title: tdTomato- cells rep1

city: Budapest

first: Zoltan

last: Wiener

address: Ulloi ut 26

country: Hungary

institute: Semmelweis University

description:
SAMPLE 2
replicate 1

hyb_protocol: Standard Illumina hybridization protocol (Whole-Genome Gene Expression Direct Hybridization Assay Guide, P/N BD-901-1002). A total of 1.5 μg of labeled cRNA was hybridized to Mouse WG-6 v2 Expression BeadChips for 18 hours at 58°C with rocking platform at speed 5

scan_protocol: BeadChips were washed, blocked and stained with streptavidin-Cy3 and scanned with Illumina iScan, using manufacturer provided protocols. The raw data was extracted using Illumina's GenomeStudio software.

data_processing: The data were normalized with quantile normalization by the Chipster software (www.chipster.csc.fi). The datasets from different time points were normalized separately with quantile and gene average normalizations and the data were then unified.

source_name: ex vivo intestinal organoid

label_protocol: The labeling and hybridization were done according to manufacturer´s instructions (TargetAmp™- Nano Labeling Kit for Illumina® Expression BeadChip®, P/N TAN07924). The starting amount of total RNA was 50 ng.

growth_protocol: Intestinal organoids were isolated and grown according to Sato T et al (Nature, 2009), but without adding growth factors

extract_protocol: Total RNA was extracted by the NucleoSpin RNA II isolation kit (Macherey-Nagel) according to the manufacturer, including DNase treatment. RNA quality was checked by Agilent Bioanalyzer

treatment_protocol: 300 nM 4-hydroxytamoxifen for 16h to activate CreERT2 in the Prox1+ cells before FACS sorting

tag: tumor stage

value: Apc-mutant intestinal adenoma

value: tdTomato- cell population (enriched for Prox1- cells)


title: tdTomato3+ (Prox1+) cells rep1

status: Public on Aug 21 2018

type: RNA

description:
SAMPLE 1
replicate 1

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type

value: tdTomato+ (Prox1+) cells


title: RNA of B3

type: SRA

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

country: China

institute: Institute of Microbiology, Guangdong Academy of Sciences

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Pseudomonas aeruginosa PAO1

source_name: Transcriptome of DDS-treated P. aeruginosa PAO1

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 150 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAO1 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 1.0E8 CFU/mL. Then DDS was added, with its concentrations were 0.64 mg/mL (three biological repeats numbered B1, B2, and B3) separately, both with a triplicate. All the  experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 150 rpm for 5 hours.

tag: treatment

value: DDS-treated sample

tag: growth

value: exponential growth phase


title: RNA of B2


title: RNA of B1


title: BS455 FFPE sample

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: BS455 FFPE sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. After eliminating  samples with poor quality data, the raw data were normalized using the cubic spline.  algorithm using the IlluminaDASL pipeline within GenePattern.

organism: Homo sapiens

source_name: Formalin-fixed paraffin-embedded (FFPE)

extract_protocol: Based on hematoxylin/eosin staining, tumor tissue was macro-dissected from non-tumor liver parenchyma by an expert liver pathologist. Total RNA was isolated from freshly cut FFPE sections using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process.

tag: tissue

value: hepatocellular carcinoma

value: Plac

tag: outcome

value: non-responder


title: BS427 FFPE sample

description: BS427 FFPE sample

value: responder


title: tdTomato3+ (Prox1+) cells rep2

description:
SAMPLE 3
replicate 2


title: tdTomato- cells rep3

description:
SAMPLE 6
replicate 3


title: Rag_cKit-_022417_C22_1

city: Worcester

first: Nicholas

last: Spidale

state: MA

address: 368 Plantation St.

department: Pathology

country: USA

institute: University of Massachusetts Medical School

data_processing: Cq values (matrix non-normalized data) are automatically calculated by the Fluidigm Realtime PCR analysis software using the Auto(Detectors) setting, which sets independent baseline and threshold values for each target gene.  Cycle 24 is considered the limit of detection, and any amplification at cycle 24 or later is recorded as 24.  Any target for which the melt curve falls outside of the set optimal paramaters for the target is also recorded as 24.  Matrix normalized data (called Log2Exp by Fluidigm) is calculted as follows:  Log2Exp = 24-Cq.  No fold change analysis is performed.

label: Eva Green

source_name: Thymus

label_protocol: RT was performed using the following reagent mix:  1.94 microliters Stop Solution (Life Technologies) + 5.84 microliters Single Cell VILO RT Mix (Life Technologies) + 3.62 microliters Single Cell SuperScript RT (Life Technologies) + 0.6 microliters Loading Reagent (Fluidigm).  RT thermal cycling protocol:  25 C, 600 s; 42 C, 3600 s; 85 C, 300 s.  Preamplification was performed using the following reagent mix:  12 microliters Single Cell PreAmp Mix (Life Technologies) + 42 microliters C1 PreAmp Dilution Reagent + 6 microliters Pooled qPCR Primers (500 nM).  PreAmp thermal cycling protocol:  95 C, 600 s; [18 cycles of:  95 C, 15 s; 60 C, 240 s]; 4 C, hold.  qPCR was performed using SsoFast EvaGreen Supermix (Bio-Rad) and assay-specific primer pairs.  qPCR thermal cycling protocol:  95 C, 60 s; [30 cycles of:  96 C, 5 s; 60 C, 20 s (read)]; 60-95 C, ramp 1 C/3 s (melt curve analysis).

