMI counts were normalized by library size factors. Genes differentially expressed across clusters were identified using likelihood ratio test.
Genome_build: mm10
Supplementary_files_format_and_content: tsv
Supplementary_files_format_and_content: matrix

growth_protocol: C57BL/6 mice were trained by subjecting them to LIP for 21 days followed by ligature removal (to enable inflammation resolution) for 14 days (21dL/14dR, L) or were not ligated during the entire period (NL, N). Hematopoietic progenitors (LSKs; Lin-cKit+Sca1+)  in mice bone marrow were sorted by FACS for single-cell transcriptomics analysis.

extract_protocol:
LSK cells from the BM of LIP-subjected mice or unligated control mice were sorted by flow cytometry and subjected to single cell RNA-sequencing.
The cell numbers were adjusted to 700–1200 cells per μl and added to 10x Chromium RT mix to achieve loading target numbers of around 20000 cells. cDNA synthesis was performed per the manufacturer’s instructions (Chromium Single Cell 3' Reagent Kits User Guide (v3.1)), and library preparation and sequencing (Novaseq SP reagent kit; 100 cycles) were performed using the Novaseq 6000 platform (Illumina) per the manufacturer’s instructions (Chromium Single Cell 3' Reagent Kits User Guide (v3.1)).

tag: cell type

value: Bone marrow LSK cells

tag: strain

tag: replicate


title: N_LSK

description: Mouse LSK cells

treatment_protocol: C57BL/6 mice were trained by subjecting them to LIP for 21 days followed by ligature removal (to enable inflammation resolution) for 14 days (21dL/14dR, L) or were not ligated during the entire period (NL, N). Hematopoietic progenitors (LSKs; Lin-cKit+Sca1+)  in mice bone marrow were sorted by FACS for single-cell transcriptomics analysis.


title: EBO1_4_WT-235

tag: genotype


title: AIHPRE015

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

tag: Sex

value: F

tag: age

value: Pre

value: serum


title: AIHPRE013

tag: disease state


title: AIHPRE014


title: EBO1_4_WT_233


title: HFF cells_G3-YSD1

description: expressed RNA after G3-YSD transfection


title: AIHPRE007


title: AIHPRE010


title: AIHPRE009


title: AIHPRE008


title: P4_WT_1

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

data_processing:
Optical duplicates were removed with clumpify using BBmap v38.34 and default settings, then Illumina adapters were trimmed with cutadapt v1.16 using a minimum overlap of 6 and minimum length of 20. Alignment to mm10/Ensembl release 102 was accomplished with STAR v2.7.9a with overhang set to 124. Trimmed reads were aligned in two pass mode to generate a BAM file, sorted by coordinates. Reads were assigned to the target with the largest overlap, and uniquely aligned, reversely stranded reads were counted with featureCounts v1.6.3. Differentially expressed genes were identified from counts using DESeq2 v1.32.0. Features with fewer than 5 reads in every sample were eliminated before DESeq was run.
Supplementary_files_format_and_content: counts.txt files contain raw counts
Supplementary_files_format_and_content: DESeq_results.txt are tab deliminated file containing the DESeq2 results
Genome_build: mm10

source_name: Retinal microglia

extract_protocol:
For P4 WT, Mertk KO, and Axl KO samples, CD11b+ CD45+ Ly6c- cells from one animal (2 retinas) were sorted directly into RLT buffer (from Qiagen RNeasy MicroRNA kit 74034) using a 4 laser BD FACSAria at the University of Utah Flow Core and stored at -80°C. 2 samples were pooled prior to RNA isolation so that each replicate was 2 animals/4 retinas. WT samples had 5470, 6134, and 7029 cells, Mertk KO samples had 4245, 4038, and 8591 cells, and AXL KO samples had 5790, 5282, and 5071 cells. We sequenced RNA from 3 samples for each genotype in a single experiment.
RNA from all samples was purified using the RNeasy Plus Micro kit. The University of Utah High-throughput Genomics core then hybridized total RNA with the NEBNext rRNA Depletion Solution human/mouse/rat to substantially diminish cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II RNA Library Prep Kit for Illumina.  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay.  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quantification Kit. Individual libraries were normalized to 10 nM, and equal volumes were pooled in preparation for Illumina sequence analysis. Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow.  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5. Samples were sequenced to a depth of 39-76 million reads.

