title: 08242017-H05-NA18508


title: 08242017-H04-NA18862

status: Public on Sep 21 2018

type: SRA

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

country: USA

institute: University of Chicago

description:
eset.rds
scqtl-counts.txt.gz
scqtl-annotation.txt
scqtl-annotation-description.txt
quality-single-cells.txt
genes-pass-filter.txt

library_source: transcriptomic

data_processing:
We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT) and ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa). Some samples included spike-in RNA from Drosophila melanogaster or Caenorhabditis elegans, so we also included the Ensembl genomes BDGP5.75 and WBcel235.75.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 54,616 genes (H. sapiens, C. elegans, D. melanogaster, ERCC) and 7,584 single cells. The file scqtl-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,151 human genes for 7,584 single cells. The file scqtl-annotation.txt is a tab-delimited plain text file that contains 40 metadata columns for the 7,584 single cells.  The file scqtl-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 40 metadata columns in scqtl-annotation.txt. The file quality-single-cells.txt is a tab-delimited plain text file (no header row) that contains a logical vector denoting whether each single cell was determined to be a high-quality cell and used in the study (TRUE) or a low-quality cell that was discarded (FALSE). The file genes-pass-filter.txt is a tab-delimited plain text file (no header row) that contains a logical vector denoting whether each human gene (total of 20,151) was determined to be expressed and included in the study (TRUE) or discarded (FALSE).

molecule: polyA RNA

organism: Homo sapiens

source_name: LCL-derived iPSC

growth_protocol: We cultured Yoruba iPSCs (Banovich et al., 2018) in feeder-free conditions for at least ten passages in E8 medium (Life Technologies) (Chen et al., 2011).

extract_protocol:
We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).

tag: experiment

tag: well

tag: individual

tag: batch


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title: 03052018-H02-NA19159


title: 03052018-G10-NA18517


title: 03052018-G04-NA18859


title: 03052018-G05-NA18859


title: 03052018-G02-NA19159


title: 03052018-F12-NA18859


title: 03052018-F10-NA18859


title: 03052018-F09-NA19159


title: 03052018-F06-NA19203


title: 03052018-F03-NA18859


title: 03052018-F08-NA19203


title: 03052018-F02-NA19203


title: 03052018-F05-NA18859


title: 03052018-F07-NA19203


title: 03052018-F04-NA18859


title: 03052018-G06-NA19159


title: 03052018-E11-NA18517


title: 03052018-E12-NA19203


title: 03052018-G01-NA18517


title: 03052018-E08-NA18859


title: 03052018-E10-NA18517


title: 03052018-F11-NA18859


title: 03052018-F01-NA19203


title: MCF10A -cys/cys, total RNA

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
FASTX to filter for read quality, remove adaptor sequences, remove short reads, and trim the 5' most nucleotide
Bowtie2 to remove rRNA, tRNA and mtRNA sequences
For ribosomal footprint samples, awk to filter for reads of footprint lengths
STAR to align reads
GenomicAlignments to filter for reads compatible with known splice variants
Replace alignments with nucleotide at central most position
Bedtools to count reads aligning to CDS regions of each gene (across only common regions between all isoforms, and excluding short regions spanning from -2 to +15 codons of each start codon, and -8 to +2 codons of each end codon)
Calculate RPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene in each sample, columns are arranged by sample name, i.e. CT2_RF1, CT2_RF2, and so on.

molecule: total RNA

source_name: Cell line

growth_protocol: HMEC-CT2 and MCF10A (Er-Src) cells were cultured under standard conditions. MCF10A cells were treated with 4HT to induce nuclear translocation of Er-Src and oncogenic transformation.

extract_protocol:
Cells were processed for ribosomal profiling using the protocol by Ingolia et al.
Libraries were constructed using the protocol by Ingolia et al.

treatment_protocol: HMEC-CT2 cells were treated with DMSO or Torin-1 for 1 h. MCF10A (Er-Src) cells were treated with vehicle control, glucose limitation, or cysteine/cystine limitation, for 30 min.

tag: treatment

value: Cys/Cys limitation

tag: molecule

value: Total RNA


title: 03052018-G03-NA18517


title: 03052018-E06-NA19203


title: MCF10A -glucose, ribosomal footprint

value: Glucose limitation

value: Ribosomal footprint RNA


title: MCF10A vehicle, total RNA

value: Vehicle


title: MCF10A -cys/cys, ribosomal footprint


title: p493 Control (MYC ON) 2

city: Philadelphia

first: Chi

middle: V

last: Dang

state: PA

address: 3601 Spruce

institute: wistar

data_processing:
The GENCODE lncRNA annotation version 22 and the GENCODE whole genome comprehensive annotation version 22 were downloaded from the official GENCODE ftp repository: ftp://ftp.sanger.ac.uk/pub/GENCODE/. The GENCODE lncRNA annotation (V22), a manually curated and evidence-based lncRNA annotation containing 15,900 genes, was used to define lncRNA genes. The GENCODE whole annotation (V22) was used to define PCGs and pseudogenes, resulting in a PCG set containing 19,814 genes; a pseudogene set containing 14,477 genes; and an “other genes” set containing 10,292 genes. All FASTQ files were aligned to the reference human genome (hg38, GRCh38) via RNA-STAR based ENCODE long RNA-Seq processing pipeline. We imported the aligned reads of each BAM file to Cufflinks RNA-Seq workflow to obtain the expression levels for genes by summarizing the fragments per kb per million mapped fragments (FPKM) values. GENCODE annotations were used to define lncRNAs, PCGs, and pseudogenes. The log-transformed FPKM values of genes were further analyzed using BRB-ArryTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) according to the instructions provided.
Genome_build: hg38, GRCh38
Supplementary_files_format_and_content: FPKM

source_name: p493-6 cells

growth_protocol: For RNA-seq analysis of MYC-ON versus MYC-OFF states, the P493-6 cells, which were engineered to have tetracycline-repressible ectopic MYC, were supplemented with 0.1 μg/mL tetracycline (Sigma) for 48 hours before harvesting for the MYC-OFF state. The RNA from these cells were compared with MYC-ON cells that had continuously expressed MYC for 48 hours grown contemporaneously with the MYC-OFF cells.