extract_protocol: Cells are lysed using the following mixture as advised by the manufacturer:  12.75 microliters Single Cell Lysis Solution (Life Technologies Single Cell-to-CT Kit) + 4.35 microliters C1 Lysis Plus Reagent (Fluidigm) + 0.9 microliters C1 DNA Dilution Reagent (Fluidigm)

tag: markers

tag: strain/genotype

value: Thymus

tag: developmental stage


title: BS139 FFPE sample

description: BS139 FFPE sample

value: Sor


title: BS147 FFPE sample

description: BS147 FFPE sample


title: Rag_cKit-_022417_C21_1


title: Rag_cKit-_022417_C20_1


title: Rag_cKit-_022417_C23_1


title: RNA of A1

source_name: Transcriptome of control of P. aeruginosa PAO1

value: native sample


title: BS103 FFPE sample

description: BS103 FFPE sample


title: RNA of A3


title: BS475 FFPE sample

description: BS475 FFPE sample


title: BS333 FFPE sample

description: BS333 FFPE sample


title: BS351 FFPE sample

description: BS351 FFPE sample


title: BS379 FFPE sample

description: BS379 FFPE sample


title: Rag_cKit-_022417_C18_1


title: BS363 FFPE sample

description: BS363 FFPE sample


title: Rag_cKit-_022417_C17_1


title: Rag_cKit-_022417_C16_1


title: Rag_cKit-_022417_C19_1


title: Sample_NC_2

city: Yangzhou

first: Lingling

last: Qiu

address: 88 South University Ave.

department: College of Animal Science and Technology

institute: Yangzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using NGS QC TOOLKIT v2.3.3, then mapped to reference genome (Gallus gallus 4.0, April 2013, Ensembl Build 85) with TopHat (version: 2.0.9)
The fragments per kilobase of transcript per million mapped reads (FPKM) method (Trapnell et al., 2010) was used to estimate each gene expression, and the total number of reads mapped to UniGenes were calculated and normalized to the FPKM for each gene.
Genome_build: Gallus gallus 4.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Gallus gallus

source_name: Spleen

extract_protocol:
Spleen samples of uninfected chickens and chickens suspected of having ALV-J infection were collected independently, washed in RNase-free water, transferred to tissue-cryopreservation tubes, immediately submerged in liquid nitrogen. Total RNA was harvested using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Black-bone silky fowls

value: Spleen

tag: gender

value: Female

tag: age

value: Twenty-week-old

tag: agent

value: uninfected


title: Rag_cKit-_022417_C14_1


title: Sample_ALV_3

value: ALV-J


title: PIM1-3

city: Tucson

first: JIN

middle: H

last: SONG

state: AZ

address: 1515 N Campbell Ave

department: Cellular and Molecular Medicine

institute: University of Arizona

description: cells were infected with lentivirus of PIM1

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: Raw data was processed using Affymetrix Expression Console

label: RFP

source_name: Rb1F/F:Trp53F/F:PB-Cre4 mice

label_protocol: sscDNA were prepared according to the standard Affymetrix GeneChip WT PLUS protocol from 500ng total RNA (GeneChip WT PLUS Reagent Kit, 2014, Affymetrix).

growth_protocol: Mouse prostate epithelial cells were grown in DMEM medium supplemented with 2.5% charcoal stripped FCS, 5 μg/mL of insulin/transferring/selenium, 10 μg/mL of bovine pituitary extract, 10 μg/mL of epidermal growth factor, and 1 μg/mL of cholera toxin.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and RNeasy kits (Qiagen).

value: prostate epithelial cancer cells

tag: transduction

value: PIM1 lentivirus


title: PIM1-1


title: Rag_cKit-_022417_C12_1


title: BS307 FFPE sample

description: BS307 FFPE sample


title: RNA of A2


title: BS301 FFPE sample

description: BS301 FFPE sample


title: Rag_cKit-_022417_C13_1


title: PIM1-2


title: EV-3

description: cells were infected with lentivirus of control empty vector

value: empty vector


title: BS305 FFPE sample

description: BS305 FFPE sample


title: tdTomato- cells rep2

description:
SAMPLE 4
replicate 2

value: Apc-mutant intestinal adenoma

value: tdTomato- cell population (enriched for Prox1- cells)


title: tdTomato3+ (Prox1+) cells rep3

description:
SAMPLE 5
replicate 3

value: tdTomato+ (Prox1+) cells


title: EV-2


title: BS319 FFPE sample

description: BS319 FFPE sample

value: hepatocellular carcinoma

value: non-responder


title: Sample_ALV_2


title: Sample_NC_1


title: BS371 FFPE sample

description: BS371 FFPE sample


title: Patient3_input

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the reference human genome version GRCh37 (hg19)
The .sam files were converted to .bam files using SAMtools
The .bam files were then processed to yield .wig files using MACS
Genome_build: hg19
Supplementary_files_format_and_content: wig files

molecule: genomic DNA

source_name: Pre-B lymphoblast cells

growth_protocol: Nalm6 cells were maintained in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) containing 10% heat-inactivated fetal calf serum (FCS) (Eurobio) supplemented with antibiotics (100 U/mL penicillin-G and 100 U/mL streptomycin, Gibco).For pre-B acute lymphoblastic leukemia (BCP-ALL) patient cells, vital mononuclear cells were isolated from bone marrow by successive centrifugations through lymphocytes separation medium (Eurobio).

extract_protocol:
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min.  Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

value: Blast from BCP-ALL patient

value: Bone marrow

tag: disease state

value: Human BCP-ALL

tag: chip antibody


title: EA72

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

description:
endocrine_dense.bed
1.4

data_processing:
reads were aligned to hg19 using Bowtie
genome segmentation was performed using ChromHMM as described in Ernst and Kellis, 2012 Nature Methods
Genome_build: hg19
Supplementary_files_format_and_content: BED file includes genome segmentation annotations based on the ChIP-Seq data and Chrom HMM analysis

source_name: Pancreas

extract_protocol: Illumina HiSeq

value: juvenile

tag: histone mark

value: endocrine


title: Sample_ALV_1

value: Black-bone silky fowls

value: Spleen

value: Female


title: EA74

description:
endocrine_dense.bed
0.8


title: EV-1


title: EA70

description:
endocrine_dense.bed
1.4


title: BS433 FFPE sample

description: BS433 FFPE sample

value: Sor


title: Patient2_input


title: Patient1_input


title: EA68

description:
endocrine_dense.bed
40

value: adult


title: BS357 FFPE sample

description: BS357 FFPE sample

value: Plac


title: BS119 FFPE sample

description: BS119 FFPE sample


title: Patient3_Runx1

value: RUNX1 (ab23980, Abcam)


