title: YJM-SEtOH-3

first: Christopher

middle: M

last: Jakobson

address: 318 Campus Dr, Clark Center W350

department: Chemical and Systems Biology

institute: Stanford University School of Medicine

description:
YJM975SEtOH3
V100006801_L*_HK500YEAoyiEAAORBAPEI-517

data_processing:
Trimming and quality filtering were performed at the Beijing Genomics Institute
Pseudo-alignment and estimated of normalized abundance was performed using kallisto [kallisto quant -t yeastIndex.idx -o sampleName -b 100 library1_1.fastq.gz library1_2.fastq.gz library2_1.fastq.gz library2_2.fastq.gz]
TPM estimates from kallisto are collated in the processed data file tpmOutput.csv
Genome_build: S. cerevisiae cDNA from Ensembl
Supplementary_files_format_and_content: .csv; columns represent biological replicates as indicated in headers

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: YJM975_S-CSM with 2% ethanol

growth_protocol: Samples of exponentially growing (OD600 ~ 0.5-1.0) 5 mL liquid cultures of homozygous diploid RM11a/α and YJM975a/α strains (in the media conditions indicated) were harvested in biological triplicate

extract_protocol:
RNA extraction, mRNA isolation by polyA enrichment were performed at the Beijing Genomics Institute
cDNA library preparation was performed at the Beijing Genomics Institute

treatment_protocol: Cells were snap-frozen and stored at -80°C.

tag: strain

tag: growth medium

value: S-CSM with 2% ethanol

value: whole yeast cells


title: AM_PIC_2h_d1

status: Public on Dec 13 2018

type: RNA

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

country: Germany

institute: Saarland University

description:
miRNA
Donor 1 PIC 2 h
Alveolar macrophages - Poly(I:C) 10 µg/ml, 2 h

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using Feature Extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

molecule: total RNA

organism: Homo sapiens

source_name: Alveolar macrophages, Poly(I:C), 2 h, donor 1

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit.

growth_protocol: Alveolar macrophages were isolated by lavage of human lung tissue obtained from patients undergoing lung resection. Cells were enriched by plastic adherence (> 95% purity as shown by CD68 staining).

extract_protocol: Total RNA including small RNAs was isolated using miRNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Cells were either left untreated or treated as follows: 1 µg/mL LPS for 2 h; 1 µg/mL Pam3CSK4 for 2 h; 10 µg/mL Poly(I:C) for 2 h; 0.1 µg LPS for 24 h (chronic low-dose exposure to induce LPS tolerance); 0.1 µg LPS for 24 h followed by rechallenge with 1 µg/mL LPS for 2 h; 1 µg Poly(I:C) for 24 h (chronic low-dose exposure).

tag: cell type

value: alveolar macrophages

tag: lung tissue donor

tag: treatment

value: PIC 2h


title: ATAC_LSD1 KO2

type: SRA

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

country: USA

institute: WCMC

description: omni-ATAC-seq

library_source: genomic

data_processing:
ATAC-seq paired-end sequencing reads were trimmed to remove adapter sequences using NGmerge with option “-a”, and trimmed reads were aligned to mm10 reference genome using bowtie2 with options “-X2000 –local”. Alignments were filtered using samtools v1.8 to retain only uniquely mapping read pairs and to discard mitochondrial mapping reads. Read duplicates were detected and removed using the MarkDuplicates program in Picard Tools 2.18.11.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BIGWIG files: Continuous value ATACseq signal.
Supplementary_files_format_and_content: BED files: Genomic locations of differential opening or closing peaks.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse GC B cells

extract_protocol:
Fifty thousand purified GC B cells were resuspended in 1ml of ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) and centrifuged at 500 r.c.f. and 4°C for 5 min. Supernatant was aspirated by pipetting and cells were resuspended in 50ul of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 3 min. Following lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and nuclei were centrifuged at 500 r.c.f. and 4°C for 10 minutes. Supernatant was then aspirated by pipetting and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl tagment DNA enzyme, 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) and incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m.
Reactions were cleaned up with Zymo DNA Clean and Concentrator columns.
DNA libraries were prepared as described (Corces et al. Nat. Methods, 2017) and sequenced on a Hi-Seq 2000 (Illumina).

treatment_protocol: Sorted viable mouse GC B splenocytes (GL7+Fas+B220+).

value: GC B splenocytes (GL7+Fas+B220+)

tag: genotype/variation

value: LSD1 KO (C<gamma>1-Cre;Lsd1fl/fl)


title: AM_untreated_d1

description:
miRNA
Donor 1 Co
Alveolar macrophages - untreated

source_name: Alveolar macrophages, untreated, donor 1

value: untreated


title: Patient 68

type: genomic

city: Salt Lake City

first: Roberto

middle: Henrique

last: Nussenzveig

state: Utah

address: 2000 Circle of Hope

department: Oncology

institute: University of Utah/Huntsman Cancer Institute

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 68

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing:
The scanned data files were processed by GenomeStudio Genotyping using the cluster file HumanOmniExpress_24v1.0 (GPL21168), HumanOmniExpress_24v1.1 (GPL22678), and InfiniumOmniExpress_24v1.2  (Platform_InfiniumOmniExpress-24v1-2_A1.txt) all provided by Illumina.
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

source_name: Prostate Cancer

label_protocol: Standard Illumina labelling protocol

extract_protocol: Extraction of genomic DNA from separated leukocytes was performed using ice-cold alkaline phenol-chloroform extraction and precipitation with isopropanol followed by ethanol.

tag: disease state

value: Prostate Cancer

tag: abir. start date

tag: abir. failure date

tag: failure (yes=1, no=0)

tag: pfs (months)

tag: logpsa (at abir start)

value: BB

value: AB

tag: tissue

value: whole blood


title: pbmc_vdj_t

city: Stanford

first: Calvin

last: Kuo

state: CA

address: 265 Campus Dr.

department: Department of Medicine, Division of Hematology

institute: Stanford University

description:
Single cell 5' VDJ-seq
PBMC_Healthy_Donor_VDJ_T_Enrichment

library_source: transcriptomic

data_processing:
The Cell Ranger (CR) Software Suite (version 2.1.0) was used for 5’ gene counting and V(D)J sequence assembly and paired clonotype calling.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv, tsv, mtx files

source_name: PBMCs from a healthy donor

growth_protocol: Tumor tissues were minced finely, washed twice in ADMEM/F12 (Invitrogen) containing 1X Normocin (InvivoGen), resuspended in Type I collagen gel (Trevigen), and layered in a double dish air-liquid culture system as previously described8. Organoids were cultured in human organoid medium (ADMEM/F12 supplemented with 50% Wnt3a, RSPO1, Noggin-conditioned media (L-WRN, ATCC), HEPES (1mM, Invitrogen), Glutamax (1X, Invitrogen), Nicotinamide (10 mM, Sigma), N-Acetylcysteine (1 mM, Sigma), B-27 without vitamin A (1X, Invitrogen), A83-01 (0.5 μM, Tocris), Pen-Strep Glutamine (1X, Invitrogen), Gastrin (10 nM, Sigma), SB-202190 (10 μM, Sigma), and EGF (50 ng/mL, Invitrogen). Organoids were passaged every 14-30 days by dissociation with 200 units ml−1 collagenase IV (Worthington) at 37 °C for 30 min, followed by three 5-min washes with 100% FBS and replating at a 1:4 split into new air-liquid interface collagen gels. Additionally, in some cases, media was supplemented with recombinant human IL-2 (Peprotech) at 600 or 6000 IU/ml.

extract_protocol:
Tumor tissues were obtained through the Stanford Tissue Bank from patients undergoing surgical resection at Stanford University Medical Center (SUMC). All experiments utilizing human material were approved by SUMC’s Institutional Review Board and performed under protocol #28908. Written informed consent for research was obtained from donors prior to tissue acquisition. Samples were confirmed to be tumor by pathological assessment at SUMC.
Cellular suspensions were loaded on a ChromiumTM Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using the ChromiumTM Single Cell 5’ Library & Gel Bead Kit (P/N 1000006, 10x Genomics). GEM-RT was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; P/N 1851197):  53 °C for 45 min, 85 °C for 5 min; held at 4 °C and stored at -20 °C. The GEMs were shipped to 10x Genomics on dry ice, then broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific; P/N 37002D) . Barcoded, full length cDNA was amplified using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 45 s; cycled 13 ×: 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter; P/N B23318) . Barcoded, full-length V(D)J segments were enriched from amplified cDNA with primers specific to TCR constant regions. The target enrichment 1 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 45 s; cycled 10 ×: 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. The target enrichment 1 was cleaned up with the SPRIselect Reagent Kit (0.8 × SPRI). The target enrichment 2 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98 °C for 45 s; cycled 10 ×: 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. The target enrichment 2 was cleaned up twice with the SPRIselect Reagent Kit (0.5 × and 0.8 × SPRI). The enrichment primers can be found in Supplementary Table 4. 5’ gene expression and enriched libraries were constructed using the reagents in the ChromiumTM Single Cell 3’/5’ Library Construction kit (P/N 1000020). For 5’ gene expression library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) post fragmentation, end repair and A-tailing cleanup with SPRIselect; (3) adaptor ligation; (4) post ligation cleanup with SPRIselect; (5) sample index PCR and cleanup. For the enriched library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) adaptor ligation; (3) post ligation cleanup with SPRIselect; (4) sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824). Sequencing libraries were loaded at concentrations on sequencers with the read configuration as specified in Table S5.

value: PBMCs from a healthy donor

tag: condition

value: Cryopreserved


title: Patient 67

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 67


title: JFE005: LA35 NI

city: Québec

first: Julie

last: Fradette

state: Québec

department: Chirurgie

country: Canada

institute: Université Laval

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: Engineered human connective tissue

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

growth_protocol: Cells were differenciated or not into adipocytes according to the protocol described in the associated publication. Reconstructed tissues were analysed at day 35 of culture.

