title: Dshibae, AI treatment, 60 min Replicate 2

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Dinoroseobacter shibae

source_name: D. shibae cultivated in minimal medium

extract_protocol:
For isolation and purification the RNeasy-kit (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cells lysis was performed enzymatically using 15 mg/mL lysozyme in Tris-EDTA-buffer (ph 8.0) and mechanically by vortexing for 3 min with acid washed glass beads. A first digestion of genomic DNA was performed on the column, using RNase-free DNase I (Qiagen) according to the manufacturer’s protocol. Total RNA was eluted in 88 µL RNase-free H2O and a second DNase I-digestion of genomic DNA was performed in solution, followed by a second RNeasy purification step. In this second purification an additional washing step with 80 % ethanol was performed prior to elution with 30µl RNase-free water. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA). Ribosomal RNA depletion:  The Ribo-Zero (gram-negative) kit to remove the prokaryotic rRNA, according to the manufacturer’s instructions.
Single end, strand specific cDNA libraries were prepared using the Scriptseq v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturers protocol. For sequencing equal volumes of libraries (12 pM) were multiplexed on a single lane. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 - HS (Illumina, San Diego, CA, USA) for 50 cycles resulting in 50 bp reads. Image analysis and base calling were performed using the Illumina pipeline v 1.8 (Illumina, San Diego, CA, USA).

tag: genotype

tag: treatment

value: AI

tag: time (min)

tag: replicate


title: Dshibae, DMSO treatment, 60 min Replicate 3

status: Public on Nov 03 2018

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain

value: DMSO


title: Dshibae, AI treatment, 40 min Replicate 2


title: Dshibae, DMSO treatment, 60 min Replicate 1


title: Dshibae, DMSO treatment, 60 min Replicate 2


title: Dshibae, AI treatment, 20 min Replicate 3


title: Dshibae, AI treatment, 60 min Replicate 1


title: Dshibae, AI treatment, 40 min Replicate 1


title: Dshibae, AI treatment, 40 min Replicate 3


title: Dshibae, AI treatment, 20 min Replicate 2


title: Dshibae, AI treatment, 20 min Replicate 1


title: Dshibae, AI treatment, 180 min Replicate 3


title: Elf FLCN KO #6 +AAVS1-FLCN-GFP 2iLif rep2

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

country: USA

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
RNA-seq reads in fastq files were aligned to hg19 using Tophat (version 2.0.13).
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCh37 gene annotations.
FeatureCounts was used to do gene-level quantification.
hg19
tab-delimited file of gene-level read counts for each sample.

organism: Homo sapiens

source_name: human embryonic stem cell

growth_protocol: Naïve hESC [Elf-1(NIH_hESC Registry #0156) were cultured as previously described. Briefly, cells were grown on a feeder layer of irradiated primary mouse embryonic fibroblasts (MEF) in naïve hESC media (2iL-I-F or 5iLA). 2iL-I-F media consisted of DMEM/F-12 media supplemented with 20% knock-out serum replacer (KSR), 0.1mM nonessential amino acids (NEAA), 1 mM sodium pyruvate, penicillin/streptomycin (all from Invitrogen, Carlsbad, CA), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), 1µM GSK3 inhibitor (CHIR99021, Selleckchem), 1µM of MEK inhibitor (PD0325901, Selleckchem), 10ng.ml-1human LIF (Chemicon), 5ng.ml-1 IGF1 (Peprotech) and 10ng.ml-1 bFGF. 5iLA media consisted of 50:50 mixture of DMEM/F12 (Invitrogen; 11320) and Neurobasal (Invitrogen; 21103) media, supplemented with 1% N2 supplement (Invitrogen; 17502048), 2% B27 supplement (Invitrogen; 17504044), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 50 mg.ml-1 BSA (Sigma), BRAF inhibitor (0.5µM), SRC inhibitor (1µM), MEK inhibitor (1µM), GSK3 inhibitor (IM-12, 1µM), ROCK inhibitor (10µM), recombinant human LIF (20ng.ml-1), and Activin A (10ng.ml-1). Cells were passaged using 0.05% Trypsin-EDTA (Life Technologies). Cells were transferred to matrigel-coated plates prior molecular analysis. Exit from the naïve state was achieved by culturing the cells in either mTeSR1 media (StemCell Technologies) or primed FGF hESC media (DMEM/F-12 media supplemented with 20% KSR, 0.1mM NEAA, 1 mM sodium pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol and 10ng.ml-1 bFGF) on matrigel-coated plates. All cells were cultured at 5% O2 and 5% CO2 between passage p20 and p40, as indicated.