title: EA64

description:
acinar_dense.bed
20

value: acinar


title: Rag_cKit-_022417_C08_1

tag: strain

value: Thymus


title: Rag_cKit-_022417_C07_1


title: Rag_cKit-_022417_C06_1


title: Patient2_Runx1

tag: cell type


title: EA62

description:
acinar_dense.bed
20


title: Rag_cKit-_022417_C04_1


title: BS315 FFPE sample

description: BS315 FFPE sample

tag: treatment

value: responder


title: BS327 FFPE sample

description: BS327 FFPE sample

value: hepatocellular carcinoma


title: BS401 FFPE sample

description: BS401 FFPE sample

value: non-responder


title: Nalm6_H3K27ac

value: Pre-B lymphoblast cells

value: Peripheral blood

tag: cell line

value: H3K27ac (ab4729, Abcam)


title: Rag_cKit-_022417_C03_1

tag: tissue


title: EA56

description:
duct_dense.bed
40

value: duct


title: BS461 FFPE sample

description: BS461 FFPE sample

tag: outcome


title: BS297 FFPE sample

description: BS297 FFPE sample


title: EA55

description:
duct_dense.bed
40


title: Rag_cKit-_022417_C02_1

tag: markers


title: EA54

description:
duct_dense.bed
40


title: Nalm6_H3K4me3

value: H3K4me3 (04-745, Merck Millipore)


title: Nalm6_H3K4me1

value: H3K4me1 (07-436, Merck Millipore)


title: Nalm6_input_rep2


title: BS477 FFPE sample

description: BS477 FFPE sample


title: Rag_cKit-_022417_C01_1

tag: strain/genotype


title: EA53

description:
duct_dense.bed
40


title: Rag_cKit-_020317_C93_1

tag: developmental stage


title: Rag_cKit-_020317_C92_1


title: Nalm6_Runx1_rep2


title: EA43

description:
duct_dense.bed
5

value: juvenile


title: Patient1_Runx1

value: Blast from BCP-ALL patient

value: Bone marrow

value: Human BCP-ALL


title: Rag_cKit-_020317_C91_1


title: BS245 FFPE sample

description: BS245 FFPE sample

value: Sor


title: EA48

description:
endocrine_dense.bed
5

value: endocrine


title: EA36

description:
duct_dense.bed
1.5


title: EA34

description:
duct_dense.bed
1.5


title: Rag_cKit-_020317_C89_1


title: Rag_cKit-_020317_C85_1


title: HC_11

city: Farmington

first: Parveen

last: Kumar

state: Connecticut

address: 10 Farmington Drive

institute: Application Computational Scientist

description:
tRNA51102
20151123_BRI2015NSDS006Catridge1_tRNA51102_02

hyb_protocol: Samples were incubated at 65°C on thermal cycler for at least 19 hours but less than 30 hours for hybridization.

scan_protocol: Hybridized samples were purified and immobilized in a sample cartridge for data collection on a GEN2 Prep Station using standard protocol prior to scanning.  All cartridges were placed on nCounter Digital Analyser for scanning with at the highest standard data resolution, 600 fields of view.

data_processing:
Raw RCC files are uploaded to nSolver Analysis software 3.0 for background subtraction using negative control probes, positive control normalization and CodeSet Content (Housekeeping) normalization. The normalized NanoString expression is then log2 transformed.
Processed data is modeled by linear mixed model in JMP Genomics 7 to account for repeated measurements. Fold change, P-value are reported as the differential expression results between baseline and later time points, for each gene. False discovery rate (FDR) corrections are provided in additional to the raw P-values.

source_name: Project 140

label_protocol: 100ng of total RNA in 5 ul of water was used as input for the NanoString Human Immunology v2 assay following the manufacturer’s protocol for the XT formulation. Following hybridization, transcripts were quantitated using the nCounter Digital Analyzer.

growth_protocol: The study was approved by Institutional Review Board (IRB 012-099), conducted in accordance with ethical guidelines (Declaration of Helsinki) and written informed consent was obtained from the patients. Eleven female patients with HER2-negative metastatic BC were recruited.

extract_protocol: Total RNA was isolated from whole blood lysed in Tempus™ Blood RNA Tubes (Applied Biosystems™) using a modified protocol for the Tempus™ Spin RNA Isolation Kit (Ambion). Following extraction, a LabChip GX instrument (Caliper Life Sciences Inc.) was used to measure the RNA Quality Score (RQS) for each sample. RNA concentration was measured using a Nanodrop 8000 (Nanodrop Technologies).

treatment_protocol: Eleven female patients with HER2-negative metastatic BC received nab paclitaxel (n=3), eribulin (n=5) or capecitabine (n=2) along with anakinra 100mg/day following 2-week treatment with anakinra only.