value: retina

value: postnatal day 4

value: Mertk +/+ Axl +/+


title: P4_WT_2


title: P4_WT_3


title: Axl_ko_3

value: Axl -/-


title: AIHPRE011

source_name: Serum

value: AIH


title: AIHPRE019


title: AIHPRE018


title: RNA-SEQ, A12-15-3, PCBN11, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-3 from patient PCBN11
processed_counts.txt
processed_TPM.txt
A12-15-3

value: prostate cancer

tag: patient id

value: male

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

value: WHITE

value: BENIGN


title: RNA-SEQ, A12-17-12, PCBN12, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-12 from patient PCBN12
processed_counts.txt
processed_TPM.txt
A12-17-12

source_name: buffy coat

tag: patient gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type


title: RNA-SEQ, A12-15-6, PCBN12, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-6 from patient PCBN12
processed_counts.txt
processed_TPM.txt
A12-15-6

tag: gender

value: TUMOR


title: Axl_ko_2

tag: strain

tag: tissue


title: RNA-SEQ, A12-17-11, PCBN11, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-11 from patient PCBN11
processed_counts.txt
processed_TPM.txt
A12-17-11

value: remission


title: HFF cells_cGAMP2

description: expressed RNA after cGAMP stimulation

tag: cell line

value: Human Foreskin Fibroblast cell line

tag: treatment

value: cGAMP stimulation


title: RNA-SEQ, A12-15-1, PCBN10, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-1 from patient PCBN10
processed_counts.txt
processed_TPM.txt
A12-15-1

tag: age


title: AIHPRE017

tag: Sex

value: F

tag: disease state


title: AIHPRE016

value: Pre


title: Axl_ko_1

tag: genotype


title: HFF cells_HSV2

description: expressed RNA after HSV infection

treatment_protocol: Transfection experiments were conducted in human HFF cells  Total RNA was prepared 6 hours after transfection. The RNA with polyA tails were isolated, ligated to the adapters, amplified, and sequenced following the standard RNAseq preparation protocol (Illumina, USA) with no modifications. The transfection experiments were conducted in duplicates.

tag: infection

value: after HSV infection


title: MerTK_ko_3

value: retina

value: Mertk -/-


title: RNA-SEQ, A12-15-4, PCBN11, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-4 from patient PCBN11
processed_counts.txt
processed_TPM.txt
A12-15-4

tag: patient id

tag: preoperative psa

tag: sample gleason score

tag: % tumor


title: HFF cells_cGAMP1

description: expressed RNA after cGAMP stimulation


title: AIHPRE012

value: serum


title: RNA-SEQ, A12-17-10, PCBN10, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-10 from patient PCBN10
processed_counts.txt
processed_TPM.txt
A12-17-10

tag: % tumor-in-normal contamination

tag: patient gleason score

tag: race

tag: pathologic stage


title: MerTK_ko_2

tag: strain

value: postnatal day 4


title: RNA-SEQ, A12-15-2, PCBN10, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-2 from patient PCBN10
processed_counts.txt
processed_TPM.txt
A12-15-2

tag: gender

tag: 5-year disease status

tag: sample type


title: HFF cells_hpRNA2

description: expressed RNA after hpRNA transfection

tag: cell line

tag: treatment

value: after hpRNA transfection


title: AIHPRE005

tag: Sex

value: M

tag: age

tag: disease state

value: AIH

tag: tissue


title: RNA-SEQ, A12-14-18, PCBN9, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-18 from patient PCBN9
processed_counts.txt
processed_TPM.txt
A12-14-18

value: prostate cancer

tag: patient id

value: male

tag: preoperative psa

value: WHITE


title: AIHPRE006


title: HFF cells_hpRNA1

description: expressed RNA after hpRNA transfection


title: MerTK_ko_Axl_ko_3

data_processing:
Optical duplicates were removed with clumpify using BBmap v38.34 and default settings, then Illumina adapters were trimmed with cutadapt v1.16 using a minimum overlap of 6 and minimum length of 20. Alignment to mm39/Ensembl release 104 was accomplished with STAR v2.7.9a with overhang set to 124. Trimmed reads were aligned in two pass mode to generate a BAM file, sorted by coordinates. Reads were assigned to the target with the largest overlap, and uniquely aligned, reversely stranded reads were counted with featureCounts v1.6.3. Differentially expressed genes were identified from counts using DESeq2 v1.32.0. Features with fewer than 5 reads in every sample were eliminated before DESeq was run.
Supplementary_files_format_and_content: counts.txt files contain raw counts
Supplementary_files_format_and_content: DESeq_results.txt are tab deliminated file containing the DESeq2 results
Genome_build: mm39