extract_protocol:
Total RNA for samples in this study were extracted with the Direct-zol RNA kit (Zymo Research) and libraries for Illumina sequencing were generated with the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems). Sequencing was run on an Illumina HiSeq 2500 in the Fred Hutchinson Cancer Research Center Shared Resources Genomics facility.
RNA libraries were prepared for sequencing using standard Illumina protocols
Total RNA for samples in this study were extracted with the Direct-zol RNA kit (Zymo Research) and libraries for Illumina sequencing were generated with the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems). Sequencing was run on an Illumina HiSeq 2500 in the Fred Hutchinson Cancer Research Center Shared Resources Genomics facility.
RNA libraries were prepared for sequencing using standard Illumina protocols
Naïve 2iL-I-F hESCs Elf1 NNMT KO (mutant 6.2.4) were crosslinked and chromatin processed as previously described with minor modifications. Briefly, cells were harvested with accutase and crosslinked in suspension with 1% formaldehyde solution for 10min at room temperature. Reaction was quenched with glycine and crosslinked cells were rinsed with ice-cold PBS. Nuclei were isolated and chromatin sonicated using a Covaris E210 to approximately 200-500bp size range. Magnetic Dynabeads were incubated overnight rotating at 4C with antibody against H3K27me3 (Active Motif, cat # 39155). Sonicated chromatin from approximately 200 thousand to 3 million cells was added to the bead-bound-antibodies and allowed to incubate at 4C rotating overnight. Beads were washed to remove unbound chromatin. Bound chromatin was eluted from beads and reverse crosslinked overnight. Purified DNA was prepared for next-generation sequencing via end repair, A-tailing, ligation of custom Y-adapters and PCR amplification to generate final DNA library following gel size selection.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naïve hESC (Elf1 2iL-I-F or WIBR3 5iLA) were spin-infected with lentiCRISPR-v2 lentiviral pools of 4 sgRNA per gene for FLCN and ESRRB in presence of 4µg.ml-1 polybrene (Supplementary Table 6A) and plated onto irradiated DR4 MEF. Two days later, cells were selected with puromycin (0.5µg.ml-1, for 2-3 days). Alternatively, SIN1 and RICTOR mutants were generated in Elf1 iCas91. Guides were ordered through Synthego (RICTOR) or as T7-gRNA primers (SIN1). A dsDNA fragment was synthesized from these primers by self-annealing PCR to a complementary scaffold primer. The dsDNA fragment was followed by Q5 High Fidelity-based PCR (New England Biolabs). This 120 bp strand served as template for IVT (MAXIscript T7 kit, applied Biosystems). The RNA was then purified using Pellet Paint® Co-Precipitant (Novagen). Elf1-iCas9 cells were treated with doxycycline (2μg.ml-1) for 2 to 3 days before and during transfection. Cells were transfected with 40 nM of gRNA using Lipofectamine RNAiMAX (Life Technologies). A second transfection was performed after 24 h. Two days after the last gRNA transfection, Elf1-iCas9 cells were dissociated into single cells and replated onto MEF-coated plates or collected for DNA analysis (pool). In the next passage, single colonies from MEF-coated plates were randomly selected and amplified. The molecular characterization of the mutant lines and their phenotype were analyzed between passage 33 and 40 using controls with matching passage number.  Genomic DNA was extracted using DNAzol reagent (Invitrogen) according to manufacturer’s instructions and quantified using Nanodrop ND-1000. Genomic regions flanking the CRISPR target sites were PCR amplified with the designed primers (Supplementary Table 6C) and send for Sanger sequencing. Alternatively, PCR were purified with the PureLink Quick PCR Purification Kit (Invitrogen), inserted into a carrier vector by Gibson Assembly, and 96 clones Sanger sequenced.

tag: culture media

tag: flcn status

value: KO + AAVS1-FLCN-GFP no Dox

tag: chip antibody


title: Elf FLCN KO 7D TeSR IWP2

value: TeSR medium

value: KO


title: Elf FLCN KO 7D TeSR DMSO


title: MF.64pLYVEpIIn.Ao.3

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Aortic Macrophage

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

organism: Mus musculus

source_name: Aorta

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: age

value: 15 weeks old

tag: sorting markers

value: CD45 CD11b CD64 MerTK LYVE-1 MHCII Dump channel

tag: cell type

value: Macrophage


title: Elf NNMT CRISPR mutant 6.2.4 input

library_source: genomic

data_processing:
ChIP-seq reads in fastq files were aligned to hg19 using Bowtie2(version 2.2.9)
MACS (version 1.4.2) was used for calling ChIP-seq peaks.
hg19
BED file of peaks (FDR<0.1) called by MACS

