title: D60C_4

source_name: Day6_differentiation with CXCL4_donor4


title: D60C_3

status: Public on Jun 01 2020

type: genomic

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

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

scan_protocol: Beadchip images were scanned on the iScan system

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

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Day6_differentiation with CXCL4_donor3

label_protocol: Standard Illumina Protocol

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

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

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

tag: donor id

tag: age

tag: Sex

value: F

tag: cell type

value: monocytes

tag: cell subtype

value: Day6_differentiation with CXCL4


title: Sample 953_Single mESC cell

type: SRA

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

country: USA

institute: Stanford University

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Single mESC cell

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

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

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 952_Single mESC cell


title: Sample 951_Single mESC cell


title: D40M_5

value: M

value: Day4_differentiation without CXCL4


title: AVAglio_GSM2225578

type: RNA

city: South San Francisco

first: Radia

last: Johnson

address: 1 DNA Way

country: United Kingdom

institute: Genentech

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

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

label: Nucleotide/fluorophore barcode

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

value: Male

tag: corticosteroids

value: Off

tag: surgical status

value: Total resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade III

tag: os (diagnosis)

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

tag: mgmt status

value: Non-methylated


title: AVAglio_GSM2225579

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

tag: age

value: On

value: Partial resection

value: Placebo

value: Unclassified

value: Classical

value: Grade IV


title: D40M_4

tag: donor id

tag: Sex

value: monocytes


title: D60C_1

source_name: Day6_differentiation with CXCL4_donor1

value: F

tag: cell type

tag: cell subtype

value: Day6_differentiation with CXCL4


title: AVAglio_GSM2225577

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

value: Female

value: Missing


title: Sample 950_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: D60M_2

value: Day6_differentiation without CXCL4


title: Sample 949_Single mESC cell


title: Sample 948_Single mESC cell


title: AVAglio_GSM2225576

value: Male

tag: corticosteroids

value: Off

tag: surgical status

value: Total resection

value: Proneural


title: AVAglio_GSM2225575

value: Partial resection

tag: treatment

tag: phillips subtype

value: Mesenchymal

value: Grade III

value: Non-methylated


title: AVAglio_GSM2225574

value: On

value: Bevacizumab

tag: tcga subtype

tag: kps

value: Grade IV


title: Sample 947_Single mESC cell


title: D40M_2

value: F

value: monocytes

value: Day4_differentiation without CXCL4


title: AVAglio_GSM2225573

tag: mmse

tag: rpa

value: Methylated


title: D40M_3


title: Sample 946_Single mESC cell

value: Differentiated mESC

value: day 0


title: AVAglio_GSM2225572

value: Female

value: Placebo

value: Unclassified

tag: os (diagnosis)

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


title: Sample 944_Single mESC cell


title: AVAglio_GSM2225585

tag: age

value: Biopsy

value: Grade V

tag: mgmt status


title: Sample 943_Single mESC cell


title: AVAglio_GSM2225570

tag: Sex

value: Off

value: Total resection

value: Mesenchymal


title: Sample 945_Single mESC cell


title: D40C_5

source_name: Day4_differentiation with CXCL4_donor5

tag: donor id

value: M

tag: cell type

value: Day4_differentiation with CXCL4


title: AVAglio_GSM2225571

value: Male

value: Bevacizumab

value: Proliferative

value: Classical

value: Grade IV

value: Non-methylated


title: AVAglio_GSM2225568

value: On

value: Partial resection

value: Grade III

value: Missing


title: Sample 942_Single mESC cell

tag: cell line

value: Differentiated mESC

value: day 0


title: D40C_3

source_name: Day4_differentiation with CXCL4_donor3

value: F

value: monocytes

tag: cell subtype


title: Sample 941_Single mESC cell

tag: day of differentiation


title: AVAglio_GSM2225567

value: Female

tag: corticosteroids

tag: surgical status

value: Placebo

value: Mesenchymal

value: Grade V


title: D40M_1

value: Day4_differentiation without CXCL4


title: D40C_2

source_name: Day4_differentiation with CXCL4_donor4

value: Day4_differentiation with CXCL4


title: AVAglio_GSM2225566

value: Male

value: Total resection

tag: treatment

tag: phillips subtype

value: Classical

value: Methylated


title: D20M_5

value: M

value: Day2_differentiation without CXCL4


title: Sample 940_Single mESC cell


title: 48h3

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

country: China

institute: Qingdao Agricultural University

data_processing:
Adapters sequences and low-quality reads were removed. Other RNAs, including rRNA, tRNA, snRNA, snoRNA, piRNA, repeats, exon and intron sequences, were removed.
The expression levels of miRNA were calculated by summing the read counts which were aligned with the temporary miRNA database with ≤ 2 mismatches.
Temporary miRNA database were  constituted of miRNAs with the highest expression for each mature miRNA family. The potentially novel miRNAs were predicted via MIREAP.
Supplementary_files_format_and_content: Two "xlsx" files include the analysis about differential expression of miRNAs in Control, HS 6h and HS 48h group.Two "fa" files include the sequences of known and novle miRNAs by our sequencing.

organism: Apostichopus japonicus

source_name: intestine tissue

growth_protocol: sea cucumber (100-120g)

extract_protocol:
Total RNA of each individua was extracted using Trizol RNA isolation reagent (Invitrogen) following the manufacturer’s instructions.
RNA molecules ranging from 18 to 30 nt were encriched by polyacrylamide gel electrophoresis (PAGE). Adapters were added repectively in 3’- and 5’ - end of RNAs.The ligation products were reverse-transcribed by PCR amplification. The PCR products in the size of 140~160 bp were encriched to generate the cDNA library. The library products were then sequenced via HiSeq.

treatment_protocol: heat stress under 26ºC

value: heat stress

tag: time point


title: CRPC_12-021I1_LUNG [re-analysis]

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
12-021I1_LUNG
CRPC lung metastasis
12-021I1_LUNG

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

source_name: CRPC lung metastasis

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

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: lung

tag: patient

tag: molecular phenotype


title: CRPC_12-021J3_PLEURAL

description:
12-021J3_PLEURAL
CRPC pleural metastasis
12-021J3_PLEURAL

source_name: CRPC pleural metastasis

value: pleural


title: AVAglio_GSM2225565

tag: age

value: Off

value: Bevacizumab

value: Proneural

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

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


title: AVAglio_GSM2225564

tag: Sex

value: On

value: Partial resection

value: Mesenchymal

value: Grade V

tag: mgmt status


title: 48h2


title: 48h1


title: CRPC_12-021FF6_BONE [re-analysis]

description:
12-021FF6_BONE
CRPC bone metastasis
12-021FF6_BONE

source_name: CRPC bone metastasis

tag: cell type

value: bone


title: D20M_3

tag: donor id

value: F

value: monocytes

tag: cell subtype


title: Sample 939_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 937_Single mESC cell


title: CRPC_12-021H6_LIVER [re-analysis]

description:
12-021H6_LIVER
CRPC liver metastasis
12-021H6_LIVER

source_name: CRPC liver metastasis

tag: gender

value: male

tag: tumor site

value: liver


title: Sample 938_Single mESC cell


title: D20C_5

source_name: Day2_differentiation with CXCL4_donor5

value: M

value: Day2_differentiation with CXCL4


title: AVAglio_GSM2225563

value: Male

tag: corticosteroids

tag: surgical status

value: Total resection

tag: treatment

tag: phillips subtype

value: Non-methylated


title: D20M_2

tag: age

value: Day2_differentiation without CXCL4


title: D20C_4

source_name: Day2_differentiation with CXCL4_donor4


title: D20M_1


title: D40C_4

value: Day4_differentiation with CXCL4


title: Sample 935_Single mESC cell


title: 6h1

value: heat stress

tag: time point


title: Sample 934_Single mESC cell


title: D20C_3

source_name: Day2_differentiation with CXCL4_donor3


title: AVAglio_GSM2225559

value: Off

value: Bevacizumab

value: Mesenchymal

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

value: Methylated


title: 6h3


title: C3

value: normal


title: D00__3

tag: donor id

tag: Sex

value: F

tag: cell type

value: monocytes


title: D40C_1

source_name: Day4_differentiation with CXCL4_donor1

tag: cell subtype


title: Sample 933_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: CRPC_12-005K3_HILAR_LUNG_LN [re-analysis]

description:
12-005K3_HILAR_LUNG_LN
CRPC hilar lung lymph node (LN) metastasis
12-005K3_HILAR_LUNG_LN

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: hilar lung lymph node (LN)

tag: patient

tag: molecular phenotype


title: D00__2

tag: age


title: AVAglio_GSM2225560

value: Male

tag: corticosteroids

tag: surgical status

value: Total resection

tag: treatment

tag: phillips subtype

value: Unclassified

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

tag: mgmt status


title: C2


title: CRPC_12-011I8_LN [re-analysis]

description:
12-011I8_LN
CRPC lymph node (LN) metastasis
12-011I8_LN

source_name: CRPC lymph node (LN) metastasis

value: lymph node (LN)


title: Sample 932_Single mESC cell


title: AVAglio_GSM2225558

value: Female

value: Off

value: Placebo

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Missing


title: C1


title: D00__4

tag: donor id

tag: Sex

value: M

tag: cell type

tag: cell subtype


title: CRPC_11-028L3_LUNG [re-analysis]

description:
11-028L3_LUNG
CRPC lung metastasis
11-028L3_LUNG

tag: gender

tag: tumor site

value: lung

tag: patient

tag: molecular phenotype


title: D20C_2

source_name: Day2_differentiation with CXCL4_donor2

tag: age

value: F

value: Day2_differentiation with CXCL4


title: CRPC_12-011J3_BLADDER [re-analysis]

description:
12-011J3_BLADDER
CRPC bladder metastasis
12-011J3_BLADDER

source_name: CRPC bladder metastasis

value: bladder


title: 6h2

tag: treatment

value: heat stress

tag: time point


title: AVAglio_GSM2225556

tag: corticosteroids

value: On

tag: surgical status

value: Partial resection

value: Bevacizumab

tag: phillips subtype

value: Proliferative

value: Classical

value: Grade IV

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

tag: mgmt status

value: Non-methylated


title: D20C_1

source_name: Day2_differentiation with CXCL4_donor1

value: monocytes


title: CRPC_12-005H6_LIVER [re-analysis]

description:
12-005H6_LIVER
CRPC liver metastasis
12-005H6_LIVER

value: male

value: prostate cancer

value: liver


title: CRPC_11-028H1_LIVER [re-analysis]

description:
11-028H1_LIVER
CRPC liver metastasis
11-028H1_LIVER


title: Sample 931_Single mESC cell

source_name: Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: D00__5

tag: donor id

tag: Sex

value: M


title: Sample 930_Single mESC cell


title: D00__1

value: F

tag: cell type

tag: cell subtype


title: Sample 936_Single mESC cell


title: AVAglio_GSM2225557

value: Female

value: Biopsy

value: Placebo

tag: tcga subtype

value: Unclassified

tag: kps

tag: mmse

tag: rpa

value: Grade V

tag: os (diagnosis)

value: Methylated


title: AVAglio_GSM2225562

tag: age

value: Off

tag: treatment

value: Mesenchymal

value: Classical

value: Missing


title: sample543_0379_N: Patient 19 adjacent normal tissue from gastric adenocarcinoma