extract_protocol:
For P7 WT and Mertk/Axl dKO, CD11b+ CD45+ cells from one animal (2 retinas) were sorted directly into RLT buffer (from Qiagen RNeasy MicroRNA kit 74034) using a 4 laser BD FACSAria at the University of Utah Flow Core and stored at -80°C. P7 samples were not pooled and thus represent 1 animal/2 retinas. For WT samples, 3783, 4083, and 4982 cells were collected. For Mertk/Axl dKO samples, 2408, 2633, and 2388 cells were collected. We sequenced RNA from 3 samples for each genotype in a single experiment.
RNA from all samples was purified using the RNeasy Plus Micro kit. The University of Utah High-throughput Genomics core then hybridized total RNA with the NEBNext rRNA Depletion Solution human/mouse/rat to substantially diminish cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II RNA Library Prep Kit for Illumina.  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay.  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quantification Kit. Individual libraries were normalized to 10 nM, and equal volumes were pooled in preparation for Illumina sequence analysis. Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow.  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5. Samples were sequenced to a depth of 39-76 million reads.

value: postnatal day 7

tag: genotype

value: Mertk -/- Axl -/-


title: RNA-SEQ, A12-15-23, PCBN21, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-15-23 from patient PCBN21
processed_counts.txt
processed_TPM.txt
A12-15-23

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

value: recurrence

value: BENIGN


title: RNA-SEQ, A12-17-9, PCBN9, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-9 from patient PCBN9
processed_counts.txt
processed_TPM.txt
A12-17-9

tag: patient gleason score

tag: race

tag: pathologic stage

value: remission


title: MerTK_ko_Axl_ko_2

tag: strain


title: MerTK_ko_1


title: HFF cells_HT-DNA2

description: expressed RNA after HT-DNA transfection

value: Human Foreskin Fibroblast cell line

value: after HT-DNA transfection


title: TGFbeta transgene mice-4

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

data_processing:
Sequencing data were assessed for quality and trimmed of the primer-adaptor sequences by the Partek® Flow® Genomic Analysis Software (Partek)
Reads were alignment to the mouse reference genome (mm10)
annotation of known miRNA based on miRBase22
Assembly: mm10
Supplementary files format and content: The number of reads for each miRNA was normalized to reads per million and quantified across all samples

source_name: atrium

extract_protocol:
Total RNA was isolated from mouse atrium with the TRIzol reagent and was further purified and concentrated by using the TriRNA Pure kit . The quality and quantity of total RNA were analyzed by using a LabChip GX
RNA libraries for RNA-seq were prepared using NEBNext kit following manufacturer's protocols.

value: cardiac-specific TGFbeta overexpression


title: AIHPRE004

value: F

value: Pre


title: TGFbeta transgene mice-3


title: RNA-SEQ, A12-14-15, PCBN8, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-15 from patient PCBN8
processed_counts.txt
processed_TPM.txt
A12-14-15

tag: gender

value: Unk

tag: 5-year disease status

tag: sample type


title: AIHPRE002

tag: Sex

tag: treatment

value: serum


title: AIHPRE003

value: M

tag: age

tag: disease state


title: AIHPRE001

value: AIH

tag: tissue


title: HFF cells_HT-DNA1

description: expressed RNA after HT-DNA transfection

tag: cell line


title: RNA-SEQ, A12-14-17, PCBN9, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-17 from patient PCBN9
processed_counts.txt
processed_TPM.txt
A12-14-17

value: prostate cancer

tag: patient id

tag: preoperative psa


title: WT_3

value: retina

tag: genotype

value: Mertk +/+ Axl +/+


title: TGFbeta transgene mice-2


title: MerTK_ko_Axl_ko_1

value: postnatal day 7


title: RNA-SEQ, A12-14-16, PCBN8, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-16 from patient PCBN8
processed_counts.txt
processed_TPM.txt
A12-14-16

