title: 1001200502_K1


title: 1001200509_M10

status: Public on Feb 18 2020

type: SRA

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

library_source: transcriptomic

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic islets

extract_protocol:
SmartSeq2 (21X-23X PCR cycles)
SmartSeq2 (21X-23X PCR cycles)

tag: cryopreserved

value: No

tag: diabetes

value: nondiabetic

tag: Sex

value: M

tag: patched

value: FACS


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title: 2333 WT

status: Public on Feb 08 2020

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

data_processing:
RNA-Seq was performed using Illumina 4000 High-seq platform
Base-calling software: Illumina Casava 1.8 software
Alignment was conducted using TopHat (version 2.0.13) and Bowtie (version 2.2.1), with default parameter settings, with exception of: "---b2-very-sensitive" for additional search of valid alignments
Expression quantitation was performed with HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: htseq raw counts

organism: Mus musculus

source_name: Cardiac ventricle

growth_protocol: Single housed

extract_protocol:
Qiagen RNeasy Plus Mini Kit
stranded TruSeq mRNA (poly A selection).

treatment_protocol: No treatment

tag: genotype

value: WT

tag: tissue

value: Cardiac ventricle


title: 1001200508_A13


title: transfection_GM12878_1_stim

status: Public on Feb 11 2020

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
A bowtie index of the ordered probe sequences and 16Ns for the barcode was created and the long reads for mapping barcodes to enhancers aligned to this index using Bowtie2. Associated barcodes were extracted and classified into those that map uniquely to a specific error-free probe, and those that do not (probe_barcode_association_3.4E6_2.map.gz).
MPRA RNA output and DNA input sequencing reads were mapped to the known tag sequences using a custom python script (quantifyRNATags.py), allowing for up to four mismatches within the constant region (the common sequence before the tag sequence) and no mismatches within the tag sequence.
The barcode counts were input, and tags having fewer than 30 reads in the input (DNA) or 4 reads in the output (RNA) were excluded from subsequent analysis.
The log(DNA/RNA) ratio (“expression”) was calculated using raw counts, scaled so that the median expression is 0, and the expression levels G+C-content normalized such that the mean expression for every %G+C was 0.
Finally, to eliminate instances where the tag sequence modifies the apparent expression level, any tags containing any one of eight blackballed 5-mer DNA sequences were excluded. Blackballed 5-mers were defined as those for which the absolute value of the average expression level of all tags containing that 5-mer was greater than 0.15.
SNPs were tested for allele-specific reporter activity by a two-sided Student’s t-test, comparing the normalized log(RNA/DNA) expression values for the tags for allele A compared to the tags for allele B. Only SNPs for which we had at least 80 good tags between the two alleles were tested. P-values were corrected for multiple hypothesis testing by Benjamini-Hochberg FDR correction. Only SNPs that had an FDR<0.1 for at least two of the replicates and where the direction of allele- specific reporter activity was consistent between all replicates were considered to be significant.
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab delimited or fasta; barcodes for each element, enhancer sequences

source_name: EBV transformed B cell line

growth_protocol: BJAB, Jurkat, U937, and GM12878 cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% L-Glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K-1M cells/mL.

extract_protocol:
Total RNA was extracted from cells using Qiagen Maxi RNeasy (Qiagen, 75162) following the manufacturer’s protocol including the on-column DNase digestion. A second DNase treatment was performed on the purified RNA using 5 μL of Turbo DNase (Life Technologies, AM2238) with buffer, in 750 μL of total volume for 1 hour at 37°C. The digestion was stopped with the addition of 7.5 μL 10% SDS and 75 μL of 0.5M EDTA followed by a 5 minute incubation at 70°C. The total reaction was then used for pulldown of GFP mRNA. Water was added to the DNase digested RNA to bring the total volume to 898 μL to which 900 μL of 20X SSC (Life Technologies, 15557-044), 1800 μL of Formamide (Life Technologies, AM9342) and 2 μL of 100 uM biotin-labeled GFP probe (GFP_BiotinCapture_1-3, IDT, Ext. Data Table 10) were added and incubated for 2.5 hours at 65°C. Biotin probes were captured using 400 μL of pre- washed Streptavidin beads (Life Technologies, 65001) eluted in 500 μL of 20X SSC. The hybridized RNA/probe bead mixture was agitated on a nutator at room temperature for 15 minutes. Beads were captured by magnet and washed once with 1x SSC and twice with 0.1x SSC. Elution of RNA was performed by the addition of 25 μL water and heating of the water/bead mixture for 2 minutes at 70°C followed by immediate collection of eluent on a magnet. A second elution was performed by incubating the beads with an additional 25 μL of water at 80°C. A final DNase treatment was performed in 50 μL total volume using 1 μL of Turbo DNase with addition of the buffer incubated for 60 minutes at 37°C followed by inactivation with 1 μL of 10% SDS and purification using RNA clean SPRI beads (Beckman Coulter, A63987).
First-strand cDNA was synthesized from half of the DNase-treated GFP mRNA with SuperScript III and a primer specific to the 3’ UTR (MPRA_v3_Amp2Sc_R) using the manufacturer’s recommended protocol, modifying the total reaction volume to 40 μL and performing the elongation step at 47°C for 80 minutes. Single-stranded cDNA was purified by SPRI and eluted in 30 μL EB.  To minimize amplification bias during the creation of cDNA tag sequencing libraries, samples were amplified by qPCR to estimate relative concentrations of GFP cDNA using 1 μL of sample in a 10 μL PCR reaction containing 5 μL Q5 NEBNext master mix, 1.7 μL Sybr green I diluted 1:10,000 (Life Technologies, S-7567) and 0.5 uM of TruSeq_Universal_Adapter and MPRA_Illumina_GFP_F primers (Ext. Data Table 10). Samples were amplified with the following qPCR conditions: 95°C for 20 seconds, 40 cycles (95°C for 20 sec, 65°C for 20 sec, 72°C for 30 sec), 72°C for 2 min. The number of cycles for sample amplification was 1-n (the number of cycles it took for each sample to pass the threshold) from the qPCR. To add Illumina sequencing adapters, 10  uL of cDNA samples and mpra:pTNFAIP3:gfp plasmid control (diluted to the qPCR cycle range of the samples) were amplified using the reaction conditions from the qPCR scaled to 50 uL, excluding Sybrgreen I. Amplified cDNA was SPRI purified and eluted in 40 μL of EB. Individual sequencing barcodes were added to each sample by amplifying the entire 40 μL elution in a 100 μL Q5 NEBNext reaction with 0.5 uM of TruSeq_Universal_Adapter primer and a reverse primer containing a unique 8 bp index (Illumina_Multiplex, Ext. Data Table 10) for sample demultiplexing post-sequencing. Samples were amplified at 95°C for 20 seconds, 6 cycles (95°C for 20 sec, 64°C for 30 sec, 72°C for 30 sec), 72°C for 2 minutes. Indexed libraries were SPRI purified and pooled according to molar estimates from Agilent TapeStation quantifications. Samples were sequenced using 1x30 bp chemistry on an Illumina HiSeq 2500 or NextSeq.   To determine oligo/barcode combinations within the MPRA pool, Illumina libraries were prepared from the mpra∆orf plasmid library by performing 4 separate amplifications with 200 ng of plasmid in a 100 μL Q5 NEBNext PCR reaction containing 0.5 uM of TruSeq_Universal_Adapter and MPRA_v3_TruSeq_Amp2Sa_F primers with the following conditions: 95°C for 20 sec, 6 cycles (95°C for 20 sec, 62°C for 15 sec, 72°C for 30 sec), 72°C for 2 minutes. Amplified material was SPRI purified using a 0.6x bead/sample ratio and eluted with 30 μL of EB. Sequencing indexes were then attached using 20 μL of the eluted product and the same reaction conditions as for the tag-seq protocol, except the number of enrichment cycles was lowered to 5. Samples were molar pooled and sequenced using 2x150 bp chemistry on Illumina HiSeq 2500 and NextSeq.
MPRA library preparation