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit

scan_protocol: Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)

data_processing: Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library.  The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Data was quantile normalized followed by log2 transform.  Signals from probes measuring same ncRNA were averaged.

source_name: adjacent normal gastric tissue from gastric adenocarcinoma patients

label_protocol: Labbeling was done according to Nimblegen one color DNA Labeling kit.

extract_protocol: Total RNA extracted using Total RNA Purification Kit from Norgen Biotek corp following manufacturer's instructions

tag: tissue

value: gastric mucosa


title: Sample 929_Single mESC cell


title: sample543_0366_N: Patient 18 adjacent normal tissue from gastric adenocarcinoma

value: Male


title: CRPC_10-056K1_LIVER [re-analysis]

description:
10-056K1_LIVER
CRPC liver metastasis
10-056K1_LIVER

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: liver

tag: patient

tag: molecular phenotype


title: sample543_0287_N: Patient 17 adjacent normal tissue from gastric adenocarcinoma


title: CRPC_10-056J1_LN [re-analysis]

description:
10-056J1_LN
CRPC lymph node (LN) metastasis
10-056J1_LN

value: lymph node (LN)


title: Sample 927_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 928_Single mESC cell


title: sample543_0461_N: Patient 20 adjacent normal tissue from gastric adenocarcinoma

tag: Sex


title: sample543_0259_N: Patient 16 adjacent normal tissue from gastric adenocarcinoma

value: Female


title: AVAglio_GSM2225561

tag: corticosteroids

tag: surgical status

value: Partial resection

value: Bevacizumab

tag: phillips subtype

value: Grade IV

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

tag: mgmt status

value: Non-methylated


title: AVAglio_GSM2225554

value: Off

value: Total resection

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade V


title: Sample 926_Single mESC cell


title: CRPC_11-028G3_ADRENAL [re-analysis]

description:
11-028G3_ADRENAL
CRPC adrenal metastasis
11-028G3_ADRENAL

source_name: CRPC adrenal metastasis

tag: cell type

value: adrenal


title: CRPC_10-039G1_LN [re-analysis]

description:
10-039G1_LN
CRPC lymph node (LN) metastasis
10-039G1_LN

tag: gender


title: CRPC_10-013L2_LN [re-analysis]

description:
10-013L2_LN
CRPC lymph node (LN) metastasis
10-013L2_LN

tag: tumor site


title: AVAglio_GSM2225552

tag: age

tag: treatment

value: Placebo

value: Mesenchymal

tag: os (diagnosis)


title: AVAglio_GSM2225551

value: Male

value: Proneural

value: Methylated


title: AVAglio_GSM2225550

value: Proliferative

value: Classical


title: Sample 925_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: AVAglio_GSM2225555

tag: Sex

value: Female

tag: corticosteroids

value: On


title: sample543_0240_N: Patient 15 adjacent normal tissue from gastric adenocarcinoma

tag: tissue

value: gastric mucosa


title: CRPC_10-013K4_DIAPHRAM [re-analysis]

description:
10-013K4_DIAPHRAM
CRPC diaphram metastasis
10-013K4_DIAPHRAM

source_name: CRPC diaphram metastasis

value: male

value: prostate cancer

value: diaphram

tag: patient

tag: molecular phenotype


title: sample543_0184_N: Patient 14 adjacent normal tissue from gastric adenocarcinoma


title: Sample 924_Single mESC cell


title: AVAglio_GSM2225549

tag: surgical status

value: Partial resection

tag: phillips subtype

tag: tcga subtype

value: Grade IV

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

tag: mgmt status

value: Non-methylated


title: sample543_0161_N: Patient 13 adjacent normal tissue from gastric adenocarcinoma


title: sample543_0155_N: Patient 12 adjacent normal tissue from gastric adenocarcinoma


title: CRPC_08-093H3_LN [re-analysis]

description:
08-093H3_LN
CRPC lymph node (LN) metastasis
08-093H3_LN

tag: gender

tag: cell type

value: lymph node (LN)


title: Sample 923_Single mESC cell


title: AVAglio_GSM2225547

tag: age

value: Male

value: Off

value: Bevacizumab

value: Mesenchymal

tag: kps

tag: mmse

tag: rpa

value: Missing


title: AVAglio_GSM2225548

tag: treatment

value: Proneural

tag: os (diagnosis)


title: CRPC_08-020T1_LN [re-analysis]

description:
08-020T1_LN
CRPC lymph node (LN) metastasis
08-020T1_LN

tag: tumor site


title: GA_110816_2038549_ASCT: Patient 10 ascites from gastric adenocarcinoma

source_name: ascites cells from gastric adenocarcinoma

tag: tissue

value: ascites cells

tag: Sex


title: CRPC_07-042L3_ADRENAL [re-analysis]

description:
07-042L3_ADRENAL
CRPC adrenal metastasis
07-042L3_ADRENAL

value: adrenal

tag: patient

tag: molecular phenotype


title: CRPC_08-020I2_DIAPHRAM [re-analysis]

description:
08-020I2_DIAPHRAM
CRPC diaphram metastasis
08-020I2_DIAPHRAM


title: Sample 920_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: AVAglio_GSM2225546

tag: corticosteroids

tag: surgical status

tag: phillips subtype

tag: tcga subtype

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


title: Sample 922_Single mESC cell


title: CRPC_07-042K2_LN [re-analysis]

description:
07-042K2_LN
CRPC lymph node (LN) metastasis
07-042K2_LN

tag: gender

value: male

tag: cell type


title: Sample 921_Single mESC cell


title: AVAglio_GSM2225545

tag: age

value: Female

value: Total resection

value: Placebo

tag: kps

tag: mmse

tag: rpa

value: Grade III

tag: mgmt status


title: Sample 918_Single mESC cell


title: GA_110816_1143494_ASCT: Patient 9 ascites from gastric adenocarcinoma

tag: tissue

tag: Sex


title: GA_092816_2004453_ASCT: Patient 8 ascites from gastric adenocarcinoma


title: AVAglio_GSM2225544

value: Partial resection

tag: treatment

value: Grade V

tag: os (diagnosis)

value: Non-methylated


title: GA_080516_1136301_ASCT: Patient 7 ascites from gastric adenocarcinoma

value: Male


title: Sample 919_Single mESC cell

tag: cell line

tag: day of differentiation


title: AVAglio_GSM2225543

tag: corticosteroids

value: Off

tag: surgical status

value: Proliferative

value: Classical

value: Grade IV


title: CRPC_12-005I5_LIVER [re-analysis]

description:
12-005I5_LIVER
CRPC liver metastasis
12-005I5_LIVER

value: prostate cancer

tag: tumor site

value: liver

tag: patient

tag: molecular phenotype


title: CRPC_06-127G3_LN [re-analysis]

description:
06-127G3_LN
CRPC lymph node (LN) metastasis
06-127G3_LN

tag: gender

tag: cell type

value: lymph node (LN)


title: Sample 917_Single mESC cell

value: Differentiated mESC

value: day 0


title: AVAglio_GSM2225542

tag: age

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

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


title: GA_072216_1223617_ASCT: Patient 6 ascites from gastric adenocarcinoma

tag: tissue

value: ascites cells

tag: Sex


title: AVAglio_GSM2225541

value: Female

value: Total resection

tag: treatment

value: Placebo

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: mgmt status

value: Missing


title: sample543_0136_N: Patient 11 adjacent normal tissue from gastric adenocarcinoma

value: gastric mucosa


title: GA_070716_2017370_ASCT: Patient 5 ascites of unknown origin

source_name: ascites cells of unknown origin


title: AVAglio_GSM2225540

tag: corticosteroids

tag: surgical status

value: Grade III


title: GA_051816_2027006_ASCT: Patient 4 ascites from gastric adenocarcinoma

value: Male


title: Sample 916_Single mESC cell

tag: cell line

tag: day of differentiation


title: Sample 915_Single mESC cell


title: GA_050416_565706_ASCT: Patient 3 ascites from gastric adenocarcinoma


title: AVAglio_GSM2225538

value: On

value: Partial resection

value: Bevacizumab

value: Grade V

value: Non-methylated


title: Sample 914_Single mESC cell


title: Sample 913_Single mESC cell


title: CRPC_05-165O1_ADRENAL [re-analysis]

description:
05-165O1_ADRENAL
CRPC adrenal metastasis
05-165O1_ADRENAL

tag: gender

value: male

tag: cell type

value: prostate cancer

tag: tumor site

value: adrenal

tag: patient

tag: molecular phenotype


title: Sample 912_Single mESC cell

value: Differentiated mESC

value: day 0


title: GA_011017_1193000_ASCT: Patient 1 ascites from gastric adenocarcinoma

value: ascites cells

tag: age

value: Female


title: AVAglio_GSM2225537

value: Total resection

value: Placebo

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

value: Grade IV

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


title: Sample 910_Single mESC cell


title: WT large intestine 5 [re-analysis]

city: San Francisco

first: Suzanne

middle: M

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

description: animals sacrificed, dissected and large intestine contents extracted

data_processing:
Real time base calling on Illumina HiSeq 4000
kallisto to align reads to genome with parameters: --plaintext --bias --single --rf-stranded -l $AvgLibSize -s $SD (AvgLibSize and SD pulled from BioAnalyzer traces)
extract estimated counts and tpms from abundances.tsv files
tpms and estimated counts = 0 replaced with 1, transcripts filtered to included only those with values greater than 10 in at least one sample
limma/voom with genotype.environment as factor to produce log base 2 fold changes and adj. p values from estimated counts
tpms were used for heat map generation
Genome_build: C. albicans SC5314 Assembly 21
Supplementary_files_format_and_content: excel files containing 1. fold changes and adjusted p-values and 2. tpms

molecule: polyA RNA

organism:
Candida albicans
Mus musculus

source_name: Murine large intestine colonization

extract_protocol:
Acid phenol chloroform extraction 4 times, phenol chloroform isoamyl extraction 4 times, additional cleanup using RNA SPRI bead mix
NEB Ultra Directional mRNA-seq

tag: strain (c. albicans/mus musculus)

tag: host mouse strain

value: BALB/c

tag: growth condition

value: large intestine

tag: time point

value: 10 days


title: GA_011317_1199751_ASCT: Patient 2 ascites from gastric adenocarcinoma

tag: tissue

tag: Sex


title: AVAglio_GSM2225536

value: Male

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: mgmt status

value: Methylated


title: WT large intestine 4 [re-analysis]