tag: subject status

value: healthy control

value: Female

tag: race

value: White

value: Non-Hispanic

value: Whole Blood

value: Tempus

value: Healthy control


title: EA32

description:
duct_dense.bed
33

tag: age

value: adult


title: HC_9

description:
tRNA51100
20151124_BRI2015NSDS006Catridge6_tRNA51100_10

tag: gender

value: African American


title: HC_10

description:
tRNA51101
20151123_BRI2015NSDS006Catridge3_tRNA51101_03


title: BS435 FFPE sample

description: BS435 FFPE sample

value: hepatocellular carcinoma

value: responder


title: EA42

description:
acinar_dense.bed
5

value: juvenile

value: acinar


title: Rag_cKit-_020317_C80_1

value: Thymus


title: Rag_cKit-_020317_C81_1


title: BS399 FFPE sample

description: BS399 FFPE sample

value: non-responder


title: Rag_cKit-_020317_C87_1


title: BS449 FFPE sample

description: BS449 FFPE sample

value: Sor


title: BS469 FFPE sample

description: BS469 FFPE sample

value: Plac


title: HC_8

description:
tRNA51099
20151123_BRI2015NSDS006Catridge2_tRNA51099_05

value: healthy control


title: HC_6

description:
tRNA51097
20151123_BRI2015NSDS006Catridge3_tRNA51097_09

value: Female


title: BS267 FFPE sample

description: BS267 FFPE sample


title: BS387 FFPE sample

description: BS387 FFPE sample


title: BS443 FFPE sample

description: BS443 FFPE sample


title: BS421 FFPE sample

description: BS421 FFPE sample


title: Sample_NC_3

tag: breed

value: Black-bone silky fowls

value: Spleen

value: Twenty-week-old

tag: agent

value: uninfected


title: EA26

description:
endocrine_dense.bed
48

value: endocrine


title: Rag_cKit-_020317_C82_1


title: Rag_cKit-_020317_C79_1


title: HC_7

description:
tRNA51098
20151124_BRI2015NSDS006Catridge4_tRNA51098_06

value: White

value: Hispanic

value: Whole Blood

value: Tempus

value: Healthy control


title: EA30

description:
duct_dense.bed
33

value: adult

value: duct


title: BS403 FFPE sample

description: BS403 FFPE sample

value: hepatocellular carcinoma

value: non-responder


title: EA14

description:
endocrine_dense.bed
66


title: HC_4

description:
tRNA51095
20151124_BRI2015NSDS006Catridge4_tRNA51095_11

value: Non-Hispanic


title: Rag_cKit-_020317_C75_1

value: Thymus


title: HC_3

description:
tRNA51094
20151123_BRI2015NSDS006Catridge3_tRNA51094_02

value: healthy control

value: Female


title: Rag_cKit-_020317_C74_1


title: Rag_cKit-_020317_C73_1


title: HC_1

description:
tRNA51092
20151124_BRI2015NSDS006Catridge6_tRNA51092_01


title: BS463 FFPE sample

description: BS463 FFPE sample

value: Sor


title: HC_5

description:
tRNA51096
20151123_BRI2015NSDS006Catridge1_tRNA51096_03


title: Rag_cKit-_020317_C68_1


title: 012-099-02-011-EOM6

description:
tRNA51091
20151124_BRI2015NSDS006Catridge5_tRNA51091_11

value: HER2-negative metastatic BC patient

value: African American

value: EOM 6


title: Rag_cKit-_020317_C69_1


title: 012-099-02-010-EOM6

description:
tRNA51084
20151124_BRI2015NSDS006Catridge4_tRNA51084_05


title: 012-099-02-010-EOM5

description:
tRNA51083
20151124_BRI2015NSDS006Catridge6_tRNA51083_03

value: EOM 5/Pre-Cycle 6


title: Rag_cKit-_020317_C65_1


title: Rag_cKit-_020317_C63_1


title: 012-099-02-010-EOM4

description:
tRNA51082
20151124_BRI2015NSDS006Catridge5_tRNA51082_08

value: EOM 4/Pre-Cycle 5


title: Rag_cKit-_020317_C62_1


title: Rag_cKit-_020317_C61_1


title: Rag_cKit-_020317_C59_1


title: BS389 FFPE sample

description: BS389 FFPE sample


title: BS419 FFPE sample

description: BS419 FFPE sample

value: responder


title: 012-099-02-011-EOM5

description:
tRNA51090
20151124_BRI2015NSDS006Catridge6_tRNA51090_05

value: Whole Blood

value: Tempus


title: EA40

description:
acinar_dense.bed
5

value: juvenile

value: acinar


title: 012-099-02-011-EOM3

description:
tRNA51089
20151124_BRI2015NSDS006Catridge5_tRNA51089_04

value: EOM 3/Pre-Cycle 4


title: BS209 FFPE sample

description: BS209 FFPE sample

value: hepatocellular carcinoma

value: Plac

value: non-responder


title: BS471 FFPE sample

description: BS471 FFPE sample


title: BS383 FFPE sample

description: BS383 FFPE sample


title: Rag_cKit-_020317_C57_1

value: Thymus


title: BS385 FFPE sample

description: BS385 FFPE sample


title: BS391 FFPE sample

description: BS391 FFPE sample


title: Rag_cKit-_020317_C55_1


title: 012-099-02-010-EOM3

description:
tRNA51081
20151123_BRI2015NSDS006Catridge3_tRNA51081_12

value: Female

value: Non-Hispanic


title: BS425 FFPE sample

description: BS425 FFPE sample


title: BS237 FFPE sample

description: BS237 FFPE sample


title: 012-099-02-008-EOM4

description:
tRNA51078
20151123_BRI2015NSDS006Catridge2_tRNA51078_12

value: HER2-negative metastatic BC patient

value: White


title: Rag_cKit-_022417_C10_1


title: 012-099-02-011-EOM2

description:
tRNA51088
20151124_BRI2015NSDS006Catridge4_tRNA51088_12

value: African American

value: EOM 2/Pre-Cycle 3


title: 012-099-02-008-EOM2

description:
tRNA51077
20151123_BRI2015NSDS006Catridge1_tRNA51077_11


title: Rag_cKit-_020317_C44_1


title: Rag_cKit-_020317_C56_1


title: 012-099-02-005-EOM6

description:
tRNA51069
20151123_BRI2015NSDS006Catridge3_tRNA51069_07

value: EOM 6