value: male

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

value: WHITE

value: TUMOR


title: HFF cells_mock2

description: expressed RNA without treatment

value: without treatment


title: WT_2


title: RNA-SEQ, A12-14-13, PCBN7, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-13 from patient PCBN7
processed_counts.txt
processed_TPM.txt
A12-14-13

tag: patient gleason score

tag: race

tag: pathologic stage

value: remission

value: BENIGN


title: TGFbeta transgene mice-1

value: cardiac-specific TGFbeta overexpression


title: HFF cells_mock1

description: expressed RNA without treatment

value: Human Foreskin Fibroblast cell line


title: wild-type mice-4

value: WT


title: RNA-SEQ, A12-14-14, PCBN7, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-14 from patient PCBN7
processed_counts.txt
processed_TPM.txt
A12-14-14

tag: gender

tag: 5-year disease status


title: wild-type mice-3


title: RNA-SEQ, A12-17-7, PCBN7, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-7 from patient PCBN7
processed_counts.txt
processed_TPM.txt
A12-17-7

tag: sample type


title: wild-type mice-1


title: WT_1

tag: strain


title: wild-type mice-2


title: vehicle

data_processing:
Aligned reads to the mm10 reference from 10X genomics (version 3.0.0 from Ensembl 93) and generated feature-barcode matrices using cellranger count v3.1.0 with expected-cells set to 5000. Filtered feature matrices from cellranger were further filtered with Seurat (v3.1.5). High-quality cells were selected by < 10% mitochondrial gene content, and high number of features (genes). Feature cut-off was specific to each sample: > 1,500 for Sample 1, > 1,000 for Sample 2, > 1,800 for vehicle, and > 2,500 for PLX-treated. Likely doublets, with high transcript counts, were also eliminated: < 27,000 counts for Sample 1, < 25,000 for Sample 2, < 47,000 for vehicle, and < 125,000 for PLX treated.
During single-cell library preparation, cells from one Bax WT and one Bax KO animal were sorted into the wrong sample so we chose to call these mixed samples Sample1 and Sample2. We used the scSplit pipeline to perform in silico genotyping and reassign these cells.
Filtered cells from all samples were then combined, without batch correction, using Seurat’s merge function and processed with the SCTransform pipeline. Mitochondrial percentage was regressed out of the model and Bax and presumed Bax-linked genes (Ftl1 and Ftl1-ps1) were excluded from the variable features list used for dimensionality reduction. From here, we subsetted the data to include only microglial cells and reran the SCTransform pipeline as before with the exception that FindClusters was run with resolution set to 0.4.
Supplementary_files_format_and_content: matrix.mtx, barcodes.tsv, featrures.tsv: Filtered feature count matrix, generated by cellranger, stored as a sparse numeric matrix and tab separated values for row and column names
Supplementary_files_format_and_content: counts_normalized.tsv: scaled gene expression data for all four samples
Supplementary_files_format_and_content: meta_data.tsv: relevant details for each cell including UMAP assignment and cell type
Genome_build: mm10

source_name: retinal microglia

extract_protocol: To ensure we captured enough cells for analysis (Liddelow, Marsh et al. 2020), we pooled 13 animals/26 retinas for each Bax WT (Sample 1) and littermate KO (Sample 2) from 6 litters. 12 animals/24 retinas for PLX3397 CX3CR1-GFP/+ and 11 animals/22 retinas were pooled for Vehicle CX3CR1-GFP/+ controls each from 2 litters. Altogether, sequencing data represent 49 animals divided into two experiments: Bax/WT and PLX/Veh. The dissociation was performed as normal, except pooling 6 retinas per tube during dissociation. CD45+ CD11b+/GFP+ CCR2- cells were sorted for Bax samples and CD45+GFP+ Ly6C- cells were sorted for PLX and Vehicle samples. Cells were sorted using a 5 laser BD FACSAria with a 70μm nozzle at 55 psi by the University of Utah Flow Core into a cold, empty tube before library generation. 15,000 cells for each Bax sample and 7,000-10,000 cells for PLX and Vehicle were loaded onto 10X chip. Single-cell libraries were generated with 10X Genomics Single Cell 3’ Gene Expression Library Prep v3 reagents at the University of Utah High Throughput Genomics core. The libraries were sequenced on a NovaSeq 6000 to generate at least 200 million paired end reads of 150 bp per sample.