title: AVAglio_GSM2225535

tag: age

value: On

value: Bevacizumab

tag: phillips subtype

value: Proneural

value: Non-methylated


title: Sample 909_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: AVAglio_GSM2225534

value: Female

value: Partial resection

tag: tcga subtype

value: Classical

tag: kps

value: Grade III

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


title: CRPC_05-011D5_LN [re-analysis]

description:
05-011D5_LN
CRPC lymph node (LN) metastasis
05-011D5_LN

tag: gender

value: male

tag: cell type

value: prostate cancer

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: CRPC_05-011G2_LUNG [re-analysis]

description:
05-011G2_LUNG
CRPC lung metastasis
05-011G2_LUNG

source_name: CRPC lung metastasis

value: lung


title: AVAglio_GSM2225533

tag: Sex

tag: corticosteroids

tag: surgical status

value: Total resection

tag: treatment

value: Placebo

value: Mesenchymal

value: Grade IV

value: Missing


title: Sample 908_Single mESC cell


title: AVAglio_GSM2225539

value: Off

value: Bevacizumab

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: mgmt status


title: AVAglio_GSM2225532

tag: age

value: Male

tag: phillips subtype

value: Proliferative

value: Methylated


title: WT large intestine 2 [re-analysis]

tag: strain (c. albicans/mus musculus)

tag: host mouse strain

value: BALB/c

tag: growth condition

value: large intestine

tag: time point

value: 10 days


title: CRPC_05-214E2_LN [re-analysis]

description:
05-214E2_LN
CRPC lymph node (LN) metastasis
05-214E2_LN

tag: gender

value: male

tag: cell type

tag: tumor site


title: Sample 907_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: CRPC_05-165K1_LUNG [re-analysis]

description:
05-165K1_LUNG
CRPC lung metastasis
05-165K1_LUNG

value: prostate cancer

value: lung

tag: patient

tag: molecular phenotype


title: Sample 911_Single mESC cell


title: WT large intestine 1 [re-analysis]


title: CRPC_04-050S1_LN [re-analysis]

description:
04-050S1_LN
CRPC lymph node (LN) metastasis
04-050S1_LN

value: lymph node (LN)


title: Sample 906_Single mESC cell


title: czf1_LI_6

data_processing:
Reads In fastq files were aligned to C. albicans transcriptome using kallisto with default parameters
Estimated counts generated from kallisto for each fastq were extracted and pair-wise comparisons between biological conditions was performed with limma using growth condition and batch as parameters in the design matrix
Supplementary_files_format_and_content: White_opaque_regulator_RNA_expression.xlsx contains log2 fold changes and adjusted p-values of pair-wise comparisons performed in limma; White_opaque_regulator_estimated_counts.xlsx contains estimated counts generated by kallisto that were used as input to limma

source_name: Large intestine lumen

growth_protocol: Candida albicans strains were grown in YEPD media overnight, then diluted to OD=0.1 and grown for 4 hours to an OD=1. These log phase cultures were either pelleted and snap frozen or used for oral gavage of mice. For mouse colonization, mice were given autoclaved food and water with penicillin and streptomycin ad libitum throughout the colonization. C. albicans colonization in mice was maintained for 10 days until the euthanization of the animals.

extract_protocol:
Acid phenol extraction followed by phenol-chloroform extraction, isopropanol preciptation, followed by SPRI bead cleanup
Followed standard protocol for NEBNext Ultra Directional Library Preparation

tag: strain

tag: time post inoculation

value: Murine gut


title: CRPC_04-050P1_LN [re-analysis]

description:
04-050P1_LN
CRPC lymph node (LN) metastasis
04-050P1_LN


title: Sample 905_Single mESC cell


title: czf1_LI_5


title: Sample 903_Single mESC cell


title: Sample 904_Single mESC cell


title: czf1_LI_4


title: AVAglio_GSM2225529

tag: Sex

tag: corticosteroids

tag: surgical status

value: Partial resection

tag: treatment

value: Placebo

value: Mesenchymal

tag: tcga subtype

value: Proneural

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

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


title: WT large intestine 3 [re-analysis]

tag: strain (c. albicans/mus musculus)

tag: host mouse strain

tag: growth condition

tag: time point


title: CRPC_03-139M5_RETROPERITONEAL [re-analysis]

description:
03-139M5_RETROPERITONEAL
CRPC retroperitoneal metastasis
03-139M5_RETROPERITONEAL

source_name: CRPC retroperitoneal metastasis

tag: gender

tag: cell type

tag: tumor site

value: retroperitoneal

tag: patient

tag: molecular phenotype


title: CRPC_03-163S5_LIVER [re-analysis]

description:
03-163S5_LIVER
CRPC liver metastasis
03-163S5_LIVER

source_name: CRPC liver metastasis

value: liver


title: AVAglio_GSM2225530

tag: age

tag: Sex

value: Female

tag: corticosteroids

value: On

tag: surgical status

tag: phillips subtype

tag: mgmt status

value: Non-methylated


title: CRPC_04-108K5_BRAIN

description:
04-108K5_BRAIN
CRPC brain metastasis
04-108K5_BRAIN

source_name: CRPC brain metastasis

value: male

value: brain


title: czf1_LI_3

tag: strain

value: BALB/c

tag: time post inoculation

value: 10 days


title: AVAglio_GSM2225527

tag: treatment

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

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


title: Sample 902_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 901_Single mESC cell


title: CRPC_03-139E5_RETROPERITONEAL [re-analysis]

description:
03-139E5_RETROPERITONEAL
CRPC retroperitoneal metastasis
03-139E5_RETROPERITONEAL

tag: gender

tag: cell type

value: prostate cancer

tag: tumor site

tag: patient

tag: molecular phenotype


title: AVAglio_GSM2225526

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

value: Partial resection

tag: phillips subtype

tag: mgmt status

value: Methylated


title: AVAglio_GSM2225531

value: Male

tag: treatment

value: Bevacizumab

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

value: Grade V


title: czf1_LI_2

tag: strain

tag: host mouse strain

tag: time post inoculation

tag: growth condition

value: Murine gut


title: czf1_LI_1


title: CRPC_03-027P3_LIVER [re-analysis]

description:
03-027P3_LIVER
CRPC liver metastasis
03-027P3_LIVER

tag: gender

tag: cell type

tag: tumor site

value: liver


title: AVAglio_GSM2225525

tag: age

value: On

value: Placebo

tag: rpa

value: Grade IV

tag: os (diagnosis)

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


title: efg1wor1_LI_5


title: CRPC_01-120C5_LN

description:
01-120C5_LN
CRPC lymph node (LN) metastasis
01-120C5_LN

value: male

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: CRPC_03-192C3_LN [re-analysis]

description:
03-192C3_LN
CRPC lymph node (LN) metastasis
03-192C3_LN


title: Sample 899_Single mESC cell

tag: cell line

tag: day of differentiation


title: AVAglio_GSM2225524

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: mgmt status

value: Non-methylated


title: efg1wor1_LI_4

tag: strain

tag: host mouse strain

value: BALB/c

tag: time post inoculation

value: 10 days

tag: growth condition


title: CRPC_01-120B1_LN

description:
01-120B1_LN
CRPC lymph node (LN) metastasis
01-120B1_LN

tag: gender

tag: cell type

value: prostate cancer

tag: tumor site


title: Sample 898_Single mESC cell

tag: cell line

value: Differentiated mESC

value: day 0


title: AVAglio_GSM2225528

tag: age

value: Female

value: Total resection

value: Classical

tag: mmse

tag: rpa

tag: os (diagnosis)

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


title: CRPC_01-002V1_LN

description:
01-002V1_LN
CRPC lymph node (LN) metastasis
01-002V1_LN

tag: patient

tag: molecular phenotype


title: Sample 897_Single mESC cell

tag: day of differentiation


title: efg1wor1_LI_2

value: Murine gut


title: AVAglio_GSM2225523

tag: Sex

value: Male

tag: corticosteroids

value: On

tag: surgical status

value: Biopsy

tag: treatment

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

value: Grade V

tag: mgmt status

value: Missing


title: CRPC_00-169F4_LN

description:
00-169F4_LN
CRPC lymph node (LN) metastasis
00-169F4_LN

tag: gender

value: male

tag: cell type

tag: tumor site

value: lymph node (LN)


title: Sample 896_Single mESC cell

tag: cell line


title: Sample 895_Single mESC cell


title: efg1wor1_LI_1

tag: strain

tag: host mouse strain

value: BALB/c

tag: time post inoculation

tag: growth condition


title: AVAglio_GSM2225522

tag: age

value: Off

value: Placebo

value: Proneural

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

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

value: Non-methylated


title: AVAglio_GSM2225521

tag: Sex

tag: corticosteroids

tag: surgical status

value: Total resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

value: Grade III

value: Methylated


title: Sample 894_Single mESC cell

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: efg1_LI_6

value: 10 days

value: Murine gut


title: Sample 900_Single mESC cell


title: CRPC_00-090P3_LN

description:
00-090P3_LN
CRPC lymph node (LN) metastasis
00-090P3_LN

tag: gender

tag: cell type

value: prostate cancer

tag: tumor site

tag: patient

tag: molecular phenotype


title: efg1_LI_5

tag: strain

tag: host mouse strain

tag: time post inoculation

tag: growth condition


title: AVAglio_GSM2225520

tag: age

value: Male

value: On

value: Partial resection

value: Unclassified

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: mgmt status


title: AVAglio_GSM2225519

tag: Sex

value: Female

tag: corticosteroids

tag: surgical status

tag: treatment

value: Placebo

tag: phillips subtype

value: Grade V

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

value: Missing


title: Sample 893_Single mESC cell

tag: cell line

tag: day of differentiation


title: CRPC_00-090B6_LN

description:
00-090B6_LN
CRPC lymph node (LN) metastasis
00-090B6_LN

tag: gender

value: male

tag: cell type

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: efg1_LI_4

tag: strain

tag: host mouse strain

value: BALB/c

tag: time post inoculation

tag: growth condition


title: AVAglio_GSM2225518

tag: age

tag: Sex

value: Off

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

tag: mgmt status

value: Non-methylated


title: Sample 892_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: CRPC_00-029N7_LN

description:
00-029N7_LN
CRPC lymph node (LN) metastasis
00-029N7_LN

tag: gender

tag: cell type

value: prostate cancer

tag: tumor site


title: Sample 891_Single mESC cell


title: efg1_LI_3

tag: strain

value: 10 days

value: Murine gut


title: efg1_LI_2

tag: host mouse strain


title: CRPC_00-029J8_LN

description:
00-029J8_LN
CRPC lymph node (LN) metastasis
00-029J8_LN

tag: patient

tag: molecular phenotype


title: efg1wor1_LI_3

tag: time post inoculation

tag: growth condition


title: Sample 890_Single mESC cell


title: AVAglio_GSM2225515

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

value: Total resection

tag: treatment

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

value: Grade III

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

value: Methylated


title: efg1_LI_1


title: AVAglio_GSM2225516

value: Male

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

tag: mgmt status


title: AVAglio_GSM2225514

value: Female

value: Classical


title: GUT_LI_5

tag: strain

tag: host mouse strain

value: BALB/c


title: Sample 888_Single mESC cell

tag: cell line

tag: day of differentiation


title: Sample 889_Single mESC cell


title: LNCaP_RB1KO_TP53KO_A18_B46_Enzalutamide

description:
LNCaP_RB1KO_TP53KO_A18_B46_Enz
LNCaP_RB1KO_TP53KO_A18_B46  cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A18_B46_Enz_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A18_B46 treated with Enzalutamide

growth_protocol: Cells were cultured in RPMI-1640, no phenol red (GIBCO, cat#11835030) with 10% FBS (GIBCO, cat#10437-02).