extract_protocol: RNA was extracted with RNeasy Lipid tissue Mini Kit (Qiagen), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Adipose-derived human stromal/stem cells differentiated into connective tissue


title: YJM-SEtOH-2

description:
YJM975SEtOH2
V100006801_L*_HK500YEAoyiEAANRBAPEI-516


title: ATAC_LSD1 KO3

description: omni-ATAC-seq


title: AM_LPS_2h_d1

description:
miRNA
Donor 1 LPS 2 h
Alveolar macrophages - LPS 1 µg/ml, 2 h

source_name: Alveolar macrophages, LPS, 2 h, donor 1

value: LPS 2h


title: Patient 65

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 65


title: JFE004: LA44 Ind

source_name: Engineered human adipose tissue

value: Adipose-derived human stromal/stem cells differentiated into adipocyte tissue


title: YJM-SEtOH-1

description:
YJM975SEtOH1
V100006801_L*_HK500YEAoyiEAAMRBAPEI-515


title: pbmc_gex

description:
Single cell 5' RNA-seq
PBMC_Healthy_Donor_GEX


title: RM-SEtOH-3

description:
RM11SEtOH3
V100006801_L*_HK500YEAoyiEAARRBAPEI-520

source_name: RM11_S-CSM with 2% ethanol


title: pbmc_vdj_b

description:
Single cell 5' VDJ-seq
PBMC_Healthy_Donor_VDJ_B_Enrichment


title: RM-SEtOH-2

description:
RM11SEtOH2
V100006801_L*_HK500YEAoyiEAAQRBAPEI-519


title: JFE003: LA40 Ind


title: Patient 64

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 64

tag: last f/u

value: AA


title: JFE002: LA36 Ind


title: RM-SEtOH-1

description:
RM11SEtOH1
V100006801_L*_HK500YEAoyiEAAPRBAPEI-518

value: S-CSM with 2% ethanol


title: JFE006: LA36 NI


title: Patient 63

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 63


title: ccRCC_B_or_vdj_t_rep1

description:
Single cell 5' VDJ-seq
Organoid_Kidney_CD45_Donor_B_VDJ_T_Enrichment_Rep1

source_name: CD45+ cells from an organoid sample

value: CD45+ cells from an organoid sample

value: Organoid


title: YJM-Sgly-3

description:
YJM975SGly3
V100006801_L*_HK500YEAoyiEAAXRBAPEI-526

source_name: YJM975_S-CSM with 2% glycerol

value: S-CSM with 2% glycerol

value: whole yeast cells


title: Patient 66

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 66


title: Patient 58

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 58


title: Patient 62

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 62


title: Patient 61

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 61


title: JFE001: LA35 Ind


title: YJM-Sgly-2

description:
YJM975SGly2
V100006801_L*_HK500YEAoyiEAAWRBAPEI-525


title: Patient 60

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 60


title: ccRCC_B_or_gex_rep2

description:
Single cell 5' RNA-seq
Organoid_Kidney_CD45_Donor_B_GEX_Rep2


title: YJM-Sgly-1

description:
YJM975SGly1
V100006801_L*_HK500YEAoyiEAAVRBAPEI-524


title: RM-Sgly-3

description:
RM11SGly3
V100006801_L*_HK500YEAoyiEABARBAPEI-532

source_name: RM11_S-CSM with 2% glycerol


title: ccRCC_B_or_vdj_t_rep2

description:
Single cell 5' VDJ-seq
Organoid_Kidney_CD45_Donor_B_VDJ_T_Enrichment_Rep2


title: ccRCC_A_or_vdj_t_rep2

description:
Single cell 5' VDJ-seq
Organoid_Kidney_CD45_Donor_A_VDJ_T_Enrichment_Rep2


title: RM-Sgly-2

description:
RM11SGly2
V100006801_L*_HK500YEAoyiEAAZRBAPEI-530


title: Patient 59

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 59


title: ccRCC_2_ft_gex_rep1

description: Single cell 5' RNA-seq

data_processing:
The Cell Ranger (CR) Software Suite (version 2.1.0) was used for 5’ gene counting and V(D)J sequence assembly and paired clonotype calling.
Genome_build: GRCh38

source_name: CD45+ cells from a fresh kidney tumor sample

growth_protocol: Tumor tissues were minced finely, washed twice in ADMEM/F12 (Invitrogen) containing 1X Normocin (InvivoGen), resuspended in Type I collagen gel (Trevigen), and layered in a double dish air-liquid culture system as previously described8. Organoids were cultured in human organoid medium (ADMEM/F12 supplemented with 50% Wnt3a, RSPO1, Noggin-conditioned media (L-WRN, ATCC), HEPES (1mM, Invitrogen), Glutamax (1X, Invitrogen), Nicotinamide (10 mM, Sigma), N-Acetylcysteine (1 mM, Sigma), B-27 without vitamin A (1X, Invitrogen), A83-01 (0.5 ?M, Tocris), Pen-Strep Glutamine (1X, Invitrogen), Gastrin (10 nM, Sigma), SB-202190 (10 ?M, Sigma), and EGF (50 ng/mL, Invitrogen). Organoids were passaged every 14-30 days by dissociation with 200 units ml?1 collagenase IV (Worthington) at 37 °C for 30 min, followed by three 5-min washes with 100% FBS and replating at a 1:4 split into new air-liquid interface collagen gels. Additionally, in some cases, media was supplemented with recombinant human IL-2 (Peprotech) at 600 or 6000 IU/ml.

extract_protocol:
Tumor tissues were obtained through the Stanford Tissue Bank from patients undergoing surgical resection at Stanford University Medical Center (SUMC). All experiments utilizing human material were approved by SUMC’s Institutional Review Board and performed under protocol #28908. Written informed consent for research was obtained from donors prior to tissue acquisition. Samples were confirmed to be tumor by pathological assessment at SUMC.
Cellular suspensions were loaded on a ChromiumTM Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using the ChromiumTM Single Cell 5’ Library & Gel Bead Kit (P/N 1000006, 10x Genomics). GEM-RT was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; P/N 1851197):  53?°C for 45 min, 85?°C for 5?min; held at 4?°C and stored at -20?°C. The GEMs were shipped to 10x Genomics on dry ice, then broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific; P/N 37002D) . Barcoded, full length cDNA was amplified using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98?°C for 45 s; cycled 13 ×: 98?°C for 20?s, 67?°C for 30?s, and 72?°C for 1?min; 72?°C for 1?min; held at 4?°C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6 × SPRI; Beckman Coulter; P/N B23318) .  Barcoded, full-length V(D)J segments were enriched from amplified cDNA with primers specific to TCR constant regions. The target enrichment 1 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98?°C for 45 s; cycled 10 ×: 98?°C for 20?s, 67?°C for 30?s, and 72?°C for 1?min; 72?°C for 1?min; held at 4?°C. The target enrichment 1 was cleaned up with the SPRIselect Reagent Kit (0.8 × SPRI).  The target enrichment 2 was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module: 98?°C for 45 s; cycled 10 ×: 98?°C for 20?s, 67?°C for 30?s, and 72?°C for 1?min; 72?°C for 1?min; held at 4?°C. The target enrichment 2 was cleaned up twice with the SPRIselect Reagent Kit (0.5 × and 0.8 × SPRI). The enrichment primers can be found in Supplementary Table 4. 5’ gene expression and enriched libraries were constructed using the reagents in the ChromiumTM Single Cell 3’/5’ Library Construction kit (P/N 1000020). For 5’ gene expression library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) post fragmentation, end repair and A-tailing cleanup with SPRIselect; (3) adaptor ligation; (4) post ligation cleanup with SPRIselect; (5) sample index PCR and cleanup. For the enriched library construction, these steps were followed: (1) fragmentation, end repair and A-tailing; (2) adaptor ligation; (3) post ligation cleanup with SPRIselect; (4) sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824). Sequencing libraries were loaded at concentrations on sequencers with the read configuration as specified in Table S5.

value: Fresh tumor


title: ccRCC_A_or_vdj_t_rep1

description:
Single cell 5' VDJ-seq
Organoid_Kidney_CD45_Donor_A_VDJ_T_Enrichment_Rep1


title: RM-Sgly-1

description:
RM11SGly1
V100006801_L*_HK500YEAoyiEAAYRBAPEI-527


title: ccRCC_A_or_gex_rep2

description:
Single cell 5' RNA-seq
Organoid_Kidney_CD45_Donor_A_GEX_Rep2


title: Patient 57

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 57


title: ccRCC_A_or_gex_rep1

description:
Single cell 5' RNA-seq
Organoid_Kidney_CD45_Donor_A_GEX_Rep1


title: YJM-SD-2

description:
YJM975SD2
V100006883_L*_HK500YEAoyiEAAERBAPEI-506

source_name: YJM975_S-CSM with 2% glucose

value: S-CSM with 2% glucose


title: ccRCC_1_or_vdj_t_rep1

description:
Single cell 5' VDJ-seq
Organoid_Kidney_CD45_Donor_1_VDJ_T_Enrichment_Rep1


title: WT CBX8 re-expression rep 3

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

data_processing:
Reads were trimmed using trimmomatic on the Galaxy web interface. Parameters used: TruSeq3; headcrop, 8; sliding window with defaults; minlen, 30.
Paired end reads were aligned to the hg38 genome using HiSat2 defaults on the Galaxy web interface
Counts matrix was generated as reads per sythnetic transcript
Mean counts per million were generated from the replicates for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for counts per transcript per replicate

source_name: T98G GBM cell line

growth_protocol: Cells were plated 72 hrs prior to the experiment, cells were grown in Eagle's modified essential medium, 10% FBS, 1% sodium pyruvate, 1% penicillin/streptomycin, 1% glutamine, 1% non-essential amino acids, grown at 37 °C and 5% CO2

extract_protocol:
RNA was isolated using Trizol followed by RNA easy
Oligo dT Library construction

treatment_protocol: Doxycycline (1 ug/mL) for 72 hours

value: wild type


title: YJM-SD-1

description:
YJM975SD1
V100006883_L*_HK500YEAoyiEAADRBAPEI-505


title: WT CBX8 re-expression rep 2


title: ccRCC_1_or_gex_rep2

description:
Single cell 5' RNA-seq
Organoid_Kidney_CD45_Donor_1_GEX_Rep2


title: Patient 56

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 56

value: Prostate Cancer

value: BB


title: ccRCC_1_or_gex_rep1

description:
Single cell 5' RNA-seq
Organoid_Kidney_CD45_Donor_1_GEX_Rep1


title: ccRCC_B_or_gex_rep1

description:
Single cell 5' RNA-seq
Organoid_Kidney_CD45_Donor_B_GEX_Rep1


title: YJM-SD-3

description:
YJM975SD3
V100006883_L*_HK500YEAoyiEAAFRBAPEI-507


title: ccRCC_1_or_vdj_t_rep2

description:
Single cell 5' VDJ-seq
Organoid_Kidney_CD45_Donor_1_VDJ_T_Enrichment_Rep2


title: Patient 55

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 55

value: whole blood


title: CBX8 KO rep 3

source_name: T98G CBX8 KO cell line

value: CBX8 KO


title: RM-SD-1

description:
RM11SD1
V100006883_L*_HK500YEAoyiEAAGRBAPEI-508

source_name: RM11_S-CSM with 2% glucose


title: Ang II induced HUVECs-1

city: Shanghai

first: Xianxian

last: Zhao

state: China

address: 168 Changhai Road

country: China

institute: Shanghai Changhai Hospital

description: Gene expression data from Ang II induced HUVECs.

hyb_protocol: Followed fragmentation, the 2nd cycle cDNAs were hybridized onto the microarray.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix)

data_processing: The original image was processed using Affymetrix GeneChip Command Console software (version 4.0, Affymetrix) through the raw data, and then the normalization of the chip was performed at the gene level and the exon level using Expression Console software (version 1.3.1, Affymetrix).

source_name: HUVECs with Ang II of 1 μM for 48 h

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

growth_protocol: HUVECs were obtained from the Cell bank of Chinese Academy of Sciences and were grown in Dulbecco's modified Eagle's medium (ScienCell Co., USA) that was supplemented with 10% fetal bovine serum (FCS) (Gibco Co., USA) in a humidified incubator with 5% CO2 at 37°C.