molecule: genomic DNA

extract_protocol:
Naïve 2iL-I-F hESCs Elf1 NNMT KO (mutant 6.2.4) were crosslinked and chromatin processed as previously described with minor modifications. Briefly, cells were harvested with accutase and crosslinked in suspension with 1% formaldehyde solution for 10min at room temperature. Reaction was quenched with glycine and crosslinked cells were rinsed with ice-cold PBS. Nuclei were isolated and chromatin sonicated using a Covaris E210 to approximately 200-500bp size range. Magnetic Dynabeads were incubated overnight rotating at 4C with antibody against H3K27me3 (Active Motif, cat # 39155). Sonicated chromatin from approximately 200 thousand to 3 million cells was added to the bead-bound-antibodies and allowed to incubate at 4C rotating overnight. Beads were washed to remove unbound chromatin. Bound chromatin was eluted from beads and reverse crosslinked overnight. Purified DNA was prepared for next-generation sequencing via end repair, A-tailing, ligation of custom Y-adapters and PCR amplification to generate final DNA library following gel size selection.
DNA libraries were prepared for sequencing using standard Illumina protocols
Total RNA for samples in this study were extracted with the Direct-zol RNA kit (Zymo Research) and libraries for Illumina sequencing were generated with the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems). Sequencing was run on an Illumina HiSeq 2500 in the Fred Hutchinson Cancer Research Center Shared Resources Genomics facility.
RNA libraries were prepared for sequencing using standard Illumina protocols
Naïve 2iL-I-F hESCs Elf1 NNMT KO (mutant 6.2.4) were crosslinked and chromatin processed as previously described with minor modifications. Briefly, cells were harvested with accutase and crosslinked in suspension with 1% formaldehyde solution for 10min at room temperature. Reaction was quenched with glycine and crosslinked cells were rinsed with ice-cold PBS. Nuclei were isolated and chromatin sonicated using a Covaris E210 to approximately 200-500bp size range. Magnetic Dynabeads were incubated overnight rotating at 4C with antibody against H3K27me3 (Active Motif, cat # 39155). Sonicated chromatin from approximately 200 thousand to 3 million cells was added to the bead-bound-antibodies and allowed to incubate at 4C rotating overnight. Beads were washed to remove unbound chromatin. Bound chromatin was eluted from beads and reverse crosslinked overnight. Purified DNA was prepared for next-generation sequencing via end repair, A-tailing, ligation of custom Y-adapters and PCR amplification to generate final DNA library following gel size selection.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: Dshibae, DMSO treatment, 180 min Replicate 3


title: Elf NNMT CRISPR mutant 6.2.4 H3K27me3

value: H3K27me3 (Active Motif, cat # 39155).


title: Dshibae, AI treatment, 180 min Replicate 2


title: Dshibae, AI treatment, 60 min Replicate 3


title: Dshibae, DMSO treatment, 180 min Replicate 2


title: Dshibae, AI treatment, 180 min Replicate 1


title: Elf FLCN KO #6 +AAVS1-FLCN-GFP 2iLif rep1


title: Elf KO FLCN #6 TeSR 7day 7-19-16 rep2


title: Elf 2iLif FLCN KO #6 7-25-16 rep2


title: Elf FLCN KO #6 +AAVS1-FLCN-GFP + Dox 4 days 2iLif rep2

value: KO + AAVS1-FLCN-GFP with Dox


title: Dshibae, DMSO treatment, 180 min Replicate 1


title: Elf TeSR 7day 7-19-16 rep2

value: WT


title: Dshibae, AI treatment, 120 min Replicate 3


title: Dshibae, AI treatment, 120 min Replicate 2


title: Elf 2iLif p25 7-22-16 rep2


title: Elf 2iLif p25 7-22-16 rep1


title: Dshibae, AI treatment, 120 min Replicate 1


title: Elf FLCN KO #6 + AAVS1-FLCN-GFP + Dox 4 days 2iLif rep1


title: Dshibae, AI treatment, 10 min Replicate 3


title: Elf 2iLif FLCN KO #6 7-25-16 rep1


title: Dshibae, AI treatment, 10 min Replicate 2


title: Elf KO FLCN #6 TeSR 7day 7-19-16 rep1


title: Dshibae, AI treatment, 10 min Replicate 1


title: Dshibae, before treatment, Replicate 3


title: Elf TeSR 7day 7-19-16 rep1


title: Dshibae, before treatment, Replicate 1


title: Dshibae, before treatment, Replicate 2


title: W3: Leaves derived in co-culturing iris and Dictyosphaerium sp. in swine wastewater

city: Hangzhou

first: Qifa

last: Zhou

address: Yuhangtang Rd

country: China

institute: Zhejiang University

data_processing:
After quality filtering sequence reads, clean reads were mapped to the genomic reference using Bowtie 2, and gene expression levels were calculated with RSEM.
Differentially expressed genes (DEGs) were determined with DEseq2.
We used BLAST or DIAMOND to map the DEGs to the PRGdb database to detect the plant disease resistant genes based on the query coverage and identity requirement.