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 10uM enzalutamide. After 48 hours, RNA was harvested.

tag: gender

value: male

value: LNCaP-RB1/TP53 double knockout human prostate tumor cell line

tag: cell type


title: GUT_LI_4

tag: time post inoculation

tag: growth condition


title: Sample 887_Single mESC cell


title: GUT_LI_3


title: AVAglio_GSM2225512

tag: age

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

value: Partial resection

tag: treatment

value: Proneural

value: Grade IV


title: AVAglio_GSM2225513

tag: phillips subtype

value: Proliferative

tag: tcga subtype

tag: kps

tag: mmse

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

value: Missing


title: AVAglio_GSM2225517

tag: rpa

tag: os (diagnosis)

tag: mgmt status

value: Non-methylated


title: LNCaP_RB1KO_TP53KO_A18_A40_Enzalutamide

description:
LNCaP_RB1KO_TP53KO_A18_A40_Enz
LNCaP_RB1KO_TP53KO_A18_A40  cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A18_A40_Enz_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A18_A40 treated with Enzalutamide

tag: gender

tag: cell line

value: prostate cancer


title: GUT_LI_2

tag: strain

tag: host mouse strain

tag: time post inoculation

value: 10 days

value: Murine gut


title: Sample 885_Single mESC cell

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: CRPC_00-090Z8_LN

description:
00-090Z8_LN
CRPC lymph node (LN) metastasis
00-090Z8_LN

source_name: CRPC lymph node (LN) metastasis

tag: cell type

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: AVAglio_GSM2225510

tag: age

tag: Sex

value: Male

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

value: Classical

value: Methylated


title: AVAglio_GSM2225508

value: Female

value: Partial resection

value: Placebo

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

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

tag: mgmt status


title: AVAglio_GSM2225509

value: Off

value: Total resection

value: Mesenchymal

value: Grade III


title: GUT_LI_1

tag: strain

tag: host mouse strain

value: BALB/c

tag: time post inoculation

value: 10 days

tag: growth condition


title: Sample 884_Single mESC cell

tag: cell line

value: Differentiated mESC

tag: day of differentiation


title: wor1_LI_5

value: Murine gut


title: Sample 883_Single mESC cell

value: day 0


title: LNCaP_Enzalutamide_4

description:
LNCaP_10uM_ENZA_2_48hrs
LNCaP cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_10uM_ENZA_2_48hrs_170328_D00300_0400_BCALEFANXX

source_name: LNCaP treated with Enzalutamide

tag: gender

value: male

value: LNCaP (ATCC, CRL-1740) human prostate tumor cell line

tag: cell type

value: prostate cancer


title: LNCaP_RB1KO_TP53KO_A15_B71_Enzalutamide

description:
LNCaP_RB1KO_TP53KO_A15_B71_Enz
LNCaP_RB1KO_TP53KO_A15_B71  cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A15_B71_Enz_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A15_B71 treated with Enzalutamide

value: LNCaP-RB1/TP53 double knockout human prostate tumor cell line


title: AVAglio_GSM2225507

tag: age

tag: Sex

tag: corticosteroids

tag: surgical status

tag: treatment

value: Proliferative

value: Proneural

value: Methylated


title: LNCaP_RB1KO_TP53KO_A15_B72_Enzalutamide

description:
LNCaP_RB1KO_TP53KO_A15_B72_Enz
LNCaP_RB1KO_TP53KO_A15_B72  cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A15_B72_Enz_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A15_B72 treated with Enzalutamide


title: LNCaP_Enzalutamide_3

description:
LNCaP_10uM_ENZA_1_48hrs
LNCaP cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_10uM_ENZA_1_48hrs_170328_D00300_0400_BCALEFANXX


title: LNCaP_RB1KO_TP53KO_A18_B25_Enzalutamide

description:
LNCaP_RB1KO_TP53KO_A18_B25_Enz
LNCaP_RB1KO_TP53KO_A18_B25  cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A18_B25_Enz_170328_D00300_0400_BCALEFANXX

source_name: LNCaP_RB1KO_TP53KO_A18_B25 treated with Enzalutamide


title: Sample 881_Single mESC cell

source_name: Single mESC cell


title: Sample 886_Single mESC cell


title: wor1_LI_3


title: LNCaP_Enzalutamide_2

description:
LNCAP_ENZA_2
LNCaP cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCAP_ENZA_2_160714_D00300_0302_AC93C7ANXX


title: wor1_LI_2


title: Sample 880_Single mESC cell


title: LNCaP_Enzalutamide_1

description:
LNCAP_ENZA
LNCaP cells cultured in 10% FBS with 10uM Enzalutamide for 48 hours and harvested
LNCAP_ENZA_160520_D00300_0274_AC8GGKANXX


title: AVAglio_GSM2225505

value: Male

value: On

value: Partial resection

value: Bevacizumab

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

value: Grade V


title: AVAglio_GSM2225506

value: Off

value: Total resection

value: Placebo

value: Unclassified

value: Mesenchymal

tag: os (diagnosis)

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

tag: mgmt status


title: AVAglio_GSM2225504

value: Grade IV

value: Non-methylated


title: Sample 879_Single mESC cell

tag: cell line

value: Differentiated mESC

value: day 0


title: wor1_LI_1

tag: strain

tag: host mouse strain

value: BALB/c

tag: time post inoculation

value: 10 days

tag: growth condition

value: Murine gut


title: WT425_LI_5


title: Sample 878_Single mESC cell

tag: day of differentiation


title: LNCaP_RB1KO_TP53KO_A18_B25_Vehicle

description:
LNCaP_RB1KO_TP53KO_A18_B25_Veh
LNCaP_RB1KO_TP53KO_A18_B25 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A18_B25_Veh_170328_D00300_0400_BCALEFANXX

source_name: LNCaP_RB1KO_TP53KO_A18_B25 treated with vehicle

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with vehicle (EtOH). After 48 hours, RNA was harvested.

tag: gender

value: male

value: LNCaP-RB1/TP53 double knockout human prostate tumor cell line

tag: cell type

value: prostate cancer


title: wor1_LI_4


title: LNCaP_RB1KO_TP53KO_A18_B46_Vehicle

description:
LNCaP_RB1KO_TP53KO_A18_B46_Veh
LNCaP_RB1KO_TP53KO_A18_B46 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A18_B46_Veh_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A18_B46 treated with vehicle


title: WT425_LI_4


title: AVAglio_GSM2225503

tag: age

tag: Sex

value: Female

tag: corticosteroids

tag: surgical status

tag: treatment

value: Bevacizumab

value: Proneural

value: Classical

value: Methylated


title: AVAglio_GSM2225502

value: Male

value: Off

value: Total resection

value: Placebo

tag: phillips subtype

value: Proliferative

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa


title: Sample 877_Single mESC cell

tag: cell line

value: Differentiated mESC

value: day 0


title: Sample 882_Single mESC cell


title: LNCaP_RB1KO_TP53KO_A18_A40_Vehicle

description:
LNCaP_RB1KO_TP53KO_A18_A40_Veh
LNCaP_RB1KO_TP53KO_A18_A40 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A18_A40_Veh_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A18_A40 treated with vehicle


title: WT425_LI_3

tag: strain

tag: host mouse strain

value: BALB/c

value: 10 days


title: AVAglio_GSM2225501

value: Mesenchymal

value: Grade V

tag: os (diagnosis)

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

tag: mgmt status

value: Non-methylated


title: AVAglio_GSM2225500

value: Female

value: On

value: Biopsy

value: Grade III


title: Sample 875_Single mESC cell

tag: day of differentiation


title: AVAglio_GSM2225499

tag: age

value: Partial resection

value: Classical


title: LNCaP_RB1KO_TP53KO_A15_B72_Vehicle

description:
LNCaP_RB1KO_TP53KO_A15_B72_Veh
LNCaP_RB1KO_TP53KO_A15_B72 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A15_B72_Veh_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A15_B72 treated with vehicle

tag: gender

value: male

value: LNCaP-RB1/TP53 double knockout human prostate tumor cell line

tag: cell type

value: prostate cancer


title: LNCaP_RB1KO_TP53KO_A15_B71_Vehicle

description:
LNCaP_RB1KO_TP53KO_A15_B71_Veh
LNCaP_RB1KO_TP53KO_A15_B71 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCaP_RB1KO_TP53KO_A15_B71_Veh_161130_D00300_0348_ACA7MHANXX

source_name: LNCaP_RB1KO_TP53KO_A15_B71 treated with vehicle


title: WT425_LI_1

source_name: Large intestine lumen

tag: time post inoculation

tag: growth condition

value: Murine gut


title: WT425_LI_2


title: LNCaP_TP53_A5_Vehicle

description:
LNCAP_TP53_A5_veh
LNCaP_TP53_A5 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_TP53_A5_veh_160714_D00300_0302_AC93C7ANXX

source_name: LNCaP_TP53_A5 treated with vehicle

value: LNCaP-TP53 knockout human prostate tumor cell line


title: Sample 873_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 874_Single mESC cell


title: AVAglio_GSM2225498

tag: Sex

value: Male

tag: corticosteroids

value: Off

tag: surgical status

tag: treatment

value: Bevacizumab

tag: phillips subtype

value: Proliferative


title: LNCaP_TP53_A3_Vehicle

description:
LNCAP_TP53_A3_veh
LNCaP_TP53_A3 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_TP53_A3_veh_160714_D00300_0302_AC93C7ANXX

source_name: LNCaP_TP53_A3 treated with vehicle

tag: cell line


title: MB468_QPRT_shRNA

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: MB-468 cells transfected with QPRT shRNA

data_processing:
Quality control: FastQC, MultiQC, ReSeqTools, Illumina CASAVA
Genome_build: Tophat v2.0.12 (Ensembl 82)
Supplementary_files_format_and_content: HTSeq v0.6.1; FPKM

source_name: Breast cancer cells

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer cells

tag: genotype/variation

value: transfected with QPRT shRNA


title: AVAglio_GSM2225497

value: Female

value: Total resection

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade IV

value: Missing


title: MB468_Control_shRNA

description: MB-468 cells transfected with control shRNA

value: transfected with control shRNA


title: Sample 872_Single mESC cell

tag: day of differentiation


title: BT20_QPRT_shRNA

description: BT-20 cells transfected with QPRT shRNA


title: BT20_Control_shRNA

description: BT-20 cells transfected with control shRNA


title: Sample 870_Single mESC cell


title: LNCaP_RB1KO_A2_Vehicle

description:
LNCAP_RB1KO_A2_veh
LNCaP_RB1KO_A2 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_RB1KO_A2_veh_160520_D00300_0274_AC8GGKANXX

source_name: LNCaP_RB1KO_A2 treated with vehicle

value: male

value: LNCaP-RB1 knockout human prostate tumor cell line

value: prostate cancer


title: LNCaP_TP53_A1_Vehicle

description:
LNCAP_TP53_A1_veh
LNCaP_TP53_A1 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_TP53_A1_veh_160520_D00300_0274_AC8GGKANXX

source_name: LNCaP_TP53_A1 treated with vehicle

value: LNCaP-TP53 knockout human prostate tumor cell line


title: AVAglio_GSM2225496

tag: age

value: On

value: Partial resection

value: Placebo

tag: os (diagnosis)