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

treatment_protocol: HUVECs at passages 3-10 were treated with Ang II of 1 μM for 48 h.

value: Human Umbilical Vein Endothelial Cells


title: Patient 73

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 73

value: AB


title: CBX8 KO rep 2


title: Ang II induced HUVECs-2


title: RM-SD-2

description:
RM11SD2
V100006883_L*_HK500YEAoyiEAAHRBAPEI-509


title: WT CBX8 re-expression rep 1


title: ccRCC_1_ft_vdj_t_rep1

description:
Single cell 5' VDJ-seq
Fresh_Tumor_Kidney_CD45_Donor_1_VDJ_T_Enrichment_Rep1

value: CD45+ cells from a fresh kidney tumor sample


title: Bvulgaris_BT

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Library strategy: DNA-Seq
The raw reads were trimmed using Trimmomatic to remove adapter sequences. Reads with an averaged value of at least 15 in a 4 nt window were trimmed from both ends. After trimming, reads pairs with at least one mate shorter that 16 bp were discarded
The remaining sequences (in average 94% of raw reads) were aligned with segemehl v0.2.0 (Hoffmann et al., 2009), with 95% accuracy threshold, to the corresponding reference genome (A.thaliana TAIR10 and the B. vulgaris RefBeet-1.2.2) including also the sequence of the BCTIV genome (accession no. JX082259).
Split read junctions were called with testrealign.x (part of segemehl toolkit) with default parameters, and junctions with at least a coverage of 10 reads and comprising the virus genome were selected for downstream analysis using R (dplyr package)
Then, the reads spanning the 10 kb locus around each selected junctions were recovered together with their mates from the original fastq files, using samtools (Li et al., 2009) and BBMap (https://sourceforge.net/projects/bbmap/)
The filtered paired read lists were used as input in the A5_miseq pipeline (Coil et al., 2015) with default parameters, for reference-unbiased de novo assembly.
We then used blastn (BLAST v2.2.25+) with default parameters to filter only the assembled scaffolds matching both the reference and the BCTIV genome, to select minicircle candidates.
Genome_build: RefBeet-1.2.2
Genome_build: TAIR10
Genome_build: Beet curly top Iran virus-[Siv] (GenBank: JX082259)
Supplementary_files_format_and_content: Assembled scaffolds matching both the reference and the BCTIV genome were used to generate a list of sequences in fasta format. If none of the assembled scaffolds matched this alignment criteria, the file was not generated (this is the case of Arabidopsis samples and the B. vulgaris mock-inoculated plant).

organism: Beta vulgaris

source_name: leaves

growth_protocol: Plants were grown in soil in greenhouse at 20–28/16–20◦C (day/night), with a 16/8 h (light/dark) photoperiod and supplementary lighting

extract_protocol:
Total nucleic acids were extracted from plant samples (100 mg) using the TLES method (Noris et al., 1996)
Before library preparation, genomic DNA was fragmented to an average insert size of 350bp using 18 cycles of 30 seconds each on a Bioruptor® Diagenode sonication device, split into three groups of 6 cycles with 2.5 minutes on ice between each set. The genomic DNA sequencing libraries were prepared using the TruSeq DNA PCR-Free LT Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA), starting from 1.1µg of sonicated DNA. Libraries were validated using the High Sensitivity D1000 screentape on the 2200 Tapestation instrument (Agilent technologies, Santa Clara, CA) and the LightCycler® 480 Instrument II using the LightCycler® 480 SYBR Green I Master mix (Roche, Basel, Switzerland).

treatment_protocol: Plants were inoculated by agroinoculation, by delivery of agrobacteria carrying 1.4mer BCTIV-Siv clone (Soleimani et al., 2013) (accession no. JX082259) or pBIN19 as control (mock).

tag: ecotype

value: Beta vulgaris L. var. vulgaris (spinach beet)

value: leaves

tag: developmental stage

value: 4 weeks post inoculation

tag: infected with

value: BCTIV


title: ccRCC_1_ft_gex_rep2

description:
Single cell 5' RNA-seq
Fresh_Tumor_Kidney_CD45_Donor_1_GEX_Rep2


title: ccRCC_1_ft_vdj_t_rep2

description:
Single cell 5' VDJ-seq
Fresh_Tumor_Kidney_CD45_Donor_1_VDJ_T_Enrichment_Rep2


title: ccRCC_1_ft_gex_rep1

description:
Single cell 5' RNA-seq
Fresh_Tumor_Kidney_CD45_Donor_1_GEX_Rep1


title: RM-SD-3

description:
RM11SD3
V100006883_L*_HK500YEAoyiEAAIRBAPEI-510

tag: strain

tag: growth medium


title: HUVECs-3

description: Gene expression data from normal HUVECs.

source_name: HUVECs

tag: cell type


title: CBX8 KO rep 1


title: Bvulgaris_HH

value: mock


title: Ang II induced HUVECs-3


title: g3

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30  and GC content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right  files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the  left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all  other parameters set default.
Gene function was annotated based on the following databases:  Nr (NCBI non-redundant protein sequences)；  Nt (NCBI non-redundant nucleotide sequences)；  Pfam (Protein family)；  KOG/COG (Clusters of Orthologous Groups of proteins)；  Swiss-Prot (A manually annotated and reviewed protein sequence database)；  KO (KEGG Ortholog database)；  GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the  bam alignment results of each sample. GATK3 software was used to perform SNP calling. Raw vcf  files were filtered with GATK standard filter method and other parameters ( cluster：3；WindowSize:  35; QD < 2.0 or FS > 60.0 or MQ < 40.0 or SOR > 4.0 or MQRankSum < -12.5 or ReadPosRankSum  < -8.0 or DP < 10).
SSR of the transcriptome were identified using MISA (http://pgrc.ipk-gatersleben.de/misa/misa.html), and primer for each SSR was designed using Primer3 (http://primer3.sourceforge.net/releases.php).
Differential expression analysis of two conditions/groups was performed using the DESeq R package  (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene  expression data using a model based on the negative binomial distribution. The resulting P values  were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.  Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample: 1. Clean data were mapped back onto the assembled transcriptome 2. Readcount for each gene was obtained from the mapping results
Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the GOseq R packages based Wallenius non-central hyper-geometric distribution （Young et al, 2010），which can adjust for gene length bias in DEGs.
KEGG (Kanehisa et al., 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS (Mao et al., 2005) software to test the statistical enrichment of differential expression genes in KEGG pathways.
The sequences of the DEGs was blast (blastx) to the genome of a related species (the protein protein interaction of which exists in the STRING database: http://string-db.org/) to get the predicted PPI of these DEGs. Then the PPI of these DEGs were visualized in Cytoscape (Shannon et al, 2003).
Genome_build: De novo transcriptome assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKMs and readcounts for each Sample

organism: Fagopyrum hailuogouense

source_name: root

growth_protocol: Roots of original buckwheat (Fagopyrum hailuogouense) were collected in 2018  in thick growth of weeds & maize fields on slopes,  Moxi Ancient Town, Luding Co., Tibetan Autonomous Prefecture Garze (Lat. 29°71’-30°11’ N, 101°59’-102°10’ E, Alt. 3100-3300 m), China. We observed that the dormancy stage was from October to the following April, and the growth stage was from April to September.Roots were collected during dormancy(February) and growth(May), respectively.

extract_protocol:
Buckwheat roots were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the transcriptome sampling, roots at dormancy and growth stages  were collected from the same individual, and roots with the same developing stage from three plants comprised of three replicates. the collected samples were flash frozen in liquid nitrogen and stored at −80°c until further use.

tag: Stage

value: Growth stage

value: root


title: HUVECs-2


title: d2

value: Dormant  stage


title: g2


title: d1


title: g1


title: d3


title: scr1_deletion_suc_R1

status: Public on Dec 12 2018

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

country: Australia

institute: Peter MacCallum Cancer Centre

description:
processed data file: scr1_counts_combined.csv
processed data file header: R121

data_processing:
basecalls were performed using Illumina CASAVA v1.8.4 pipeline
raw reads were cleaned using Cutadapt v1.9.1 with default parameters and assessed for quality using FastQC
cleaned reads were aligned to the S. pombe ASM294v2.25 genome using Tophat2 v2.1.1 with a max intron size of 5000bp and library-type of fr-firststrand (for stranded samples) or fr-unstranded (for unstranded samples)
reads mapping to gene features were counted with featureCounts v1.5.2 using -s 2 (for stranded samples)
Differential gene expression was performed using DESeq2 v1.12.3
Genome_build: ASM294v2
Supplementary_files_format_and_content: csv file includes read counts for each sample

organism: Schizosaccharomyces pombe

source_name: Whole cell

growth_protocol: Cells were cultured in YES 3% glucose for four hours at 32 degrees before being collected by centrifugation, washed twice in sterile water and shifted to YES 3% glucose, YES 3% sucrose, YES 3% glycerol + 0.1% glucose or YES 3% glycerol and cultured at 32 degrees for a further four hours

extract_protocol:
Cells were harvested by centrifugation and the hot phenol method (Lyne et al. 2003, BMC Genomics 4:27) was used to isolate total RNA from cells
Libraries for R72, R73, R74, R81 and R82 were prepared from ribo-depleted RNA using the Illumina TruSeq unstranded protocol. All other samples were prepared from ribo-depleted RNA using the Illumina TruSeq stranded protocol.

value: D163_scr1 deletion

tag: genotype


title: WT_glyc_gluc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R126

value: Y44_Wild Type

value: h-


title: scr1_disrupt_gluc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R81


title: WT_suc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R87


title: scr1_disrupt_suc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R96


title: WT_suc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R73


title: scr1_disrupt_gluc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R95


title: WT_glyc_gluc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R74


title: scr1_deletion_gluc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R120


title: WT_glyc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R88


title: scr1_deletion_gluc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R129

value: D165_scr1 deletion


title: WT_gluc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R86


title: scr1_disrupt_suc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R82


title: WT_glyc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R110


title: WT_gluc_R1

description:
processed data file: scr1_counts_combined.csv
processed data file header: R72


title: scr1_deletion_suc_R2

description:
processed data file: scr1_counts_combined.csv
processed data file header: R130


title: PolII_glycerol_CHIP_R2

description:
ChIP
none

data_processing:
basecalls were performed using Illumina CASAVA v1.8.4 pipeline
raw reads were cleaned using Cutadapt v1.9.1 with default parameters and assessed for quality using FastQC
cleaned reads were aligned to the S. pombe ASM294v2.25 genome using Bowtie2 v2.3.1 with the following parameters: --very-sensitive- local --minins 0 --maxins 600 -t --threads 8.
ChIP-seq peak calling was performed for transcription factor ChIPs using MACS2 v2.1.1 with the following parameters: -bw 300 --gsize 12.5E6 -B -q 0.01 -m 4 50 -extsize 150 —fix- bimodal. The Irreproducible Discovery Rate (IDR) statistic v2.0.2 (https://github.com/nboley/idr) was calculated for pairs of ChIP-seq replicates and used to filter MACS2 peak calls for reproducible and high quality peaks.
bigwigs were generated for RNA-PolII Ser5 ChIPs using deeptools BAM compare
Genome_build: ASM294v2
Supplementary_files_format_and_content: peak files contain high confidence peaks that passed IDR thresholds per sample

growth_protocol: Cells were cultured in YES 3% glucose for four hours at 32 degrees before being collected by centrifugation, washed twice in sterile water and shifted to YES 3% glucose, YES 3% sucrose, or YES 3% glycerol and cultured at 32 degrees for a further four hours

