title: OCH-101 chronic hepatitis C


title: VTC004_2_74_S47

status: Public on Jan 24 2020

type: SRA

city: San Antonio

first: Chun-Lin

last: Lin

state: Texas

address: 7703 Floyd Curl Dr., MC8257, 233 STRF

country: USA

institute: University of Texas Health Science Center at San Antonio

library_source: transcriptomic

data_processing:
Illumina Real-Time Analysis software used for basecalling.
Sequenced reads were mapped to GRCh38 human genome using STAR-2.5.3a
Fragments Per Kilobase of transcript per Million mapped reads were calculated for each sample using RSEM software
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: CTCs from prostate patients' blood sample

growth_protocol: Patients CTCs were isolated from blood sample by using Ficoll and cultured in Prime-EX tumorsphere SFM medium for a week.

extract_protocol:
single cell cDNA generation with Fluidigm C1 Single-Cell Auto Prep System
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit with Nextera XT Index Kit v2 Set A and B index primers.
single cell RNA-seq

tag: cell type

value: circulating tumor cells from prostate cancer patients


title: OCH369 chronic hepatitis C

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: liver tissue

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Liver tissue was obtained by liver biopsy.

extract_protocol: Total RNA from liver biopsy was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Liver tissue sample was obtained before anti-viral treatment.

tag: disease state

value: chronic hepatitis C


title: OCH410 chronic hepatitis C


title: SC-32-C

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

description:
genome Putnam et al. (2007)
South Carolina, 32 C,replicate C
S71

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

source_name: whole-organism

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
RNA was extracted from whole organisms using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: MA animals were exposed to 20C or 30C; ME animals were exposed to 20C, 28C, or 30C;  NC animals were exposed to 20C , 30C or 32C; NS animals were exposed to 20C, 28C, or 30C; SC animals were exposed to 20C, 30C or 32C. Sample sizes: nTotal=52; nMA = 8; nME = 10; nNC = 11; nNS = 11; nSC = 12

tag: developmental stage

value: adult

tag: geographic location

value: USA:South Carolina

tag: temperature


title: NS-28-A

description:
genome Putnam et al. (2007)
Nova Scotia, 28 C,replicate A
S70

value: Canada:Nova Scotia


title: VTC004_2_73_S49


title: VTC004_2_72_S62


title: OCH-255 chronic hepatitis C


title: ME-30-C

description:
genome Putnam et al. (2007)
Maine, 30 C, replicate C
S69


title: VTC004_2_70_S59


title: OCH-242 chronic hepatitis C


title: NC-20-C

description:
genome Putnam et al. (2007)
North Carolina, 20 C, replicate C
S68

value: USA:North Carolina


title: VTC004_2_69_S200


title: T24_Control_rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Gene expression data from untreated T24 cells

hyb_protocol: The cDNA was hybridized to Human Gene 1.0 ST v1 arrays

scan_protocol: Affymetrix Standard protocol

data_processing:
Gene level analysis was performed using the Affymetrix® Expression Console™ software with the default settings of the RMA-sketch workflow.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

label: biotin

source_name: T24 untreated for 24 hrs

label_protocol: Fragmentation and labeling was performed using the Affymetrix GeneChip WT terminal Labeling Kit.

growth_protocol: T24 bladder carcinoma cells were maintained in DMEM supplemented with 2mM glutamine and 10% FCS

extract_protocol: Total RNA was extracted using EZ-RNA total isolation kit (Biological Industries, Israel)

treatment_protocol: T24 cells were transfected with 50 MOI of either RAdMock or RAdnCD40L (RAd expressing membrane-bound noncleavable CD40L) for 24 hours or treated with soluble CD40L (1µg/ml) for 24 hours or left as untreated control

tag: cell line

value: bladder carcinoma cells

tag: treated/infected with

value: none (untreated)


title: MA-20-D

description:
genome Putnam et al. (2007)
Massachusetts, 20 C, replicate D
S75


title: MA-20-C

description:
genome Putnam et al. (2007)
Massachusetts, 20 C, replicate C
S67


title: VTC004_2_60_S61


title: SB1003_rep3_10_min

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description: Sample of replicate 3 after 10 minutes of photooxidative stress

data_processing:
Strand-specific RNA-seq cDNA library preparation and barcode introduction based on RNA adapter ligation
Quality of the libraries was validated using Agilent 2100 Bioanalyzer (Agilent Technologies)
Cluster generation using Illumina cluster station, single-end sequencing on the HiSeq2500 (standard protocol)
Fluorescent images were processed to sequences and transformed to FastQ format using the Genome Analyzer Pipeline Analysis software 1.8.2 (Illumina)
The fastq-mcf and fastq-multx tool of ea-utils (Aronesty, 2011) were used to controll the sequence output for general quality features, sequencing adapter clipping
Analysis of sequencing output quality via FastQC (Babraham Bioinformatics)
Identified adapter contamination and remaining artificial sequence (barcode) have been removed using program fastx_trimmer from the FASTX-210 toolkit version 0.0.13
On the 3’-end, reads were trimmed if the per base Phred score falls short of 20. Trimmed reads with a remaining length < 20 nucleotides were discarded
Sequenced libraries were mapped to the R. capsulatus genome (accession nr. NC_014034) and the pRCB133 plasmid (accession nr. NC_014035.1) using Bowtie2 (version 2.1.0) in end-to-end alignment mode (Langmead and Salzberg, 2012)
bam files were filtered for uniquely mapped reads using SAMtools (both strands) (Li et al., 2009)
Uniquely mapped read counts analyzed via DESeq2 (Love et al., 2014) for pairwise detection and quantification of differential gene expression
DESeq2 parametrization using a beta prior and disabled Cook distance cut off filtering
RPKM values were computed for each library from the raw gene counts
Genome_build: Chromosome NC_014034, plasmid NC_014035.1
Supplementary_files_format_and_content: fold changes, raw values, DESeq2NormCounts.RPKM values for each sample

organism: Rhodobacter capsulatus SB 1003

source_name: Bacterial cells

growth_protocol: Cultivation of strains in flat glass bottles at 32°C in the dark in minimal medium containing malate as a carbon source (van Niel, 1944) and with 0.2 µM methylene blue. Cultures were gassed with air.

extract_protocol:
Total RNA was isolated using the hot phenol methoden followed by two of chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol. RNA was resolved in Rnase free water (Roth) 0and concentrations were determined at a NanoDrop 1000 Spectrophotometer (PeqLab).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aerated cultures were stressed with 800 w m-2 white light for 10 min.

tag: tissue

value: exponentially grown cultures of Rhodobacter capsulatus wild type SB1003

tag: genotype

value: Wild type


title: SC-32-B

description:
genome Putnam et al. (2007)
South Carolina, 32 C,replicate B
S63


title: OCH-132 chronic hepatitis C


title: VTC004_2_58_S58


title: Singlecut_pri-mir-92a-1

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The 3' and 5' adapters in the raw reads were removed using cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC). We then used fastq-join (default parameter) to join the paired-end reads before removing low quality reads and deduplicating the reads with the same barcodes using fastq_quality_filter (-q 20 -p 90) and fastx_collapser (default parameter) from FASTX-Toolkit, respectively. After trimming the barcode sequences from both ends (6 nt random sequences at the 5' end, and 4 nt random sequences at the 3' end), the trimmed reads were mapped to the pri-mir-92a-1 sequence using BWA.
Genome_build: n/a
Supplementary_files_format_and_content: Tab-delimited text files, containing the raw read counts.

molecule: other

organism: synthetic construct

source_name: synthetic

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
The DNA sequences encoding pri-miRNAs were amplified from human HCT116 genomic DNA using specific primers. Pri-miRNAs were synthesized by in vitro transcription (IVT),  visualized on 10% UREA-PAGE and gel-eluted followed by isopropanol precipitation. The NLS Microprocessor complex (composed of NLS-D3 fragment of DROSHA and DGCR8) or minimal Microprocessor complex (composed of D3 fragment of DROSHA and G4 dimer of DGCR8)  was co-expressed and purified in HEK293E cells. Purified Microprocessor complex was used in in vitro processing assay for pri-miRNAs. After visualized in 10% UREA-PAGE, the fragments from the reaction mixture which are longer than pre-miRNAs, 5p and 3p basal segments were sliced from the gel and cloned to construct a DNA library for next generation sequencing.

tag: barcode

value: TGGTCA


title: SB1003_rep2_10_min

description: Sample of replicate 2 after 10 minutes of photooxidative stress


title: Cells from diagnosis (Dx) specimen of Pt-12

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

description:
Oligo-d(T) primed mRNA and antibody-derived tag reads.
processed data file: count_matrix.tsv
processed data file: cell_metadata.tsv

data_processing:
Combined CITE-seq UMI count matrices (mRNA and ADT) were generated using the 10X Genomics Cell Ranger (3.1.0) pipeline with default parameters.
The Seurat package in R was then used to aggregate the samples, which were further filtered to exclude cells not passing the following QC measures: fewer than 25% of UMIs derived from mitochondria and fewer than 4000 genes, to exclude low quality cells and likely doublets, respectively.
Antibody-derived UMIs and mRNA UMIs were normalized using Seurat's centered log-ratio (CLR) normalization and standard log normalization, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: count_matrix.tsv contains UMI feature counts per gene per cell (mRNA suffixed "_RNA" and antibody-derived tags suffixed "_ADT").
Supplementary_files_format_and_content: cell_metadata.tsv contains information about each cell in the count matrix.

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Freshly thawed patient specimen, no culture involved.

extract_protocol:
Cells were processed using the 10X Genomics Chromium platform to generate paired (mRNA and ADT) CITE-seq libraries.
10X Genomics 3' end library kit (v3).

tag: patient

tag: cell populations

value: All subpopulations, no enrichment

tag: aml disease stage

value: Diagnosis (Dx)


title: Cells from relapse (Rl) specimen of Pt-12

value: Relapse (Rl)


title: SC-30-D

description:
genome Putnam et al. (2007)
South Carolina, 30 C, replicate D
S62


title: VTC004_2_44_S43


title: OCH433 chronic hepatitis C


title: OCH-235 chronic hepatitis C


title: SB1003_rep1_10_min

description: Sample of replicate 1 after 10 minutes of photooxidative stress


title: ME-30-B

description:
genome Putnam et al. (2007)
Maine, 30 C, replicate B
S61


title: OCH-319 chronic hepatitis C


title: T24_Control_rep1


title: dof2.1-KO_mock_2

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

institute: The University of Tokyo

description: Gene expression in mock condition

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Arabidopsis Oligo Microarray Version 4)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: WT and dof2.1-KO plants were grown on the peat under continuous light condition.

extract_protocol: RNA was prepared using the Isospin Plant RNA kit following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Rosette leaves from 3-week-old WT and dof2.1-KO were treated with 3 mM MES buffer (mock control) or 3 mM MES buffer containing 100 μM MEJA for 2 days.