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

tag: mgmt status

value: Methylated


title: Sample 876_Single mESC cell

value: Differentiated mESC

value: day 0


title: LNCaP_RB1KO_A18_Vehicle

description:
LNCAP_RB1KO_A18_veh
LNCaP_RB1KO_A18 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_RB1KO_A18_veh_160714_D00300_0302_AC93C7ANXX

source_name: LNCaP_RB1KO_A18 treated with vehicle

tag: gender

tag: cell type


title: Sample 869_Single mESC cell


title: AVAglio_GSM2225493

tag: Sex

value: Male

tag: corticosteroids

value: Off

value: Bevacizumab

value: Non-methylated


title: AVAglio_GSM2225494

tag: surgical status

tag: treatment

value: Mesenchymal

value: Grade III


title: Sample 868_Single mESC cell

tag: cell line


title: AVAglio_GSM2225495

value: Female

value: Total resection

tag: phillips subtype

value: Proneural

value: Grade IV


title: LNCaP_RB1KO_A15_Vehicle

description:
LNCAP_RB1KO_A15_veh
LNCaP_RB1KO_A15 cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_RB1KO_A15_veh_160714_D00300_0302_AC93C7ANXX

source_name: LNCaP_RB1KO_A15 treated with vehicle

value: male

value: LNCaP-RB1 knockout human prostate tumor cell line

value: prostate cancer


title: LNCaP_EtOH_Vehicle_2

description:
LNCAP_EtOH_2
LNCaP cells cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_EtOH_2_160714_D00300_0302_AC93C7ANXX

source_name: LNCaP treated with vehicle

value: LNCaP (ATCC, CRL-1740) human prostate tumor cell line


title: AVAglio_GSM2225491

value: On

value: Partial resection

tag: tcga subtype


title: Sample 867_Single mESC cell

value: Differentiated mESC

value: day 0


title: LNCaP_EtOH_Vehicle_1

description:
LNCAP_EtOH
LNCaP cells cultured in 10% FBS with vehicle (EtOH) for 48 hours and harvested
LNCAP_EtOH_160520_D00300_0274_AC8GGKANXX


title: Sample 871_Single mESC cell


title: Sample 866_Single mESC cell


title: AVAglio_GSM2225492

value: Male

tag: kps


title: Sample 629_Single MCF7 cell

source_name: Single MCF7 cell

value: MCF7 cell


title: Sample 631_Single MCF7 cell


title: Sample 630_Single MCF7 cell


title: LNCaP_DMSO_Vehicle_2

description:
LNCaP_DMSO_Veh_2_48hrs
LNCaP cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested
LNCaP_DMSO_Veh_2_48hrs_170328_D00300_0400_BCALEFANXX

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with vehicle (DMSO). After 48 hours, RNA was harvested.


title: LNCaP_DMSO_Vehicle_1

description:
LNCaP_DMSO_Veh_1_48hrs
LNCaP cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested
LNCaP_DMSO_Veh_1_48hrs_170328_D00300_0400_BCALEFANXX


title: Sample 865_Single mESC cell


title: Sample 864_Single mESC cell


title: Sample 633_Single MCF7 cell


title: Sample 628_Single MCF7 cell


title: Sample 627_Single MCF7 cell


title: AVAglio_GSM2225490

value: Off

value: Bevacizumab

value: Proliferative

tag: mmse

value: Non-methylated


title: AVAglio_GSM2225489

value: Placebo

value: Mesenchymal

value: Unclassified

tag: rpa

value: Missing


title: Sample 632_Single MCF7 cell

tag: day of differentiation


title: RNA-seq of siFEN1 MCF-7 cells treated with E2 - replicate 4

city: Amsterdam

first: Koen

last: Flach

address: Plesmanlaan 121

institute: NKI

data_processing:
Sequences were generated by theHiSeq 2500 High Output Mode, and aligned to the Human Reference Genome (assembly hg19, February 2009). Peak calling over input was performed using MACS peak caller (Zhang et al., 2008) version 1.3.7.1 and  DFilter (Kumar et al., 2013), only considering peaks shared by both peak callers. RNA seq Read counts were mapped using Salmon v0.14.1 and Differential expression (DE) was performed using DESeq2 with an FDR (adjusted p-value) < 0.05. Median of ratios normalization was performed across all samples and differentially expressed genes were identified between E2 vs Vehicle and siFEN1 vs siControl conditions
Genome_build: Hg19

source_name: MCF-7 siFEN1 E2 #4

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

extract_protocol: Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)

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


title: AVAglio_GSM2225488

tag: age

value: Female

value: Grade IV

value: Methylated


title: AVAglio_GSM2225487

value: Total resection

value: Proneural

value: Grade V

tag: os (diagnosis)


title: Sample 863_Single mESC cell

source_name: Single mESC cell

value: Differentiated mESC

value: day 0


title: RNA-seq of siFEN1 MCF-7 cells treated with E2 - replicate 3

source_name: MCF-7 siFEN1 E2 #3


title: Sample 626_Single MCF7 cell

value: MCF7 cell


title: RNA-seq of siFEN1 MCF-7 cells treated with E2 - replicate 2

source_name: MCF-7 siFEN1 E2 #2


title: Sample 625_Single MCF7 cell


title: AVAglio_GSM2225485

value: Off

value: Classical

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


title: Sample 862_Single mESC cell


title: AVAglio_GSM2225486

value: Bevacizumab

tag: mgmt status


title: RNA-seq of siFEN1 MCF-7 cells treated with E2 - replicate 1

source_name: MCF-7 siFEN1 E2 #1


title: Sample 861_Single mESC cell


title: Sample 624_Single MCF7 cell


title: Sample 860_Single mESC cell


title: Sample 623_Single MCF7 cell


title: RNA-seq of siFEN1 MCF-7 cells treated with vehicle - replicate 4

source_name: MCF-7 siFEN1 Veh #4


title: Sample 622_Single MCF7 cell


title: Sample 858_Single mESC cell


title: RNA-seq of siFEN1 MCF-7 cells treated with vehicle - replicate 3

source_name: MCF-7 siFEN1 Veh #3


title: Sample 621_Single MCF7 cell


title: AVAglio_GSM2225483

value: Male

value: On

value: Non-methylated


title: AVAglio_GSM2225484

value: Partial resection

value: Placebo

value: Mesenchymal


title: Sample 857_Single mESC cell


title: RNA-seq of siFEN1 MCF-7 cells treated with vehicle - replicate 1

source_name: MCF-7 siFEN1 Veh #1


title: RNA-seq of siFEN1 MCF-7 cells treated with vehicle - replicate 2

source_name: MCF-7 siFEN1 Veh #2


title: RNA-seq of siControl MCF-7 cells treated with E2 - replicate 4

source_name: MCF-7 siControl E2 #4


title: Sample 620_Single MCF7 cell


title: AVAglio_GSM2225481


title: AVAglio_GSM2225480

value: Grade IV


title: AVAglio_GSM2225479

value: Methylated


title: RNA-seq of siControl MCF-7 cells treated with E2 - replicate 3

source_name: MCF-7 siControl E2 #3


title: Sample 855_Single mESC cell


title: Sample 619_Single MCF7 cell


title: Sample 854_Single mESC cell


title: RNA-seq of siControl MCF-7 cells treated with E2 - replicate 2

source_name: MCF-7 siControl E2 #2


title: Sample 618_Single MCF7 cell


title: Sample 617_Single MCF7 cell


title: RNA-seq of siControl MCF-7 cells treated with E2 - replicate 1

source_name: MCF-7 siControl E2 #1


title: AVAglio_GSM2225478

value: Total resection

value: Proliferative


title: Sample 859_Single mESC cell


title: Sample 853_Single mESC cell


title: AVAglio_GSM2225477


title: Sample 852_Single mESC cell


title: AVAglio_GSM2225476

value: Proneural


title: AVAglio_GSM2225482


title: RNA-seq of siControl MCF-7 cells treated with vehicle - replicate 4

source_name: MCF-7 siControl Veh #4


title: Sample 851_Single mESC cell

value: Differentiated mESC


title: Sample 856_Single mESC cell

value: day 0


title: AVAglio_GSM2225475


title: Sample 615_Single MCF7 cell

value: MCF7 cell


title: Sample 614_Single MCF7 cell


title: RNA-seq of siControl MCF-7 cells treated with vehicle - replicate 3

source_name: MCF-7 siControl Veh #3


title: Sample 850_Single mESC cell


title: RNA-seq of siControl MCF-7 cells treated with vehicle - replicate 2

source_name: MCF-7 siControl Veh #2


title: Sample 613_Single MCF7 cell

source_name: Single MCF7 cell


title: Sample 612_Single MCF7 cell


title: AVAglio_GSM2225473

value: Off


title: RNA-seq of siControl MCF-7 cells treated with vehicle - replicate 1

source_name: MCF-7 siControl Veh #1


title: Sample 616_Single MCF7 cell


title: Sample 611_Single MCF7 cell


title: Chip-seq of ERα in proliferating MCF-7 cells treated with FEN1 inhibitor

library_source: genomic

source_name: ERα proliferating FEN1 inhibitor

extract_protocol:
ChIP experiments were performed as described previously (Zwart et al., 2011).
ChIP DNA was amplified as described (Jansen et al., 2013). Sequences were generated by theHiSeq 2500 High Output Mode, and aligned to the Human Reference Genome (assembly hg19, February 2009).