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared according to Wong et al. 2013 Curr Protoc Mol Biol Chapter 7:Unit 7 11

treatment_protocol: Cells were crosslinked for 30 mins in 1% formaldehyde. Following this the crosslinking reaciton was quenched with glycine

value: h+ ura4-d18 leu1-32 ade6-m216 scr1::TAP-KanMX6

tag: chip antibody

value: Anti-RNA polymerase II subunit B1 (phospho-CTD Ser-5) clone 3E8 (Merck Millipore 04-1572)


title: PolII_sucrose_CHIP_R2

description:
ChIP
none


title: PolII_glycerol_CHIP_R1

description:
ChIP
none


title: AM_PIC_24h_d4

description:
miRNA
Donor 4 PIC 24 h
Alveolar macrophages - Poly(I:C) 1 µg/ml, 24 h

source_name: Alveolar macrophages, Poly(I:C), 24 h, donor 4

value: alveolar macrophages

tag: lung tissue donor

tag: treatment

value: PIC 24h


title: AM_untreated_d4

description:
miRNA
Donor 4 Co
Alveolar macrophages - untreated

source_name: Alveolar macrophages, untreated, donor 4

value: untreated


title: PolII_glucose_CHIP_R1

description:
ChIP
none

value: Y44_Wild type


title: PolII_glucose_CHIP_R2

description:
ChIP
none


title: HUVECs-1

description: Gene expression data from normal HUVECs.

value: Human Umbilical Vein Endothelial Cells


title: Rst2_sucrose_CHIP_R2

description:
ChIP
Rst2_sucrose_IDR_filtered.narrowPeak

value: h+ ura4-d18 leu1-32 ade6-m216 rst2::TAP-KanMX6

value: Protein A (clone SPA-27, Sigma P2921)


title: Rst2_glycerol_CHIP_R1

description:
ChIP
Rst2_glycerol_IDR_filtered.narrowPeak


title: Scr1_sucrose_INPUT_R1

description:
Input Control
none


title: Rst2_glucose_CHIP_R2

description:
ChIP
Rst2_glucose_IDR_filtered.narrowPeak


title: Rst2_glycerol_CHIP_R2


title: Scr1_glucose_INPUT_R2

description:
Input Control
none


title: PolII_sucrose_CHIP_R1

description:
ChIP
none


title: Scr1_glycerol_INPUT_R1

description:
Input Control
none


title: Rst2_glucose_CHIP_R1


title: d8H1+ins_CD31+_rep1

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg38 genome using RSEM.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: hg38
Supplementary_files_format_and_content: Excel table files of gene names and FPKM values for each sample.

growth_protocol: Undifferentiated hESCs was cultured in E8 medium without feeders.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase free DNase.
RNA library was prepared following the instruction of TruePrepTM DNA Library Prep Kit V2 for Illumina

treatment_protocol: For monolayer based endothelial and hematopoietic differentiation, we modified a protocol published by Wang et al (Wang et al., 2012).  On day 5 and of differentiation, CD31+CD34+ were sorted.On day 8 of differentiation,  CD31+CD34+CD43+ and CD31+CD34+CD43- cells were sorted

tag: cell line

value: human embryonic stem cell line

tag: passage

tag: insulin supplement

value: yes

tag: cell subtype

value: day 8 CD31+CD34+


title: d8H1+ins_CD31+_rep2


title: d8H1-ins_CD31+_rep2

value: no


title: Tup11_glycerol_CHIP_R2

description:
ChIP
Tup11_glycerol_IDR_filtered.narrowPeak

value: h+ ura4-d18 leu1-32 ade6-m216 tup11::TAP-KanMX6


title: d8H1-ins_CD31+_rep1


title: Rst2_sucrose_CHIP_R1


title: d8iPS-ins_CD31+_rep1

value: human induced pluripotent stem cells (iPSCs) from CD34+ cord blood


title: d8iPS+ins_CD31+_rep1


title: Tup11_sucrose_CHIP_R1

description:
ChIP
Tup11_sucrose_IDR_filtered.narrowPeak


title: Tup11_sucrose_CHIP_R2


title: Tup11_glycerol_CHIP_R1


title: d8iPS+ins_CD31+_rep2


title: d8iPS-ins_CD31+_rep2


title: Tup11_glucose_CHIP_R2

description:
ChIP
Tup11_glucose_IDR_filtered.narrowPeak


title: Tup11_glucose_CHIP_R1


title: Scr1_glycerol_CHIP_R2

description:
ChIP
Scr1_glycerol_IDR_filtered.narrowPeak


title: d5iPS+ins_CD31+_rep1

value: day 5 CD31+CD34+


title: d5iPS+ins_CD31+_rep2


title: d5iPS-ins_CD31+_rep2


title: d5H1+ins_CD31+_rep2


title: d5H1-ins_CD31+_rep2


title: d5H1+ins_CD31+_rep1


title: Scr1_sucrose_CHIP_R1

description:
ChIP
Scr1_sucrose_IDR_filtered.narrowPeak


title: Scr1_glucose_CHIP_TR_R1

description:
ChIP
Scr1_glucose_IDR_filtered.narrowPeak


title: Scr1_glucose_CHIP_TR_R2


title: Scr1_sucrose_CHIP_R2


title: Scr1_glucose_CHIP_R1


title: iPSC-_CD43-_rep1


title: iPSC-_CD43+_rep1


title: d5H1-ins_CD31+_rep1


title: BB21_HS_20_9

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

data_processing:
reads were processed and aligned to the C. elegans WS220 reference genome. The expression levels for each gene were evaluated by read counts. DESeq2 package in R  was used to identify differentially expressed genes.
Genome_build: C. elegans WS220
Supplementary_files_format_and_content: DEseq2 results based on normalized read counts; excel

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: worms were grown at 20°C on enriched NGM with OP50 as food

extract_protocol:
Frozen worms were grinded to powder using pre-chilled mortar and pestle. RNA was extracted using Direct-Zol RNA MiniPrep Plus (Zymo research) according to the manufacture instructions.
Illumina TruSeq® RNA Sample Preparation kit.

treatment_protocol: For heat shock treatment, L4 larva were transferred from 20°C incubator to 34°C water bath for 75 min incubation. Next, worms were allowed to recover at room-temperature for 20 min and then returned back to 20°C incubator for additional 3 h. Control plates were kept under 20°C all time long. Before collecting the worms, the heat-exposed and the control worms were washed several times with M9 media to avoid contamination with bacteria, and then snap-frozen in liquid nitrogen and stored in -80°C

tag: genotype/variation

value: ADAR mutant

tag: tissue

value: whole worm

tag: bio replicate no

tag: tech replicate no


title: BB21_HS_12_7


title: H1_CD43-_rep1


title: BB4_HS_12_7


title: H1_CD43-_rep2


title: iPSC-_CD43-_rep2


title: Scr1_glucose_CHIP_R2

value: h+ ura4-d18 leu1-32 ade6-m216 scr1::TAP-KanMX6


title: H1_CD43+_rep2


title: iPSC-_CD43+_rep2


title: H1_CD43+_rep1


title: Scr1_glycerol_CHIP_R1


title: BB4_C_4_9


title: BB4_HS_28_6


title: d5iPS-ins_CD31+_rep1


title: BB21_C_12_7


title: BB4_C_12_7


title: BB4_C_28_6


title: BB4_HS_5_9


title: N2_HS_30_8

value: wild type


title: N2_HS_28_6


title: BB21_C_20_9


title: N2_HS_12_7


title: N2_C_12_7


title: N2_C_30_8


title: N2_C_28_6


title: 89290T

first: Pengbo

last: Cao

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The TopHat (v2.0.10) was used to align reads to human reference genome (hg19 release) and RefSeq annotated genes, and to discover transcript splice sites.
The Cufflinks (v2.1.1) was used to estimate the gene expression levels based on the map generated by TopHat.
The expression levels for each gene were normalized to fragments per kilobase of exon per million fragments mapped (FPKM) to facilitate the comparison of transcript levels among samples.
Genome_build: hg19
Supplementary_files_format_and_content: Textfiles include FPKM values for each sample

source_name: tumor tissue

extract_protocol:
Total RNA from ICC tissue samples was extracted by TRIzol (Sigma, USA). Briefly, 2 μg of total RNA was used to synthesize cDNA with the PrimeScript RT Master Mix (RR037A, TaKaRa, Japan), following the standard protocols provided by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: female

tag: age

value: Intrahepatic cholangiocarcinoma


title: 88674T

value: male


title: 88724N

source_name: adjacent non-tumor tissue

value: adjacent non-tumor liver tissue


title: 88674N


title: 96484N


title: 88659T


title: 88659N


title: 86960T


title: 96484T


title: 88724T


title: 89290N


title: 87823N


title: 87823T


title: 86960N


title: 86279T


title: 86279N


title: Th9(IL4+TGF-b+IL-1b)

city: Winston-Salem

first: Yong

last: Lu

address: 575 N. Patterson Ave

department: Dept of Microbiology and Immunology

institute: wake forest school of medicine

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Expression Console produced RMA values

source_name: Th9(IL4+TGF-b+IL-1b) cells

label_protocol: Affymetrix protocol

growth_protocol: T cell culture condition

extract_protocol: RNeasy Mini Kit (Qiagen)

value: cultured murine Th cells


title: 85421T


title: 85421N


title: Th1

source_name: Th1 cells


title: Th2

source_name: Th2 cells


title: Th9(IL4+IL-1b)

source_name: Th9(IL4+IL-1b) cells


title: Th9(IL4+TGFb)

source_name: Th9(IL-4+TGFb) cells


title: 81032N


title: 81032T


title: 81023T


title: 81023N


title: 11770T


title: 11770N


title: 099535T


title: 098699N


title: 090608T


title: 098699T


title: 090608N


title: H2

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

data_processing:
Adaptor sequences and low quality score bases were trimmed and resulting reads were aligned to the human genome reference sequence (GRCh38).
The two lanes were then merged and processed. The number of read fragments overlapping with transcripts of genes was obtained using kallisto on gene annotation version E87.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing combined expression pseudo-count values for each sample (sample multiplexed over 2 lanes).