treatment_protocol: Jurkat T cells were stimulated with 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour prior to harvesting. BJAB and GM12878 B cells were stimulated with 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours. U937 monocytes were stimulated with 100 ng/mL LPS for 2 hours.

tag: stim condition

value: 2.5ug/ml anti-IgM + 2.0 ug/ml anti-CD40 2 hours

tag: cell line

tag: vector delivery

value: transfection

tag: replicate


title: transfection_GM12878_3_stim


title: 2329 WT


title: transfection_GM12878_2_stim


title: transfection_GM12878_2_unstim


title: 2337 KO

value: Scn1b KO


title: 2324 KO


title: 2478 WT


title: 2338 KO


title: Sample 127465: eGFP6

data_processing:
RNA-Seq was performed using Illumina NovaSeq-6000, paired-end 50 cycle
Base-calling software: Illumina Casava 1.8 software
Alignment was conducted using TopHat (version 2.0.13) and Bowtie (version 2.2.1), with default parameter settings, with exception of: "---b2-very-sensitive" for additional search of valid alignments
Expression quantitation was performed with HTSeq
Genome_build: CriGri_1.0
Supplementary_files_format_and_content: htseq raw counts

molecule: polyA RNA

organism: Cricetulus griseus

source_name: lung

growth_protocol: Incubator; 37 degrees C and 5% CO2

value: eGFP

value: lung


title: 2336 KO


title: Sample 127463: eGFP4


title: Sample 127462: eGFP3


title: Sample 127464: eGFP5


title: Sample 127461: WTICD5


title: Sample 127459: WTICD3


title: transfection_GM12878_3_unstim


title: Sample 127458: WTICD1


title: Sample 127460: WTICD4


title: TW_2_2

status: Public on Feb 05 2020

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

country: China

institute: Peking University

description: polyA RNA, cultured with traveling waves

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling. Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the human reference genome (hg19) using Tophat software.
We quantified the relative expression level as log2(FPKM + 1) to perform PCA analysis and hierarchical clustering. Uniquely mapped reads counted by HTSeq were used to conduct differential-expression analysis in DEseq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_expression_FPKM.txt: Tab-delimited text files include the FPKM values of RefSeq genes.

source_name: hiPSC derived cardiomyocytes

growth_protocol: Human iPSCs 253G1 derived cardiomyocytes cultured in medium.

extract_protocol:
Total RNA in tissue was harvested using Trizol reagent (Life Technologies) according to manufacturer instructions. The purified mRNAs were used to construct the cDNA library with the NEB RNA library construct kit. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.
A total of 1.5 μg RNA per sample was used as input material for RNA sample preparations. Sequencing libraries were generated using a NEBNext UltraTM RNA library prep kit Illumina (New England Biolabs, Ipswich, MA, USA) according to manufacturer instructions, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and fragmentation was performed using divalent cations under an elevated temperature in NEBNext First Strand Synthesis reaction buffer (5×; New England Biolabs). First-strand cDNA was synthesized using a random hexamer primer and M-MuLV reverse transcriptase (RNase H−; New England Biolabs). Second-strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptor (New England Biolabs) with a hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of the correct length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, MA, USA), after which 3 µL USER enzyme (New England Biolabs) was incubated with size-selected, adaptor-ligated cDNA at 37°C for 15 min, followed by 5 min at 95°C. PCR was performed using a Phusion high-fidelity DNA polymerase, universal PCR primers, and an Index (X) primer (New England Biolabs). Products were purified (AMPure XP; Beckman Coulter), and library quality was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies).

treatment_protocol: The cardiomyocytes were cultured for 14 day with or without traveling wave.

tag: cell type

value: hiPSC derived cardiomyocytes


title: transfection_GM12878_1_unstim


title: TW_2_1


title: TW_1_2


title: TW_0_2

description: polyA RNA, cultured without traveling waves


title: TW_0_1


title: 2326 WT


title: TW_1_1


title: N07

status: Public on Feb 03 2020

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

department: Pathology

country: South Korea

institute: Cha University

data_processing:
Alignment of the sequences to the reference immuneresponse V3.1 and counting of the sequencing reads were performed using the ImmuneResponseRNA Report plug-in in Torrent Suite software (Version 5.2)
Targets of the panel (Oncomine Immune Response Panel) are about 400 genes
Genome_build: hg19
Supplementary_files_format_and_content: TPM.tsv file was generated by calculating TPM (Transcripts Per Million) by normalizing each gene length and the total read counts. Scores represent TPM.
Supplementary_files_format_and_content: raw_count.tsv file was generatedy by using ImmuneResponseRNA Report plug-in in Torrent Suite Software (Version 5.2). Scores represent raw read counts.

source_name: non-small cell lung cancer cells

growth_protocol: Cases showing a partial or complete response to anti-PD-1 antibody (nivolumab or pembrolizumab) by Response Evaluation Criteria in Solid Tumor (RECIST) v1.1 lasting >24 weeks or stable disease lasting >24 weeks were considered as having a durable clinical benefit (DCB). Cases showing progression of disease or stable disease lasting ≤24 weeks were considered as showing no durable benefit (NDB).

extract_protocol:
For RNA extraction, 2–10 sections of 10 µm-thick formalin-fixed paraffin-embedded tissue were prepared. After macrodissection of the tumor area, RNA were extracted using the Recover All Total Nucleic Acid Isolation kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol. RNA concentrations were determined with the Qubit RNA HS Assay Kit and Qubit 3.0 Fluorometer (Thermo Fisher Scientific).
RNA was reverse-transcribed into cDNA using the SuperScript VILO™ cDNA synthesis kit (Thermo Fisher Scientific). Libraries were prepared manually using the Ion AmpliSeq™ Library kit 2.0 (Life Technologies, Carlsbad, CA, USA) and Oncomine™ Immune Response Research Assay (Thermo Fisher Scientific). A 50-pM pool of RNA libraries was used for sequencing of a 395-gene panel focused on diverse immunological processes including tumor infiltration by immune cells, and other key immune functions. Template preparation and enrichment were performed using an Ion Chef™ system (Thermo Fisher Scientific) and Ion 520™ & Ion 530™ Kit – Chef (Thermo Fisher Scientific). Sequencing was performed on an Ion S5™ XL Sequencer using an Ion 530 Chip and Ion S5™ sequencing kit (all from Thermo Fisher Scientific).