treatment_protocol: Plx animals were treated with Pexidartinib (PLX3397) (AdooQ BioScience A15520) dissolved in corn oil (Sigma-Aldrich C8267) and 10% DMSO (Fisher Scientific BP231) and administered to postnatal pups by daily intraperitoneal injection P3-P5 or P4-P6 at 0.25 mg/g body weight. Vehicle control animals recieved IP injection of corn oil and 10% DMSO.

tag: age

value: postnatal day 6 and 7

tag: treatment

value: Vehicle


title: RNA-SEQ, A12-14-11, PCBN6, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-11 from patient PCBN6
processed_counts.txt
processed_TPM.txt
A12-14-11

tag: disease state


title: RNA-SEQ, A12-14-12, PCBN6, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-12 from patient PCBN6
processed_counts.txt
processed_TPM.txt
A12-14-12


title: RNA-SEQ, A12-17-8, PCBN8, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-8 from patient PCBN8
processed_counts.txt
processed_TPM.txt
A12-17-8

value: Unk


title: Bax_ko

value: Bax -/-


title: Bax_wt

value: Bax +/+


title: KO_TCDD_3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM.
Differential expression analysis was done using Cuffdiff.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: genematrix.tsv: Tab-delimited text file containing FPKM for all samples and genes.

source_name: Liver

growth_protocol: Fmo3+/+ or Fmo3-/- genotype on C57Bl6/J Background.

extract_protocol:
Mice were euthanized, and perfused with saline. The liver was removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent/Qiagen RNeasy Kit.
RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NovaSeq 6000.

treatment_protocol: Corn oil vehicle or 25ug/kg TCDD weekly via intraperitoneal injection for 6 weeks.

tag: tissue

value: Liver

value: TCDD


title: Brown adipose tissue, cBATKO_TH_10

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

country: France

institute: IGFL-ENS

description:
TH kinetics.txt
BATKO_TH_10

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Read were counted using htseqcount Galaxy version 0.6.1galaxy3 using these parameters // Mode : Union / Stranded : Reverse / Minimul alignement quality : 10 / Feature type : exon / ID Attribute : gene name
Differential gene expression analysis was performed with DESeq2 (R package, Version 1.34.0) using the following thresholds: adjusted p-value <0.05; average expression > 10 reads per million, log2 fold-change > 0.6 or < -0.6. The effect of mutations on both cold exposure and HFD was obtained using the interaction model (Ge, 2021). Thresholds for the interaction were the following: average expression > 10 reads per million, adjusted p-value < 0.05.
Differentially expressed genes expression was visualized as clustered heatmaps using Pheatmap R package (RRID:SCR_016418)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts of all samples from the same experiment (TH injection for target genes, cold exposure and HFD in 3 different tables. Each sample is preceded by a, b or c, which allows to quickly identify the 3 different experiments)

source_name: Brown adipose tissue

extract_protocol:
RNAs were extracted using Trizol. Total RNA was converted to cDNA using MMLV reverse transcriptase. 1ug of total RNA was used for the construction of sequencing libraries
cDNA libraries were prepared using the total RNA SENSE kit (Lexogen, Vienna, Austria) and analyzed on a Nextseq 500 sequencer (Illumina)

value: Brown adipose tissue

value: 8-12 weeks

tag: Sex

value: Male

tag: background strain

value: BATKO

value: PTU+TH 24h


title: Brown adipose tissue, cBATKO_TH_7

description:
TH kinetics.txt
BATKO_TH_7

tag: genotype


title: HFF cells_HSV1

description: expressed RNA after HSV infection

tag: cell line

tag: infection

value: after HSV infection


title: KO_TCDD_0


title: Brown adipose tissue, cBATKO_TH_15

description:
TH kinetics.txt
BATKO_TH_15


title: Brown adipose tissue, cBATKO_PTU_17

description:
TH kinetics.txt
BATKO_PTU_17

value: PTU


title: RNA-SEQ, A12-17-6, PCBN6, buffy coat

city: Bethesda

first: Adam

last: Sowalsky

institute: National Cancer Institute

description:
Paired-end RNA-seq for buffy coat sample A12-17-6 from patient PCBN6
processed_counts.txt
processed_TPM.txt
A12-17-6