molecule: polyA RNA

organism: Iris tectorum

source_name: Leaves

growth_protocol: The plants were cultured in swine wastewater in a glasshouse,with average flooding height of 12.3 ± 0.8 cm (n = 18).

extract_protocol:
Total RNA was extracted using an RNAprep pure plant kit (TIANGEN Biotech Co., Ltd., Beijing, China)
1) mRNA enrichment: Oligo dT Selection or rRNA depletion; 2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer; 3)End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments; 4)PCR amplification: The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5)Denature and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) Sequencing on BGISEQ-500 platform.

treatment_protocol: The  plants were cultured alone or co-cultured with the microalgae.

tag: tissue

value: Leaves

tag: culture


title: W2: Leaves derived in co-culturing iris and Dictyosphaerium sp. in swine wastewater


title: Hermaphrodite animal nr.4

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: CEL-seq

data_processing:
We aligned the 50 base pair paired-end reads to the C. elegans references transcriptome, which was compiled from the C. elegans reference genome WS249.  See: online methods and supplementary of the manuscript
Genome_build: C. elegans reference genome WS249
Supplementary_files_format_and_content: Read-, UMI (Barcode)-, Transcript-, count tables for mapped reads per section as tab separated values (.tsv) per animal.

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Unless noted otherwise, C. elegans strains were cultured at 20°C using standard conditions (Lewis and Fleming, 1995). For RNA tomography, young adult Bristol N2 males and hermaphrodites, or young adult glp-1(q231) mutants (grown at the restrictive temperature of 25°C) were used.

extract_protocol:
mRNA extraction, barcoding, reverse transcription and in vitro transcription were performed as described (Junker et al., 2014) according to the CEL-seq protocol (Hashimshony et al., 2012) using the Message Amp II kit (Ambion). Illumina sequencing libraries were subsequently prepared according to the CEL-seq2 protocol  (Hashimshony et al., 2016) using the SuperScript® II Double-Stranded cDNA Synthesis Kit (Thermofisher), Agencourt AMPure XP beads (Beckman Coulter), and randomhexRT for converting aRNA to cDNA using random priming. See online methods and supplementary of the manuscript
CEL-Seq v1, as in (Junker et al 2014); See online methods and supplementary of the manuscript

treatment_protocol: Live young adult males or hermaphrodites were oriented perpendicular to the sectioning axis, frozen and cryo-sectioned as described (Junker et al., 2014) with a sectioning width of 20 mm. See online methods and supplementary of the manuscript

tag: sex/germline

value: Hermaphrodite


title: N3: Leaves derived in culturing iris in swine wastewater


title: Hermaphrodite animal nr.2

description: CEL-seq


title: Hermaphrodite animal nr.1

description: CEL-seq


title: Hermaphrodite animal nr.3

description: CEL-seq


title: Male animal nr.4

description: CEL-seq

value: Male


title: Male animal nr.3

description: CEL-seq


title: Bone Marrow proB and preB cells of WT mouse, bio rep 4

type: RNA

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from WT bone marrow proB and preB cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label: biotin

source_name: WT 4

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Not applicable

tag: genotype/variation

value: bone marrow proB and preB


title: N2: Leaves derived in culturing iris in swine wastewater


title: Bone Marrow proB and preB cells of WT mouse, bio rep 2

source_name: WT 2


title: Leukemic Bone Marrow cells of AID-/- + Pax5+/- mouse, bio rep 1

description: Gene expression data from  AID-/- + Pax5+/- bone marrow leukemic cells

value: total bone marrow


title: Leukemic Bone Marrow cells of AID-/- + Pax5+/- mouse, bio rep 2


title: Leukemic Bone Marrow cells of AID+/- + Pax5+/- mouse, bio rep 5

description: Gene expression data from  AID+/- + Pax5+/- bone marrow leukemic cells