tag: tumor type

value: squamous cell carcinoma

value: male

tag: survival

value: recurrence:1, progression-free-survival_days:64, live, overall-survival_days:145


title: N11

value: recurrence:1, progression-free-survival_days:53, dead, overall-survival_days:71


title: 1001200508_A16

value: No


title: N04

value: adenocarcinoma

value: female

value: recurrence:1, progression-free-survival_days:37, dead, overall-survival_days:105


title: D05

value: recurrence:0, progression-free-survival_days:281, live, overall-survival_days:281


title: N09

value: recurrence:1, progression-free-survival_days:21, dead, overall-survival_days:914


title: N12

value: recurrence:1, progression-free-survival_days:45, live, overall-survival_days:271


title: N02

value: recurrence:1, progression-free-survival_days:8, dead, overall-survival_days:8


title: N03

value: recurrence:1, progression-free-survival_days:52, dead, overall-survival_days:121


title: D08

value: Large cell neuroendocarine carcinoma

value: recurrence:1, progression-free-survival_days:191, dead, overall-survival_days:376


title: N01

value: lung

value: recurrence:1, progression-free-survival_days:35, dead, overall-survival_days:39


title: D02

value: squamous cell carcinoma

value: recurrence:0, progression-free-survival_days:357, live, overall-survival_days:357


title: D01

value: recurrence:1, progression-free-survival_days:144, live, overall-survival_days:234


title: D03

value: male

value: recurrence:0, progression-free-survival_days:1088, live, overall-survival_days:1088


title: N10

value: adenocarcinoma-squamous cell carcinoma

value: recurrence:1, progression-free-survival_days:70, dead, overall-survival_days:70


title: D04

value: adenocarcinoma

value: recurrence:1, progression-free-survival_days:315, live, overall-survival_days:315


title: N06

value: recurrence:1, progression-free-survival_days:54, dead, overall-survival_days:147


title: D06

value: recurrence:1, progression-free-survival_days:253, dead, overall-survival_days:262


title: ZG302383_PL

status: Public on Jan 21 2020

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

description:
Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using bowtie2 with default parameters.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: ProcessedDataMatrix_biofilm_isolates.xlsx: Processed data file is a data matrix that contains raw unique gene reads.

organism: Pseudomonas aeruginosa

growth_protocol: Biofilm cells were grown statically in LB for 12h to 48h (96-well microtiter plates); planktonic cultures were grown in LB to an OD600=2 (shaking).

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) were used according to the manufacturer’s instruction.
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).

treatment_protocol: Directly after cultivation the biofilm cells were treated with one volume of RNAlater (Qiagen); planktonic cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C.

tag: isolate

value: clinical

tag: location

value: Gorlitz

tag: infection side

value: nd/other

tag: growth condition

value: planktonic


title: ZG316717_PL

value: ear infection


title: ZG8038581181_PL

value: Chemnitz

value: respiratory tract


title: Psae1656_PL

value: Munich


title: D07

value: lung

value: female

value: recurrence:1, progression-free-survival_days:259, dead, overall-survival_days:259


title: PSAE1837_PL

value: Gera


title: PSAE1934_PL

value: Bremen


title: PA14_PL_replicate2

value: Liberati et al. 2007

value: burn wound


title: N08

value: squamous cell carcinoma

value: male

value: recurrence:1, progression-free-survival_days:28, dead, overall-survival_days:329


title: PA14_PL_replicate1

value: clinical

value: Liberati et al. 2006


title: MHH17704_PL

value: Hannover Medical School

value: nd/other

value: planktonic


title: MHH17767_PL

value: respiratory tract


title: N05

value: adenocarcinoma

value: recurrence:1, progression-free-survival_days:64, dead, overall-survival_days:260


title: MS5_PL

value: University Hospital Munster


title: MHH17546_PL


title: D09

value: lung

value: recurrence:1, progression-free-survival_days:362, dead, overall-survival_days:362


title: MHH16951_PL


title: MHH15103_PL

value: wound infection


title: MHH16798_PL


title: MHH16563_PL


title: MHH1525_PL


title: MHH16050_PL


title: ZG302442_PL

value: Gorlitz

value: ear infection


title: M70646077_PL

value: rectal infection


title: ZG8510487_PL

value: Leipzig

value: urinary tract


title: M70639645_PL

value: clinical


title: M70564993_PL


title: MHH15015_PL


title: M70647319_PL


title: F2166_PL

value: University Hospital Frankfurt


title: F2224_PL


title: F2856_PL


title: F2165_PL


title: F2059_PL


title: F2056_PL


title: F2055_PL


title: F2020_PL


title: F2006_PL


title: F2044_PL


title: F1959_PL


title: F1864_PL


title: F1997_PL


title: F1862_PL


title: F1764_PL


title: F1659_PL


title: ZG8038581181_BF48_dyn

description:
Cells were grown in static biofilm cultures (96-well microtiter plates) for 48h and incubated for 10 min in RNAlater reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx

value: Chemnitz

value: biofilm

tag: growth time


title: ESP076_PL

value: University Hospital Palma de Mallorca, Spain

value: nd/other

value: planktonic


title: ESP088_PL


title: ZG8038581181_BF24_dyn

description:
Cells were grown in static biofilm cultures (96-well microtiter plates) for 24h and incubated for 10 min in RNAlater reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx

value: respiratory tract


title: ZG8038581181_BF36_dyn

description:
Cells were grown in static biofilm cultures (96-well microtiter plates) for 36h and incubated for 10 min in RNAlater reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx


title: ESP067_PL


title: ESP063_PL


title: ESP083_PL


title: F2081_PL


title: F2030_PL


title: ESP032_PL


title: PSAE1656_BF48_dyn

value: Munich


title: ESP058_PL


title: ESP046_PL


title: ESP031_PL


title: ESP027_PL


title: CH5591_PL

value: Charite Berlin


title: CH4681_PL


title: CH4634_PL


title: CH4703_PL


title: PSAE1656_BF36_dyn


title: PSAE1656_BF24_dyn


title: PSAE1656_BF12_dyn

description:
Cells were grown in static biofilm cultures (96-well microtiter plates) for 12h and incubated for 10 min in RNAlater reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx


title: MHH17767_BF48_dyn

value: Hannover Medical School


title: CH4035_PL


title: CH3462_PL


title: CH2860_PL


title: ZG8038581181_BF12_dyn


title: CH4528_PL


title: MHH17767_BF24_dyn


title: MHH17767_BF36_dyn


title: CH2747_PL


title: CH3466_PL

value: sepsis


title: CH2724_PL


title: CH2706_PL


title: CH2685_PL


title: CH2690_PL


title: CH2682_PL


title: F2059_BF36_dyn

value: wound infection


title: F2059_BF24_dyn


title: F2059_BF48_dyn


title: CH2680_PL


title: CH4591_PL


title: CH2678_PL


title: CH2677_PL


title: CH2665_PL


title: CH2597_PL


title: F2059_BF12_dyn


title: F2020_BF48_dyn


title: CH2582_PL


title: CF592_Iso2_PL

value: University Hospital Essen


title: CH2824_PL


title: F2020_BF36_dyn


title: MHH17767_BF12_dyn


title: ZG8038581181_BF48_replicate2


title: F2020_BF24_dyn


title: ZG8510487_BF48


title: ZG8038581181_BF48_replicate1


title: F2020_BF12_dyn


title: ZG316717_BF48_replicate2

value: Gorlitz

value: ear infection


title: ZG316717_BF48_replicate1


title: ZG302442_BF48


title: PSAE1934_BF48

value: Bremen


title: PSAE1837_BF48

value: clinical

value: Gera


title: ESP067_BF24_dyn


title: ESP067_BF36_dyn


title: ZG302383_BF48


title: ESP067_BF12_dyn


title: PA14_BF48

value: Liberati et al. 2006

value: burn wound


title: PSAE1656_BF48

value: biofilm


title: MHH17546_BF48


title: MHH17767_BF48


title: MHH17704_BF48_replicate2

value: nd/other


title: MHH17704_BF48_replicate1


title: MHH16798_BF48


title: MS5_BF48

value: University Hospital Munster


title: MHH16951_BF48

value: respiratory tract


title: MHH16050_BF48


title: MHH16563_BF48_replicate1


title: M70647319_BF48_replicate2


title: MHH15103_BF48


title: MHH1525_BF48


title: ESP067_BF48_dyn

value: University Hospital Palma de Mallorca, Spain


title: M70647319_BF48_replicate1


title: M70639645_BF48

value: urinary tract


title: M70646077_BF48

value: rectal infection


title: F2856_BF48

value: University Hospital Frankfurt


title: F2224_BF48


title: M70564993_BF48


title: F2166_BF48


title: F2137_BF48

value: wound infection


title: F2165_BF48


title: F2056_BF48


title: F2055_BF48


title: F2044_BF48


title: F2059_BF48


title: F2081_BF48


title: F2006_BF48_replicate2


title: F1997_BF48

description:
Cells were grown in static biofilm cultures (96-well microtiter plates) for 48h and incubated for 10 min in RNAlater reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
F1997_BF
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx


title: F2006_BF48_replicate1


title: F1864_BF48


title: F2030_BF48


title: MHH15015_BF48

value: Hannover Medical School


title: F1959_BF48


title: F2020_BF48


title: F1764_BF48_replicate2


title: F1764_BF48_replicate1


title: F1764_BF48_replicate3


title: F1862_BF48


title: F2137_PL

value: planktonic


title: ESP083_BF48


title: ESP088_BF48


title: F1659_BF48


title: ESP076_BF48


title: ESP067_BF48


title: ESP058_BF48


title: ESP046_BF48


title: ESP063_BF48


title: ESP031_BF48


title: ESP032_BF48


title: ESP027_BF48_replicate2


title: ESP027_BF48_replicate1


title: CH4703_BF48

value: Charite Berlin


title: CH4634_BF48_replicate2


title: CH5591_BF48


title: CH4681_BF48


title: CH4634_BF48_replicate1


title: CH4528_BF48_replicate2


title: CH4035_BF48


title: CH4528_BF48_replicate1


title: CH3462_BF48


title: CH2860_BF48


title: CH3466_BF48

value: sepsis


title: CH2824_BF48

value: clinical


title: CH2747_BF48


title: CH2724_BF48


title: CH2706_BF48


title: CH2685_BF48


title: CH2690_BF48


title: CH2682_BF48_replicate1


title: CH2682_BF48_replicate2


title: CH2677_BF48


title: CH2678_BF48


title: CH2665_BF48


title: CH2597_BF48


title: CF592_Iso2_BF48

value: University Hospital Essen


title: CH4591_BF48


title: CH2582_BF48


title: Sample_C1_NOHDI_200U-R1

status: Public on Jan 01 2020

city: TALLAHASSEE

first: LAUREN

middle: A

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

description: Normal

library_source: genomic

data_processing:
Basecalls performed with CAVASA version v1.8.4.
Sequencing data aligned to the HG19 genome using bowtie2 version 2.2.2, --wrapper basic -0 --end-to-end -p 23 --no-mixed --no-discordant -I 0 -X 500 -q -x -S
Using samtools via the R package gyro (https://github.com/dvera/gyro), raw files converted from sam to bam files, minQual=20.
Bed files were generated using bedtools via the R package travis (https://github.com/dvera/travis) and mat10 files were created using the package genmat (https://github.com/dvera/genmat). Nucleosome distributions were calculated by fragments per million for each bp in the 2kb surrounding each TSS (bedtoolsCoverage). Midpoints for nucleosome distributions were determined through the calculation of center fragments in 60 bp windows at a 10 bp step in the 2kb surrounding each TSS.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: mat10 files

molecule: genomic DNA

source_name: B-Lymphocyte

growth_protocol: GM12878 cells were grown in RPM1 1640 media, supplemented with 15% Fetal Bovine Serum and 1X PSG.

extract_protocol:
Nuclei were isolated in nucleus isolation buffer containing: 10 mM HEPES at pH 7.8, 2 mM MgOAc2, 0.3 M sucrose, 1 mM CaCl2, and 1% Nonidet P-40. The nuclei were then pelleted by centrifugation at 1000g for 5 min at 4°C.
Using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), DNA sequencing libraries were prepared for the mononucleosomal-sized and sub-nucleosomal-sized fragments for each sample. DNA was end-prepped using NEB Prep enzyme mix, end-repair reaction buffer (10X), and 30 ng of DNA for each samples, then held at 30 degrees Celsius for 30 minutes and then at 65 degrees Celsius for 30 minutes. Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted ligated products. The universal and indexed sequences were added by PCR using 23 ul of adaptor-ligated DNA fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina. Then PCR was done for 8 cycles (not including the initial denaturation and final extension). The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted products. The libraries were quality-checked using Agilent 2100 Bioanalyzer High-Sensitivity. Across the libraries, the samples ranged between 200-400bp and there were no adapter or primer dimers.

treatment_protocol: For HKST treatment, GM12878 cells were stimulated with 1.0X10e9 heat-killed Salmonella typhimurium for 20 minutes, 40 minutes and 60 minutes and subsequently harvested.

value: B-lymphoblastoid cell line

tag: treatment

value: Untreated

tag: mnase digest

value: Heavy


title: human fallopian tube scRNA-seq (benign donors) [sc_b1_K09]

status: Public on Jan 10 2020

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequencing files were trimmed by Trim Galore!, mapped to UCSC hg19 human genome assembly by STAR (Dobin et al., 2012) and counted by FeatureCount (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: read counts in txt format

source_name: human fallopian tube

extract_protocol:
The fallopian tube samples were processed in 1 hour, after being collected from the hospital. The tissues were dissociated with Human Tumor Dissociated kit (Miltenyi Biotec) and filtered using 100µm SmarterStrainers (Miltenyi Biotec).
SMART-seq2 for single-cell RNA-seq

value: normal fallopian tube cells


title: Sample_C1_NOHDI_20U-R1

description: Normal

value: Light


title: Sample_20m_NOHDI_200U-R1

description: Normal

value: 20 minute incubation with HKST


title: Sample_40m_NOHDI_20U-R1

description: Normal

value: 40 minute incubation with HKST


title: Sample_60m_NOHDI_200U-R1

description: Normal

value: 60 minute incubation with HKST


title: CH2680_BF48

value: nd/other

value: biofilm


title: SBT_2

status: Public on Dec 31 2019

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

description:
iCDC-P30
SB431542 inhibitor-treated iCDC at passage 30.
Heart ventricle
processed data file: all_compare.txt
processed data file: gene.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: all_compare.txt
Supplementary_files_format_and_content: gene.txt

source_name: cardiosphere derived cells

extract_protocol:
Primary CDCs, iCDC and SB431542-treated iCDC RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: iCDC were treated with SB431542 for 3 days.