tag: plant name

tag: treatment

value: Mock


title: dof2.1-KO_mock_3

description: Gene expression in mock condition


title: dof2.1-KO_MeJA_1

description: Gene expression during MeJA treatment

value: MeJA


title: VTC004_2_26_S42


title: WT_mock_2

description: Gene expression in mock condition

value: WT (wild type)


title: dof2.1-KO_mock_1

description: Gene expression in mock condition


title: WT_mock_3

description: Gene expression in mock condition


title: NC-20-B

description:
genome Putnam et al. (2007)
North Carolina, 20 C, replicate B
S60


title: SB1003_rep3_0_min

description: Sample of replicate 3 right before stress induction


title: dof2.1-KO_MeJA_3

description: Gene expression during MeJA treatment


title: WT_MeJA_1

description: Gene expression during MeJA treatment


title: WT_mock_1

description: Gene expression in mock condition


title: dof2.1-KO_MeJA_2

description: Gene expression during MeJA treatment


title: WT_MeJA_2

description: Gene expression during MeJA treatment


title: VTC004_2_17_S54

value: circulating tumor cells from prostate cancer patients


title: MA-20-B

description:
genome Putnam et al. (2007)
Massachusetts, 20 C, replicate B
S59


title: SB1003_rep1_0_min

description: Sample of replicate 1 right before stress induction


title: SC-32-A

description:
genome Putnam et al. (2007)
South Carolina, 32 C,replicate A
S55


title: VTC004_2_15_S195


title: VTC004_2_22_S56


title: Cloning single worm pRNA+pppRNA 2

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

description: single worm 2

data_processing:
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Genome_build: C. elegans WS215
Supplementary_files_format_and_content: tabbed txt file containing sequence and read number for the analysis

organism: Caenorhabditis elegans

source_name: adult worms

growth_protocol: N2 worms were grown on NGM plates with OP50 at 20 °C.

extract_protocol:
RNAs were extracted with TRIzol
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker.
5' RNA ligation and 3' RNA ligation

treatment_protocol: For cloning 22G-RNA, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours; for cloning csRNA, the sample is treated with 1 U/μl CIP at 37 °C for 1 hour, extracted, precipitated, and treated with 0.5 μM hDcp2 at 20 °C for 2 hours.

tag: sample type

value: single adult worm 2


title: SC-30-C

description:
genome Putnam et al. (2007)
South Carolina, 30 C, replicate C
S54

value: adult


title: VTC004_2_07_S198


title: Cloning single worm pRNA+pppRNA 1

description: single worm 1

value: single adult worm 1


title: ME-30-A

description:
genome Putnam et al. (2007)
Maine, 30 C, replicate A
S53


title: Cloning pRNA+pppRNA

description: pRNA+pppRNA

value: with PIR-1


title: NC-20-A

description:
genome Putnam et al. (2007)
North Carolina, 20 C, replicate A
S52

value: USA:North Carolina


title: WT_MeJA_3

description: Gene expression during MeJA treatment


title: Cloning pRNA

description: pRNA

value: without PIR-1


title: VTC004_2_06_S51


title: PIR from mouse injected with iCM-Ex, biological rep2

city: Stanford

first: Phillip

last: Yang

address: 269 Campus Drive, CCSR 3120

institute: Stanford University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on rotation onto Clariom S Mouse Array gene chips (Thermo Fisher Scientific).

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner.

data_processing: Data were analyzed with Expression Console and Transcription Analysis Console softwares (Thermo Fisher Scientific) using default settings.

organism: Mus musculus

source_name: heart

label_protocol: 5.5 μg of sense-strand cDNA was labeled with biotin according to the Clariom S microarray protocol (Thermo Fisher Scientific).

growth_protocol: Female 80-100 day-old SCID mice were purchased from Charles River Laboratories (MA). iCMs were differentiated from iPSCs and cultured until spontaneous contractions were observed. iCM-Ex were precipitated from iCMs.

extract_protocol: Trizol extraction of total RNA was performed using miRNeasy Mini Kit (Qiagen) according to the manufacturers’ instruction.

treatment_protocol: 4 weeks post-MI, mice were sacrificed by isofluorane and cervical dislocation. Hearts were explanted and the peri-infarct region was identified via microscopy, dissected out. Samples were rinsed with PBS twice and placed in Trizol (Thermo Fisher Scientific).

value: heart PIR

value: iCM-Ex


title: VTC004_2_02_S196


title: SB1003_rep2_0_min

description: Sample of replicate 2 right before stress induction

value: exponentially grown cultures of Rhodobacter capsulatus wild type SB1003

value: Wild type


title: MA-20-A

description:
genome Putnam et al. (2007)
Massachusetts, 20 C, replicate A
S51


title: Cloning csRNA

description: cRNA


title: VTC004_2_09_S194


title: PIR from mouse injected with iCMs, biological rep3

value: iCMs


title: Hap1 SPRING KO clone 26 + sterols

status: Public on Jan 23 2020

city: Amsterdam

first: Noam

last: Zelcer

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: AUMC

description: 3864_8_Hap1_C12orf49_clone_26_sterol_depletion_GGCTACA_S32

data_processing:
Basecalling and demultiplexing was performed using the standard Illumina pipeline
The reads were mapped to the human reference genome (GRCh38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script, based on HTSeq-count, that generates counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: Hap1 cells

growth_protocol: Cells were plated and subsequently cultured in sterol-contaning or sterol-depletion medium for 24 hrs before extraction of RNA

extract_protocol:
RNA was extracted with the Trizol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: dna content

value: Haploid


title: Hap1 CTRL - sterols


title: Pat 2 Left Krukenberg Tumour

city: Singapore

first: Johnny

middle: Chin-Ann

last: Ong

state: Singapore

address: 11 Hospital Drive

department: Division of Surgical Oncology

country: Singapore

institute: National Cancer Centre Singapore

description:
Pat_2_Genes_FPKM.txt
Pat_2_Genes_Count.txt

data_processing:
Fastq raw files were uploaded onto the DNANexus platform.
DNANexus modules were used to process data.
TopHat (Known Genes) (v1.2.0)
Cuffdiff (v1.0.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including gene count and FPKM values for each sample

source_name: Tumour derived from metastasis in the left ovary

extract_protocol:
Human biopsies were flash freezed and subsequently prepared on membrane slides at a thickness of 10µm. Sections were microdissected using the Arcturus XT Laser Capture Microdissection Instrument to obtain the stroma and tumour/normal epithelial component. Qiagen RNAeasy micro kit was used to extract the RNA.
Ovation FFPE RNA-Seq Multiplex System was used to prepare the sequencing library. The amount of RNA used ranged from 3-60ng.


title: Hap1 SPRING KO clone 26 - sterols

description: 3864_7_Hap1_C12orf49_clone_26_IMDM_TAGCTTA_S31


title: Hap1 CTRL + sterols

description: 3864_2_Ctrl_Hap1_sterol_depletion_ACAGTGA_S26


title: Hap1 SPRING KO clone 14 - sterols

description: 3864_3_Hap1_C12orf49_clone_14_IMDM_GCCAATA_S27


title: PIR from mouse injected with iCM-Ex, biological rep1


title: Hap1 SPRING KO clone 14/rescue - sterols

description: 3864_5_Hap1_C12orf49_clone_14_rescue_IMDM_ACTTGAA_S29


title: PIR from mouse injected with saline control, biological rep3

value: saline


title: PIR from mouse injected with iCMs, biological rep2


title: PIR from mouse injected with saline control, biological rep1


title: PIR from mouse injected with saline control, biological rep2


title: PIR from mouse injected with iCMs, biological rep1


title: Pat 2 Right Krukenberg Tumour

source_name: Tumour derived from metastasis in the right ovary


title: Hap1 SPRING KO clone 26/rescue - sterols

description: 3864_9_Hap1_C12orf49_clone_26_rescue_IMDM_CTTGTAA_S33


title: Pat 2 Primary CRC Stroma

source_name: Stroma derived from primary colorectal tumour


title: Hap1 SPRING KO clone 26/rescue + sterols

description: 3864_10_Hap1_C12orf49_clone_26_rescue_sterol_depletion_AGTCAAC_S34


title: Pat 2 Colonic Mucosa Epithelial

source_name: Epithelium derived from colonic mucosa

value: Epithelium derived from colonic mucosa


title: Pat 1 Krukenberg Tumour

description:
Pat_1_Genes_FPKM.txt
Pat_1_Genes_Count.txt

source_name: Tumour derived from metastasis in the ovary


title: Pat 1 Primary CRC Tumour

source_name: Tumour derived from primary colorectal tumour


title: Hap1 SPRING KO clone 14/rescue + sterols

description: 3864_6_Hap1_C12orf49_clone_14_rescue_sterol_depletion_GATCAGA_S30


title: Pat 2 Left Krukenberg Stroma

source_name: Stroma derived from metastasis in the left ovary


title: Pat 1 Primary CRC Stroma

value: Stroma derived from primary colorectal tumour


title: Pat 1 Colonic Mucosa Epithelial


title: Hap1 SPRING KO clone 14 + sterols

description: 3864_4_Hap1_C12orf49_clone_14_sterol_depletion_CAGATCA_S28


title: Pat 2 Right Krukenberg Stroma

source_name: Stroma derived from metastasis in the right ovary


title: SJTALL221

city: Memphis

first: Robert

middle: Joseph

last: Autry

state: TN

address: 262 Danny Thomas Pl, MS 313

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description: Patient RNA Seq Data

data_processing:
STAR Aligner used to align reads
edgeR TIMM normalization
LIMMA used to generate FPKM
Genome_build: hg19
Supplementary_files_format_and_content: csv file with FPKM

source_name: B-lineage ALL

growth_protocol: Cells were grown for 4 days at 37C 5% CO2 in RPMI without Phenol-RED +20% FBS +2mM glutamine +ITS + anti/anti

extract_protocol:
RNA was extracted using either TRI-reagent or Qiagen RNAeasy
Libraries were constructed using standard Illumina procedures