source_name: Vd1+ IELs

extract_protocol:
IELs were isolated from duodenal biopsies via mechanical disruption. Briefly, duodenal tissues were shaken at 250 rpm for 30 min at 37°C in 7 mL of RPMI 1640 medium supplemented with 1% dialyzed fetal bovine serum (Biowest), 2 mM EDTA (Corning), and 1.5 mM MgCl2 (Thermo Fisher Scientific). The procedure was repeated once with fresh medium to enhance cell recovery. Cells were harvested from the biopsy-free media via centrifugation and pooled for subsequent analyses.
Full-length cDNA and sequencing libraries were generated using a modified version of the single-cell Smart-seq2 protocol (Picelli et al., 2014). Briefly, 50–100 NCR+ (NKp46+) or NCR– (NKp46–) Vd1+ IELs were sorted into a lysis buffer containing oligo-dT and dNTPs. Reverse transcription was performed after hybridization of oligo-dT to poly-A RNA. The resulting cDNA was amplified over 18 thermocycles, purified using an AMPure XP Kit (Beckman Coulter), and quality controlled using a Bioanalyzer High Sensitivity DNA Kit (Agilent). A total of 0.25 ng of cDNA from each sample was tagmented, ligated with adapters (Nextera XT), amplified over 12 thermocycles, and quality controlled using a Bioanalyzer High Sensitivity DNA Kit (Agilent). Libraries were then pooled in equimolar amounts and sequenced on two lanes in duplicate using a HiSeq4000 System (Illumina).

tag: group

value: Active

tag: compartment

value: Duodenum

tag: Sex

value: F

tag: cell number


title: HEK293T_SIRT7_++_nucl_3

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 1.12
Mapping to rRNA reference sequence using Bowtie2 v. 2.2.6
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Human rRNA sequences
Supplementary_files_format_and_content: MS Excel files. Contains 5' and 3' read count over the rRNA sequence and the calculated RiboMeth-seq score and statistical analyses

molecule: nuclear RNA

source_name: HEK293T cell line

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific), according to the manufacturers instructions
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and adaptors added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description


title: H5

tag: cell type

value: M


title: HEK293T_SIRT7_++_nucl_1


title: H1


title: HEK293T_SIRT7_++_nucl_2


title: H6


title: 099535N


title: HEK293T_siSIRT7_cyto_2

molecule: cytoplasmic RNA


title: G2

value: GFD


title: HEK293T_siCtrl_cyto_3


title: HEK293T_siSIRT7_cyto_1


title: G1


title: G10

value: Control


title: F11


title: G9


title: HEK293T_SIRT7_--_nucl_1


title: HEK293T_siCtrl_cyto_2


title: F8


title: HEK293T_SIRT7_--_nucl_2


title: HEK293T_SIRT7_--_cyto_3


title: F7


title: HEK293T_siSIRT7_cyto_3


title: E11


title: HEK293T_SIRT7_++_cyto_3


title: E10


title: HEK293T_siCtrl_cyto_1


title: HEK293T_SIRT7_++_cyto_1


title: E7


title: E6


title: E4


title: ChIP-Seq Input (Control), 0 hr, Series 2

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description: Liver homogenate of mice

data_processing:
Alignment: The first fifty nucleotides of each sequence were mapped onto the UCSC mouse genome version NCBI37/mm9 via the eland_extended mode of ELAND v2e in the Illumina CASSAVA pipeline v1.8.2. We first retrieved fragments with unique matches at both ends. The tags with multiple matches on the mouse genome were then aligned via fetchGWI with an allowed maximum of 500 matches per tag. When tag alignment revealed multiple possible fragments for a tag pair, all possible fragments were kept and given a weight corresponding to the normalized size probability as determined from the size probability distribution of the unique fragments. Fragments sequenced more than once were counted only once (non-redundant only).
Scores were computed as the log2-ratio between counts in paired ChIPs and Input samples to which a pseudocount value of 16 was added. For RPC4 ChIP scores, the counts were assigned to a previously defined list of mouse annotated pol III genes and pol III occupied loci (see Table S3 in {Renaud, 2014 #11}, with each annotated RNA-coding region extended by 150 bp on each side. For H3K4me3 and RPB2, the regions considered extended 1000 bp upstream and downstream of the pol III loci TSSs. One fragment was worth one count, and fractional counts were attributed in case of a partial overlap between a fragment and an extended locus.
Genome_build: Ensembl 67/NCBI 37
Supplementary_files_format_and_content: BigWig files generated from the initial mapped bed file using first bedtools genomecov -bg to generate a bedgraph and then bedGraphToBigWig  to generate the final BigWig file

source_name: Liver

extract_protocol:
ChIP-seq was performed with the ‘MicroPlex Library Preparation’ kit, from Diagenode
10 ng of immunoprecipitated material was used for sequencing library preparation. Total input was also prepared for sequencing at each time point and replicate. Paired-end sequencing libraries were prepared with the ‘MicroPlex Library Preparation’ kit, from Diagenode, following the instructions of the manufacturer (Diagenode, catalog no C05010011).  No size selection was performed and the chromatin was amplified with 14 cycles of PCR. 100 nucleotides at the fragment ends were sequenced with paired-end sequencing technology from HiSeq 2500 (Illumina).

tag: strain

tag: experiment

value: ChIP-Seq

tag: age (weeks)

tag: chip antibody

tag: time point

value: 0 h


title: ChIP-Seq Input (Control), 48 hrs, Series 2

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 60 hrs, Series 2

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 48 hrs, Series 2

description: Liver homogenate of mice

value: anti-POLR2B Santa Cruz Cat N. SC-67318 (H-201)


title: D9


title: E1


title: HEK293T_SIRT7_--_cyto_2

tag: cell line


title: ChIP-Seq Input (Control), 36 hrs, Series 2

description: Liver homogenate of mice


title: D5


title: ChIP-Seq Pol II, 36 hrs, Series 2

description: Liver homogenate of mice


title: D8


title: C11


title: F4


title: HEK293T_SIRT7_--_cyto_1


title: ChIP-Seq Pol II, 0 hr, Series 2

description: Liver homogenate of mice


title: ChIP-Seq H3K4me3, 60 hrs, Series 2

description: Liver homogenate of mice

value: anti-H3K36me3 Abcam Cat N. ab9050 batch 927884


title: C10


title: ChIP-Seq H3K4me3, 48 hrs, Series 2

description: Liver homogenate of mice


title: C7


title: HEK293T_SIRT7_++_cyto_2


title: ChIP-Seq Pol II, 60 hrs, Series 2

description: Liver homogenate of mice


title: D12


title: B12


title: D4


title: ChIP-Seq Pol III, 60 hrs, Series 2

description: Liver homogenate of mice

value: anti-Rpc4 (Bonhoure et al, 2014)


title: ChIP-Seq H3K4me3, 0 hr, Series 2

description: Liver homogenate of mice


title: ChIP-Seq Pol III, 48 hrs, Series 2

description: Liver homogenate of mice


title: B5


title: B11


title: ChIP-Seq Pol III, 36 hrs, Series 2

description: Liver homogenate of mice


title: A5


title: A2


title: A6


title: ChIP-Seq Input (Control), 48 hrs, Series 1

description: Liver homogenate of mice


title: ChIP-Seq H3, 60 hrs, Series 1

description: Liver homogenate of mice

value: anti-H3 Abcam Cat N. ab1791-100 batch 377098


title: ChIP-Seq H3K4me3, 36 hrs, Series 2

description: Liver homogenate of mice


title: KYSE30-RNA-P1

city: Luoyang

first: liu

last: Ke

state: Henan

address: 24 Jinghua Road, Jianxi Qu

department: Cancer Hospital

institute: The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology

data_processing:
The Solexa pipeline version 1.8 (off-line Base Caller software, version 1.8) was used for image processing and Base recognition
The reads were removed after the sequencing quality evaluation by FastQC software, and the reference genomes of the corresponding species were compared by Hisat2 software (v2.0.4).
Transcription abundance was estimated using StringTie software (v1.2.3) with reference to the official database annotation information
FPKM was calculated at the gene level and transcript level using Ballgown
Genome_build: hg19

source_name: CELL

extract_protocol:
After total RNA was extracted from KYSE30 cells treated with Porphyromonas gingivalis or PBS, quality of the isolated RNA was assessed by agarose gel electrophoresis.Quantity of RNA was measured using NanoDrop 1000 instrument.
Oligo(dT) magnetic beads were used for enrichment of mRNA. cDNA libraries were constructed according to Illumina protocols. The quality of cDNA libraries were assessed using Agilent 2100 platform and the quantity of cDNA libraries were determined using RealTime PCR. Sequencing of samples was run on an Illumina HiSeq 4000.

tag: treatment

value: P. gingivalis


title: KYSE30-RNA-P2

growth_protocol: After total RNA was extracted from KYSE30 cells treated with Porphyromonas gingivalis or PBS, quality of the isolated RNA was assessed by agarose gel electrophoresis.


title: C4


title: KYSE30-RNA-C3

value: PBS


title: KYSE30-RNA-P3


title: ChIP-Seq Input (Control), 0 hr, Series 1

description: Liver homogenate of mice


title: KYSE30-RNA-C1


title: ChIP-Seq Pol II, 48 hrs, Series 1

description: Liver homogenate of mice


title: KYSE30-RNA-C2


title: ChIP-Seq Input (Control), 60 hrs, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Input (Control), 36 hrs, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 0 hr, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Pol II, 36 hrs, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Pol III, 0 hr, Series 2

description: Liver homogenate of mice


title: ChIP-Seq Pol III, 0 hr, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Pol III, 60 hrs, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Pol III, 48 hrs, Series 1

description: Liver homogenate of mice


title: ChIP-Seq Pol III, 36 hrs, Series 1

description: Liver homogenate of mice


title: HEK293T AQ-seq 1

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: small RNA-seq

data_processing:
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the human genome (hg38) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.

growth_protocol: HEK293T and HeLa cells were grown in DMEM media (Welgene) supplemented with 10% FBS (Welgene).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNA was mixed with thirty synthetic miRNA-like spike-in oligos. The RNA mixture was size-fractionated by 15% urea-polyacrylamide gel electrophoresis to enrich miRNA species. Small RNA libraries were constructed using either TruSeq small RNA library preparation kit (Illumina) according to manufacturer's instructions or AQ-seq as follows: miRNA-enriched RNA was ligated to 3′ randomized adapter with 20% PEG 8000, then ligated to 5′ randomized adapter with 20% PEG 8000, reverse-transcribed, and amplified. The cDNA was sequenced using a HiSeq 2500 platform.