tag: strain/background

value: iCDC

tag: passage


title: SBT_3


title: SBT_1


title: P0_3

description:
Primary CDCs isolated from heart explant culture.
Heart ventricle
processed data file: all_compare.txt
processed data file: gene.txt

value: Primary CDC


title: P0_2


title: P30_1

description:
iCDC-P30
hTERT immortalized CDCs (iCDC) at passage 30.
Heart ventricle
processed data file: all_compare.txt
processed data file: gene.txt


title: ATAC.rep3.gTKO.743

status: Public on Dec 05 2019

city: Boston

first: Eric

last: Engelbrecht

address: 1 Blackfan Street

department: Vascular Biology Program

institute: Boston Children's Hospital

description:
ATAC.rep3.gTKO.743
processed data file:
GEO_retina_ATACseq_HOMER_results.xlsx
GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx
retina.gTKO_peaks.narrowPeak.bed
Ret.gTKO.cat.743.438.440.final.sorted.bw

data_processing:
ATAC-seq: Read alignment to the MGSCv37 (mm9) genome assembly was performed with bowtie2 (Langmead & Salzberg, 2012) and the options: --very-sensitive –X 2000 –no-mixed –no-discordant. Duplicated fragments were removed using the Picard “MarkDuplicates” script with the options: Remove_Duplicates=true Validation_stringency=lenient (http://broadinstitute.github.io/picard/).   Paired-end reads were separated, centered on Tn5 cut sites, and trimmed to 10 bp using a custom in-house script. Peaks were called using the MACS2 “callpeak” script (Zhang et al., 2008) with options: -B –keep-dup all –nomodel –nolambda –shift -75 –extsize 150. Reads mapping to murine blacklisted regions and mitochondrial DNA were masked out of peak lists using the Bedtools “intersect -v” script (Quinlan & Hall, 2010).   Replicates from each biological group were merged using the bedops “merge” script to generate one high-confidence peak set for each of the two biological groups (Control and gTKO) (Neph et al., 2012). These two peak sets were then merged to generate a final merged peak set of 62,748 peaks. For each replicate, reads covering consensus peak intervals were counted using the Bedtools “coverage” script with the “-counts” option (Quinlan & Hall, 2010). The resultant count table was input to edgeR (M. D. Robinson et al., 2010) to determine differentially accessible peaks (DAPs), which can be found in the excel file “GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx”. HOMER results from different peak inputs are in the excel file “GEO_retina_ATACseq_HOMER_results.xlsx”.
Base calls were performed using Illumina CASAVA 1.8.2
bigWig files:  Nucleotide-resolution coverage (bigWig) tracks were generated by first combining trimmed reads from each replicate, then inputting the resultant .bam files to the DeepTools (Ramirez et al., 2016) “bamCoverage” script with options “—normalizeUsing RPGC –binSize 1”.
bulk RNA-seq: Reads from each sample were aligned to the MGSCv37 (mm9) genome assembly using STAR (Dobin et al., 2013) with the options: --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM. Gene-level counts over UCSC annotated exons were calculated using the Rsubread package and “featureCounts” script (Liao, Smyth, & Shi, 2013) with options: -M –O –p –d 30 –D 50000. The resultant count table was input to edgeR (M. D. Robinson, McCarthy, & Smyth, 2010) for differential gene expression analysis.
bulk RNA-seq: The .bam files from STAR were input to the RSEM (B. Li & Dewey, 2011) script “rsem-calculate-expression” with default parameters to generate FPKMs for each replicate. FPKMs are located in the excel files called "GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx" and “GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx”.
Genome_build: mm9
Supplementary_files_format_and_content: The excel files "GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx" and “GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx” include RSEM-generated FPKMs and the edgeR output for RNA-seq experiments.     The excel file “GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx” includes the edgeR output for the ATAC-seq experiment. HOMER results from different peak inputs are in the excel file “GEO_retina_ATACseq_HOMER_results.xlsx”.     All 58,311 and 50,178 merged Control and gTKO peaks, respectively, are included in the .bed files “retina.Control_peaks.narrowPeak.bed”, and “retina.gTKO_peaks.narrowPeak.bed”. The bigWig files were generated as described in "data processing".

growth_protocol: Mice were housed in our animal facility with food ad libitum and 12 hr light/dark cycles. Animals were used in accordance with protocols approved by the Institutional Animal Care and Use Committees (IACUC) of Boston Children’s Hospital and the French Department of Education.

extract_protocol:
bulk RNA-seq: Cells were sorted into either 0.1% FAF-BSA/PBS or buffer RLT (Qiagen) supplemented with beta-mercaptoethanol for ATAC-seq and RNA-seq, respectively. Cells sorted into buffer RLT were subjected to total RNA extraction using the RNeasy Micro Kit (Qiagen).
ATAC-seq: ATAC-seq libraries were prepared according to the previously described fast-ATAC protocol (Corces et al., 2016). Briefly, 5,000-8,000 FACS-isolated cells in 0.1% FAF-BSA/PBS were pelleted by centrifugation at 400 xg at 4 ˚C for 5 min. Supernatant was carefully removed to leave the cell pellet undisturbed, then cells were washed once with 1 mL ice-cold PBS. The transposition mix [25 µL buffer TD, 2.5 µL TDE1 (both from Illumina FC-121-1030), 1 µL of 0.5% digitonin (Promega, G9441) and 16 µL nuclease-free water] was prepared and mixed by pipetting, then added to the cell pellet. Pellets were disrupted by gently flicking the tubes, followed by incubation at 37 ˚C for 30 minutes in an Eppendorf ThermoMixer with constant agitation at 300 rpm. Tagmented DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, 28204), and subjected to cycle-limiting PCR as previously described (Buenrostro et al., 2013). Transposed fragments were purified using the MinElute PCR Purification Kit (Qiagen, 28004) and Agilent DNA Tapestation D1000 High Sensitivity chips (Agilent) were used to quantify libraries.
RNA-seq: Double-stranded cDNA was synthesized from 5-10 ng RNA using the SMART-Seq2 v4 Ultra Low RNA Kit for Sequencing (Takara) according to the manufacturer’s instructions.

treatment_protocol: "Control" and "gTKO" pups were given intraperitoneal injections of tamoxifen (100 ug) from P1-P3. "JunB.Control" and "JunB.ECKO" pups were given subcutaneous injections of 4-hydroxytamoxifen (50 ug) from P1-P3.