tag: tissue type

value: Bone Marrow

tag: patient diagnosis

value: acute lymphoblastic leukemia

tag: cell type

value: primary leukemia cells


title: Pat 2 Colonic Mucosa Stroma

source_name: Stroma derived from colonic mucosa

value: Stroma derived from colonic mucosa


title: Pat 1 Krukenberg Stroma

source_name: Stroma derived from metastasis in the ovary


title: Pat 1 Colonic Mucosa Stroma


title: SJTALL035

description: Patient RNA Seq Data


title: SJTALL030212

description: Patient RNA Seq Data


title: SJTALL030359

description: Patient RNA Seq Data


title: SJTALL030249

description: Patient RNA Seq Data


title: SJTALL030527

description: Patient RNA Seq Data


title: SJTALL033

description: Patient RNA Seq Data


title: SJTALL030338

description: Patient RNA Seq Data


title: SJTALL073

description: Patient RNA Seq Data


title: SJTALL040

description: Patient RNA Seq Data


title: SJTALL071

description: Patient RNA Seq Data


title: SJTALL030134

description: Patient RNA Seq Data


title: SJTALL030189

description: Patient RNA Seq Data


title: SJTALL030071

description: Patient RNA Seq Data


title: SJTALL030064

description: Patient RNA Seq Data


title: SJTALL030

description: Patient RNA Seq Data


title: SJTALL026

description: Patient RNA Seq Data


title: SJTALL025

description: Patient RNA Seq Data


title: SJTALL027

description: Patient RNA Seq Data


title: SJTALL022066

description: Patient RNA Seq Data


title: SJTALL080

description: Patient RNA Seq Data


title: SJTALL021918

description: Patient RNA Seq Data


title: SJTALL032

description: Patient RNA Seq Data


title: SJTALL021912

description: Patient RNA Seq Data


title: SJTALL021911

description: Patient RNA Seq Data


title: SJTALL021917

description: Patient RNA Seq Data


title: SJTALL021906

description: Patient RNA Seq Data


title: Pat 2 Primary CRC Tumour

value: Tumour derived from primary colorectal tumour


title: SJMLL022031

description: Patient RNA Seq Data


title: SJHYPER022032

description: Patient RNA Seq Data


title: SJTALL021919

description: Patient RNA Seq Data


title: SJHYPER022039

description: Patient RNA Seq Data


title: SJINF022043

description: Patient RNA Seq Data


title: SJHYPO022024

description: Patient RNA Seq Data


title: SJETV022026

description: Patient RNA Seq Data


title: SJHYPER022008

description: Patient RNA Seq Data


title: SJETV022010

description: Patient RNA Seq Data


title: SJHYPER021928

description: Patient RNA Seq Data


title: SJETV022049

description: Patient RNA Seq Data


title: SJETV022004

description: Patient RNA Seq Data


title: SJETV022023

description: Patient RNA Seq Data


title: SJTALL011

description: Patient RNA Seq Data


title: SJETV022015

description: Patient RNA Seq Data


title: SJHYPER021999

description: Patient RNA Seq Data


title: SJETV021993

description: Patient RNA Seq Data


title: SJETV021981

description: Patient RNA Seq Data


title: SJETV021990

description: Patient RNA Seq Data


title: SJETV021977

description: Patient RNA Seq Data


title: SJETV021969

description: Patient RNA Seq Data


title: SJETV021949

description: Patient RNA Seq Data


title: SJTALL030263

description: Patient RNA Seq Data


title: PIR from mouse injected with iCM-Ex, biological rep3


title: SJETV021945

description: Patient RNA Seq Data


title: SJETV057

description: Patient RNA Seq Data


title: SJHYPER022017

description: Patient RNA Seq Data


title: SJHYPER021984

description: Patient RNA Seq Data


title: SJETV021967

description: Patient RNA Seq Data


title: SJETV021942

description: Patient RNA Seq Data


title: SJETV021937

description: Patient RNA Seq Data


title: SJBALL048061

description: Patient RNA Seq Data


title: SJBALL047363

description: Patient RNA Seq Data

value: Peripheral Blood


title: SJBALL104

description: Patient RNA Seq Data


title: SJBALL047029

description: Patient RNA Seq Data


title: SJBALL047026

description: Patient RNA Seq Data


title: SJBALL047030

description: Patient RNA Seq Data


title: SJBALL047019

description: Patient RNA Seq Data


title: SJBALL047037

description: Patient RNA Seq Data


title: SJBALL047039

description: Patient RNA Seq Data


title: SJBALL047038

description: Patient RNA Seq Data


title: SJE2A063

description: Patient RNA Seq Data


title: SJBALL047021

description: Patient RNA Seq Data


title: SJBALL046138

description: Patient RNA Seq Data


title: SJBALL047034

description: Patient RNA Seq Data


title: SJBALL044901

description: Patient RNA Seq Data


title: SJBALL044896

description: Patient RNA Seq Data


title: SJBALL044890

description: Patient RNA Seq Data


title: SJBALL044889

description: Patient RNA Seq Data


title: SJBALL044884

description: Patient RNA Seq Data


title: SJBALL043686

description: Patient RNA Seq Data


title: SJBALL043684

description: Patient RNA Seq Data


title: SJBALL043675

description: Patient RNA Seq Data


title: SJBALL043666

description: Patient RNA Seq Data


title: SJBALL043680

description: Patient RNA Seq Data


title: SJBALL043685

description: Patient RNA Seq Data


title: SJBALL030726

description: Patient RNA Seq Data


title: SJBALL043663

description: Patient RNA Seq Data


title: SJBALL047023

description: Patient RNA Seq Data


title: SJBALL030675

description: Patient RNA Seq Data


title: SJBALL043681

description: Patient RNA Seq Data


title: SJBALL030659

description: Patient RNA Seq Data


title: SJBALL030572

description: Patient RNA Seq Data


title: SJBALL030700

description: Patient RNA Seq Data


title: SJBALL030563

description: Patient RNA Seq Data


title: SJBALL030543

description: Patient RNA Seq Data


title: SJBALL030574

description: Patient RNA Seq Data


title: SJBALL030535

description: Patient RNA Seq Data


title: SJBALL030569

description: Patient RNA Seq Data


title: SJBALL030541

description: Patient RNA Seq Data


title: SJBALL030463

description: Patient RNA Seq Data


title: SJBALL030474

description: Patient RNA Seq Data


title: SJBALL030414

description: Patient RNA Seq Data


title: SJBALL030520

description: Patient RNA Seq Data


title: SJBALL043687

description: Patient RNA Seq Data


title: SJBALL030434

description: Patient RNA Seq Data


title: SJBALL030404

description: Patient RNA Seq Data


title: SJBALL030413

description: Patient RNA Seq Data


title: SJBALL030384

description: Patient RNA Seq Data


title: SJBALL030379

description: Patient RNA Seq Data


title: SJBALL030351

description: Patient RNA Seq Data


title: SJBALL030334

description: Patient RNA Seq Data


title: SJBALL030350

description: Patient RNA Seq Data


title: SJBALL030662

description: Patient RNA Seq Data


title: SJBALL030331

description: Patient RNA Seq Data


title: SJBALL030318

description: Patient RNA Seq Data


title: SJBALL030337

description: Patient RNA Seq Data


title: SJBALL030325

description: Patient RNA Seq Data


title: SJBALL030294

description: Patient RNA Seq Data


title: SJBALL030295

description: Patient RNA Seq Data


title: SJBALL030313

description: Patient RNA Seq Data


title: SJBALL030288

description: Patient RNA Seq Data


title: SJBALL030276

description: Patient RNA Seq Data


title: SJBALL030258

description: Patient RNA Seq Data


title: SJBALL030267

description: Patient RNA Seq Data


title: SJBALL030219

description: Patient RNA Seq Data


title: SJBALL030227

description: Patient RNA Seq Data


title: SJBALL030215

description: Patient RNA Seq Data


title: SJBALL030247

description: Patient RNA Seq Data


title: SJBALL030344

description: Patient RNA Seq Data


title: SJBALL030724

description: Patient RNA Seq Data


title: SJBALL030207

description: Patient RNA Seq Data


title: SJBALL030174

description: Patient RNA Seq Data


title: SJBALL030103

description: Patient RNA Seq Data


title: SJBALL030127

description: Patient RNA Seq Data


title: SJBALL030130

description: Patient RNA Seq Data


title: SJBALL030132

description: Patient RNA Seq Data


title: SJBALL030150

description: Patient RNA Seq Data


title: SJBALL030095

description: Patient RNA Seq Data


title: SJBALL030090

description: Patient RNA Seq Data


title: SJBALL030091

description: Patient RNA Seq Data


title: SJBALL030285

description: Patient RNA Seq Data


title: SJBALL030275

description: Patient RNA Seq Data


title: SJBALL030270

description: Patient RNA Seq Data


title: SJBALL030072

description: Patient RNA Seq Data


title: SJBALL030059

description: Patient RNA Seq Data


title: SJBALL030036

description: Patient RNA Seq Data


title: SJBALL030248

description: Patient RNA Seq Data


title: SJBALL030034

description: Patient RNA Seq Data


title: SJBALL022052

description: Patient RNA Seq Data


title: SJBALL022047

description: Patient RNA Seq Data


title: SJBALL022020

description: Patient RNA Seq Data


title: SJBALL022035

description: Patient RNA Seq Data


title: SJBALL022002

description: Patient RNA Seq Data


title: SJBALL021968

description: Patient RNA Seq Data


title: SJBALL021973

description: Patient RNA Seq Data


title: SJBALL030170

description: Patient RNA Seq Data


title: SJBALL021924

description: Patient RNA Seq Data


title: 714_E. cloacae+HuNoV_Group3

city: Seoul

first: BYUNGJOO

last: PARK

address: 120, Neungdong-ro, Gwangjin-gu,

department: Infectious disease

country: South Korea

institute: College of Veterinary medicine, Konkuk University

data_processing:
mRNA-Seq reads were mapped using TopHat software tool in order to obtain the alignment file
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools
The RT (Read Count) data were processed based on Quantile normalization method using EdgeR within R using Bioconductor
The alignment files also were used for assembling transcripts, estimating their abundances and detecting differential expression of genes or isoforms using cufflinks.
we used the FPKM (fragments per kilobase of exon per million fragments) as the method of determining the expression level of the gene regions. Gene classification was based on searches done by DAVID
Genome_build: Sus Scrofa (NCBI; Sscrofa11.1)
Supplementary_files_format_and_content: Excel

organism: Sus scrofa

source_name: E. cloacae+HuNoV_ileum

extract_protocol:
Ileum tissues were collected and RNA was harvested using Trizol reagent
SENSE mRNA-Seq Library Prep Kit

tag: animal model

value: gnotobiotic pigs

tag: age

value: E. cloacae+HuNoV

value: ileum


title: 713_E. cloacae+HuNoV_Group3


title: SJALL060414

description: Patient RNA Seq Data


title: SJALL060412

description: Patient RNA Seq Data


title: 500_HuNoV only_Group1

source_name: HuNoV only_ileum

value: HuNoV only


title: 711_E. cloacae only_Group2

source_name: E. cloacae only_ileum

value: E. cloacae only


title: SJBALL030045

description: Patient RNA Seq Data


title: 712_E. cloacae only_Group2


title: 499_HuNoV only_Group1


title: SJALL060406

description: Patient RNA Seq Data


title: 497_HuNoV only_Group1


title: 498_HuNoV only_Group1


title: 490_Negative control group

source_name: Negative control_ileum

value: Negative control


title: SJALL060398

description: Patient RNA Seq Data


title: SJALL060397

description: Patient RNA Seq Data


title: SJALL060407

description: Patient RNA Seq Data


title: SJALL060400

description: Patient RNA Seq Data


title: SJALL060394

description: Patient RNA Seq Data


title: 428_Negative control group


title: SJALL059544

description: Patient RNA Seq Data


title: 427_HuNoV only_Group1


title: SJALL060391

description: Patient RNA Seq Data


title: SJALL059538

description: Patient RNA Seq Data


title: 429_Negative control group


title: 426_HuNoV only_Group1


title: 425_HuNoV only_Group1


title: 424_HuNoV only_Group1


title: SJALL059526

description: Patient RNA Seq Data


title: 423_HuNoV only_Group1


title: SJALL059527

description: Patient RNA Seq Data


title: 422_HuNoV only_Group1


title: SJALL059523

description: Patient RNA Seq Data


title: SJALL059522

description: Patient RNA Seq Data


title: SJALL059525

description: Patient RNA Seq Data


title: 407_E. cloacae+HuNoV_Group3


title: SJALL059521

description: Patient RNA Seq Data


title: SJBALL030568

description: Patient RNA Seq Data


title: 408_E. cloacae+HuNoV_Group3


title: 405_E. cloacae+HuNoV_Group3


title: 404_Negative control group


title: 406_E. cloacae only_Group2


title: 403_Negative control group


title: SJALL059518

description: Patient RNA Seq Data


title: 173_E. cloacae only_Group2


title: SJALL059329

description: Patient RNA Seq Data


title: SJALL059333

description: Patient RNA Seq Data


title: SJALL059332

description: Patient RNA Seq Data


title: 172_E. cloacae only_Group2


title: SJALL059326

description: Patient RNA Seq Data


title: SJALL057950

description: Patient RNA Seq Data


title: SJALL059325

description: Patient RNA Seq Data


title: SJALL057949

description: Patient RNA Seq Data


title: SJALL057948

description: Patient RNA Seq Data


title: Mitochondria of fish

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description: zb-mito

data_processing:
For circular RNA (circRNA) prediction, we identified the candidates with find_circ (Memczak et al., 2013) and the junction reads were calculated as Transcripts Per Kilobase Million (TPM).
Genome_build: hg19, mm9, danRer11
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Danio rerio