title: BS437 FFPE sample

description: BS437 FFPE sample


title: 012-099-02-008-EOM1

description:
tRNA51076
20151124_BRI2015NSDS006Catridge5_tRNA51076_05

value: EOM 1/Pre-Cycle 2


title: Rag_cKit-_020317_C41_1


title: BS331 FFPE sample

description: BS331 FFPE sample

value: Sor


title: BS487 FFPE sample

description: BS487 FFPE sample


title: Rag_cKit-_020317_C45_1


title: 012-099-02-010-EOM1

description:
tRNA51080
20151123_BRI2015NSDS006Catridge1_tRNA51080_01

value: Whole Blood

value: Tempus


title: HC_2

description:
tRNA51093
20151124_BRI2015NSDS006Catridge5_tRNA51093_06

value: healthy control

value: Healthy control


title: 012-099-02-011-EOM1

description:
tRNA51087
20151123_BRI2015NSDS006Catridge2_tRNA51087_06


title: Rag_cKit-_020317_C39_1


title: 012-099-02-005-EOM3

description:
tRNA51066
20151124_BRI2015NSDS006Catridge4_tRNA51066_04

value: EOM 3/Pre-Cycle 4


title: Rag_cKit-_020317_C43_1


title: Rag_cKit-_020317_C35_1


title: BS213 FFPE sample

description: BS213 FFPE sample

value: hepatocellular carcinoma


title: BS217 FFPE sample

description: BS217 FFPE sample

value: Plac

value: non-responder


title: BS485 FFPE sample

description: BS485 FFPE sample

value: responder


title: 012-099-01-007-EW

description:
tRNA51073
20151124_BRI2015NSDS006Catridge5_tRNA51073_02

value: Female

value: Hispanic

value: Early Withdrawal


title: 012-099-02-011-B

description:
tRNA51085
20151123_BRI2015NSDS006Catridge1_tRNA51085_09

value: HER2-negative metastatic BC patient

value: African American

value: Non-Hispanic

value: Baseline


title: Rag_cKit-_020317_C37_1

value: Thymus


title: Rag_cKit-_020317_C38_1


title: 012-099-02-011-RI

description:
tRNA51086
20151123_BRI2015NSDS006Catridge3_tRNA51086_06

value: Whole Blood

value: Run In


title: Rag_cKit-_020317_C33_1


title: BS165 FFPE sample

description: BS165 FFPE sample

value: Sor


title: BS235 FFPE sample

description: BS235 FFPE sample


title: BS479 FFPE sample

description: BS479 FFPE sample


title: BS423 FFPE sample

description: BS423 FFPE sample


title: BS239 FFPE sample

description: BS239 FFPE sample


title: Rag_cKit-_020317_C31_1


title: 012-099-02-003-EW

description:
tRNA51055
20151123_BRI2015NSDS006Catridge1_tRNA51055_07

value: White

value: Tempus


title: 012-099-02-008-RI

description:
tRNA51075
20151123_BRI2015NSDS006Catridge3_tRNA51075_08


title: dGATA_3: K.O. mouse lung treated with OVA

city: Chiba

first: Yuki

last: Morimoto

state: Chiba

address: 1-8-1, Inohana, Chuoku

department: Graduate school of Medicine

country: Japan

institute: Chiba University

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: K.O. mouse lung treated with OVA

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

treatment_protocol: K.O. mouse was treated with OVA

value: BALB/c

value: lung

tag: group

value: Knock out


title: Rag_cKit-_020317_C29_1


title: Rag_cKit-_020317_C34_1


title: 012-099-01-007-EOM1

description:
tRNA51071
20151123_BRI2015NSDS006Catridge1_tRNA51071_04

value: EOM 1/Pre-Cycle 2


title: 012-099-02-005-EOM2

description:
tRNA51065
20151124_BRI2015NSDS006Catridge4_tRNA51065_03

value: Female

value: EOM 2/Pre-Cycle 3


title: Rag_cKit-_020317_C27_1


title: 012-099-02-010-RI

description:
tRNA51079
20151123_BRI2015NSDS006Catridge2_tRNA51079_03


title: dGATA_2: K.O. mouse lung treated with OVA


title: dGATA_1: K.O. mouse lung treated with OVA


title: Rag_cKit-_020317_C26_1


title: Balbc_3: W.T. mouse lung treated with OVA

source_name: W.T. mouse lung treated with OVA

treatment_protocol: W.T. mouse was treated with OVA

value: Control


title: 012-099-02-008-B

description:
tRNA51074
20151124_BRI2015NSDS006Catridge6_tRNA51074_04

value: HER2-negative metastatic BC patient


title: BS491 FFPE sample

description: BS491 FFPE sample

value: hepatocellular carcinoma

value: Plac

value: responder


title: BS481 FFPE sample

description: BS481 FFPE sample


title: BS493 FFPE sample

description: BS493 FFPE sample


title: 012-099-01-007-B

description:
tRNA51070
20151123_BRI2015NSDS006Catridge2_tRNA51070_02

value: Hispanic

value: Baseline


title: 012-099-01-007-US

description:
tRNA51072
20151124_BRI2015NSDS006Catridge6_tRNA51072_11

value: Whole Blood

value: Unscheduled


title: Rag_cKit-_020317_C20_1

value: Thymus


title: Rag_cKit-_020317_C21_1


title: 012-099-02-003-EOM4

description:
tRNA51054
20151124_BRI2015NSDS006Catridge4_tRNA51054_02

value: White

value: Non-Hispanic

value: Tempus

value: EOM 4/Pre-Cycle 5


title: Rag_cKit-_020317_C23_1


title: 012-099-02-004-EOM3

description:
tRNA51060
20151124_BRI2015NSDS006Catridge4_tRNA51060_01

value: EOM 3/Pre-Cycle 4


title: 4_A: Eosinophils cultured with Amphiregulin for 3 days

treatment_protocol: Eosinophils were cultured with Amphiregulin  for 3 days in vitro.

value: BALB/c

value: Eosinophils

value: Treat


title: Balbc_1: W.T. mouse lung treated with OVA

value: lung

value: Control


title: Rag_cKit-_020317_C28_1


title: 3_A: Eosinophils cultured with Amphiregulin for 3 days


title: 4_C: Eosinophils cultured without Amphiregulin for 3 days

treatment_protocol: Eosinophils were cultured without Amphiregulin  for 3 days in vitro.