title: HEK293T AQ-seq 2

description: small RNA-seq


title: HEK293T TruSeq 1

description: small RNA-seq


title: ChIP-Seq Pol II, 60 hrs, Series 1

description: Liver homogenate of mice


title: A1


title: 22rv1-sinc-72h-rep1

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

data_processing:
Align to GRCh38 using version STAR 2.4.1
Count reads using featureCounts (default settings, strand specific mode)
FPKM - upper quartile normalized using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level expression estimates

growth_protocol: Most cell lines were originally purchased from the American Type Culture Collection (ATCC) and were cultured as per the standard ATCC protocols. LNCaP-AR and LAPC4 cells were gifts from Dr. Charles Sawyers lab (Memorial Sloan-Kettering Cancer Center, New York, NY). Until otherwise stated, for all the experiments LNCaP, PNT2, LNCaP-AR, C42B, 22RV1, DU145, PC3 cells were grown in the RPMI 1640 medium (Gibco) and VCaP cells in the DMEM with Glutamax (Gibco) medium supplemented with 10% Full Bovine Serum (FBS; Invitrogen). LAPC4 cells were grown in IMEM (Gibco) medium supplemented with 15%FBS and 1nM of R1881. Immortalized normal prostate cells: RWPE1 were grown in keratinocyte media with regular supplements (Lonza); PNT2 were grown in RPMI medium with 10%FBS. HEK293 cells were grown in DMEM (Gibco) medium with 10% FBS. All cells were grown in a humidified 5%CO2 incubator at 37℃. All cell lines were biweekly tested to be free of mycoplasma contamination and genotyped every month at the University of Michigan Sequencing Core using Profiler Plus (Applied Biosystems) and compared with corresponding short tandem repeat (STR) profiles in the ATCC database to authenticate their identity in culture between passages and experiments.

extract_protocol:
In brief, tumor genomic DNA and total RNA were purified from the same sample using the AllPrep DNA/RNA/miRNA kit (QIAGEN). Matched normal genomic DNA from blood, buccal swab, or saliva was isolated using the DNeasy Blood & Tissue Kit (QIAGEN).
In-house dUTP based strand-specific RNA-seq protocol with polyA selection

treatment_protocol: Cells were seeded in a 6-wells plate at 200,000 cells/well density and transiently transfected with 2.5ug of lentiCRISPR-V2 (Addgene: #52961) vector using the Lipofectamine 3000 reagent (Cat#: L3000008), encoding the Cas9 protein and sgRNA that cuts either at amino acid 271 (5’-GTCAAGTGCGAGAAGCAGCCG-3’) or 359 (5’-GCCGGGCCCGGAGCTTATGGG-3’) in Exon2 of FOXA1. Cells were treated with non-targeting control sgRNA (5’-GACCGGAACGATCTCGCGTA-3’) vector to generate isogenic WT clones. Transfected cells were selected with puromycin (Gibco) for 3-4 days and FACS-sorted as single cells into 96-well plates. Cells were maintained in 96-wells for 4-6 weeks with replacement of the growth medium every 7days to allow for the expansion of clonal lines. Clones that successfully seeded, were further expanded and genotyped for FOXA1 using Sanger sequencing and immunoblotting with the N-terminal FOXA1 antibody. Sequence and expression validated 22RV1 and LNCaP clones with distinct class2 mutations were used for growth, invasion and metastasis assays as described. To generate stable cells, doxycyclline-inducible vectors coding different FOXA1 variants or GFP (control) were packaged into viral particle through the University of Michigan Vector Core. PCa cells were seeded in a 6-well plate at 100,000-250,000cells/well density and infected with 0.5ml of 10X viral titres packaged at the UofM Vector Core. This was followed by 3-4 days of puromycin (Gibco) selection to generate stable lines.

tag: foxa1 genotype

value: WT/WT

value: siNC (control)

tag: crispr genotype


title: 22rv1-sitle3-72h-rep2


title: 22rv1-sinc-72h-rep2


title: 22rv1-sitle3-72h-rep1


title: 22rv1-crispr-#wt3-rep2


title: Mixture_Sample_27

city: Cambridge

first: Kai

last: Kang

state: MA

address: 32 Vassar Street

department: CSAIL

institute: MIT

data_processing:
Generation of FASTQ files performed using Illumina bcl2fastq2
FASTQ files from each sequencing run concatenated into single file per library
Adapter sequence trimmed using cutadapt 1.12
Trimmed reads aligned using STAR version 2.5.2b to GRCh38 assembly
Counts per gene determined using featureCounts version 1.5.1 based on Ensembl release 90 GRCh38 annotations
Coverage tracks generated using genomeCoverageBed (bedtools v2.25.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig (.bw) containing raw read coverage; tab-delimited text (.txt) containing raw read counts per gene for all samples

growth_protocol: MCF7 cells were  cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS). Namalwa cells were a gift from Dr. Sandeep Dave, Duke University, and were cultured in RPMI medium supplemented with 10% FBS. Hs343T and hTERT-HME1 (ATCC) were cultured in HuMEC Ready medium (Thermo Fisher Scientific).

extract_protocol:
RNeasy kit
TruSeq RNA sample preparation kit v2

treatment_protocol: No treatment

tag: origin

value: cell line

tag: sample name

tag: tumor-mcf7 proportions

tag: cafs-hs_343.t proportions

tag: normal_breast-hmecs-htert proportions

tag: lymphocytes-namalwa proportions

value: control


title: Mixture_Sample_32


title: Mixture_Sample_28


title: Mixture_Sample_29


title: Lymphocytes_Namalwa_pure_2

value: Lymphocytes-Namalwa


title: 22rv1-crispr-#wt2-rep2


title: Normal_breast-hMECs-hTERT_pure_2


title: Mixture_Sample_31


title: Mixture_Sample_30


title: CAFs-Hs_343.T_pure_2


title: Mixture_Sample_25


title: Mixture_Sample_26


title: Tumor-MCF7_pure_2


title: 22rv1-crispr-#57-rep1


title: 22rv1-crispr-#57-rep2


title: 22rv1-crispr-#wt2-rep1


title: 22rv1-parental-rep2

value: parental


title: 22rv1-parental-rep1


title: Mixture_Sample_22


title: Mixture_Sample_24


title: Mixture_Sample_21


title: 22rv1-foxa1-r261g-v5-ar-milli-rep2

data_processing:
Alignment using STAR version 2.4.1 (splicing disabled)
Peak calling using MAC2 (default parameters)
BigWig created using bedtools and kent utils
Coverage was normalized to total sequencing depth
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig (coverage) and BED (peak calls)

extract_protocol:
8-10 million cells ectopically overexpressing different V5-tagged FOXA1 variants and WT AR (or TLE3) were fractionated to isolated intact nuclei using the NE-PER kit reagents (Thermo Fisher Scientific; Cat#: 78835) and lysed in the complete IP lysis buffer (Thermo Fisher Scientific; Cat#: 87788). Nuclear lysates were incubated for 2 hours at 4C with 30ul of magnetic Protein-G Dynabeads (Thermo Fisher Scientific; Cat#: 10004D) for pre-clearing. A fraction of the cleared lysate was saved as input and the remainder was incubated overnight (12-16 hours) with 10ug of target protein antibody at 4C with gentle mixing. Next day, 50ul of Dynabeads Protein-G beads were added to the lysate-antibody mixture and incubated for 2h at 4C. Beads were washed 3 times with IP buffer (150nM NaCl; Thermo Fisher Scientific) and directly boiled in 1X NuPage LDS/reducing agent buffer (ThermoFisher Scientific; Cat#: NP0007 and NP0009) to elute and denature the precipitated proteins. These samples were then immunoblotted as described above with the exception of using protein A-HRP secondary (GE HealthCare, Cat#: NA9120-1ML) antibody for detection.
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).

value: WT/WT + exo R261G

tag: target

value: AR

tag: foxa1 antibody

tag: crispr clone

value: no

tag: overexpression

value: yes


title: 22rv1-foxa1-r261g-v5-foxa1-cst-rep2

value: CST


title: 22rv1-crispr-#wt3-rep1


title: Mixture_Sample_20


title: Mixture_Sample_19


title: Mixture_Sample_18


title: 22rv1-foxa1-i176m-v5-ar-milli-rep2

value: WT/WT + exo I176M


title: Mixture_Sample_23


title: 22rv1-foxa1-i176m-v5-foxa1-cst-rep2


title: Mixture_Sample_14


title: Mixture_Sample_16


title: Mixture_Sample_15


title: Mixture_Sample_17


title: 22rv1-foxa1-wt-v5-ar-milli-rep2

value: WT/WT + exo WT


title: Mixture_Sample_12


title: Mixture_Sample_13


title: 22rv1-crispr-#36-tle3


title: 22rv1-foxa1-wt-v5-foxa1-cst-rep2


title: 22rv1-crispr-#57-tle3


title: 22rv1-foxa1-r261g-v5-ar-milli-rep1


title: 22rv1-parental-tle3


title: 22rv1-foxa1-r261g-v5-foxa1-cst-rep1


title: 22rv1-foxa1-i176m-v5-ar-milli-rep1


title: Mixture_Sample_7


title: 22rv1-foxa1-wt-v5-ar-milli-rep1


title: Mixture_Sample_9


title: Mixture_Sample_8


title: Mixture_Sample_10


title: Mixture_Sample_6


title: 22rv1-foxa1-i176m-v5-foxa1-cst-rep1


title: Mixture_Sample_11


title: 22rv1-foxa1-wt-v5-foxa1-cst-rep1


title: 22rv1-crispr-#wt3-tle3


title: Mixture_Sample_5


title: hek293-foxa1-r261g-v5-foxa1-tfs

value: FOXA1-negative + exo R261G

value: TFS


title: hek293-foxa1-i176m-v5-foxa1-tfs

value: FOXA1-negative + exo I176M


title: Mixture_Sample_3


title: hek293-foxa1-wt-v5-foxa1-tfs

value: FOXA1-negative + exo WT


title: Mixture_Sample_4


title: Mixture_Sample_2


title: lapc4-parental-tle3


title: Mixture_Sample_1


title: lncap-parental-tle3

source_name: LNCAP

value: LNCAP

value: WT/WT


title: 22rv1-crispr-#70-foxa1-tfs


title: c42b-parental-tle3


title: 22rv1-crispr-#70-foxa1-cst


title: hek293-egfp-v5-foxa1-tfs

value: FOXA1-negative + exo eGFP


title: Lymphocytes-Namalwa_pure_1

value: cell line

value: control


title: 22rv1-crispr-#36-armilli


title: CAFs-Hs_343.T_pure_1


title: Normal_breast-hMECs-hTERT_pure_1


title: Replicate 3 for wild type (Col-0)

city: Pozuelo de Alarcón

last: Oñate-Sánchez

state: Madrid

address: Campus de Montegancedo, Autopista M-40 (Km 38)

country: Spain

institute: Centro de Biotecnología y Genómica de plantas (Universidad Politécnica de Madrid)

data_processing:
Quality was assessed using FastQC v0.11.5 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc).
In order to evaluate the expression levels of the reads aligned, the cuffdiff protocol under local Galaxy interface v.2.2.1.0 (Afgan et al., 2016) was used.
The reads were aligned against the genome using TopHat v2.1.0 (Langmead et al., 2009)
The expression was obtained with Cuffdiff v2.2.1.3 (Trapnell et al., 2010).
Genome_build: Araport 11
Supplementary_files_format_and_content: Excel file with columns specifying: gene_id, gene name, sample 1 (identity), sample 2 (identity), status, log2 (fold change), p_value, q_value, significant?.