extract_protocol:
Total RNA from P493-6 cells was extracted using TRIzol (Invitrogen) and an RNeasy Plus Mini Kit (Qiagen).
es. Poly-A enriched library preparation and sequencing were performed at the Penn Next-Generation Sequencing Core following standard protocols. Briefly, mRNA was purified using poly(A) selection or rRNA depletion before the RNA was chemically fragmented and converted into single-stranded cDNA using random hexamer priming. The second strand was generated to create double-stranded cDNA. Library construction began with the generation of blunt-end DNA fragments from ds-cDNA. Then, A-bases were added to blunt-ends to prepare them for the ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina). Fragments of approximately 300 to approximately 400 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using an Illumina HiSeq 2000, which generated approximately 50 to approximately 100 million unfiltered reads per sample.

treatment_protocol: MYC OFF treated with  0.1 μg/mL tetracycline (Sigma) for 48 hours

tag: cell type

value: p493-6 cells

tag: condition

value: Control (MYC ON)


title: p493 Control (MYC ON) 1


title: p493 TET (MYC OFF) 1

value: TET (MYC OFF)


title: p493 TET (MYC OFF) 2


title: MCF10A -glucose, total RNA


title: 03052018-E07-NA18517


title: MCF10A vehicle, ribosomal footprint


title: 03052018-E05-NA18517


title: 03052018-E04-NA19203


title: 03052018-E03-NA19203


title: 03052018-E02-NA19159


title: 03052018-D12-NA18859


title: 03052018-D10-NA18859


title: 02212018-C10-NA19185


title: 02212018-C11-NA19098


title: 03052018-D11-NA19159


title: 03052018-E09-NA18859


title: IL-1b 12h replicate 2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
IL-1b_12h_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

data_processing:
Constructed libraries were sequenced on a NextSeq 500 Illumina platform, producing 2x100nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Sequencing and cell quality control of the primary sequencing data were performed using Illumina's SureCell scRNA-seq application in Basespace.
Alignments to the hg38 genome and subsequent counts were generated using Illumina's SureCell scRNA-seq application.
Following count generation, all processing steps (batch correction, normalization, differential expression) were performed using Seurat v2.3.4.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: All_counts_passfilter_all_merged.csv: Comma-separated text file includes counts.

source_name: A549 cells

extract_protocol:
Single cells were individually partitioned into subnanoliter droplets on a cartridge using a one-touch ddSEQ Single-Cell Isolator. Cell lysis and cell barcoding occur inside individual droplets, and single-cell-barcoded RNA-Seq libraries are subsequently prepared using Nextera technology.
SureCell WTA 3′ Library Prep Kit for the ddSEQ System.

treatment_protocol: A549 cells were treated with IL-1β for 3h, 6h, or 12h.

tag: cell line

value: alveolar basal epithelial cells

value: IL-1b 12h


title: IL-1b 12h replicate 1

description:
IL-1b_12h_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: Mock 12h replicate 1

description:
Mock_12h_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

value: Mock 12h


title: 02212018-C09-NA18913


title: 02212018-C07-NA18913


title: 02212018-C06-NA19098


title: Mock 12h replicate 2

description:
Mock_12h_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: IL-1b 6h replicate 2 experiment 2

description:
IL-1b_6h_2_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

value: IL-1b 6h


title: 02212018-C05-NA19098


title: 02212018-C03-NA18913


title: 02212018-C08-NA19098


title: IL-1b 6h replicate 1 experiment 2

description:
IL-1b_6h_1_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: 02212018-C01-NA19143


title: 02212018-C02-NA18505


title: 02212018-C04-NA18913


title: 03052018-E01-NA19203


title: Mock 6h replicate 1 experiment 2

description:
Mock_6h_1_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

value: Mock 6h


title: Mock 6h replicate 2 experiment 1

description:
Mock_6h_2_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: IL-1b 6h replicate 1 experiment 1

description:
IL-1b_6h_1_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: Mock 6h replicate 2 experiment 2

description:
Mock_6h_2_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: 02212018-B12-NA18913


title: Mock 6h replicate 1 experiment 1

description:
Mock_6h_1_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: IL-1b 3h replicate 2

description:
IL-1b_3h_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

value: IL-1b 3h


title: IL-1b 6h replicate 2 experiment 1

description:
IL-1b_6h_2_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: 02212018-B11-NA18913


title: 02212018-B10-NA18505


title: 02212018-B09-NA18505


title: IL-1b 3h replicate 1

description:
IL-1b_3h_1
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv


title: 02212018-B08-NA19098


title: Mock 3h replicate 2

description:
Mock_3h_2
ddSEQ
PolyA RNA
processed data file: All_counts_passfilter_all_merged.csv

value: Mock 3h


title: HMEC-CT2 DMSO rep 2

value: DMSO

tag: replicate number


title: 02212018-B07-NA18505


title: 02212018-B05-NA18505


title: HMEC-CT2 Torin-1 rep 2


title: 02212018-B04-NA19098


title: HMEC-CT2 Torin-1 rep 1


title: 02212018-B03-NA18913


title: 02212018-B02-NA18913


title: 02212018-B01-NA18913


title: 02212018-A12-NA19143


title: 02212018-A11-NA18505


title: 02212018-A10-NA19098


title: 02212018-A09-NA19098