title: AVAglio_GSM2225472

value: Classical


title: Chip-seq of ERα in proliferating MCF-7 cells treated with vehicle

source_name: ERα proliferating vehicle


title: Sample 610_Single MCF7 cell


title: AVAglio_GSM2225470

value: Bevacizumab

value: Unclassified

value: Grade III

value: Missing


title: Sample 846_Single mESC cell

source_name: Single mESC cell


title: Sample 609_Single MCF7 cell


title: Chip-seq of ERα in MCF-7 cells stimulated for 30 min with E2 and pretreated with FEN1 inhibitor

source_name: ERα 30 min E2 FEN1 inhibitor


title: Sample 845_Single mESC cell


title: Sample 608_Single MCF7 cell


title: AVAglio_GSM2225474

value: Female

value: On

value: Non-methylated


title: Chip-seq of ERα in MCF-7 cells stimulated for 30 min with E2 and pretreated with vehicle

source_name: ERα 30 min E2 Vehicle


title: Sample 607_Single MCF7 cell


title: AVAglio_GSM2225469

value: Male

value: Partial resection

value: Placebo

value: Grade IV


title: (+)siD1_10 FGC1391_s_2

city: Miinneapolis

first: Jeffrey

middle: H

last: Albrecht

state: MN

address: One Veterans Drive

department: Medicine - Gastroenterology

institute: University of Minnesota

description:
FBS(+) Cyclin-D1 siRNA rep-10
(+)siD1_10
RawTranscriptCounts_SkHep1.xls

data_processing:
Illumina's bcl2fastq-v2.17.1.14 software was used to convert BCL basecall files to fastq files.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to respective genomes and Refseq transcriptome. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
ChIP-Seq: Peak calling on HNF4a ChIP samples was done using HOMER in factor mode and FDR cut off of 0.01 with respect to corresponding Input. Bioconductor's diffBind package was used for differential binding analysis.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Excel file with raw transcript counts
Supplementary_files_format_and_content: Tab-delimited peak files listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.

source_name: SK-HEP-1 cells (ATCC® HTB-52™)

growth_protocol:
RNA-Seq: AML12, HepG2, and Sk-Hep1 cells were cultured in the presence or absence of serum along with control or cyclin D1 siRNA (see PMID 27351284 and 22751438 for the culture conditions). HepG2 and SK-HEP-1 cells were cultured in the presence of control or cyclin D1 siRNA (see PMID 27351284 for the culture conditions)
ChIP-Seq: Male BALB/c mice were transduced with recombinant adenoviruses encoding cyclin D1-HA-FLAG or cyclin D1-RD-FLAG (see PMID: 22751438 and 27351284 for details). Livers were harvested 24 hours later for ChIP-seq.

extract_protocol:
RNA-Seq: RNA was extracted using Qiazol followed by purification using the miRNeasy kit (Qiagen)
ChIP-Seq: DNA was exgtracted from mouse liver as previously described (PMID: 18556755).
RNA-Seq: Libraries were prepared using TruSeq Stranded mRNA HT kit using standard Illumina protocols
ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions.

treatment_protocol:
RNA-Seq: AML 12 cells were cultured in 10% FBS (FBS(+)) or had withdrawal of serum 24 hours before harvest (FBS(-)). 45 hours before harvest, AML 12, HepG2 and SK-Hep-1 cells were treated with control or cyclin D1 siRNA (Dharmacon On-Target plus SMARTpool, catalog # L-042441-00-0020).
ChIP-Seq:  Mice were treated with recombinant adenoviruses as above.

tag: strain


title: Sample 849_Single mESC cell


title: (+)siD1_10 FGC1301_s_1


title: Sample 848_Single mESC cell


title: Sample 844_Single mESC cell


title: Sample 606_Single MCF7 cell


title: AVAglio_GSM2225471

value: Proneural

value: Methylated


title: Sample 847_Single mESC cell

value: Differentiated mESC

value: day 0


title: AVAglio_GSM2225467

value: Total resection


title: AVAglio_GSM2225468

value: Off


title: AVAglio_GSM2225466

value: Bevacizumab


title: (+)siD1_10 FGC1293_s_3


title: (+)siD1_9 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-9
(+)siD1_9
RawTranscriptCounts_SkHep1.xls


title: Sample 605_Single MCF7 cell

value: MCF7 cell


title: AVAglio_GSM2225464

value: Mesenchymal


title: Sample 841_Single mESC cell


title: Sample 603_Single MCF7 cell


title: AVAglio_GSM2225465

value: Biopsy

value: Unclassified

value: Grade V

value: Missing


title: Sample 604_Single MCF7 cell


title: Sample 842_Single mESC cell


title: Sample 840_Single mESC cell


title: Sample 839_Single mESC cell


title: (+)siD1_9 FGC1293_s_3


title: (+)siD1_9 FGC1301_s_1


title: Sample 843_Single mESC cell


title: (+)siD1_8 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-8
(+)siD1_8
RawTranscriptCounts_SkHep1.xls


title: Sample 601_Single MCF7 cell


title: Sample 602_Single MCF7 cell


title: AVAglio_GSM2225462

value: Female

value: On

value: Classical

value: Non-methylated


title: AVAglio_GSM2225461

value: Partial resection

value: Grade IV


title: (+)siD1_8 FGC1301_s_1


title: Sample 838_Single mESC cell

value: Differentiated mESC


title: Sample 837_Single mESC cell

value: day 0


title: Sample 600_Single MCF7 cell


title: (+)siD1_8 FGC1293_s_3


title: Sample 599_Single MCF7 cell


title: Sample 836_Single mESC cell


title: AVAglio_GSM2225460

value: Proneural


title: Sample 835_Single mESC cell


title: AVAglio_GSM2225459

value: Off

value: Total resection

value: Placebo


title: (+)siD1_7 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-7
(+)siD1_7
RawTranscriptCounts_SkHep1.xls


title: AVAglio_GSM2225458

value: Male


title: AVAglio_GSM2225463

value: Mesenchymal


title: Sample 834_Single mESC cell


title: (+)siD1_7 FGC1301_s_1


title: Sample 597_Single MCF7 cell

value: MCF7 cell


title: Sample 596_Single MCF7 cell


title: (+)siD1_6 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-6
(+)siD1_6
RawTranscriptCounts_SkHep1.xls


title: (+)siD1_7 FGC1293_s_3


title: Sample 595_Single MCF7 cell


title: AVAglio_GSM2225454

value: Bevacizumab


title: AVAglio_GSM2225456

value: Methylated


title: (+)siD1_6 FGC1301_s_1


title: Sample 830_Single mESC cell


title: Sample 831_Single mESC cell


title: Sample 598_Single MCF7 cell


title: AVAglio_GSM2225457

value: Unclassified


title: Sample 832_Single mESC cell


title: Sample 593_Single MCF7 cell


title: Sample 592_Single MCF7 cell


title: Sample 829_Single mESC cell


title: Sample 828_Single mESC cell


title: AVAglio_GSM2225452

value: Female

value: On

value: Grade V


title: (+)siD1_5 FGC1301_s_1

description:
FBS(+) Cyclin-D1 siRNA rep-5
(+)siD1_5
RawTranscriptCounts_SkHep1.xls


title: AVAglio_GSM2225453

value: Partial resection

value: Classical


title: (+)siD1_6 FGC1293_s_3


title: Sample 833_Single mESC cell

value: Differentiated mESC


title: Sample 591_Single MCF7 cell


title: (+)siD1_5 FGC1391_s_2


title: Sample 827_Single mESC cell

value: day 0


title: AVAglio_GSM2225451

value: Grade IV


title: AVAglio_GSM2225450

value: Off

value: Non-methylated


title: Sample 590_Single MCF7 cell


title: (+)siD1_4 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-4
(+)siD1_4
RawTranscriptCounts_SkHep1.xls


title: (+)siD1_5 FGC1293_s_3


title: Sample 594_Single MCF7 cell


title: Sample 589_Single MCF7 cell


title: Sample 826_Single mESC cell


title: AVAglio_GSM2225449

value: Total resection


title: AVAglio_GSM2225448

value: Male

value: Proneural

value: Missing


title: Sample 588_Single MCF7 cell

value: MCF7 cell


title: Sample 824_Single mESC cell


title: Sample 825_Single mESC cell


title: Sample 587_Single MCF7 cell


title: AVAglio_GSM2225447

value: Placebo

value: Mesenchymal


title: Sample 586_Single MCF7 cell


title: Sample 821_Single mESC cell


title: (+)siD1_3 FGC1293_s_3

description:
FBS(+) Cyclin-D1 siRNA rep-3
(+)siD1_3
RawTranscriptCounts_SkHep1.xls


title: (+)siD1_3 FGC1391_s_2


title: (+)siD1_3 FGC1301_s_1


title: AVAglio_GSM2225445

value: Female

value: Bevacizumab

value: Methylated


title: Sample 820_Single mESC cell


title: Sample 584_Single MCF7 cell


title: AVAglio_GSM2225444

value: Grade III


title: Sample 585_Single MCF7 cell


title: Sample 583_Single MCF7 cell


title: (+)siD1_2 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-2
(+)siD1_2
RawTranscriptCounts_SkHep1.xls


title: Sample 819_Single mESC cell


title: AVAglio_GSM2225442


title: (+)siD1_2 FGC1301_s_1


title: (+)siD1_4 FGC1301_s_1


title: Sample 582_Single MCF7 cell


title: AVAglio_GSM2225443

value: Partial resection

value: Proliferative

value: Classical


title: (+)siD1_4 FGC1293_s_3


title: Sample 818_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 823_Single mESC cell


title: AVAglio_GSM2225446

value: On

value: Grade V


title: Sample 581_Single MCF7 cell


title: AVAglio_GSM2225441

value: Male

value: Off


title: Sample 817_Single mESC cell


title: (+)siD1_1 FGC1391_s_2

description:
FBS(+) Cyclin-D1 siRNA rep-1
(+)siD1_1
RawTranscriptCounts_SkHep1.xls


title: AVAglio_GSM2225440

value: Biopsy

value: Missing


title: Sample 822_Single mESC cell


title: Sample 580_Single MCF7 cell

value: MCF7 cell


title: AVAglio_GSM2225439

value: Total resection

value: Mesenchymal

value: Non-methylated


title: Sample 579_Single MCF7 cell


title: Sample 816_Single mESC cell


title: Sample 815_Single mESC cell


title: Sample 578_Single MCF7 cell


title: (+)siD1_1 FGC1293_s_3


title: AVAglio_GSM2225437

value: Bevacizumab

value: Grade IV

value: Methylated


title: (+)siC_10 FGC1391_s_2

description:
FBS(+) Control siRNA rep-10
(+)siC_10
RawTranscriptCounts_SkHep1.xls