organism: Arabidopsis thaliana

source_name: Seeds at 12 hai (hours after imbibition)

extract_protocol:
RNA extraction was carried out as described previously (protocol 2 in Oñate-Sánchez and Vicente-Carbajosa, 2008) except that: in step 2, the mix containing the sample, phenol and chloroform was applied to a Phase Lock (5-PRIME) eppendorf previous to centrifugation to prevent organic contamination of the aqueous phase. RNA isolation was followed by RNA cleanup by the RNeasy mini kit (Qiagen).
Stranded library for HiSeq Sequencing v4 Chemistry

tag: tissue

value: seed


title: Tumor-MCF7_pure_1


title: Replicate 2 for wild type (Col-0)


title: Replicate 3 for nac25-KO


title: 22rv1-crispr-#36-foxa1-cst


title: 22rv1-crispr-#wt3-foxa1-tfs


title: 22rv1crispr-#wt3-armilli


title: 22rv1-crispr-#36-foxa1-tfs


title: 22rv1-parental-armilli


title: Replicate 3 for nac1L-KO


title: 22rv1-crispr-#wt3-foxa1-cst


title: Replicate 1 for nac25-KO


title: 22rv1-parental-foxa1-tfs


title: Replicate 1 for wild type (Col-0)


title: 22rv1-parental-foxa1-cst


title: Replicate 2 for nac1L-KO


title: 22rv1-crispr-#57-armilli


title: Replicate 2 for nac25-KO


title: 22rv1-crispr-#57-foxa1-tfs


title: RFPadultZ

city: Würzburg

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

description:
Adult murine hearts
barcode file: CEL-Seq2_UMI_barcodes.csv.gz

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the hearts of adult Ki67TagRFP mice [Z]

extract_protocol:
Live single cells were sorted in 384- well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain background

tag: genotype/variation

value: adult

value: Heart


title: Replicate 1 for nac1L-KO


title: RFPIRInfX

description:
Murine hearts 14 days after ischemia/reperfusion
barcode file: CEL-Seq2_UMI_barcodes.csv.gz

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-I/R surgery [X]

tag: time point

tag: heart region

value: infarcted area


title: 22rv1-crispr-#57-foxa1-cst

tag: cell line

tag: foxa1 genotype

value: no


title: RFPSHInfW

description:
Murine hearts 14 days after sham-surgery
barcode file: CEL-Seq2_UMI_barcodes.csv.gz

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex of hearts of Ki67TagRFP mice 14 days post-sham surgery [W]

value: apex


title: lncap-foxa1-p358fs-v5-foxa1-tfs

value: WT/WT + exo P358fs

value: yes


title: WTMIInfV

description:
Murine hearts 14 days after myocardial infarction
barcode file: CEL-Seq2_UMI_barcodes.csv.gz

source_name: Extracted RNA from living cells of the infarcted area of hearts of WT mice 14 days post-MI surgery [V]

value: WT


title: WTadultY

source_name: Extracted RNA from living cells of the hearts of adult Ki67TagRFP mice [Y]


title: lncap-foxa1-p358fs-v5-foxa1-cst

value: CST


title: Fibroblast HFFO4I3 0.5 µM

city: Frankfurt am Main

first: Xinlai

last: Cheng

state: Hessen

address: Max-von-Laue-Strasse 15. R. 3.652

department: Chemical Biology

institute: Goethe Frankfurt University. BMLS

description:
This cell line expresses EGFP under the control of the LTR7 promoter
SW-XC31_200737910047_G

hyb_protocol: No modifications were made to the recommended manufacturer's protocol for BeadChips

scan_protocol: Standard protocol for a BeadArray Reader

data_processing: The data were obtained from Beadstudio Software and transferred to R Software. The data were quantile-normalized across all hybridizations on BeadArrays.

label: Biotin

source_name: Treated human fibroblasts

label_protocol: The Illumina Totalprep RNA Amplification Kit was used to synthesize cDNA as well as to amplify biotinylated cRNA.

growth_protocol: Cell were culturted in standard DMEM medium enriched with FCS 10% and with Penicillin/Streptomycin added. The cells were cultured for at least 40 passages.

extract_protocol: Total RNA was extracted and purified by means of the Guanadine thyocyanate-phenol-chloroform extraction method using QIAzol Lysis Reagent.

treatment_protocol: Non-treated cells were kept in unaltered medium, while the other two samples were treated with a commercially available cocktail of empisomal vectors and with additional treatments of O4I3 (1 and 10 nM).

tag: passage


title: RFPneoU

description:
Neonatal murine hearts
barcode file: CEL-Seq2_UMI_barcodes.csv.gz

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the hearts of neonatal Ki67TagRFP mice [U]

value: neonate


title: iPSC O4I3 10 nM

source_name: hiPSC treated with O4I3 10 nM


title: Fibroblast HFF NT

description:
This cell line expresses EGFP under the control of the LTR7 promoter
SW-XC26_200737910047_B

source_name: Non treated human fibroblasts


title: lapc4-foxa1-wt-v5-foxa1-cst

value: WT/P358fs + exo WT


title: WTadultT

source_name: Extracted RNA from living cells of the hearts of adult Ki67TagRFP mice [T]


title: 96484N

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
From raw.CEL file, Copy-number estimation using Robust Multichip Analysis (CRMA) was used to pre-process the probe signal intensities. The procedure included that signal intensities were calibrated for offset and crosstalk between alleles, and normalized for probe sequence effects. After summarizing to probe-set level signals, fragment-length effects were normalized. Next, raw copy numbers was calculated by paired analysis, taking paired tumor-adjacent tissue as a reference for every tumor tissue. Then segmented copy number profiles were analyzed using Circular binary segmentation (CBS) algorithm2 with default parameters in the R package “DNA-copy” (http://www.r-project.org/).
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: adjacent non-tumor tissue

label_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by an Affymetrix service facility (CapitalBio Corporation, China).

extract_protocol: Genomic DNA from tumor and matched non-tumor liver tissues was isolated using QIAamp DNA Mini kits (Qiagen).

treatment_protocol: For all tumors and non-tumor tissues, samples were snap frozen and stored at -80°C. Tumor sections had to contain more than 70% tumor cell nuclei and less than 20% necrosis in all tumor samples.

tag: gender

value: male

tag: age

value: adjacent non-tumor liver tissue


title: iPSC O4I3 1 nM

source_name: hiPSC treated with O4I3 1 nM


title: 89290T

source_name: tumor tissue

value: female

value: Intrahepatic cholangiocarcinoma


title: lapc4-foxa1-wt-v5-foxa1-tfs

value: TFS


title: 96484T


title: 87823T


title: RFPIRInfS

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-I/R surgery [S]


title: iPSC NT

source_name: Non-treated hiPSC


title: lapc4-dht-foxa1-tfs


title: lapc4-dht-foxa1-cst


title: 89290N


title: 88659N


title: 88724T


title: RFPadultR

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the hearts of adult Ki67TagRFP mice [R]


title: c42b-parental-foxa1-tfs

value: WT/WT


title: 88724N


title: c42b-parental-foxa1-cst


title: Sorafenib

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

description: PLC-PRF-5 cells were treated with sorafenib (10 μM)

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

growth_protocol: PLC cells (5 × 10^3 cells/mL) were seeded in 96-well culture plates for 20h

extract_protocol: TRIzol Reagent (Invitrogen) was then used to lyse cells and extract the total RNA

treatment_protocol: PLC-PRF-5 cells were treated with sorafenib (50 μM), sorafenib probe (50μM) or DMSO for 24 h.

tag: cell type

value: liver hepatoma

tag: agent

value: sorafenib (10 uM)


title: 86279N


title: RFPadultQ

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the hearts of adult Ki67TagRFP mice [Q]

value: adult

value: Heart


title: Sorafenib probe

description: PLC-PRF-5 cells were treated with sorafenib probe (10μM)

value: sorafenib probe (10 uM)


title: Control vs alkaline stressed-cells

city: Fukuoka

first: Yujiro

last: Higuchi

address: 744 Motooka

country: Japan

institute: Kyushu University

description: Control cells were untreated, and alkaline-stressed cells were harvested after 2 h exposure at pH 8.0.

hyb_protocol: Hybridization buffer (Toray 3D-Gene Hybridization Buffer) was added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on a GenePix4000B (Molecular Devices) scanner

data_processing: GenePix Pro 5.1 was used

source_name: Fission yeast cells

label_protocol: 1 µg of total RNA were primed with 1 µl of T7 Oligo dT primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of Reverse Transcription Master Mix (Thermo). Labeling was performed using Cy3 and HyPer5 Post-Labeling Reactive Dye Pack (GE Healthcare).

growth_protocol: S. pombe ARC001 strain was cultured onvernight in YES (pH 5.4).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following manufacturer's instructions

treatment_protocol: Alkaline stress treatment was performed by culturing cells in YES supplemented with 200 mM MOPS (pH 8.0).

tag: strain

source_name: Fission yeast cells treated with alkaline stress


title: 86960T


title: lncap-parental-foxa1-cst

source_name: LNCAP

value: LNCAP

tag: target

value: no


title: 86960N


title: 85421N


title: 88659T


title: 88674T


title: 86279T


title: SAM2

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Raw sequence data were obtained via the RNA high-throughput sequencing process, and then filtered to remove contaminating reads, adapter sequences, poly-A tails, and other artifacts. All high-quality sequences, including those with only a single unique read, were used for further analysis.
Sequences reads were mapped to the Populus trichocarpa genome database downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/775/GCA_000002775.2_Poptr2_0/ by SOAP according to the default settings. The GenBank and Rfam  databases were employed to annotate the rRNAs, snRNAs, snoRNAs, and tRNAs in the sRNA library. Repeat overlapping sequences were annotated as repeat-associated sRNAs. Matching sRNAs without annotation were stored in an unannotated file.
To identify known miRNAs from the SAM and leaves of P. tomentosa, the bioinformatics pipeline was used to annotate known miRNAs, both conserved and lineage-specific. In the present study, all miRNAs belonging to families already annotated in the miRBase Registry (http://www.mirbase.org) in the P. trichocarpa database were defined as known. Potentially novel miRNAs and their hairpin precursors were predicted using the MIREAP (http://sourceforge.net/projects/mireap/) software from the remaining unannotated reads. The essential criteria of plant miRNAs were used to screen the novel miRNA candidates.
The expression frequency of miRNAs was normalized to one million by total clean reads of miRNAs in each library (TPM = miRNA count/total count of clean reads×1,000,000). The differential expression change of miRNA reads between the SAM and leaf libraries was calculated as follows: The fold change = log2 (SAM/Leaf). Both fold change > 1 and FDR < 0.05 were used to define the differentially expressed miRNAs.
Genome_build: Populus trichocarpa genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/775/GCA_000002775.2_Poptr2_0/)
Supplementary_files_format_and_content: The tab-delimited text file includes miRNA_name; SAM; leaf; log2FC; FDR; Regulated; Target Geneid and Swissprot_annotation(.txt)

organism: Populus tomentosa

source_name: SAM

growth_protocol: Healthy shoot tips and surrounding leaves of P. tomentosa, were collected from 20-year-old plants growing under natural conditions at Yangzhou University, Yangzhou, China (32.39°N, 119.42°E).