title: 012-099-02-005-EOM1

description:
tRNA51064
20151123_BRI2015NSDS006Catridge2_tRNA51064_07

value: HER2-negative metastatic BC patient

value: Female

value: EOM 1/Pre-Cycle 2


title: 2_A: Eosinophils cultured with Amphiregulin for 3 days


title: Rag_cKit-_020317_C19_1


title: Balbc_2: W.T. mouse lung treated with OVA


title: Rag_cKit-_020317_C25_1


title: Rag_cKit-_020317_C14_1


title: Rag_cKit-_020317_C15_1


title: 2_C: Eosinophils cultured without Amphiregulin for 3 days


title: BS457 FFPE sample

description: BS457 FFPE sample

value: hepatocellular carcinoma

value: Sor

value: non-responder


title: Rag_cKit-_020317_C13_1

value: Thymus


title: 012-099-02-005-RI

description:
tRNA51063
20151123_BRI2015NSDS006Catridge2_tRNA51063_10

value: White

value: Whole Blood

value: Run In


title: 012-099-02-005-EOM4

description:
tRNA51067
20151124_BRI2015NSDS006Catridge6_tRNA51067_07

value: Non-Hispanic

value: Tempus

value: EOM 4/Pre-Cycle 5


title: 012-099-02-005-B

description:
tRNA51062
20151124_BRI2015NSDS006Catridge5_tRNA51062_12

value: Baseline


title: Rag_cKit-_020317_C12_1


title: 6_ST2high_IL33_IL2: ST2 high memory Th2 cells cultured with IL-2 + IL-33 for 3 days

treatment_protocol: ST2 high memory Th2 cells were cultured with IL-2 + IL-33  for 3 days in vitro.

value: BALB/c

value: ST2 high memory Th2 cells

value: Treat


title: 5_ST2high_IL2: ST2 high memory Th2 cells cultured with IL-2 for 3 days

treatment_protocol: ST2 high memory Th2 cells were cultured with IL-2  for 3 days in vitro.

value: Control


title: 012-099-02-003-RI

description:
tRNA51051
20151123_BRI2015NSDS006Catridge3_tRNA51051_10

value: HER2-negative metastatic BC patient

value: Female


title: Rag_cKit-_020317_C11_1


title: Rag_cKit-_020317_C09_1


title: 012-099-02-005-EOM5

description:
tRNA51068
20151123_BRI2015NSDS006Catridge1_tRNA51068_05

value: EOM 5/Pre-Cycle 6


title: Rag_cKit-_020317_C07_1


title: 012-099-02-004-RI

description:
tRNA51057
20151123_BRI2015NSDS006Catridge2_tRNA51057_08


title: 012-099-02-004-B

description:
tRNA51056
20151124_BRI2015NSDS006Catridge6_tRNA51056_06


title: 3_C: Eosinophils cultured without Amphiregulin for 3 days

value: Eosinophils


title: 012-099-02-004-EW

description:
tRNA51061
20151124_BRI2015NSDS006Catridge5_tRNA51061_10

value: Early Withdrawal


title: 3_ST2High_IL2: ST2 high memory Th2 cells cultured with IL-2 for 3 days


title: 2_ST2High_IL33_IL2: ST2 high memory Th2 cells cultured with IL-2 + IL-33 for 3 days


title: Rag_cKit-_020317_C05_1

value: Thymus


title: 1_ST2High_IL2: ST2 high memory Th2 cells cultured with IL-2 for 3 days


title: 012-099-02-004-EOM2

description:
tRNA51059
20151123_BRI2015NSDS006Catridge1_tRNA51059_12

value: White

value: EOM 2/Pre-Cycle 3


title: Rag_cKit-_020317_C01_1


title: Rag_cKit-_012317_C95_1


title: 012-099-02-004-EOM1

description:
tRNA51058
20151123_BRI2015NSDS006Catridge3_tRNA51058_01

value: Whole Blood

value: EOM 1/Pre-Cycle 2


title: Rag_cKit-_012317_C93_1


title: Rag_cKit-_012317_C94_1


title: BS299 FFPE sample

description: BS299 FFPE sample

value: hepatocellular carcinoma

value: Sor

value: non-responder


title: 012-099-02-003-B

description:
tRNA51050
20151123_BRI2015NSDS006Catridge2_tRNA51050_01

value: Non-Hispanic

value: Tempus

value: Baseline


title: 4_ST2High_IL33_IL2: ST2 high memory Th2 cells cultured with IL-2 + IL-33 for 3 days