tag: strain background

tag: genotype/variation

value: S1pr3-/- S1pr1flox/flox S1pr2flox/flox Rosa26-CreERT2

tag: age

value: postnatal day 6

value: FACS-sorted adult mouse retinal endothelial cells


title: P30_2


title: P0_1


title: P30_3


title: ATAC.rep2.Control.437

description:
ATAC.rep2.Control.437
processed data file:
GEO_retina_ATACseq_HOMER_results.xlsx
GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx
retina.Control_peaks.narrowPeak.bed
Ret.Control.cat.742.437.439.sorted.sorted.bw

value: S1pr3-/- S1pr1flox/flox S1pr2flox/flox


title: mEmbryoE85_03_plate2

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institue

description:
SvdB12h-2-3-Tomo-20um-E8p75MouseEmbryo2-Plate2-Run1_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h-2-3-Tomo-20um-E8p75MouseEmbryo2-Plate2-Run1_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h-2-3-Tomo-20um-E8p75MouseEmbryo2-Plate2-Run1_cbc_trimmed_star_spliced.coutt.tsv.gz

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 93 of the mouse genome
Supplementary_files_format_and_content: Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell.

growth_protocol: 120h Mouse gastruloids from IB10 mESCs were generated as described previously (van den Brink et al., Development, 2014; Baillie-Johnson et al., 2014), with the following modifications: After neutralization of trypsin with ESLIF, cells were washed with PBS twice. Next cells, were resuspended in N2B27 medium, and the concentration was determined while cells were already in N2B27. Cells were then diluted in N2B27 to a concentration of 7.5 cells/µl (37.500 cells in 5 ml of N2B27 for a full 96-wells plate), and 40 µl (300 cells) of this suspension was transferred to each well of a U-bottomed 96-wells plate. N2B27 was ordered by Takara (NDiff 227 medium, 500 ml, Y40002) and was thawed and aliquotted to prevent the formation of protein aggregates

extract_protocol:
After cryosectioning, sections are sorted into 96 well plates containing mineral oil, and uniquely barcoded cell specific primers (celseq1 or celseq2 barcodes) for mRNA detection, Spike-in controls inhibitor.
Tomo-seq-celseq: celseq1 runs contain the cell-specific barcode in the first 8 nucleotides in Read 1, followed by the 4-nucleotide long UMI. Celseq2 runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode
Illumina TruSeq adapaters

tag: experiment

value: tomo-seq

tag: protocol/barcodes

tag: section thickness

tag: embryonic stage

tag: sequencing runs

value: 1 from 1

tag: plates

tag: gastruloid barcodes

value: from 1 to 72


title: Sample_60m_NOHDI_20U-R1

description: Normal

tag: cell line

tag: cell type

value: B-lymphoblastoid cell line


title: ATAC.rep1.Control.439

description:
ATAC.rep1.Control.439
processed data file:
GEO_retina_ATACseq_HOMER_results.xlsx
GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx
retina.Control_peaks.narrowPeak.bed
Ret.Control.cat.742.437.439.sorted.sorted.bw


title: ATAC.rep1.gTKO.440

description:
ATAC.rep1.gTKO.440
processed data file:
GEO_retina_ATACseq_HOMER_results.xlsx
GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx
retina.gTKO_peaks.narrowPeak.bed
Ret.gTKO.cat.743.438.440.final.sorted.bw


title: Sample_20m_NOHDI_20U-R1

description: Normal


title: Sample_40m_NOHDI_200U-R1

description: Normal

value: Heavy


title: mEmbryoE85_03_plate1

description:
SvdB12h-2-2-Tomo-20um-E8p85MouseEmbryo2-Plate1-Run1_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h-2-2-Tomo-20um-E8p85MouseEmbryo2-Plate1-Run1_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h-2-2-Tomo-20um-E8p85MouseEmbryo2-Plate1-Run1_cbc_trimmed_star_spliced.coutt.tsv.gz

value: from 60 to 96


title: mEmbryoE85_01_plate2_seqrun2

description:
SvdB12h1-2-2-Tomo-20um-E7p75MouseEmbryo-Plate2-Run1Run2_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h1-2-2-Tomo-20um-E7p75MouseEmbryo-Plate2-Run1Run2_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h1-2-2-Tomo-20um-E7p75MouseEmbryo-Plate2-Run1Run2_cbc_trimmed_star_spliced.coutt.tsv.gz

value: 2 from 2

value: from 2 to 86


title: mEmbryoE85_02_plate2_seqrun2

description:
SvdB12h2-3-2-Tomo-20um-E8p75MouseEmbryo-Plate2-Run1Run2_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h2-3-2-Tomo-20um-E8p75MouseEmbryo-Plate2-Run1Run2_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h2-3-2-Tomo-20um-E8p75MouseEmbryo-Plate2-Run1Run2_cbc_trimmed_star_spliced.coutt.tsv.gz

value: from 1 to 69


title: mEmbryoE85_02_plate2_seqrun1

value: 1 from 2


title: mEmbryoE85_01_plate2_seqrun1


title: mEmbryoE85_02_plate1_seqrun1

description:
SvdB12h2-3-1-Tomo-20um-E8p75MouseEmbryo-Plate1-Run1Run2_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h2-3-1-Tomo-20um-E8p75MouseEmbryo-Plate1-Run1Run2_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h2-3-1-Tomo-20um-E8p75MouseEmbryo-Plate1-Run1Run2_cbc_trimmed_star_spliced.coutt.tsv.gz

value: from 43 to 96


title: mEmbryoE85_01_plate1_seqrun1

description:
SvdB12h1-2-1-Tomo-20um-E7p75MouseEmbryo-Plate1-Run1Run2_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h1-2-1-Tomo-20um-E7p75MouseEmbryo-Plate1-Run1Run2_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h1-2-1-Tomo-20um-E7p75MouseEmbryo-Plate1-Run1Run2_cbc_trimmed_star_spliced.coutt.tsv.gz

value: from 54 to 96


title: mEmbryoE85_01_plate1_seqrun2


title: TCCSUPPi_R2

status: Public on Nov 25 2019

city: Serdang

first: Abhimanyu

last: Veerakumarasivam

state: Selangor

address: Jalan Puchong

department: Biomedical Science

country: Malaysia

institute: Universiti Putra Malaysia

description:
cDNA
processed data file: txicounts_TCCSUP.csv
processed data file: diffexpr-results_TCCSUP.csv

data_processing:
Quality control of the sequencing reads was assessed using FastQC and MultiQC analyses.
All ribosomal RNA (rRNA) sequences were filtered out using bbduk and Greengenes rRNA db.
Quality reads were mapped to a human reference genome (hg19) using HISAT2 aligner. Reads that mapped to the reference genome was used to quantify the transcriptome assembly using StringTie (Pertea et al., 2015). Quantification of the transcripts abundance was carried out using Salmon’s quasimapping strategy which count the number of reads that map to a given transcript (Patro et al., 2017) calculated in fragments per kilobase of gene model per million mapped (FPKM) of the coding genes in each samples.
Differential transcripts analysis (DEGs) was carried out using DESeq2 package (Love et al., 2014) via tximport in R environment/
Genome_build: human reference genome (hg19, GRCh37)
Supplementary_files_format_and_content: txicountsTCCSUP.csv: Comma-separated values file includes FPKM values for each sample.
Supplementary_files_format_and_content: txicounts_EJ28.csv: Comma-separated values file includes FPKM values for each sample.
Supplementary_files_format_and_content: diffexpr-results_TCCSUP.csv: Comma-separated values file includes differential expression results.
Supplementary_files_format_and_content: diffexpr-results_EJ28P.csv: Comma-separated values file includes differential expression results.