value: prostate cancer

tag: patient id

value: male

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

value: WHITE

value: remission


title: plx

value: postnatal day 6 and 7


title: WT tumor

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

data_processing:
sequencer-generated bcl files were converted to fastqs using the cellranger mkfastq (cellranger version 1.2) command with default parameters.
fastq files were aligned to the mouse reference genome (with ENSEMBL v84 annotation) using cellranger count (cellranger version 1.2). This step also generated the submitted raw feature-barcode matrices
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv: all cellranger barcodes (shared by all samples); genes.tsv: all genes from mm10 (shared by all samples); *.mtx: matrix exchange file from cellranger to generate a feature-barcode matrix; All processed files were generated by cellranger: More information on 10X filetypes at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

source_name: tumor

extract_protocol:
Tumor tissue was digested with 0.2mg/ml DNase I (Sigma-Aldrich), 100U/ml Collagenase I (Worthington Biochemical), and 500U/ml Collagenase Type IV (Worthington Biochemical) for 30 minutes at 37°C while under constant agitation. Blood was collected via cardiac puncture from mice that were euthanized by overdose with 2.5% Avertin. Blood samples were treated with 175 mM NH4Cl for 5 minutes at room temperature to lyse red blood cells. All samples were stained with Zombie NIR fixable viability dye for 30 minutes at 4°C and antibodies for 30 minutes at 4°C. Myeloid cells (CD45+ CD90- NK1.1- Ly6G- B220- SigF- CD11b+ and/or CD11c+) were sorted.
Sorted cells were resuspended at a concentration of 1x103 cells/𝜇l in media (DPBS, 0.04% BSA) and loaded onto the Chromium Controller (10X Genomics). Samples underwent single-cell encapsulation and cDNA library preparation using the Chromium Single Cell 3’ v2 Reagent Kits (10X Genomics). The cDNA library was sequenced on an Ilumina HiSeq 4000.

value: control

tag: tumor model

value: subcutaneous B16F10


title: Brown adipose tissue, cBATKO_PTU_11

description:
TH kinetics.txt
BATKO_PTU_11


title: KO_TCDD_2


title: Brown adipose tissue, cBATKO_PTU_4

description:
TH kinetics.txt
BATKO_PTU_4


title: WT tumor-bearing blood

source_name: blood


title: WT_TCDD_2


title: RNA-SEQ, A12-14-9, PCBN5, prostate tissue

address: 37 Convent Drive Building 37 Room 1062B

description:
Paired-end RNA-seq for prostate tissue sample A12-14-9 from patient PCBN5
processed_counts.txt
processed_TPM.txt
A12-14-9

tag: gender

tag: patient gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type

value: BENIGN


title: Brown adipose tissue, cBATKO_TH_9

description:
TH kinetics.txt
BATKO_TH_9

tag: tissue

tag: age

tag: Sex

tag: treatment


title: Brown adipose tissue, cBATKO_TH_8

description:
TH kinetics.txt
BATKO_TH_8

tag: background strain

tag: genotype


title: KO_TCDD_1

tag: strain

value: Liver

value: TCDD


title: FoxP3 DTR tumor

value: treg-depleted


title: RNA-SEQ, A12-17-5, PCBN5, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-5 from patient PCBN5
processed_counts.txt
processed_TPM.txt
A12-17-5

tag: disease state

tag: patient id

tag: preoperative psa

tag: sample gleason score


title: WT_TCDD_3


title: RNA-SEQ, A12-14-10, PCBN5, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-10 from patient PCBN5
processed_counts.txt
processed_TPM.txt
A12-14-10

tag: gender

tag: % tumor

tag: % tumor-in-normal contamination

value: TUMOR


title: WT_TCDD_1


title: RNA-SEQ, A12-14-8, PCBN4, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-8 from patient PCBN4
processed_counts.txt
processed_TPM.txt
A12-14-8