extract_protocol:
Total RNAs were extracted from the shoot tips (SAM) and surrounding leaves via the Trizol method with a slight modification to the manufacturer’s instructions for the TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: shoot tips


title: lncap-parental-foxa1-tfs

tag: foxa1 antibody


title: 81023T


title: SAM1


title: lapc4-parental-foxa1-cst

value: CST

tag: crispr clone


title: 87823N


title: RFPMIInfM

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-MI surgery [M]

value: infarcted area


title: 81032T


title: 88674N


title: leaf2

source_name: leaf

value: leaves


title: RFPIRInfN

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the infarcted area of hearts of Ki67TagRFP mice 14 days post-I/R surgery [N]


title: 81032N

value: male


title: 85421T


title: leaf1


title: lapc4-parental-foxa1-tfs

tag: overexpression


title: RFPSHInfL

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex of hearts of Ki67TagRFP mice 14 days post-sham surgery [L]

tag: tissue

value: apex


title: 15143-63_2292

status: Public on Dec 11 2018

city: Fredericton

first: Helen

middle: H.

last: Tai

state: New Brunswick

address: P. O. Box 20280, 850 Lincoln Rd.

department: Potato Research Centre

institute: Agriculture and Agri-Food Canada

data_processing:
*_arn*.txt: Adapter and barcode sequences were trimmed
*1x3.txt: Sequences that were not present in at least one of the three replicates were removed (1X3 tags)
Tag count data were transformed into a data matrix using in-house Perl scripts and transformed to the relative unit of counts per million.
Supplementary_files_format_and_content: tab delimited txt file with tag sequence and tag counts

organism: Solanum tuberosum

source_name: 15143-63_foliage from field-grown plants

extract_protocol:
The smallest leaflet from the 4th fully expanded compound leaf was removed from each of the five plants per plot and pooled for each replicate plot.  Leaf tissue was ground in the Lysing Matrix D tubes using a Geno Grinder 2000 (SPEX CertiPrep) machine for 2 min at speed 5. Samples were kept frozen. One ml RNA lysis buffer (200 mM sodium borate decahydrate (Borax), pH 9.0, 30 mM ethylene glygol bis (aminoethyl ether)-N-N’-tetraacetic acid (EGTA), 1% (w/v) sodium dodecyl sulfate (SDS), and 10 mM dithiothreitol) plus 1 % (w/v) sodium deoxycholate and 2% (w/v) polyvinylpyrrolidone (PVP) (Mr 40,000))  was added to ground leaf tissue in each tube.
Template DNA hybridization and sequencing on an Illumina Genome Analyzer II (Illumina, San Diego, USA) according to the manufacturer's instructions.

tag: genotype/variety

value: 15146 diploid mapping population clone

tag: clone id

value: foliage from field-grown plants

tag: run

value: RunB

tag: adapter b barcode

value: CCT

tag: channel


title: RFPadultP

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the hearts of adult Ki67TagRFP mice [P]

tag: strain background

tag: genotype/variation

tag: time point


title: 15143-81_2196

source_name: 15143-81_foliage from field-grown plants

value: 15144 diploid mapping population clone


title: 15143-23_2300

source_name: 15143-23_foliage from field-grown plants

value: 15143 diploid mapping population clone

value: RunA


title: 15143-40_2299

source_name: 15143-40_foliage from field-grown plants


title: 15143-09_2295

source_name: 15143-09_foliage from field-grown plants


title: 15143-25_2291

source_name: 15143-25_foliage from field-grown plants

value: RunC

value: GTT


title: 15143-41_2293

source_name: 15143-41_foliage from field-grown plants


title: 15143-98_2294

source_name: 15143-98_foliage from field-grown plants


title: 15143-04_2296

source_name: 15143-04_foliage from field-grown plants


title: 15143-28_2288

source_name: 15143-28_foliage from field-grown plants


title: 15143-51_2289

source_name: 15143-51_foliage from field-grown plants


title: 15143-42_2286

source_name: 15143-42_foliage from field-grown plants


title: Russet Burbank_2287

source_name: Russet Burbank_foliage from field-grown plants

value: tetraploid variety

value: Russet Burbank


title: 15143-84_2098

source_name: 15143-84_foliage from field-grown plants

value: 15145 diploid mapping population clone


title: 81023N

city: Beijing

source_name: adjacent non-tumor tissue

tag: gender

value: female

tag: age

value: adjacent non-tumor liver tissue


title: 11770N


title: 15143-01_2285

source_name: 15143-01_foliage from field-grown plants


title: Green Mountain_2298

source_name: Green Mountain_foliage from field-grown plants

value: Green Mountain


title: 11770T

source_name: tumor tissue

value: male

value: Intrahepatic cholangiocarcinoma


title: 15143-55_2281

source_name: 15143-55_foliage from field-grown plants

value: AGC


title: 15143-91_2283

source_name: 15143-91_foliage from field-grown plants

value: foliage from field-grown plants


title: 15143-79_2280

source_name: 15143-79_foliage from field-grown plants


title: 12120-03_2282

source_name: 12120-03_foliage from field-grown plants


title: 15143-54_2279

source_name: 15143-54_foliage from field-grown plants


title: 15143-70_2278

source_name: 15143-70_foliage from field-grown plants


title: 99535N


title: 15143-76_2275

source_name: 15143-76_foliage from field-grown plants

value: ACA


title: RFPSHInfO

source_name: Extracted RNA from Ki67-RFP+ or Ki67-RFP- cells of the apex of hearts of Ki67TagRFP mice 14 days post-sham surgery [O]

value: adult

value: Heart

tag: heart region

value: apex


title: Hindenburg_2273

source_name: Hindenburg_foliage from field-grown plants

value: Hindenburg


title: 15143-47_2274

source_name: 15143-47_foliage from field-grown plants

value: 15143 diploid mapping population clone

value: RunC


title: 15143-84_2277


title: 15143-49_2290

source_name: 15143-49_foliage from field-grown plants

value: GTT


title: 15143-29_2271

source_name: 15143-29_foliage from field-grown plants


title: 15143-95_2276

source_name: 15143-95_foliage from field-grown plants


title: 15143-50_2272

source_name: 15143-50_foliage from field-grown plants


title: Shepody_2297

source_name: Shepody_foliage from field-grown plants

value: tetraploid variety

value: Shepody

value: RunA

value: CCT


title: 15143-33_2268

source_name: 15143-33_foliage from field-grown plants


title: 15143-32_2267

source_name: 15143-32_foliage from field-grown plants

value: ATG


title: 15143-78_2269

source_name: 15143-78_foliage from field-grown plants


title: 15143-87_2266

source_name: 15143-87_foliage from field-grown plants


title: 98699N

source_name: adjacent non-tumor tissue

value: male

value: adjacent non-tumor liver tissue


title: 15143-48_2262

source_name: 15143-48_foliage from field-grown plants


title: 99535T

source_name: tumor tissue

value: female

value: Intrahepatic cholangiocarcinoma


title: 15143-96_2270

source_name: 15143-96_foliage from field-grown plants

value: foliage from field-grown plants

value: ACA


title: 15143-75_2264

source_name: 15143-75_foliage from field-grown plants


title: 15143-37_2261

source_name: 15143-37_foliage from field-grown plants


title: 15143-94_2265

source_name: 15143-94_foliage from field-grown plants


title: 15143-19_2258

source_name: 15143-19_foliage from field-grown plants

value: CGG


title: 15143-22_2260

source_name: 15143-22_foliage from field-grown plants


title: 15143-81_2256

source_name: 15143-81_foliage from field-grown plants


title: 98699T


title: 15143-03_2257

source_name: 15143-03_foliage from field-grown plants


title: 90608N


title: 15143-05_2255

source_name: 15143-05_foliage from field-grown plants


title: 15143-27_2263

source_name: 15143-27_foliage from field-grown plants


title: Control

description: PLC-PRF-5 cells were treated with DMSO

source_name: PLC-PRF-5 cells were treated with DMSO

tag: cell line

tag: cell type

value: liver hepatoma

tag: agent

value: DMSO


title: 07506-01_2253

source_name: 07506-01_foliage from field-grown plants

value: parental clone


title: Atlantic-1_2248

source_name: Atlantic-1_foliage from field-grown plants

value: RunC

value: CAA


title: 15143-88_2252

source_name: 15143-88_foliage from field-grown plants

value: 15143 diploid mapping population clone


title: 15143-31_2250

source_name: 15143-31_foliage from field-grown plants


title: 15143-44_2254

source_name: 15143-44_foliage from field-grown plants


title: 15143-57_2247

source_name: 15143-57_foliage from field-grown plants


title: 15143-35_2249

source_name: 15143-35_foliage from field-grown plants


title: 15143-02_2244

source_name: 15143-02_foliage from field-grown plants


title: 15143-71_2245

source_name: 15143-71_foliage from field-grown plants


title: 15143-36_2246

source_name: 15143-36_foliage from field-grown plants


title: 15143-69_2251

source_name: 15143-69_foliage from field-grown plants


title: 15143-61_2243

source_name: 15143-61_foliage from field-grown plants

value: CTC


title: 15143-46_2241

source_name: 15143-46_foliage from field-grown plants


title: 90608T

source_name: tumor tissue


title: 15143-38_2242

source_name: 15143-38_foliage from field-grown plants


title: 15143-53_2097

source_name: 15143-53_foliage from field-grown plants


title: 15143-59_2237

source_name: 15143-59_foliage from field-grown plants


title: 15143-43_2240

source_name: 15143-43_foliage from field-grown plants


title: 15143-45_2233

source_name: 15143-45_foliage from field-grown plants

value: TGT


title: 15143-73_2231

source_name: 15143-73_foliage from field-grown plants


title: 15143-18_2236

source_name: 15143-18_foliage from field-grown plants


title: 15143-65_2235

source_name: 15143-65_foliage from field-grown plants


title: 15143-72_2228

source_name: 15143-72_foliage from field-grown plants


title: 15143-90_2226

source_name: 15143-90_foliage from field-grown plants

value: TAG