source_name: whole fish

extract_protocol:
The isolated mitochondria were homogenized in TRizol reagent (Life Technologies) by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole fish


title: SJALL057946

description: Patient RNA Seq Data


title: egg extract rep3

city: Lausanne

first: Philippe

last: Reymond

address: Biophore building

department: Department of Plant Molecular Biology

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were checked for quality and adapters trimmed using cutadapt v1.5
Reads were mapped to the Arabidopsis genome using star
The number of read counts (log2) per gene locus was summarized with htseq-count
Library sizes were scaled using TMM normalization (EdgeR v 3.4.0)
Differential expression was computed with limma (v 3.2) using a moderated t-test and a Benjamini-Hochberg corrected p-values
Genome_build: Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: tab-delimited text file

source_name: leaf

growth_protocol: Arabidopsis thaliana ecotype Col-0 plants were vernalized for 2 days at 4°C and cultivated in pots containing moist compost. Plants were grown in a controlled environmental chamber with a 10 h day / 14 h night cycle (100 mmol m-2 sec-1) at RH 60%. Experiments were conducted with four- to five-week-old plants.

extract_protocol:
Total RNA was extracted using an RNeasy® plant mini kit (Qiagen). DNase treatment was added to the protocol. For cDNA synthesis, RNA samples were purified by NaAC 3M and EtOH precipitation.
Library were synthetized from 500 ng of purified total RNA using the TrueSeq stranded mRNA kit (Illumina). RNA and library quality was assessed with a fragment analyzer from Advanced Analytical. Library were sequenced with the Illumina HiSeq 2500.

treatment_protocol: For experiments with natural oviposition, 15 plants were placed in a 60 x 60 x 60 cm tent containing approximately 30 P. brassicae butterflies. After 24 h, four plants containing one egg batch on two leaves were placed in a growth chamber for 4 days. Just before hatching, eggs were gently removed with a forceps. For egg extract application, 2 x 2 µl of egg extract were spotted under the surface of each of two leaves of each treated plant. Four plants were treated with egg extract for 5 days. Treated or oviposited leaves were harvested and quickly stored in liquid N2. Untreated plants were used as controls

tag: organ

value: leaf

value: five weeks


title: oviposition rep3


title: egg extract rep2


title: oviposition rep2


title: oviposition rep1


title: SJALL057945

description: Patient RNA Seq Data


title: egg extract rep1


title: SJALL055895

description: Patient RNA Seq Data


title: SJALL059345

description: Patient RNA Seq Data


title: control rep3


title: SJALL055898

description: Patient RNA Seq Data


title: SJALL054756

description: Patient RNA Seq Data


title: SJALL055635

description: Patient RNA Seq Data


title: SJALL054752

description: Patient RNA Seq Data


title: control rep1


title: at-microspore.RNAseq.WT.replicate1

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Arabidopsis thaliana microspore of wt (Columbia-0)
at.microspore.RNAseq.rpkm.txt.gz

data_processing:
Bisulfite-seq: For each sample, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were  trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the Capsella reference genome using the Bismark read mapper (Krueger and Andrews, 2011) using the single end mode. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
small-RNA: Adapters were removed from the 50 bp long single sRNA reads in each library. The resulting18-30 bp long reads were mapped to the reference genomes. Mapped reads from both replicates were pooled together, sorted in two categories (21-22-nt and 24-nt long) and remapped to the same reference masked genome mentioned above using ShorStack (--mismatches 2 --mmap f) in order to improve the localization of sRNAs mapping to multiple genomic locations. We normalized the alignments by converting coverage values to reads per million mapped reads (RPM) values.
RNA-seq: For each replicate, reads were mapped to the respective eference genomes using TopHat v2.1.0 (Trapnell et al, 2009)in single end mode. Gene and TE expression was normalized to reads per kilobase per million mapped reads (RPKM) using GFOLD.
WGS and TE insertion analysis: For each accession the 150 bp long reads were mapped to the Capsella reference genome using TEPID (Stuart el al 2016) in paired-end mode with default parameters.
Genome_build: TAIR10, Caprub1_0
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: small-RNA: Unique small RNAs (between 18-30 nts)  that mapped to the reference genomes. Accumulation number (raw reads) are represented in a three column format file: <sequence_smallRNA> <number_of_reads><read_length_bp> for each sample.
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes and transposable elements in both genomes for each condition and replicate.
Supplementary_files_format_and_content: WGS and TE insertion analysis: Identified new TE insertions are shown for the six samples. Rows indicate chromosome (scaffold) and insertion position and values indicate TE identity.

source_name: AT microspore wt

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
RNA of Arabidopsis microspores was isolated using the TRIzoL following the manufacturer’s protocol (Thermofischer: cat-15596018)
Total RNA was treated with the Poly(A) mRNA Magnetic Isolation Module kit (NEB #E7490) . Libraries were prepared from the resulting mRNA with the NEBNext® Ultra™ II kit (NEB #E7770S).

treatment_protocol: Material was generated by Percoll percoll gradient following previously published procedures (Duplakova et al., 2016)

value: microspore

value: wt (Col-0)


title: at-microspore.RNAseq.WT.replicate2


title: at-microspore.RNAseq.nrpd1a-3.replicate2

description:
Arabidopsis thaliana microspore of nrpd1a-3 (Columbia-0)
at.microspore.RNAseq.rpkm.txt.gz

source_name: AT microspore nrpd1a-3

value: nrpd1a-3 (Col-0)


title: SJALL054754

description: Patient RNA Seq Data

value: Bone Marrow

value: acute lymphoblastic leukemia


title: SJALL054557

description: Patient RNA Seq Data

value: primary leukemia cells


title: at-microspore.sRNA.WT.replicate2

description: Arabidopsis thaliana microspore of wt (Columbia-0)

extract_protocol:
Total RNA was treated with DNAseI (Thermofischer: cat-EN0521) and then loaded on a 15% TBE-Urea polyacrylamide gel. RNA with a size of 15-27-nt was retrieved and eluted by crushing the gel in PAGE elution buffer (1M Tris pH7.5, 2.5M NaOAc, 0.5M EDTA pH8) followed by an overnight incubation and a new TRizoL extraction.
sRNA seq libraries were generated with the NEBNext® Multiplex Small RNA kit (NEB #E7300S).


title: SJALL054545

description: Patient RNA Seq Data


title: at-microspore.sRNA.WT.replicate1


title: SJBALL021941

description: Patient RNA Seq Data


title: at-microspore.sRNA.nrpd1a-3.replicate2

description: Arabidopsis thaliana microspore of nrpd1a-3 (Columbia-0)


title: SJALL054537

description: Patient RNA Seq Data


title: SJALL054554

description: Patient RNA Seq Data


title: control rep2


title: at-microspore.sRNA.nrpd1a-3.replicate1


title: Mitochondria of Hela cells treated with negative control

description: NC-PNP-mito

source_name: Hela cells

tag: cell line

value: HeLa

value: treated with negative control


title: SJALL054523

description: Patient RNA Seq Data

value: Peripheral Blood


title: Nuclei of Hela cells

library_source: genomic

molecule: genomic DNA


title: Mitochondria of Hela cells treated with knockdown PNP1

value: treated with knockdown PNP1


title: SJALL054532

description: Patient RNA Seq Data


title: SJALL054530

description: Patient RNA Seq Data


title: SJALL054529

description: Patient RNA Seq Data


title: Mitochondria of RPE-1 cells

description: RPE-mito

source_name: RPE-1 cells


title: Cytoplasm of Hela cells

description: Hela-cyto


title: Mitochondria of Hela cells

description: Hela-mito


title: SJALL054521

description: Patient RNA Seq Data


title: SJALL054525

description: Patient RNA Seq Data


title: Mitochondria of Hela cells - genomic


title: SJALL050551

description: Patient RNA Seq Data


title: SJALL050543

description: Patient RNA Seq Data


title: SJALL050541

description: Patient RNA Seq Data


title: KSHV (-) tumors [DS027accepted_hitsmouse]

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
We performed 76 nt paired-end sequencing using an Illumina NextSeq500 platform.
Illumina Casava software was used for basecalling.
The short-read sequences  were mapped to the mouse reference genome (GRCm38.82) by the splice junction aligner TopHat V2.1.0.
The number of reads mapped to each gene based on the TxDb. Mmusculus gene ensembls were counted, reported and annotated using the Rsamtools, GenomicFeatures, GenomicAlignments packages.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Tab-delimited text files include log2 count per million values for each Sample

source_name: KSHV (-) tumors

growth_protocol: mECK36 cells KSHV (+) were obtained and cultured as previously described (Mutlu et al., 2007). mECK36 KSHV (+) tumors were obteined as previously described (Mutlu et al., 2007). KSHV (-) tumor cells were obtained from mECK36 tumor explants after Bac36 episome loss achieved by growth without hygromycin selection as previously described (Mutlu et al., 2007). KSHV (-) tumors were obteined by subcutaneous injection of KSHV (-) tumor cells in nude mice as previously described (Ma et a., 2013).

extract_protocol:
RNA was isolated and purified using the RNeasy mini kit (Qiagen). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
mRNA from cell lines and tumor samples were processed for directional mRNA-seq library construction using the Preparation Kit according to the manufacturer's protocol.