value: BALB/c

value: ST2 high memory Th2 cells

value: Treat


title: 012-099-02-003-EOM3

description:
tRNA51053
20151124_BRI2015NSDS006Catridge5_tRNA51053_09

value: HER2-negative metastatic BC patient

value: Female

value: EOM 3/Pre-Cycle 4


title: 012-099-01-001-EW

description:
tRNA51049
20151124_BRI2015NSDS006Catridge6_tRNA51049_08

value: Early Withdrawal


title: Rag_cKit-_012317_C91_1

value: Thymus


title: 012-099-02-003-EOM2

description:
tRNA51052
20151124_BRI2015NSDS006Catridge6_tRNA51052_09

value: White

value: EOM 2/Pre-Cycle 3


title: 012-099-01-001-US

description:
tRNA51048
20151124_BRI2015NSDS006Catridge4_tRNA51048_08

value: Whole Blood

value: Unscheduled


title: Rag_cKit-_012317_C90_1


title: Rag_cKit-_012317_C92_1


title: OE RNAseq rep2

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

data_processing:
Adaptors in single-end sequencing reads were trimmed by using the cutadapt program with parameters ‘-m16 -e 0.2’ plus ‘-a AGATCGGAAGAGCACACGTCTGAACTC’ for eCLIP-seq and ‘-a ATCTCGTATGCCGTCTTCTGCTTGAAA’ for Ribo-seq data, respectively. Gene annotation from human refGene (hg19) was downloaded from UCSC genome browser for mapping. The ensemble of mRNA sequences named as hmg was constructed by joining mRNA sequences (with 1kb N) of coding genes, and the longest isoform was chosen as the representative isoform for each transcript. The first random 6nt of eCLIP-seq reads were used to remove PCR products, and only those equal to or longer than 16 nt were mapped to hmg by using Bowtie2 in the end-to-end model. The first 4nt barcode sequence from Ribo-seq and RNA-seq reads was removed before mapping to hmg by using STAR. For each group of mapped reads with same genomic position and same barcode, only one is retained to avoid PCR products. For each replicate group of eCLIP-seq libraries, peak calling was performed by using CLIPper on combined reads from WT and OE miR-17/20a samples. The Ago2 peaks were filtered on the relative enrichment of Ago2 CLIP reads counts over those in input control samples. The reads counts of peaks were computed by using featureCounts program and the enrichment was calculated with edgeR package. The peaks corresponding to miR17/20a were computed in a similar manner by comparing eCLIP under miR-17/20a OE over WT.
Genome_build: hg19. Gene annotation from human refGene (hg19) was downloaded from UCSC genome browser. The ensemble of mRNA sequences, named as hmg, was constructed by joining mRNA sequences (with 1kb N) of coding genes, and the longest isoform was chosen as the representative isoform for each transcript.
Supplementary_files_format_and_content: bigWig for normalized coverage signals in forward strand of hmg

molecule: polyA RNA

source_name: OE RNAseq

growth_protocol: HeLa cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS) plus 100 U penicillin/streptomycin (Gibico) at 37oC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted by TRIZOL reagent.
For Aog2 CLIP-seq, HeLa cells grown on 15 cm plates were first UV irradiated at 400 mj and collected by scraping the cells. After IP, the 3’ RNA adapter was ligated to RNA fragments on beads, which was followed by reverse transcription and ligation of a 3’ single-stranded DNA adapter to the cDNA. Libraries were sequenced by Hi-Seq 2500. For Ribo-seq, transfected cells were collected and resuspended with ice-cold lysis buffer (10 mM Tris-Cl pH7.4, 5mM MgCl2, 100 mM KCl, 1% Triton X-100) and placed on ice for 20 min. The cell lysate were centrifuged at 12000g for 20 min, and then the supernatant was loaded on a 10%-50% linear sucrose gradient and centrifuged at 36400 rpm for 3 hrs in SW41Ti rotor (Beckman). After centrifugation, ribosome and polyribosome fractions were collected and monitored by UV254. The collected fractions were pelleted by ultracentrifuge at 50,000 rpm in SW60 rotor for 6 hrs and ribosomal bound RNAs were digested with RNase I (Ambion). The RNA fragments were size selected (~30 nt) and rRNA depleted by antisense oligo and RNase H strategy. Ribosome protected fragments(RPFs) were ligated with the 5’ and 3’ adaptor and sequenced on Hi-Seq 2500. For RNA-seq, A fraction of total RNA from the same cells was each isolated using TRIZOL Reagent (Ambion) and fragmented using reverse transcriptase buffer (Invitrogen) at 94oC for 10 min. RNA fragments were size selected (180-220 nt) and rRNA depleted by antisense oligo and RNase H strategy, and then ligated with 5′ and 3′ adaptor. The libraries were sequenced on Hi-Seq X10.

treatment_protocol: microRNA mimics were transfected into cells with  RNAi Max. Cells were harvested 48 hrs post-transfection for subsequent analysis.

value: HeLa

value: cervical adenocarcinoma cells

tag: genotype/variation

value: miR17/20a OE


title: Rag_cKit-_012317_C89_1

tag: strain


title: Rag_cKit-_012317_C88_1


title: OE RNAseq rep1

tag: cell type


title: HaCat-E5

city: Atlixco

first: Verónica

last: Vallejo-Ruiz

state: Puebla

address: Km 4.5 Carretera Federal Atlixco-Metepec

department: Centro de Investigación Biomédica de Oriente

country: Mexico

institute: Instituto Mexicano del Seguro Social

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10 µm resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

label: Alexa 647

source_name: HaCat cell_HPV-16 E5

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: HaCat immortal keratinocyte cells (Hacat/E5, HaCat/pMSG) (Kabsch and Alonso, 2002) were maintained in Dulbecco Modiﬁed Eagle Medium  (DMEM); supplemented with 10% Fetal Bovine Serum containing penicillin (100 U/ml), and streptomycin (100 µg/ml). The cells were grown in 25cm2 tissue culture ﬂasks in a (5% CO2) at 37°C and routinely passaged when conﬂuent.

extract_protocol: Total RNA from HaCaT/E5 and HaCaT/pMSG monocultures was obtained with ReliaPrep™ RNA Cell Miniprep System (Promega)

value: HaCaT

value: human skin keratinocyte cells

value: stably transfected with HPV-16 E5 (Kabsch and Alonso, 2002)


title: 012-099-01-001-EOM1

description:
tRNA51047
20151123_BRI2015NSDS006Catridge3_tRNA51047_05

value: Non-Hispanic

value: Tempus

value: EOM 1/Pre-Cycle 2


title: 012-099-01-001-RI

description:
tRNA51046
20151124_BRI2015NSDS006Catridge5_tRNA51046_07

value: HER2-negative metastatic BC patient

value: Female

value: Run In


title: Rag_cKit-_012317_C87_1

value: Thymus


title: 012-099-01-001-B

description:
tRNA51045
20151123_BRI2015NSDS006Catridge1_tRNA51045_10

value: White

value: Baseline


title: WT RNAseq rep2

source_name: WT RNAseq

value: WT


title: Rag_cKit-_012317_C86_1


title: Rag_cKit-_012317_C85_1


title: DMSO-treated Apc mutant organoids

city: Helsinki

first: Jenny

last: Hogstrom

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package for QC, filtering and analysis of the data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on UMI counts and percentage of mitochondrial genes. Cells with more than 5% of mitochondrial genes were filtered out
The expression matrix was further filtered by removing genes with expression in less than 10 cells and cells with less than 800 expressed genes. The minimum expression threshold was set at 1
To be able to compare the two samples, we performed canonical correlation analysis (CCA) to identify shared correlation structures and aligned the dimensions using dynamic time warping
Genome_build: mm10
Supplementary_files_format_and_content: Filtered data was combined for CCA and further analysis, and saved as notch-combi.Robj