tag: patient gleason score

tag: race

tag: pathologic stage


title: RNA-SEQ, A12-17-4, PCBN4, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-4 from patient PCBN4
processed_counts.txt
processed_TPM.txt
A12-17-4

tag: 5-year disease status

tag: sample type


title: RNA-SEQ, A12-14-7, PCBN4, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-7 from patient PCBN4
processed_counts.txt
processed_TPM.txt
A12-14-7

tag: age


title: WT_TCDD_0

tag: tissue

tag: treatment


title: Brown adipose tissue, cBATKO_PTU_3

description:
TH kinetics.txt
BATKO_PTU_3

value: Brown adipose tissue

value: 8-12 weeks

tag: Sex

value: Male

tag: background strain

tag: genotype

value: BATKO


title: KO_Bone_GFP-Tm+_3

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

institute: The University of Tokyo

data_processing:
Sequenced reads were trimmed for adaptor and low-quality sequence, then aligned to mouse reference sequence mm10 with STAR.
Aligned reads were counted with featureCounts.
Raw counts were analyzed by DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts.

source_name: Bone cells

extract_protocol:
Total RNA were extracted from sorted cells with the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and SMARTer ThruPLEX DNA-Seq Kit (Takara Bio).

value: postnatal day 21

value: Conditional PTH1R KO

tag: cell type

value: Bone cells


title: KO_Coil_3

tag: strain

value: Corn Oil Vehicle


title: RNA-SEQ, A12-14-5, PCBN3, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-5 from patient PCBN3
processed_counts.txt
processed_TPM.txt
A12-14-5

tag: disease state

value: prostate cancer

tag: patient id

value: male

tag: preoperative psa

tag: sample gleason score

value: WHITE


title: RNA-SEQ, A12-17-3, PCBN3, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-3 from patient PCBN3
processed_counts.txt
processed_TPM.txt
A12-17-3

tag: gender

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

value: recurrence


title: Brown adipose tissue, cBATKO_PTU_2

description:
TH kinetics.txt
BATKO_PTU_2

value: PTU


title: KO_Bone_GFP-Tm+_1


title: KO_Bone_GFP-Tm+_2


title: KO_Coil_2

value: Liver


title: KO_Coil_1


title: KO_Bone_GFP+_3


title: RNA-SEQ, A12-14-3, PCBN2, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-3 from patient PCBN2
processed_counts.txt
processed_TPM.txt
A12-14-3

value: UNKNOWN

tag: race

tag: pathologic stage

value: Unk

tag: 5-year disease status

value: remission

tag: sample type

value: BENIGN


title: Brown adipose tissue, cPTU+TH_24H_B26

description:
TH kinetics.txt
PTU+TH_24H_B26

tag: tissue

value: Brown adipose tissue

tag: age

value: 8-12 weeks

tag: Sex

value: Wild-type

tag: treatment

value: PTU+TH 24h


title: Brown adipose tissue, cPTU+TH_24H_B27

description:
TH kinetics.txt
PTU+TH_24H_B27

value: Male

tag: background strain

tag: genotype


title: KO_Coil_0

tag: strain


title: Brown adipose tissue, cPTU+TH_24H_B28

description:
TH kinetics.txt
PTU+TH_24H_B28


title: KO_Bone_GFP+_1

value: postnatal day 21

value: Conditional PTH1R KO

tag: cell type

value: Bone cells


title: RNA-SEQ, A12-14-4, PCBN2, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-4 from patient PCBN2
processed_counts.txt
processed_TPM.txt
A12-14-4

tag: disease state

value: prostate cancer

tag: patient id

value: male

tag: preoperative psa

tag: sample gleason score

value: TUMOR


title: WT_Coil_2

value: Corn Oil Vehicle


title: Brown adipose tissue, cPTU+TH_24H_B24

description:
TH kinetics.txt
PTU+TH_24H_B24


title: Brown adipose tissue, cPTU+TH_12H_B23

description:
TH kinetics.txt
PTU+TH_12H_B23

value: PTU+TH 12h


title: RNA-SEQ, A12-17-2, PCBN2, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-2 from patient PCBN2
processed_counts.txt
processed_TPM.txt
A12-17-2

tag: gender

value: UNKNOWN

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

value: WHITE