tag: tissue/cell type

value: KSHV-negative mECK36 tumors


title: KSHV (-) tumors [DS029accepted_hitsmouse]


title: SJALL050540

description: Patient RNA Seq Data


title: SJALL054538

description: Patient RNA Seq Data


title: SJALL050484

description: Patient RNA Seq Data


title: KSHV (-) tumor cells [DS023accepted_hitsmouse]

source_name: KSHV (-) tumor cells

value: tumorigenic KSHV-negative mECK36 cells


title: SJALL049687

description: Patient RNA Seq Data


title: SJALL049685

description: Patient RNA Seq Data


title: KSHV (-) tumor cells [DS021accepted_hitsmouse]


title: KSHV (-) cells [DS017accepted_hitsmouse]

source_name: KSHV (-) cells

value: KSHV-negative mECK36 cells


title: KSHV (-) cells [DS019accepted_hitsmouse]


title: KSHV (+) tumors [DS011accepted_hitsmouse]

source_name: KSHV (+) tumors

value: KSHV-positive mECK36 tumors


title: SJALL049684

description: Patient RNA Seq Data

source_name: B-lineage ALL


title: KSHV (+) tumors [DS013accepted_hitsmouse]


title: SJALL049489

description: Patient RNA Seq Data


title: SJALL049485

description: Patient RNA Seq Data


title: SJALL050544

description: Patient RNA Seq Data


title: SJALL049493

description: Patient RNA Seq Data


title: KSHV (+) tumors [DS009accepted_hitsmouse]


title: SJALL049109

description: Patient RNA Seq Data


title: KSHV (-) tumors [DS025accepted_hitsmouse]


title: KSHV (+) tumors [DS007accepted_hitsmouse]


title: KSHV (+) tumors [DS005accepted_hitsmouse]


title: SJALL048693

description: Patient RNA Seq Data


title: SJALL048691

description: Patient RNA Seq Data


title: KSHV (+) cells [DS001accepted_hitsmouse]

source_name: KSHV (+) cells

value: KSHV-positive mECK36 cells


title: SJALL048510

description: Patient RNA Seq Data


title: Mitochondria of N2a cells

source_name: N2a cells


title: SJALL048503

description: Patient RNA Seq Data


title: SJALL048502

description: Patient RNA Seq Data


title: Mitochondria of mouse muscle

source_name: mouse muscle

tag: tissue

value: muscle

tag: strain


title: KSHV (+) tumors [DS015accepted_hitsmouse]


title: Mitochondria of 3T3 cells

source_name: 3T3 cells


title: SJALL047978

description: Patient RNA Seq Data


title: KSHV (+) cells [DS003accepted_hitsmouse]


title: PDGFRa H2BGFP+ cells_undamaged+7d_post_LAD ligation

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

data_processing:
Demultiplexing and alignment to the mm10 reference genome was performed using the cellranger count pipeline (10X Genomics).
Filtering was performed using the cellranger count pipeline (10X Genomics).
Further filtering and quality control of low quality cells (cells with more than 10% mitochondrial genes and/or < 200 genes filtered out) was performed using Seurat v.2.1 R package
Genome_build: mm10
Supplementary_files_format_and_content: matrix file plus genes and barcodes tab-separated files for each single cell sequencing experiment

source_name: heart

extract_protocol:
After the target cell suspension was examined for quality and cells counted using a hemocytometer, they were delivered into a Chromium Controller (10X Genomics), captured and libraried with the Chromium single cell 3’ reagent kit v2 (10X Genomics).   Demultiplexing and alignment to the modified mm10 reference genome was performed using the cellranger count pipeline (10X Genomics
cDNA libraries were sequenced on a Nextseq 500 (Illumina) to a minimum depth of 20,000 mean reads per cell.
single cell RNA-seq

treatment_protocol: Mice hearts were either collected undamaged or 7 days after LAD ligation and subjected to drop-seq using 10x genomics platform.

tag: genotype

value: PDGFRa H2BEGFP+

value: heart

tag: time point

value: undamaged+7days post LAD


title: SJALL047977

description: Patient RNA Seq Data


title: SJALL048081

description: Patient RNA Seq Data


title: Hic1 citrine+ cells_undamaged

value: C57BL/6 (Hic1 Citrine)

value: Hic1 Citrine+

value: undamaged


title: SJALL048689

description: Patient RNA Seq Data

value: acute lymphoblastic leukemia

value: primary leukemia cells


title: SJALL047974

description: Patient RNA Seq Data

value: Bone Marrow


title: Hic1 CreERT2 tdTomato+ cells_7d post LAD ligation

value: C57BL/6 (Hic1 CreERT2 tdTomato)

value: Hic1 CreERT2 tdTomato+

value: 7 days post LAD


title: 28d_LAD_R60-60-B6pos

data_processing:
Illumina sequencing output generated bcl files were de-multiplexed by bcl2fastq2
Demultiplexed read sequences were then aligned to the Mouse Genome mm10 reference sequence using TopHat splice junction mapper with Bowtie 2 (http://ccb.jhu.edu/software/tophat/index.shtml) or STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886) aligners.
Assembly and differential expression was estimated using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts of sequencing reads for each sample separatley at text files.

extract_protocol:
Total RNA was isolated from hearts using RNeasy plus micro kits (Qiagen, 74004) as per manufacturer’s instructions. Sample integrity was tested on an Agilent Bioanalyzer 2100 RNA 6000 Nano or Pico kits. RNA samples with a RNA Integrity Number > 8 were used to prepare libraries following the standard protocol for the TruSeq Stranded mRNA library kit (Illumina) on the Illumina Neoprep automated microfluidic library prep instrument.
Paired end sequencing was performed on the Illumina NextSeq 500 using the High Output 150 cycle Kits and libraries were prepared  using standard Illumina protocols.

treatment_protocol: Mice underwent left anterior descending (LAD) coronary artery ligation hearts were collected at 7, 14 and 28 days after ligation and compared to undamaged hearts

value: D28 post LAD ligation


title: SJALL047971

description: Patient RNA Seq Data


title: SJALL044302

description: Patient RNA Seq Data


title: 28d_LAD_R60-60-B4pos


title: SJALL047968

description: Patient RNA Seq Data


title: Hic1 CreERT2 tdTomato+ cells_undamaged


title: 28d_LAD_F2pos


title: Mitochondria of mouse heart

source_name: mouse heart


title: 28d_LAD_R60-60-B6neg


title: 28d_LAD_E4neg


title: SJALL044300

description: Patient RNA Seq Data


title: 28d_LAD_R60-60-B4neg


title: 28d_LAD_E2pos


title: SJALL048085

description: Patient RNA Seq Data


title: SJALL040124

description: Patient RNA Seq Data


title: SJALL048082

description: Patient RNA Seq Data


title: 14d_LAD_R60-65-D9pos

value: D14 post LAD ligation


title: SJALL040122

description: Patient RNA Seq Data


title: SJALL040108

description: Patient RNA Seq Data


title: 14d_LAD_R60-65-D1neg


title: SJALL040101

description: Patient RNA Seq Data


title: 7d_LAD_R60-66-4B

value: D7 post LAD ligation


title: 14d_LAD_R60-65-D1pos


title: SJALL040121

description: Patient RNA Seq Data


title: SJALL047967

description: Patient RNA Seq Data


title: 14d_LAD_R60-65-D9neg


title: 7d_LAD_R60-63-1A


title: SJALL040098

description: Patient RNA Seq Data


title: SJALL040097

description: Patient RNA Seq Data


title: SJALL040127

description: Patient RNA Seq Data


title: SJALL040095

description: Patient RNA Seq Data


title: SJALL040091

description: Patient RNA Seq Data


title: 7d_LAD_R60-63-1B


title: SJALL040090

description: Patient RNA Seq Data


title: Undamaged Sca-1_pos 67_B7pos


title: 7d_LAD_PDGFRa-Sca1Neg_


title: 7d_LAD_PDGFRa-Sca1pos


title: SJALL040065

description: Patient RNA Seq Data


title: at-microspore.RNAseq.nrpd1a-3.replicate1

value: microspore

value: nrpd1a-3 (Col-0)


title: SJBALL014876

description: Patient RNA Seq Data

data_processing:
STAR Aligner used to align reads
edgeR TIMM normalization
LIMMA used to generate CPM (counts per million)
Genome_build: hg19
Supplementary_files_format_and_content: Each processed file contains Counts for each gene, columns are related to each sample

source_name: acute lymphoblastic leukemia patient

treatment_protocol: Diagnostic Bone marrow or peripheral blood at Diagnosis with ALL with associated Prednisolone LC50 treated with drug from 0.015uM-503.5 uM values above maximum and minimum were assigned 1/2 lowest concentration or 2x's highest concentration

tag: prednisolone lc50


title: SJALL040064

description: Patient RNA Seq Data


title: Undamaged Sca-1_neg 67_B7neg

value: PDGFRa H2BEGFP+


title: Undamaged Sca-1_neg 67_A6neg

value: heart


title: Undamaged Sca-1_pos 67_A6pos


title: SJALL047544

description: Patient RNA Seq Data


title: Undamaged Sca-1_neg_F3


title: 7d_LAD_R60-66-4A


title: SJALL047541

description: Patient RNA Seq Data


title: SJALL047543

description: Patient RNA Seq Data


title: Undamaged Sca-1_neg_E5


title: Undamaged Sca-1_pos_E3


title: Undamaged Sca-1_pos_E1


title: SJALL047540

description: Patient RNA Seq Data


title: Undamaged Sca-1_pos_F3


title: SJALL040089

description: Patient RNA Seq Data


title: SJALL047539

description: Patient RNA Seq Data


title: SJALL047537

description: Patient RNA Seq Data


title: SJALL047538

description: Patient RNA Seq Data


title: MM_LysM_Adrb2_flox_plus_input_1

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Reads were aligned using Kallisto v0.40 to Mouse Ensembl v91. Transcript abundance files were then used in the DESeq2 R package, which was used for all downstream differential expression analysis.
Genome_build: Ensembl Mus musculus release 91: GRCm38.p5 (GCA_000001635.7)
Supplementary_files_format_and_content: abundance measurements

source_name: Input fraction ribosome-bound mRNA from the ileum muscularis of LysM:Adrb2floxplus:RiboTag mice

extract_protocol: For intestine immunoprecipitation (IP) mice were sacrificed and tissue remove and divided as above. Samples were washed of fecal contents in PBS with cycloheximide (0.2 mg/mL) (PBS/CHX).  Mesenteric fat was removed and the muscularis was separated from the mucosa as described above and samples were washed 5 times in PBS/CHX. For nodose tissues were isolated as described above. The RiboTag immunoprecipitation protocol (http://depts.washington.edu/mcklab/RiboTagIPprotocol2014.pdf)  was then followed with the following modifications: All samples were homogenized by hand with a dounce homogenizer in 2.5 mL supplemented homogenization buffer (changes per 2.5 mL: 50 µl Protease Inhibitor, 75 µl heparin (100 mg/mL stock), 25 µl SUPERase In RNase Inhibitor). Samples were then centrifuged for 10 minutes at 10,000 G, after which 800 µl of supernatant was removed and 5µL of anti-HA antibody (Abcam, ab9110) was added. For input samples, 40uL of supernatant was removed and 60uL of PicoPure lysis buffer was added. These input samples were then put at -80°C. Immunoprecipitated samples were kept rotating at 4°C with antibody for 1 hour. 200 µl of Thermo Protein magnetic A/G beads were washed with homogenization buffer, added to the sample, and kept rotating for 30 minutes at 4°C. The beads were washed four times with high-salt buffer and samples were eluted with 100 µl of PicoPure lysis buffer.  RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

value: Ileum muscularis


title: MM_LysM_Adrb2_flox_plus_input_2


title: SJALL047535

description: Patient RNA Seq Data


title: MM_LysM_Adrb2_flox_plus_ip_2

source_name: Immunoprecipitated ribosome-bound mRNA from the ileum muscularis of LysM:Adrb2floxplus:RiboTag mice


title: SJALL047534

description: Patient RNA Seq Data


title: MM_LysM_Adrb2_flox_plus_ip_1


title: SJALL047532

description: Patient RNA Seq Data


title: MM_LysM_Adrb2_flox_flox_input_2

source_name: Input fraction ribosome-bound mRNA from the ileum muscularis of LysM:Adrb2floxflox:RiboTag mice