source_name: Bladder cancer cells

growth_protocol: Cells were grown in a monolayer in culture flasks with normal complete growth media (RPMI1640 and MEM alpha) placed in a humidified chamber at 37°C in 5% CO2/air until confluence.

extract_protocol:
Total RNA was extracted from each of the persistently infected cells and the cell lines without NDV infection (negative control) using Qiagen RNeasy micro kit (Qiagen, Germany) following the manufacturer’s protocol. RNA quality and RNA integrity number (RIN) were assessed by spectrophotometer (NanoDrop 2000) and Bioanalyzer 21000 expert software system (Agilent Technologies, Santa Clara, CA, USA). RNA Integrity Number (RIN) were of good quality being in the range between 8.0 to 9.0.
Transcriptome library was constructed based on TruSeq Stranded mRNA library preparation kit v2 protocols (Illumina, San Diego, CA) using a total of 3 μg of RNA per sample.

treatment_protocol: EJ28 and TCCSUP cells were infected with NDV AF2240 at MOI of 1 and 0.1, respectively. Cells were incubated at 37oC and rocked at every 15 minutes interval for an hour to allow for viral absorption. Majority of the cells died leaving small subpopulation of cells which were re-infected three more times. These cells were named EJ28Pi and TCCSUPPi cell lines respectively.

value: TCCSUP

value: Bladder cancer cells

tag: infection

value: Newcastle disease virus


title: EJ28M_R2

description:
cDNA
processed data file: txicounts_EJ28.csv
processed data file: diffexpr-results_EJ28P.csv


title: ATAC.rep2.gTKO.438

description:
ATAC.rep2.gTKO.438
processed data file:
GEO_retina_ATACseq_HOMER_results.xlsx
GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx
retina.gTKO_peaks.narrowPeak.bed
Ret.gTKO.cat.743.438.440.final.sorted.bw

value: S1pr3-/- S1pr1flox/flox S1pr2flox/flox Rosa26-CreERT2

value: postnatal day 6

value: FACS-sorted adult mouse retinal endothelial cells


title: EJ28M_R3


title: ATAC.rep3.Control.742

description:
ATAC.rep3.Control.742
processed data file:
GEO_retina_ATACseq_HOMER_results.xlsx
GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx
retina.Control_peaks.narrowPeak.bed
Ret.Control.cat.742.437.439.sorted.sorted.bw

value: S1pr3-/- S1pr1flox/flox S1pr2flox/flox


title: TCCSUPM_R3


title: EJ28Pi_R2


title: TCCSUPPi_R1


title: sciPlex3_A549_MCF7_K562_screen

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

state: NY

department: Biomedical Engineering

institute: Columbia University

description: sci-Plex of pooled single-nucleus transcriptional profiling of A549, MF7 and K562 cells exposed to one of 188 compounds or dmso vehicle control. Half of this drug library was composed of  compounds that target regulators of transcription and half targeted diverse cellular processes.

data_processing:
Expression matrices, cell annotations and gene annotations were generated accodring to the protocol described in our manuscript as well as in Cao et al. 2017 Science 357(6352) p. 661-667 (two level sci-RNA-seq) and Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).
Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 2, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only pertains to sciPlex3, associated metadata to deconvolve hash combinations can be found in sciPlex3_A549_MCF7_K562_hashTable_metadata.txt). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out files) for each nuclear transcriptome in the  experiment. Tab delimited columns of hashTable.out files correspond to a sample id, the cell  barcode identified for that hash, a "_" delimited string with treatment metadata, an  axis id for each hash (important for multiple hash per well experiments such as in sci-Plex3) and umi counts for each hash. The first tab delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. For sciPlex1, the first "_" delimited string corresponds to the cell type, for sciPlex2 the first "_" delimited string corresponds to treatment  and the second to dose, for sciPlex4 the first "_" delimited string corresponds to an identifier that, with the hash, is identified using the metedata in sciPlex3_A549_MCF7_K562_hashTable_metadata.txt and for sciPlex4 the first "_" delimited string corresponds to the dose of the compounds in the second  "_" delimited string and similarly the third corresponds to the dose of the compounds in the fourth  "_" delimited string. For all experiments the last "_" string corresponds to the treatment well from multiwell plates.
Genome_build: GRCh38 and mm10
Supplementary_files_format_and_content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

source_name: A549, MCF7 and K562 cells

growth_protocol: All cell lines were cultured in DMEM supplemented with 10% FBS and 1% penn-strep.

extract_protocol:
24 hours after drug exposure, cells were harvested following the sci-Plex protocol as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
Nucle were subjected to two or three level sci-RNA-seq following the protocols described in Cao et al. 2017 Science 357(6352) p. 661-667 (two level sci-RNA-seq) and Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq).

treatment_protocol: Cells were seeded at 25,000 cells per well in 96 well plates. 24 hours after seeding cells were exposed to increasing doeses of small molecules or dmso vehicle control.

value: A549 human lung adenocarcinoma, MCF7 breast adenocarcinoma and K562 chronic myelogenous leukemia cells

tag: treatment

value: Cells were treated with increasing doses of a library of 188 small molecule inhibitors or dmso vehicle control.


title: EJ28M_R1


title: EJ28Pi_R1


title: MHH16563_BF48_replicate2

description:
Cells were grown in static biofilm cultures (96-well microtiter plates) for 48h and incubated for 10 min in RNAlater reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
processed data file: ProcessedDataMatrix_clinical_isolates.xlsx

tag: isolate

value: clinical

tag: location

value: Hannover Medical School

tag: infection side

value: nd/other

tag: growth condition

value: biofilm

tag: growth time


title: mEmbryoE85_03_plate3

description:
SvdB12h-2-4-Tomo-20um-E8p75MouseEmbryo2-Plate3-Run1_cbc_trimmed_star_spliced.coutb.tsv.gz
SvdB12h-2-4-Tomo-20um-E8p75MouseEmbryo2-Plate3-Run1_cbc_trimmed_star_spliced.coutc.tsv.gz
SvdB12h-2-4-Tomo-20um-E8p75MouseEmbryo2-Plate3-Run1_cbc_trimmed_star_spliced.coutt.tsv.gz

value: tomo-seq

value: 1 from 1

value: from 1 to 35


title: TCCSUPM_R1


title: TCCSUPM_R2


title: HSC_CB_2

status: Public on Nov 13 2019

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description: CD45+/CD34+/CD38-/CD45RA-/CD90high/CD49fhigh cord blood hematopoietic stem cells