title: AVAglio_GSM2225436

value: Partial resection

value: Proneural


title: (+)siD1_2 FGC1293_s_3


title: Sample 813_Single mESC cell

value: Differentiated mESC


title: (+)siC_10 FGC1301_s_1


title: Sample 576_Single MCF7 cell


title: Sample 577_Single MCF7 cell


title: Sample 812_Single mESC cell

value: day 0


title: (+)siC_10 FGC1293_s_3


title: (+)siD1_1 FGC1301_s_1


title: Sample 575_Single MCF7 cell


title: AVAglio_GSM2225435

value: On

value: Placebo


title: Sample 811_Single mESC cell


title: AVAglio_GSM2225434

value: Female


title: Sample 574_Single MCF7 cell


title: (+)siC_9 FGC1391_s_2

description:
FBS(+) Control siRNA rep-9
(+)siC_9
RawTranscriptCounts_SkHep1.xls


title: Sample 810_Single mESC cell


title: AVAglio_GSM2225433

value: Unclassified

value: Classical

value: Grade V


title: Sample 573_Single MCF7 cell

value: MCF7 cell


title: (+)siC_9 FGC1301_s_1


title: AVAglio_GSM2225432

value: Grade III

value: Missing


title: AVAglio_GSM2225438

value: Male

value: Non-methylated


title: Sample 572_Single MCF7 cell


title: Sample 809_Single mESC cell


title: Sample 814_Single mESC cell


title: (+)siC_9 FGC1293_s_3


title: AVAglio_GSM2225431

value: Proliferative

value: Grade IV


title: AVAglio_GSM2225430

value: Partial resection

value: Bevacizumab


title: Sample 571_Single MCF7 cell


title: Sample 807_Single mESC cell

value: Differentiated mESC


title: Sample 570_Single MCF7 cell


title: (+)siC_8 FGC1301_s_1

description:
FBS(+) Control siRNA rep-8
(+)siC_8
RawTranscriptCounts_SkHep1.xls


title: Sample 569_Single MCF7 cell


title: (+)siC_8 FGC1293_s_3


title: Sample 805_Single mESC cell

value: day 0


title: Sample 806_Single mESC cell


title: Sample 568_Single MCF7 cell


title: AVAglio_GSM2225428

value: On

value: Mesenchymal


title: AVAglio_GSM2225429

value: Proneural


title: Sample 567_Single MCF7 cell


title: Sample 804_Single mESC cell


title: AVAglio_GSM2225427

value: Total resection

value: Placebo


title: Sample 566_Single MCF7 cell


title: (+)siC_7 FGC1391_s_2

description:
FBS(+) Control siRNA rep-7
(+)siC_7
RawTranscriptCounts_SkHep1.xls


title: (+)siC_7 FGC1301_s_1


title: (+)siC_7 FGC1293_s_3


title: Sample 803_Single mESC cell


title: AVAglio_GSM2225426

value: Female

value: Unclassified

value: Classical

value: Methylated


title: Sample 802_Single mESC cell


title: Sample 808_Single mESC cell


title: Sample 565_Single MCF7 cell

value: MCF7 cell


title: (+)siC_6 FGC1391_s_2

description:
FBS(+) Control siRNA rep-6
(+)siC_6
RawTranscriptCounts_SkHep1.xls


title: (+)siC_8 FGC1391_s_2


title: AVAglio_GSM2225425

value: Male

value: Grade V


title: AVAglio_GSM2225424

value: Off

value: Non-methylated


title: Sample 801_Single mESC cell


title: (+)siC_6 FGC1301_s_1


title: Sample 800_Single mESC cell


title: (+)siC_6 FGC1293_s_3


title: Sample 563_Single MCF7 cell


title: Sample 798_Single mESC cell


title: Sample 562_Single MCF7 cell


title: Sample 799_Single mESC cell


title: AVAglio_GSM2225422

value: Partial resection

value: Grade IV


title: (+)siC_5 FGC1391_s_2

description:
FBS(+) Control siRNA rep-5
(+)siC_5
RawTranscriptCounts_SkHep1.xls


title: (+)siC_5 FGC1301_s_1


title: AVAglio_GSM2225421

value: Missing


title: AVAglio_GSM2225420

value: On

value: Proliferative


title: Sample 796_Single mESC cell

value: Differentiated mESC

value: day 0


title: (+)siC_2 FGC1391_s_2

description:
FBS(+) Control siRNA rep-2
(+)siC_2
RawTranscriptCounts_SkHep1.xls


title: Sample 560_Single MCF7 cell


title: Sample 559_Single MCF7 cell


title: Sample 558_Single MCF7 cell


title: Sample 797_Single mESC cell


title: Sample 561_Single MCF7 cell


title: Sample 795_Single mESC cell


title: AVAglio_GSM2225423

value: Biopsy

value: Bevacizumab

value: Proneural


title: Sample 564_Single MCF7 cell


title: (+)siC_2 FGC1293_s_3


title: AVAglio_GSM2225419


title: (+)siC_2 FGC1301_s_1


title: AVAglio_GSM2225418

value: Total resection

value: Classical


title: Sample 794_Single mESC cell


title: AVAglio_GSM2225417

value: Female


title: AVAglio_GSM2225416

value: Male

value: Placebo

value: Methylated


title: (+)siC_1 FGC1391_s_2

description:
FBS(+) Control siRNA rep-1
(+)siC_1
RawTranscriptCounts_SkHep1.xls


title: AVAglio_GSM2225415

value: Off

value: Unclassified


title: Sample 792_Single mESC cell


title: (+)siC_5 FGC1293_s_3


title: Sample 555_Single MCF7 cell

value: MCF7 cell


title: (+)siC_1 FGC1301_s_1


title: (+)siC_1 FGC1293_s_3


title: Sample 556_Single MCF7 cell


title: Sample 791_Single mESC cell


title: AVAglio_GSM2225414

value: Grade IV

value: Non-methylated


title: (+)siD1_6 FGC1312_s_1

description:
FBS(+) Cyclin-D1 siRNA rep-6
(+)siD1_6
RawTranscriptCounts_HEPG2.xls

source_name: Hep G2 cells (ATCC® HB-8065™)


title: Sample 554_Single MCF7 cell


title: AVAglio_GSM2225413

value: Mesenchymal


title: (+)siD1_6 FGC1293_s_4


title: Sample 557_Single MCF7 cell


title: (+)siD1_5 FGC1312_s_1

description:
FBS(+) Cyclin-D1 siRNA rep-5
(+)siD1_5
RawTranscriptCounts_HEPG2.xls


title: Sample 788_Single mESC cell

value: Differentiated mESC


title: Sample 552_Single MCF7 cell


title: Sample 553_Single MCF7 cell


title: Sample 550_Single MCF7 cell


title: AVAglio_GSM2225411

value: On

value: Proliferative

value: Grade V

value: Missing


title: Sample 787_Single mESC cell

value: day 0


title: Sample 551_Single MCF7 cell


title: (+)siD1_5 FGC1293_s_4


title: Sample 793_Single mESC cell


title: AVAglio_GSM2225410

value: Total resection

value: Bevacizumab

value: Proneural


title: AVAglio_GSM2225409

value: Male

value: Partial resection

value: Placebo

value: Classical


title: Sample 786_Single mESC cell


title: (+)siD1_4 FGC1312_s_1

description:
FBS(+) Cyclin-D1 siRNA rep-4
(+)siD1_4
RawTranscriptCounts_HEPG2.xls


title: Sample 785_Single mESC cell


title: Sample 549_Single MCF7 cell

value: MCF7 cell


title: Sample 548_Single MCF7 cell


title: Sample 790_Single mESC cell


title: (+)siD1_4 FGC1293_s_4


title: Sample 547_Single MCF7 cell


title: (+)siD1_2 FGC1312_s_1

description:
FBS(+) Cyclin-D1 siRNA rep-2
(+)siD1_2
RawTranscriptCounts_HEPG2.xls


title: AVAglio_GSM2225408

value: Female

value: Off

value: Biopsy


title: Sample 784_Single mESC cell

value: Differentiated mESC


title: Sample 783_Single mESC cell


title: AVAglio_GSM2225406

value: On

value: Unclassified

value: Grade IV

value: Non-methylated


title: AVAglio_GSM2225407

value: Mesenchymal


title: Sample 782_Single mESC cell

value: day 0


title: AVAglio_GSM2225405

value: Bevacizumab


title: (+)siC_10 FGC1312_s_1

description:
FBS(+) Control siRNA rep-10
(+)siC_10
RawTranscriptCounts_HEPG2.xls


title: Sample 545_Single MCF7 cell


title: (+)siD1_2 FGC1293_s_4


title: Sample 781_Single mESC cell


title: Sample 546_Single MCF7 cell


title: AVAglio_GSM2225404

value: Total resection

value: Grade V


title: Sample 544_Single MCF7 cell


title: (+)siC_10 FGC1293_s_4


title: Sample 780_Single mESC cell


title: AVAglio_GSM2225403

value: Male

value: Proneural


title: AVAglio_GSM2225402

value: Placebo


title: Sample 543_Single MCF7 cell

value: MCF7 cell


title: (+)siC_9 FGC1312_s_1

description:
FBS(+) Control siRNA rep-9
(+)siC_9
RawTranscriptCounts_HEPG2.xls


title: (+)siC_9 FGC1293_s_4


title: Sample 542_Single MCF7 cell


title: Sample 778_Single mESC cell


title: Sample 779_Single mESC cell


title: (+)siC_8 FGC1312_s_1

description:
FBS(+) Control siRNA rep-8
(+)siC_8
RawTranscriptCounts_HEPG2.xls


title: (+)siC_8 FGC1293_s_4


title: Sample 777_Single mESC cell


title: AVAglio_GSM2225400

value: Methylated


title: AVAglio_GSM2225401


title: Sample 540_Single MCF7 cell


title: Sample 539_Single MCF7 cell


title: Sample 776_Single mESC cell


title: Sample 775_Single mESC cell


title: Sample 538_Single HEK293T cell

source_name: Single HEK293T cell

value: HEK293T cell


title: (+)siC_6 FGC1293_s_4

description:
FBS(+) Control siRNA rep-6
(+)siC_6
RawTranscriptCounts_HEPG2.xls


title: (+)siC_6 FGC1312_s_1


title: (+)siC_5 FGC1312_s_1

description:
FBS(+) Control siRNA rep-5
(+)siC_5
RawTranscriptCounts_HEPG2.xls


title: Sample 774_Single mESC cell


title: AVAglio_GSM2225398

value: Off


title: Sample 789_Single mESC cell

value: Differentiated mESC


title: Sample 537_Single HEK293T cell


title: AVAglio_GSM2225397

value: On

value: Partial resection


title: Sample 773_Single mESC cell


title: Sample 541_Single MCF7 cell


title: Sample 536_Single HEK293T cell


title: (+)siC_5 FGC1293_s_4


title: AVAglio_GSM2225399

value: Grade IV


title: Sample 772_Single mESC cell


title: Sample 535_Single HEK293T cell


title: AVAglio_GSM2225395


title: Sample 771_Single mESC cell


title: (+)siC_1 FGC1312_s_1

description:
FBS(+) Control siRNA rep-1
(+)siC_1
RawTranscriptCounts_HEPG2.xls


title: AVAglio_GSM2225394

value: Female

value: Non-methylated


title: (+)siC_1 FGC1293_s_4


title: Sample 534_Single HEK293T cell


title: Sample 533_Single HEK293T cell


title: Non_functional_cap_in_vivo_half_life_5h_rep2

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

description: Randomly synthesized 10 nt RNA oligos

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

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

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

value: HEK293, stably expressing H-2Kb

value: Non-functional cap, in vivo half life. RNA levels at 5h time point


title: Non_functional_cap_in_vivo_half_life_2h_rep2

description: Randomly synthesized 10 nt RNA oligos

value: Non-functional cap, in vivo half life. RNA levels at 2h time point


title: Sample 532_Single HEK293T cell


title: AVAglio_GSM2225396


title: Sample 770_Single mESC cell

value: day 0


title: Sample 768_Single mESC cell


title: AVAglio_GSM2225391

value: Male

value: Total resection

value: Bevacizumab

value: Mesenchymal


title: Non_functional_cap_in_vivo_half_life_5h_rep1

description: Randomly synthesized 10 nt RNA oligos


title: Sample 530_Single HEK293T cell


title: Non_functional_cap_in_vivo_half_life_2h_rep1

description: Randomly synthesized 10 nt RNA oligos


title: Sample 767_Single mESC cell


title: AVAglio_GSM2225412

value: Placebo

value: Classical

value: Grade V

value: Missing


title: AVAglio_GSM2225392

value: On

value: Proliferative

value: Proneural


title: Sample 531_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225389

value: Female

value: Biopsy


title: In_vitro_Half_life_60min

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vitro half life. RNA levels at 60 min time point