title: SJALL047533

description: Patient RNA Seq Data


title: SJALL047531

description: Patient RNA Seq Data


title: MM_LysM_Adrb2_flox_flox_ip_2

source_name: Immunoprecipitated ribosome-bound mRNA from the ileum muscularis of LysM:Adrb2floxflox:RiboTag mice


title: MM_LysM_Adrb2_flox_flox_input_1


title: Nodose_ip_5

source_name: Immunoprecipitated ribosome-bound mRNA from the nodose ganglion of Snap25:RiboTag mice

value: Nodose ganglion


title: SJALL047530

description: Patient RNA Seq Data


title: Nodose_ip_4


title: SJALL047542

description: Patient RNA Seq Data


title: SJALL047529

description: Patient RNA Seq Data


title: Nodose_ip_2


title: Nodose_ip_1


title: SJALL047536

description: Patient RNA Seq Data


title: Nodose_ip_3


title: SJALL047527

description: Patient RNA Seq Data


title: SJALL047526

description: Patient RNA Seq Data


title: SJALL047528

description: Patient RNA Seq Data


title: SJALL047525

description: Patient RNA Seq Data


title: Ileum_ip_4

source_name: Immunoprecipitated ribosome-bound mRNA from the ileum muscularis of Snap25:RiboTag mice


title: SJALL047523

description: Patient RNA Seq Data


title: SJALL047524

description: Patient RNA Seq Data


title: MM_LysM_Adrb2_flox_flox_ip_1


title: Ileum_ip_2


title: Ileum_ip_1


title: SJALL047521

description: Patient RNA Seq Data


title: Ileum_ip_3


title: SJALL047518

description: Patient RNA Seq Data


title: 1048

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using RNA-Seq Alignment version 1.1.0 (Illumina BaseSpace software application). The application uses Tophat 2 for alignment and RNAReadCounter to generate count tables.
Differential expression analysis of count tables was performed using the default settings of DESeq2 (1.6.3, Benjamini-Hochberg FDR correction).
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel Worksheet (.xlsx), contains unnormalized counts for each sample generated by RNAReadCounter. The raw counts were used by DESeq2 for differential expression analysis.

source_name: Left Ventricle

growth_protocol: Male and female mice were kept on a 12 hour light-dark cycle at FSU Animal Facility. Food and water were provided ad libitum. Animals of all strains were group housed. Euthanization by isoflourane exposure followed by cervical dislocation.

extract_protocol:
The left ventricle was immediately isolated after extraction, flash frozen in liquid nitrogen, and pulverized cold. Total RNA was isolaged from pulverized tissue using miRNeasy minikit (Qiagen), according to manufacturer’s instructions.
cDNA libraries were generated from the isolated mRNA using an NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs) and a unique 6 nucleotide index primer (NEBNext multiplex oligos for Illumina) was incorporated into each sample.  The library construction was done according to NEB instructions, modified for use with a Beckman Biomek 4000 at the Florida State University Biological Sciences core lab.  The unique index (barcode) was added to each library to multiplex the sixteen libraries into two lanes of the sequencing run. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies).  12 pM of the pooled sample was sequenced, with single end, 100 base reads on an Illumina HiSeq 2500 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

value: Wild Type

tag: Sex

value: F

value: 5M = 150 days

value: Left Ventricle


title: 1047


title: 1046


title: 1041

value: M


title: 1045


title: SJALL047517

description: Patient RNA Seq Data

value: acute lymphoblastic leukemia


title: SJALL047516

description: Patient RNA Seq Data


title: 1059


title: 1040


title: SJALL047515

description: Patient RNA Seq Data


title: SJALL047513

description: Patient RNA Seq Data


title: 1028

value: Homozygous


title: SJALL047514

description: Patient RNA Seq Data


title: SJALL047512

description: Patient RNA Seq Data


title: SJALL047522

description: Patient RNA Seq Data


title: 1026


title: 1025


title: SJALL047510

description: Patient RNA Seq Data


title: SJALL047519

description: Patient RNA Seq Data


title: SJALL047511

description: Patient RNA Seq Data


title: 988

value: 5M 9D = 159 days


title: SJALL047520

description: Patient RNA Seq Data


title: 1009

value: 5M 2D = 152 days


title: SJALL040135

description: Patient RNA Seq Data


title: 984


title: SJALL040131

description: Patient RNA Seq Data


title: SJALL040136

description: Patient RNA Seq Data


title: SJALL040130

description: Patient RNA Seq Data


title: SJALL040128

description: Patient RNA Seq Data


title: SJALL040132

description: Patient RNA Seq Data


title: ML3173 (Pxyl-dcas9(Sth3)) in xylose 2hr

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

description: Strains were grown in PYE + supplements to OD600~0.2 and RNA was extracted and processed into sequencing libraries as previously reported (Culviner and Laub, 2018).

data_processing:
Reads were aligned to Caulobacter NC_011916.1 (NA1000) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
The change in gene expression was calculated by taking log2-RPKM ratio of each gene from the experimental condition to the control condition (dcas9 grown in xylose / dcas9 grown in glucose; sgRNA-ctrA grown in xylose / sgRNA-ctrA grown in glucose).
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position. For RNA-seq, two files are provided, one for forward and reverse strand.

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus CB15N

growth_protocol: Caulobacter crescentus was grown in PYE+0.2% glucose to OD ~ 0.05-0.1. Cultures were split and 0.3% xylose was added to to one flask to induce the CRISPR system. RNA was harvested after 2hr.

extract_protocol:
RNA was extracted as previously reported (Culviner and Laub, 2018).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).

tag: growth stage

value: exponential phase

tag: media

value: PYE + 0.2% glucose + 0.3% xylose


title: ML3174 (Pxyl-dcas9(Sth3) Pconstitutive-sgRNA(Sth3)_ctrA) in xylose 2hr


title: 981


title: SJALL040126

description: Patient RNA Seq Data


title: ML3174 (Pxyl-dcas9(Sth3) Pconstitutive-sgRNA(Sth3)_ctrA) in glucose

value: PYE + 0.2% glucose


title: ML3173 (Pxyl-dcas9(Sth3)) in glucose


title: 1058


title: SJALL040123

description: Patient RNA Seq Data


title: SJALL040117

description: Patient RNA Seq Data


title: SJALL040116

description: Patient RNA Seq Data


title: 302_whole_33_H21_hCS

first: Nasa

last: Sinnott-Armstrong

address: 318 Campus Drive, Clark Center S240

department: Genetics

institute: Stanford University

description: nucleic acid

data_processing:
Illumina base calling
SeqPurge trimming: SeqPurge -a1 CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -a2 CTGTCTCTTATACACATCTGACGCTGCCGACGA
bowtie2 alignment: bowtie2 -X 2000 --threads {threads} --rg-id {wildcards.sample_label} --fr --rg 'SM:{wildcards.sample_label}' -x [REFERENCE_FILE] -1 {input.left} -2 {input.right} | samtools view -hb -S - | samtools sort -o bams/unprocessed/{wildcards.sample_label}.bam -
macs2 peaks calling: macs2 callpeak -g 3e9  --treatment <sample BAM> --format BAMPE --nomodel --call-summits --nolambda --keep-dup all -p 0.01 -B –SPMR
bedtools overlap counts with multiBamCov
Genome_build: hg38

source_name: forebrain spheroid

growth_protocol: The generation and maintenance of hCS and hSS was performed as previously described (Birey et al., 2017; Paşca et al., 2015; Sloan et al., 2017). In brief, intact hiPS cell colonies were enzymatically lifted using dispase (0.35 mg/mL, Life Technologies, 17105) and transferred into ultralow-attachment plates in hiPS medium supplemented with the SMAD inhibitors dorsomorphin (5 μM, Sigma-Aldrich) and SB-431542 (10 μM, Tocris), and the ROCK inhibitor Y-27632 (10 μM, Selleckchem). The hiPS cell medium was changed and supplemented with dorsomorphin and SB-431542 every day. On the sixth day in suspension, the medium was switched to neural medium containing neurobasal A (Life Technologies, 10888), B-27 supplement without vitamin A (Life Technologies, 12587), GlutaMax (1:100, Life Technologies), penicillin and streptomycin (1:100, Life Technologies) and supplemented with EGF (20 ng/ml, R&D Systems) and FGF-2 (20 ng/ml, R&D Systems). The neural medium was changed every day until day 17 and then every other day until day 24. For the generation of hSS, the medium was additionally supplemented with the WNT pathway inhibitor IWP-2 (5 μM, Selleckchem) on days 4-24, the SHH pathway agonist SAG (100 nM, Selleckchem) on days 12-24, retinoic acid (RA, 100 nM, Sigma-Aldrich) on days 12-15 and allopregnanolone (100 nM, Cayman Chemicals, 16930) on days 15-24. From day 25 to day 43, the neural medium for both hCS and hSS was changed every other day and supplemented with BDNF (20 ng/ml, Peprotech) and NT3 (20 ng/ml, Peprotech). From day 45 onwards, hCS and hSS were maintained in neural medium without growth factors with medium changes every four to six days.

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., Corces et al.) with modifications. Briefly, 10,000-50,000 cells were washed in ice-cold PBS, centrifuged at 4C for 5 min at 500 rcf, washed in ice-cold Resuspension Buffer (RSB, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH=7.4) and centrifuged again. Cells were resuspended in 50 uL Lysis Buffer (RSB plus 0.1 % NP-40 and 0.1% Tween-20) and centrifuged at 4C for 10 min at 500 rcf.
Pelleted nuclei were resuspended gently in 50 uL transposition mix (25 uL 2X Tagment DNA Buffer, 2.5 uL Tn5 Tagment DNA Enzyme 1, 0.1% Tween -20, H20) and incubated for 30 minutes at 37 C. DNA was cleaned using Qiagen MinElute columns, and PCR amplified 5 cycles in a 50 uL reaction with Illumina Nextera adaptors using NEBNext High Fidelity 2x Master Mix. A side qPCR reaction was performed using 10% of the pre-amplified PCR to determine the number of additional cycles to amplify. Final PCR products were cleaned using Qiagen MinElute columns and quantified by qPCR against a PhiX standard curve prior to pooling and sequencing to an average depth of ~10M filtered, deduplicated reads per sample on the Illumina NextSeq platform. Whole tissue samples were processed as previously described (Corces et al., 2017). Briefly, tissue samples were dounce homogenized and nuclei were isolated by gradient centrifugation prior to library preparation.