data_processing:
Primary data analysis, including base calling and quality scoring is performed by real-time analysis or RTA (Version 2.4.11) on the sequencing instrument (NextSeq550). RTA performs image analysis and base calling during the sequencing run.
Raw data was processed by converting the BCL files into FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina)
The FASTQ files were adapted and quality trimmed using Trim Galore! (Version 0.4.1)
FASTQ files were mapped against a the human reference genome hg19 using STAR (version 2.5.0c) . BAM files were built in a 2-pass mapping (--twopassMode Basic) and were finally sorted (--outSAMtype BAM SortedByCoordinate).
Read counting was performed by featureCounts as part of the Subread (Liao et al.) software package (version 1.6.1) using gencode.v28lift37
Genome_build: hg19
Supplementary_files_format_and_content: text file with hgnc symbols and  raw counts for each gene

source_name: Cord Blood HSCs

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer. Ribosomal RNA was removed using NEBNext rRNA Depletion Kit.
5 ng total RNA was used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (Takara). Libraries were barcoded by a dual indexing approach and were amplified by 11 PCR cycles. Fragment length distribution was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (Agilent). Quantification was performed with the ‘Qubit® dsDNA HS Assay Kit’ (ThermoFisher). The combined library pools were denatured with sodium hydroxide and were finally diluted to 1.5 pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina, San Diego, USA). 1.3 mL of each denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for 75 bp single reads (#FC-404-2005; Illumina).

tag: facs


title: Brain 2m WT Rep1

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

data_processing:
Sequenced reads were quality trimmed and filtered using Trimmomatic tool and reads passing the quality filtering were mapped to the mouse mm10 reference genome using ‘bowtie’ algorithm.
HTSeq Python package was used to calculate raw read counts per transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts values for each Sample ...

source_name: Whole brain

extract_protocol:
Left retinas and left brain hemispheres were dissected and snap frozen for preservation of RNA for gene expression studies. Total RNA was extracted using Trizol (Invitrogen, CA).
mRNA was purified from total RNA using biotin-tagged poly dT oligonucleotides and streptavidin-coated magnetic beads and quality was assessed using an Agilent Technologies 2100 Bioanalyzer.

tag: age

value: 2 months

tag: genotype

value: WT

tag: Sex

value: female


title: August6R4High

status: Public on Nov 04 2019

description:
Reduced, biological replicate 5
Sample_70816

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (WS220) (http://genome.ucsc.edu/) using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation and differential expression analysis, using WS220 as the reference genome sequence. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff2. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: WS220
Supplementary_files_format_and_content: raw counts, txt

organism: Caenorhabditis elegans

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - oxidized biol.replicate 5

growth_protocol: Worms were grown on standard NGM plates at 20oC

extract_protocol:
Worms were grounded in Trizol reagent (Life Technologies) with sea sand and pestle. After filtering of the sand, samples were vigorously shaken with chloroform, allowed to stand for 3 minutes at room temperature, and then centrifuged at 16,000 g at 4°C. The aqueous phase was then collected and RNA was purified using QIAGEN RNeasy RNA extraction columns as per manufacturers’ recommendations.
Total RNA was assessed for quality using the TapeStation (Agilent). Samples were prepared using the Illumina TruSeq Stranded Total RNA Library Prep kit (Illumina). 100 ng of total RNA was rRNA-depleted using Ribo-Gone (Takara Bio USA). The rRNA-depleted RNA was then fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The products were purified and enriched by PCR (15 cycles) to create the final cDNA library. The 3’ prime ends of the cDNA were adenylated and ligated to adapters, including a 6-nt barcode unique for each sample. Final libraries were checked for quality and quantity by TapeStation and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems, Wilmington MA).
The samples were pooled, clustered on an Illumina cBot and sequenced on one lane of an Illumina HiSeq4000 flow cell, as paired-end 50 nt reads. The quality of the raw reads data for each sample (e.g. low-quality scores, over-represented sequences, inappropriate GC content) was checked using FastQC (version v0.11.3).

treatment_protocol: Age - synchronized eggs were extracted using alkaline hypochlorite solution and allowed to hatch by overnight incubation in M9 medium during gentle shaking. Newly hatched, arrested L1 larvae were transferred onto standard nematode growth medium (NGM) plates seeded with live E. coli OP50.

tag: redox

value: reduced

tag: source


title: July7R5Low

description:
Oxidized, biological replicate 3
Sample_70813

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - oxidized biol.replicate 3

value: oxidized


title: August6R5Low

description:
Oxidized, biological replicate 5
Sample_70817

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - reduced biol.replicate 5


title: EJ28Pi_R3

value: Bladder cancer cells

value: Newcastle disease virus


title: mEmbryoE85_02_plate1_seqrun2

tag: experiment

tag: protocol/barcodes

tag: section thickness

tag: embryonic stage

tag: sequencing runs

value: 2 from 2

tag: plates

value: from 43 to 96


title: June28R4Low2

description:
Oxidized, biological replicate 2
Sample_70811

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - oxidized biol.replicate 2


title: July7R4High

description:
Reduced, biological replicate 3
Sample_70812

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - reduced biol.replicate 3


title: June28Low

description:
Oxidized, biological replicate 1
Sample_70809

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - oxidized biol.replicate 1


title: June28High

description:
Reduced, biological replicate 1
Sample_70808

source_name: L2 staged N2jrIs2[Prpl-17::Grx1-roGFP2] - reduced biol.replicate 1


title: Ad-378 rep2

status: Public on Nov 02 2019

city: shanghai

first: chao

last: sun

state: shanghai

address: 320 Yueyang Road, Xuhui District, Shanghai, China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy ofSciences

description:
Ad-378-2
processed data file: RNA-SEQ_Ad_Ctrl_vs_378.xlsx

data_processing:
RNA were pooled for deep sequencing by using Illumina Hiseq Xten (2 × 150) platforms at the CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China. Raw read qualities were evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, v0.11.5). Adaptor sequences and read sequences on both ends with Phred quality scores below 30 were trimmed. Trimmed reads were then mapped with the Hisat2 algorithm (Hisat2 v2.1.0) to target sequences. Gene expression levels were quantified by the software package HTSeq (v0.6.1p1).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA-SEQ_Ad_Ctrl_vs_378.xlsx: Excel file includes RPKM values for each Sample.

source_name: liver

growth_protocol: Eight-week-old male mice were injected with adenovirus 1x10^9 PFU, and liver tissue was collected two weeks later.

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The corresponding adenovirus was injected into the tail vein, and the liver was taken two weeks later.

tag: strain/background

tag: genotype/variation

value: Hepatic miR-378 overexpression

value: Male

value: 10 weeks

tag: tissue

value: Liver


title: Ad-378 rep1

department: Shanghai Institutes for Biological Sciences

description:
Ad-378-1
processed data file: RNA-SEQ_Ad_Ctrl_vs_378.xlsx


title: Ad-ctrl rep2

description:
Ad-Ctrl-2
processed data file: RNA-SEQ_Ad_Ctrl_vs_378.xlsx

value: Control


title: Ad-378 rep3

description:
Ad-378-3
processed data file: RNA-SEQ_Ad_Ctrl_vs_378.xlsx


title: Ad-ctrl rep1

description:
Ad-Ctrl-1
processed data file: RNA-SEQ_Ad_Ctrl_vs_378.xlsx