source_name: Apc mutant organoids

growth_protocol: Intestinal organoids were grown according to Sato et al (Nature, 2009)

extract_protocol:
The cells were loaded into Chromium Single Cell Chip v2 (10x Genomics, Pleasanton, CA) and gel beads in emulsion (GEM) generation was performed aiming at 3000 cell captures per sample
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina) with following read lengths: 26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 91bp (Read 2) resulting in 115 754 and 113 705 mean reads per cell for the sample vehicle and DBZ respectively

treatment_protocol: 300nM 4-OH-tam, 10uM DBZ

value: 3-4 months

value: intestinal organoid


title: WT RNAseq rep1

value: HeLa

value: cervical adenocarcinoma cells


title: HaCat-pMSG

label: Alexa 555

source_name: HaCat cell_pMSG

value: HaCaT

value: stably transfected with the empty vector pMSG (Kabsch and Alonso, 2002)


title: DBZ-treated Apc mutant organoids


title: S48P3P160125UOXZP22H06.R1.star.bam

status: Public on Aug 20 2018

city: Cardiff

first: Viola

last: Volpato

address: Maindy Rd

department: UK DRI

country: United Kingdom

institute: Cardiff University

data_processing:
SC alignment: RNA-seq data were mapped to the hg19 assembly via STAR version 2.2.0. Read alignments were merged in single BAM file output per sample.
SC filtering: Reads were filtered to remove those not uniquely mapped and all ribosomal and mitochondrial RNA reads. We excluded libraries with: less than 2000 expressed genes; low complexity, where the % of 200 most expressed features (genes and ERCC-spike in) represented more than 50% of total number of counts; low % of endogenous RNA, for which the % of  ERCC spike-in > 14%; low number of mapped read for which the total counts < 10e-6.
SC generation of abundances measures: Gene-level read counts were obtained using FeatureCount (Liao et al., 2014).
SC normalisation: We computed the normalized log-expression values with R package scran (1.0.4) by adding one to each count, dividing by the size factor for that cell, and log transforming.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalised values for filtered Samples

extract_protocol:
Single cell suspensions were generated using accutase dissociation followed by single cell filtration of iPSC-derived cortical neurons. The single cell suspension was sorted into a 96-well PCR plate containing a lysis mix. Sorting gates were set to include only live (DAPI negative) single cells. Stream alignment and sort efficiency was checked using Accudrop beads (Becton Dickinson). Single iPSC derived cortical neurons were isolated by FACS onto 96-well plates in 2ul lysis buffer.
Libraries were prepared following the Smart-Seq2 protocol. Libraries were pooled in 288- or 384-plexes and each pool sequenced on 1 lane of HiSeq4000 at 75bp paired end

value: iPSC-derived neurons

tag: time point

tag: site

value: E

tag: well

tag: batch


title: S71P3P160125UOXZP22G09.R1.star.bam

tag: cell line


title: S36P3P160125UOXZP22D05.R1.star.bam


title: S23P3P160125UOXZP22G03.R1.star.bam


title: S60P3P160125UOXZP22D08.R1.star.bam


title: S24P4P160125UOXCC12H03.R1.star.bam

value: D


title: S24P3P160125UOXZP22H03.R1.star.bam


title: S12P4P160125UOXCC12D02.R1.star.bam


title: S96P4P160125UOXCC1BULK2NA.R1.star.bam


title: S72P4P160125UOXCC12H09.R1.star.bam


title: S96P3P160125UOXZP2BULK2NA.R1.star.bam


title: S12P3P160125UOXZP22D02.R1.star.bam


title: S84P3P160125UOXZP22D11.R1.star.bam


title: S72P3P160125UOXZP22H09.R1.star.bam


title: S95P4P160125UOXCC1BULK1NA.R1.star.bam


title: S84P4P160125UOXCC12D11.R1.star.bam


title: S48P4P160125UOXCC12H06.R1.star.bam


title: S60P4P160125UOXCC12D08.R1.star.bam


title: S36P4P160125UOXCC12D05.R1.star.bam


title: S95P3P160125UOXZP2BULK1NA.R1.star.bam


title: S71P4P160125UOXCC12G09.R1.star.bam


title: S11P3P160125UOXZP22C02.R1.star.bam


title: S59P3P160125UOXZP22C08.R1.star.bam


title: S83P3P160125UOXZP22C11.R1.star.bam


title: S47P3P160125UOXZP22G06.R1.star.bam


title: S83P4P160125UOXCC12C11.R1.star.bam


title: S35P3P160125UOXZP22C05.R1.star.bam


title: S47P4P160125UOXCC12G06.R1.star.bam


title: S11P4P160125UOXCC12C02.R1.star.bam


title: S23P4P160125UOXCC12G03.R1.star.bam


title: S35P4P160125UOXCC12C05.R1.star.bam


title: S10P3P160125UOXZP22B02.R1.star.bam


title: S94P3P160125UOXZP22F12.R1.star.bam


title: S34P3P160125UOXZP22B05.R1.star.bam


title: S46P3P160125UOXZP22F06.R1.star.bam


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title: S82P4P160125UOXCC12B11.R1.star.bam


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title: BS187 FFPE sample

description: BS187 FFPE sample

tag: tissue

value: hepatocellular carcinoma

tag: treatment

value: Sor

tag: outcome

value: responder


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