treatment_protocol: Dissociation of neural spheroids and human tissue into single cells was performed as previously described (Birey et al., 2017; Paşca et al., 2015; Sloan et al., 2017; Zhang et al., 2016). Briefly, tissue was chopped and incubated in 40 U/ml papain enzyme solution at 37 °C for 90 minutes. The number of neural spheroids used per sample ranged from 3 to 15 depending on their age and size. After digestion, samples were washed with a protease inhibitor solution and gently triturated to achieve a single cell suspension.  Single cell suspensions were then either FACS-sorted or immunopanned to achieve astrocyte- or neuron-enriched populations. For FACS-sorting, cells were resuspended in 0.2% BSA and DAPI-negative live cells were separated based on their expression of either GFP (pLV-GFAP-eGFP glia) or mCherry (AAV-DJ-hSYN1::mCherry neurons). Positive cells were sorted into ice-cold PBS. For immunopanning, the single cell suspension was added to a series of plastic petri dishes pre-coated with cell type-specific antibodies and incubated for 10-30 minutes at room temperature. Unbound cells were transferred to the subsequent petri dish, while the dish with bound cells was rinsed with PBS to wash away loosely bound contaminating cell types. An anti-Thy1 antibody (CD90, BD Biosciences, 550402) was used to harvest neurons, and an anti-HepaCAM antibody (R&D, MAB4108) was used to harvest astrocytes. Bound cells were then incubated in a trypsin solution (for glia) or Accutase (for neurons) at 37 °C for 3-5 minutes then gently pipetted off the plates with trypsin or Accutase. Cells were then spun down at 200 x g for 5 minutes, and resuspended in cold 0.2% BSA in PBS prior to RNA-seq and ATAC-seq.

tag: purification

value: whole

tag: differentiation media

value: hCS

tag: individual

tag: day of differentiation

tag: isolation method

value: nuclei

tag: sample source

value: forebrain spheroid

tag: cell count

tag: assay batch


title: 300_whole_33_H20_hCS

description: nucleic acid


title: 299_whole_33_H20_hCS

description: nucleic acid


title: 301_whole_33_H21_hCS

description: nucleic acid


title: 298_whole_27_2242.1_hCS

description: nucleic acid


title: SJALL040111

description: Patient RNA Seq Data


title: 297_whole_27_2242.1_hCS

description: nucleic acid


title: 1014

tag: age


title: SJALL040120

description: Patient RNA Seq Data

tag: tissue


title: 295_whole_27_8858.1_hCS

description: nucleic acid


title: 296_whole_27_8858.1_hCS

description: nucleic acid


title: SJALL040086

description: Patient RNA Seq Data


title: SJALL040115

description: Patient RNA Seq Data


title: SJALL040082

description: Patient RNA Seq Data


title: SJALL040085

description: Patient RNA Seq Data


title: 290_glial_125_8858.1_hSS

description: nucleic acid

value: glial

value: hSS

value: immunopanning


title: 294_whole_42_2242.1_hCS

description: nucleic acid


title: 293_whole_42_2242.1_hCS

description: nucleic acid


title: SJALL040078

description: Patient RNA Seq Data


title: SJALL040077

description: Patient RNA Seq Data


title: SJALL040110

description: Patient RNA Seq Data


title: 287_neuronal_125_1205.4_hSS

description: nucleic acid

value: neuronal


title: 288_neuronal_125_8858.1_hSS

description: nucleic acid


title: 289_glial_125_1205.4_hSS

description: nucleic acid


title: SJALL040074

description: Patient RNA Seq Data


title: SJALL040073

description: Patient RNA Seq Data


title: SJALL040072

description: Patient RNA Seq Data


title: 285_whole_59_8858.1_hSS

description: nucleic acid


title: 286_whole_59_1205.4_hSS

description: nucleic acid


title: 291_whole_42_8858.1_hCS

description: nucleic acid


title: SJALL040070

description: Patient RNA Seq Data


title: 292_whole_42_8858.1_hCS

description: nucleic acid


title: SJALL040081

description: Patient RNA Seq Data


title: 283_whole_41_8858.1_hSS

description: nucleic acid


title: SJALL040068

description: Patient RNA Seq Data


title: 284_whole_41_1205.4_hSS

description: nucleic acid


title: 282_whole_41_0524.1_hSS

description: nucleic acid


title: SJALL040061

description: Patient RNA Seq Data


title: SJALL040063

description: Patient RNA Seq Data


title: SJALL040066

description: Patient RNA Seq Data


title: 279_whole_25_0524.1_hCS

description: nucleic acid


title: 280_whole_25_8858.1_hCS

description: nucleic acid


title: 277_whole_46_0524.1_hCS

description: nucleic acid


title: 278_whole_46_8858.1_hCS

description: nucleic acid


title: SJALL040060

description: Patient RNA Seq Data


title: SJALL040059

description: Patient RNA Seq Data


title: SJALL040069

description: Patient RNA Seq Data


title: SJALL040055

description: Patient RNA Seq Data


title: 276_glial_206_8858.1_hCS

description: nucleic acid


title: SJALL040067

description: Patient RNA Seq Data


title: SJALL040057

description: Patient RNA Seq Data


title: 275_glial_206_1205.4_hCS

description: nucleic acid


title: 274_neuronal_206_8858.1_hCS

description: nucleic acid


title: 272_neuronal_179_0524.1_hCS

description: nucleic acid


title: 273_neuronal_206_1205.4_hCS

description: nucleic acid


title: 254_whole_140_hfb.2

description: nucleic acid

source_name: hfb

value: hfb


title: WILMAR-P_PolII_Molasses_R2

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

country: Australia

institute: Peter MacCallum Cancer Centre

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

organism: Schizosaccharomyces pombe

source_name: Whole cell

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

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

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

tag: strain

value: Wilmar-P Scr1-TAP

value: h90 scr1::TAP-KanMX6

tag: chip antibody

value: RNA Pol II Ser5 (clone 3E8, Merck 04-1572)

tag: treatment

value: molasses


title: WILMAR-P_PolII_Glucose_R1

value: Wilmar-P

tag: genotype

value: 3% glucose


title: 253_whole_140_hfb.2

description: nucleic acid


title: WILMAR-P_PolII_Glucose_R2


title: WILMAR-P_Scr1_Molasses_INPUT_R1


title: SJALL040103

description: Patient RNA Seq Data

value: acute lymphoblastic leukemia

tag: prednisolone lc50


title: WILMAR-P_PolII_Molasses_R1


title: WILMAR-P_Scr1_Glucose_INPUT_R1


title: 252_whole_140_hfb.2

description: nucleic acid


title: WILMAR-P_Scr1_Molasses_R2

description: Y23_Scr1_chip-molasses-R2_peaks.narrowPeak

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


title: 249_glial_140_hfb.2

description: nucleic acid


title: 248_glial_140_hfb.2

description: nucleic acid


title: 247_glial_140_hfb.2

description: nucleic acid


title: WILMAR-P_Scr1_Molasses_R1

description: Y23_Scr1_chip-molasses-R1_peaks.narrowPeak


title: 246_neuronal_140_hfb.2

description: nucleic acid


title: WILMAR-P_Scr1_Glucose_R2

description: Y23_Scr1_chip-glucose-R2_peaks.narrowPeak


title: 245_neuronal_140_hfb.2

description: nucleic acid


title: 244_neuronal_140_hfb.2

description: nucleic acid


title: WILMAR-P_Scr1_Glucose_R1

description: Y23_Scr1_chip-glucose-R1_peaks.narrowPeak


title: 227_neuronal_220_8858.1_hCS

description: nucleic acid


title: LAB_Scr1_Molasses_INPUT_R1

value: 972h- Scr1-TAP

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


title: LAB_PolII_Molasses_R1


title: LAB_Scr1_Molasses_R2

description: WT_Scr1_chip-molasses-R2_peaks.narrowPeak


title: 221_glial_220_8858.1_hCS

description: nucleic acid

value: hCS


title: 220_neuronal_220_8858.1_hCS

description: nucleic acid

value: forebrain spheroid


title: LAB_Scr1_Molasses_R1

description: WT_Scr1_chip-molasses-R1_peaks.narrowPeak


title: 222_glial_220_8858.1_hCS

description: nucleic acid

value: glial


title: Og-NSC

city: seoul

first: Hyun-Seob

last: Lee

address: 71 Daehak-ro, Jongno-gu

department: Biomedical research institute

institute: Seoul national University Hospital

description: single cells RNA sequencing

data_processing:
Cell ranger v2.1.1
Seurat 3.0
Genome_build: hg19

source_name: H9 hESC Midbrain Organoid derived NPC

extract_protocol: Construction of single cell RNA-sequencing libraries was conducted using the Single Cell 3' Reagent Kit (10X Genomics, Pleasanton, USA) in accordance with the manufacturer's protocol.

tag: cell type

value: H9 hESC-derived NPC


title: 2D-NSC

description: single cells RNA sequencing

source_name: H9 hESC-derived NPC


title: Pat 4 Krukenberg Tumour

description:
Pat_4_Genes_FPKM.txt
Pat_4_Genes_Count.txt

source_name: Tumour derived from metastasis in the ovary


title: 213_neuronal_394_2242.1_hSS

description: nucleic acid

value: hSS

value: immunopanning


title: Pat 3 Krukenberg Tumour

description:
Pat_3_Genes_FPKM.txt
Pat_3_Genes_Count.txt

value: Tumour derived from metastasis in the ovary


title: 216_glial_394_2242.1_hSS

description: nucleic acid


title: 215_glial_394_2242.1_hSS

description: nucleic acid


title: 214_neuronal_394_2242.1_hSS

description: nucleic acid

value: neuronal


title: 210_glial_394_2242.1_hCS

description: nucleic acid


title: Pat 4 Krukenberg Stroma

source_name: Stroma derived from metastasis in the ovary


title: 219_neuronal_220_8858.1_hCS

description: nucleic acid


title: Pat 3 Krukenberg Stroma

value: Stroma derived from metastasis in the ovary


title: 209_glial_394_2242.1_hCS

description: nucleic acid


title: Pat 3 Primary CRC Tumour

source_name: Tumour derived from primary colorectal tumour


title: 208_neuronal_394_2242.1_hCS

description: nucleic acid


title: 207_neuronal_394_2242.1_hCS

description: nucleic acid


title: LAB_PolII_Molasses_R2

value: RNA Pol II Ser5 (clone 3E8, Merck 04-1572)


title: 204_glial_532_8858.1_hCS

description: nucleic acid


title: parA_nd

city: Worcester

first: Jan

last: Czerminski

state: Massachusetts

address: 55 Lake Ave N, S6-241

department: Neurology

institute: UMass Medical School

description: 10X genomics single cell RNAseq

data_processing:
Alignment, filtering, barcode counting, and UMI counting was performed using the Cell Ranger pipeline (10x Genomics - v2.1.1)
Further normalization, filtering, and analysis was performed using the Seurat R package (v2.3.4)
Genome_build: hg19
Supplementary_files_format_and_content: barcode (cell) x gene matrix output of cellranger count function

source_name: ips-derived neural cells

growth_protocol: iPSCs were dissociated into single cells and plated at a density of 50,000 cells/well in a vitronectin-coated 24-well plate with 10µM of the ROCK inhibitor Y-27632 (Tocris Bioscience). The next day, media was changed to Neural differentiation media (NDM) consisting of 50% DMEM/F12, 50% Neurobasal, 0.5X Glutamax, 1X N-2 supplement (all from ThermoFisher) and supplemented with 2uM DMH1 and SB431542 (both from Tocris Bioscience). After 14 days, cells were broken into clumps after EDTA treatment and cultured in suspension for 7 days in NDM. On day 21 of differentiation, neurospheres were dissociated into single cells with StemPro Accutase (ThermoFisher) and plated onto coverslips (Electron Microscopy Sciences) coated with Matrigel (Corning) at a density of 25,000-50,000 cells/coverslip and fed every 2-3 days with Neuron media consisting of Neurobasal, 1X N-2, 0.5X B-27 without vitamin A, 1X Penicillin/Streptomycin, 1X Glutamax, 0.3% Glucose, 10ng/ml GDNF (Peprotech), 10ng/ml BDNF (Peprotech), 10ng/ml ascorbic acid (Sigma-Aldrich), and 1µM cyclic AMP (Sigma-Aldrich).