title: AVAglio_GSM2225393


title: Sample 764_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 766_Single mESC cell


title: AVAglio_GSM2225388

value: Male

value: Off

value: Total resection

value: Grade IV

value: Non-methylated


title: In_vitro_Half_life_30min

description: Randomly synthesized 10 nt RNA oligos

value: In vitro half life. RNA levels at 30 min time point


title: Sample 769_Single mESC cell


title: AVAglio_GSM2225387

value: Placebo

value: Mesenchymal

value: Classical

value: Grade V

value: Missing


title: AVAglio_GSM2225386

value: On

value: Proneural


title: In_vitro_Half_life_10min

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vitro half life. RNA levels at 10 min time point


title: Sample 527_Single HEK293T cell

value: HEK293T cell


title: Sample 763_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 762_Single mESC cell


title: In_vitro_Half_life_0min

description: Randomly synthesized 10 nt RNA oligos

value: In vitro half life. RNA levels at 0 min time point


title: AVAglio_GSM2225390

value: Male

value: Off

value: Biopsy


title: Sample 526_Single HEK293T cell


title: In_vivo_Half_life_5h_rep2

description: Randomly synthesized 10 nt RNA oligos

value: In vivo half life. RNA levels at 5h time point


title: AVAglio_GSM2225384

value: Female

value: Total resection

value: Bevacizumab

value: Proliferative

value: Methylated


title: AVAglio_GSM2225385

value: Partial resection

value: Mesenchymal

value: Grade IV

value: Missing


title: Sample 525_Single HEK293T cell

value: HEK293T cell


title: In_vivo_Half_life_2h_rep2

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vivo half life. RNA levels at 2h time point


title: Sample 761_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 529_Single HEK293T cell


title: Sample 528_Single HEK293T cell


title: Sample 765_Single mESC cell


title: Sample 524_Single HEK293T cell


title: In_vivo_Half_life_5h_rep1

description: Randomly synthesized 10 nt RNA oligos


title: Sample 523_Single HEK293T cell


title: Sample 760_Single mESC cell


title: AVAglio_GSM2225383

value: Male

value: Off

value: Placebo

value: Classical


title: Sample 758_Single mESC cell


title: Sample 522_Single HEK293T cell


title: Sample 757_Single mESC cell


title: In_vivo_Gating_GFP_high_rep2

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation,  FACS GFP positive cells


title: AVAglio_GSM2225382


title: In_vivo_Half_life_2h_rep1

description: Randomly synthesized 10 nt RNA oligos


title: Sample 521_Single HEK293T cell


title: Sample 520_Single HEK293T cell


title: Sample 756_Single mESC cell


title: In_vivo_Gating_25D_high_rep2

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation,  FACS 25D positive cells


title: AVAglio_GSM2225381

value: Proneural

value: Grade V

value: Non-methylated


title: Sample 519_Single HEK293T cell


title: AVAglio_GSM2225380

value: Total resection

value: Bevacizumab

value: Proliferative

value: Grade III


title: In_vivo_Gating_GFP_low_rep2

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vivo translation,  FACS GFP negative cells


title: Sample 755_Single mESC cell

value: Differentiated mESC


title: In_vivo_Gating_25D_low_rep2

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation,  FACS 25D negative cells


title: AVAglio_GSM2225378

value: Female

value: On

value: Partial resection

value: Mesenchymal

value: Methylated


title: Sample 518_Single HEK293T cell

value: HEK293T cell


title: Sample 753_Single mESC cell

value: day 0


title: In_vivo_Gating_GFP_low_rep1

description: Randomly synthesized 10 nt RNA oligos


title: In_vivo_Gating_GFP_high_rep1

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation,  FACS GFP positive cells


title: Sample 517_Single HEK293T cell


title: Sample 759_Single mESC cell


title: Sample 754_Single mESC cell


title: AVAglio_GSM2225374

value: Male

value: Off

value: Classical

value: Grade V

value: Non-methylated


title: Sample 516_Single HEK293T cell


title: AVAglio_GSM2225373

value: Bevacizumab

value: Proneural

value: Grade IV


title: AVAglio_GSM2225375

value: Placebo

value: Grade III


title: Sample 752_Single mESC cell

value: Differentiated mESC


title: Sample 751_Single mESC cell


title: In_vivo_Gating_25D_high_rep1

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vivo translation,  FACS 25D positive cells


title: Sample 515_Single HEK293T cell


title: Sample 750_Single mESC cell


title: Non_functional_cap_Ribosome_bound

description: Randomly synthesized 10 nt RNA oligos

value: Non-funtional cap, in vivo translation. Sucrose gradient:Ribosome bound fraction


title: Sample 514_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225371

value: On

value: Partial resection

value: Methylated


title: AVAglio_GSM2225372

value: Female

value: Off

value: Mesenchymal


title: Sample 513_Single HEK293T cell


title: In_vivo_Gating_25D_low_rep1

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation,  FACS 25D negative cells


title: Sample 749_Single mESC cell

value: day 0


title: AVAglio_GSM2225377

value: Male

value: Bevacizumab

value: Proliferative

value: Proneural

value: Grade V

value: Missing


title: Sample 748_Single mESC cell

value: Differentiated mESC


title: Sample 512_Single HEK293T cell


title: AVAglio_GSM2225370

value: Total resection

value: Classical

value: Grade IV

value: Non-methylated


title: In_vivo_Ribosome_free_rep2

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vivo translation. Sucrose gradient:Ribosome free fraction


title: Non_functional_cap_Ribosome_free

description: Randomly synthesized 10 nt RNA oligos

value: Non-funtional cap, in vivo translation. Sucrose gradient:Ribosome free fraction


title: AVAglio_GSM2225369

value: Off


title: Sample 511_Single HEK293T cell

value: HEK293T cell


title: Sample 747_Single mESC cell

value: day 0


title: Sample 746_Single mESC cell


title: In_vivo_Ribosome_free_rep1

description: Randomly synthesized 10 nt RNA oligos


title: Sample 510_Single HEK293T cell


title: In_vivo_Polysome_rep2

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation. Sucrose gradient:Polysome fraction


title: AVAglio_GSM2225367

value: Male

value: Partial resection

value: Placebo

value: Mesenchymal

value: Methylated


title: Sample 509_Single HEK293T cell


title: In_vivo_Monosome_rep2

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation. Sucrose gradient:Monosome fraction


title: Sample 745_Single mESC cell

value: Differentiated mESC


title: Sample 508_Single HEK293T cell


title: Sample 744_Single mESC cell


title: AVAglio_GSM2225364

value: Female

value: On

value: Biopsy

value: Bevacizumab

value: Proneural

value: Grade III


title: AVAglio_GSM2225365

value: Off

value: Total resection

value: Classical

value: Grade IV


title: AVAglio_GSM2225366

value: Male

value: Grade V


title: In_vivo_Polysome_rep1

description: Randomly synthesized 10 nt RNA oligos

value: HEK293, stably expressing H-2Kb

value: In vivo translation. Sucrose gradient:Polysome fraction


title: Sample 743_Single mESC cell

value: day 0


title: In_vivo_Monosome_rep1

description: Randomly synthesized 10 nt RNA oligos

value: In vivo translation. Sucrose gradient:Monosome fraction


title: Sample 742_Single mESC cell

value: Differentiated mESC


title: Sample 505_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225363

value: Partial resection

value: Placebo

value: Non-methylated


title: AVAglio_GSM2225368

value: On

value: Bevacizumab

value: Proliferative


title: Randomly_synthesized_oligos

description: Randomly synthesized 10 nt RNA oligos

value: Originally synthesized oligo pool


title: AVAglio_GSM2225362

value: Off

value: Proneural


title: Sample 504_Single HEK293T cell


title: Sample 502_Single HEK293T cell


title: Sample 503_Single HEK293T cell


title: Sample 739_Single mESC cell


title: Sample 740_Single mESC cell


title: CIT_24_A

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

description: HepG2 Cells

data_processing:
Reads Aligned against whole genome Manifest (BioSpyder) Human and counted
Raw Counts summed to Unique Gene
Raw Counts from Biospyder – removed features without at least 4 samples > 1 count across all samples
Remaining 13,133 unique features. Samples < 100 counts/gene removed

source_name: HepG2 Cells

extract_protocol:
Cell lysates from plates were prepared using TempO-Seq lysis buffer (BioSpyder). After 10-min incubation at room temperature, lysates were stored at −80 °C until testing.
Sequencing libraries were prepared using  the TempO-Seq protocol (BioSpyder).

tag: exposure

value: Citrate

tag: treatment concentration

value: 1.2 ug/mL


title: AVAglio_GSM2225361

tag: Sex

value: Female

tag: corticosteroids

value: Total resection

value: Mesenchymal

value: Grade IV

value: Methylated


title: CIT_24_B

description: HepG2 Cells


title: CIT_24_C

description: HepG2 Cells


title: Sample 738_Single mESC cell

value: Differentiated mESC

value: day 0


title: AVAglio_GSM2225359

tag: surgical status

tag: treatment

value: Placebo


title: Sample 506_Single HEK293T cell

tag: cell line

value: HEK293T cell


title: AVAglio_GSM2225360

value: Male

value: On

tag: phillips subtype

tag: tcga subtype

value: Non-methylated


title: Sample 501_Single HEK293T cell


title: Sample 500_Single HEK293T cell


title: Sample 507_Single HEK293T cell