extract_protocol:
dissociated into single cells with accutase and run on 10X genomics chip per manufacturers instructions
10x Genomics Chromium™ Single Cell 3’ Library and Gel Bead Kit v2 per manufacturer’s instructions

treatment_protocol: Doxycycline diluted in distilled water was added to the culture media starting at various time points at a concentration of 500ng/ml.

tag: cell line

value: parentalA

tag: dox treatment

value: no dox


title: 203_glial_532_8858.1_hCS

description: nucleic acid

tag: purification

tag: differentiation media


title: parA_d0

description: 10X genomics single cell RNAseq

value: d0 dox


title: dis_nd

description: 10X genomics single cell RNAseq

value: disomic


title: 202_neuronal_532_8858.1_hCS

description: nucleic acid

tag: individual

tag: day of differentiation


title: c5a_nd

description: 10X genomics single cell RNAseq


title: 201_neuronal_532_8858.1_hCS

description: nucleic acid

tag: isolation method

tag: sample source


title: c5a_d14

description: 10X genomics single cell RNAseq

value: d14 dox


title: 198_glial_532_2242.1_hCS

description: nucleic acid

tag: cell count

tag: assay batch


title: c5a_d0

description: 10X genomics single cell RNAseq


title: 197_glial_532_2242.1_hCS

description: nucleic acid


title: diff8.day28.par.nd

data_processing:
removed contaminating ribosomal RNA reads
TopHat2 (v2.0.14) was used to map the remaining reads to the reference genome
HTseq was used to count the mapped reads
DEseq2 was used to determine differential expression and generate FPKM (fragments per kilobase of transcript per million mapped reads) values.
Genome_build: hg19
Supplementary_files_format_and_content: monolayer_rawcounts.txt is a comma-seperated text file containing a gene x sample matrix of raw counts. Genes are in the first column (gene_id) and samples with associated raw counts in the subsequent columns with the column name identical to sample name given above.

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher) according to manufacturer’s instructions. RNA samples were cleared of contaminating genomic DNA by DNAse I (Roche) treatment for 1hr at 37°C. RNA cleanup and DNAse I removal was performed using RNeasy MinElute columns (Qiagen) according to manufacturer’s instructions. Clean RNA was assessed for quality on an Advanced Analytical Fragment Analyzer, and all samples had a RQN > 7.5.
100ng of RNA per sample was used to prepare mRNA strand-specific sequencing libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® in conjunction with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs).

tag: differentiation

value: parental

tag: dox condition


title: diff8.day28.par.d0dox

value: day 0 dox


title: diff8.day28.c5a.nd

value: clone 5a


title: diff8.day28.dis.nd


title: 195_neuronal_532_2242.1_hCS

description: nucleic acid

value: hCS

value: forebrain spheroid


title: 190_neuronal_595_6593.8_hCS

description: nucleic acid


title: 196_neuronal_532_2242.1_hCS

description: nucleic acid


title: 192_glial_595_6593.8_hCS

description: nucleic acid

value: glial


title: Pat 3 Primary CRC Stroma

data_processing:
Fastq raw files were uploaded onto the DNANexus platform.
DNANexus modules were used to process data.
TopHat (Known Genes) (v1.2.0)
Cuffdiff (v1.0.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including gene count and FPKM values for each sample

source_name: Stroma derived from primary colorectal tumour

extract_protocol:
Human biopsies were flash freezed and subsequently prepared on membrane slides at a thickness of 10µm. Sections were microdissected using the Arcturus XT Laser Capture Microdissection Instrument to obtain the stroma and tumour/normal epithelial component. Qiagen RNAeasy micro kit was used to extract the RNA.
Ovation FFPE RNA-Seq Multiplex System was used to prepare the sequencing library. The amount of RNA used ranged from 3-60ng.

tag: tissue


title: diff8.day28.c5a.d0dox


title: 189_neuronal_595_6593.8_hCS

description: nucleic acid


title: diff8.day28.c5a.d21dox

value: day 21 dox


title: diff8.day28.c5a.d14dox

value: day 14 dox


title: diff8.day21.c5a.nd


title: 180_glial_588_2242.1_hCS

description: nucleic acid

value: immunopanning


title: 178_neuronal_588_2242.1_hCS

description: nucleic acid

value: neuronal


title: 179_glial_588_2242.1_hCS

description: nucleic acid


title: 177_neuronal_588_2242.1_hCS

description: nucleic acid


title: diff8.day21.c5a.d0dox


title: diff8.day21.C5a.d14dox


title: 174_glial_107_2242.1_hSS

description: nucleic acid

value: hSS


title: diff7.day28.dis.nd


title: diff7.day28.c5a.nd


title: 191_glial_595_6593.8_hCS

description: nucleic acid


title: diff7.day28.c5a.d0dox


title: 172_neuronal_107_2242.1_hSS

description: nucleic acid


title: 173_glial_107_2242.1_hSS

description: nucleic acid


title: diff7.day21.c5a.nd


title: 165_neuronal_114_2242.1_hCS

description: nucleic acid


title: 167_glial_114_2242.1_hCS

description: nucleic acid


title: diff7.day28.c5a.d14dox


title: diff7.day21.c5a.d0dox


title: diff7.day21.c5a.d14dox


title: 166_neuronal_114_2242.1_hCS

description: nucleic acid


title: 168_glial_114_2242.1_hCS

description: nucleic acid


title: 162_glial_491_6593.8_hCS

description: nucleic acid


title: 161_glial_491_6593.8_hCS

description: nucleic acid


title: diff10.day28.par.nd


title: 129_ipsc_0_2242.1

description: nucleic acid

value: ipsc

value: nuclei


title: diff6.day28.par.nd

value: no dox


title: diff10.day28.par.d0dox


title: diff6.day28.par.d0dox


title: 124_ipsc_0_8858.1

description: nucleic acid

value: dissociated


title: diff10.day28.dis.nd

value: disomic


title: 171_neuronal_107_2242.1_hSS

description: nucleic acid


title: diff10.day28.c5a.nd


title: 122_ipsc_0_8858.1

description: nucleic acid


title: diff10.day28.c5a.d0dox


title: diff7.day28.c5a.d21dox


title: 120_ipsc_0_2242.1

description: nucleic acid


title: diff10.day28.c5a.d21dox


title: 121_ipsc_0_8858.1

description: nucleic acid


title: SJALL040104

description: Patient RNA Seq Data

source_name: acute lymphoblastic leukemia patient

extract_protocol:
RNA was extracted using either TRI-reagent or Qiagen RNAeasy
Libraries were constructed using standard Illumina procedures

value: acute lymphoblastic leukemia


title: diff10.day28.c5a.d14dox


title: 119_ipsc_0_2242.1

description: nucleic acid


title: diff10.day21.c5a.nd


title: 118_ipsc_0_2242.1

description: nucleic acid


title: diff10.day21.c5a.d0dox


title: diff10.day21.c5a.d14dox


title: 115_whole_25_8858.1_hSS

description: nucleic acid

value: whole


title: 117_ipsc_0_2242.1

description: nucleic acid


title: RXL_input control

description: Input control

data_processing:
BWA v 0.014aligner to align reads
MACS2 v 0.015
peaks were called at FDR <0.05
Genome_build: hg19
Supplementary_files_format_and_content: Process file contains peaks for PAX5 binding vs control in NALM6 cells

source_name: NALM6 leukemia cell line

growth_protocol: Cells were grown for 4 days at 37C 5% CO2 in RPMI without Phenol-RED +10% FBS +2mM glutamine

extract_protocol:
DNA was extracted using Qiagen kit
Libraries were constructed using standard Illumina procedures

treatment_protocol: No Treatment

tag: antibody


title: 123_ipsc_0_8858.1

description: nucleic acid


title: SJALL040106

description: Patient RNA Seq Data


title: IPSC3

city: Sydney

first: John

middle: William

last: Manion

address: Charles Perkins Centre, John Hopkins Drive

department: SOLES

institute: The University of Sydney

data_processing:
QC: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30  and GC content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We  selected TopHat as the mapping tool for that TopHat can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
Quantification of gene expression level  HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length  for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Ensembl release 90 Human genome
Supplementary_files_format_and_content: Txt file contains FPKM and Raw Reads

source_name: Stem cell derived

extract_protocol:
Total RNAwas harvested from hiPSC and GABAergic neuron cultures by using the Favorgen Blood/Cultured Cell Total RNA kit (Favorgen Biotech Corp.). RNA was treated with DNase in solution using On-Column DNase I Digestion Set (Sigma) and maintained with Ribosafe RNase inhibitor (Bioline) 40U per sample. Quality and quantity of RNA were assessed by absorbance spectroscopy (Nanodrop, Thermo Fisher Scientific Life Sciences), Agilent Bio-analyser and Agarose gel electrophoresis.
Library preparation was performed using the NEBNext Ultra RNA library prep kit for Illumina. Index coded samples were clustered using the HiSeq PE Cluster Kit cBot-HS (illumina) and the resultant libraries were sequenced on an illumine hiseq platform and 125/150BP paired end reads were generated

value: iPSC


title: IPSC2


title: 111_whole_25_8858.1_hCS

city: Stanford

description: nucleic acid


title: 112_whole_25_8858.1_hCS

description: nucleic acid


title: 130_ipsc_0_8858.1

description: nucleic acid


title: 109_whole_25_2242.1_hSS

description: nucleic acid


title: IPSC1


title: Sensory_Neuron4

value: stem cell-derived Sensory neuron


title: Sensory_Neuron3


title: 108_whole_25_2242.1_hSS

description: nucleic acid


title: Sensory_Neuron2


title: Sensory_Neuron1


title: 101_whole_140_hfb.1

description: nucleic acid

value: hfb


title: 114_whole_25_8858.1_hSS

description: nucleic acid

value: forebrain spheroid


title: GABA_Neuron1

value: stem cell-derived GABA neuron


title: NALM6_PAX5 CHIP-seq

description: NALM6_PAX5 CHIP-seq

value: PAX5, Abcam :ab15164


description:
697_24hr_htseq-count.txt
697-240-1-24-3
697 shCELSR2 24hr prednisolone replicate 3

data_processing:
STAR Aligner used to align reads
edgeR TIMM normalization
LIMMA used to generate CPM (counts per million) filtered for at least 10 counts per transcript
p.adjust function used to assign FDR
Genome_build: hg19
Supplementary_files_format_and_content: Each processed file contains Counts for each gene, columns are related to each sample (replicates of three) in each time point 0hr prednislone or 24 hr prednisolone in either NALM6 cell line or 697 cell line.

source_name: 697 shCELSR2 24hr prednisolone

growth_protocol: Leukemia cell lines Nalm-6 or 697 were grown in standard conditions RPMI-1640 10%FBS 200mM glutamine with puromycin to select shRNA vectors

treatment_protocol: 0 hr or 24 hr prednisolone treatment

tag: knockdown

value: 697 shCELSR2


title: GABA_Neuron3


title: GABA_Neuron2