title: Leukemic Bone Marrow cells of AID+/- + Pax5+/- mouse, bio rep 3


title: W1: Leaves derived in co-culturing iris and Dictyosphaerium sp. in swine wastewater


title: Bone Marrow proB and preB cells of WT mouse, bio rep 3

source_name: WT 3


title: Leukemic Bone Marrow cells of AID+/- + Pax5+/- mouse, bio rep 1


title: Male animal nr.1

description: CEL-seq


title: Day3-2

first: Hua

last: Liu

state: Zhejiang

address: #866 Yu Hang Tang Rd

department: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province

institute: School of Medicine,Zhejiang University

description: Gene expression in IFN-gamma treated for 3day hESC-MSCs

hyb_protocol: Labeled controls and test samples labeled with Cy5-dCTP and Cy3-dCTP were dissolved in 80 mL hybridization solution containing 3¡ÁSSC, 0.2% SDS, 5¡ÁDenhardt¡¯s solution and 25% formamide. DNA in hybridization solution was denatured at 95¡æ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42¡æ and washed with two consecutive solutions

scan_protocol: CapitalBio Technology Human LncRNA Array v4 was designed with four identical arrays per slide (4 x 180K format), with each array containing probes interrogating about 41,000 human lncRNAs and about 34,000 human mRNAs.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used thresholdvalues of ¡Ý2 and ¡Ü_2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: human ESC-MSCs, IFN-gamma treated for 3days, replicate 2

label_protocol: cDNA labeled with a fluorescent dye (Cy5 or Cy3-dCTP) was produced by Eberwine¡¯s linear RNA amplification method and subsequent enzymatic reaction

growth_protocol: hESC-MSCs were kept in an undifferentiated state by using 10%FBS and 90%L-DMEM

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: human IFN-gamma treats the hESC-MSCs for 0, 1, 3 days respectively

tag: agent

value: IFN-gamma

tag: time point

value: h1ESCs obtained from WiCell


title: Leukemic Bone Marrow cells of AID-/- + Pax5+/- mouse, bio rep 3


title: N1: Leaves derived in culturing iris in swine wastewater


title: Leukemic Bone Marrow cells of AID+/- + Pax5+/- mouse, bio rep 4


title: Day3-1

source_name: human ESC-MSCs, IFN-gamma treated for 3days, replicate 1


title: Day3-3

source_name: human ESC-MSCs, IFN-gamma treated for 3days, replicate 3


title: glp-1 mutant animal nr.2

description: CEL-seq

value: glp-1 mutant (germline deficient)


title: glp-1 mutant animal nr.1

description: CEL-seq


title: Bone Marrow proB and preB cells of WT mouse, bio rep 1

source_name: WT 1


title: Day1-1

description: Gene expression in IFN-gamma treated for 1day hESC-MSCs

source_name: human ESC-MSCs, IFN-gamma treated for 1day, replicate 1


title: Day1-3

source_name: human ESC-MSCs, IFN-gamma treated for 1day, replicate 3


title: Day0-3

description: Gene expression in IFN-gamma nontreated hESC-MSCs

source_name: human ESC-MSCs, IFN-gamma nontreated, replicate 3


title: Male animal nr.2

description: CEL-seq


title: Donor2_MIX_H9

status: Public on Nov 02 2018

city: New Haven

first: Yi-Chien

last: Lu

state: Connecticut

address: 10 Amistad Street

department: Laboratory Medicine

institute: Yale Medical School

description: Fluidigm C1 single cell sequencing fastq file

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were  masked for low-quality sequence and aligned to human hg19 reference genome by using Bowtie2-TopHat standard command with defult setting.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD34+ selected PBSC

extract_protocol:
Standard Fluidigm C1 single cell capture protocol
Clontech® SMARTer Ultra® Low RNA Kit for the Fluidigm C1 System and  Illumina Nextera XT DNA library preparation  protocol for single-cell mRNA sequencing library preparation for sequencing from cDNA acquired from the C1 system.

tag: sorting gate

value: MKP+ERP

tag: donor

value: Donor 2


title: Donor2_MIX_H8


title: Leukemic Bone Marrow cells of AID+/- + Pax5+/- mouse, bio rep 2


title: Donor2_MIX_H7


title: Donor2_MIX_H6


title: MCF-7 FAT1 CR rep1

city: NEW YORK

first: Sarat

last: CHANDARLAPATY

address: 417 E 68th Street

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files

source_name: Human breast cancer cell line

growth_protocol: MCF-7 parental cells and FAT1 crispr cells were grown in DMEM/F-12 medium supplied with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted from MCF7 cells or FAT1-CR-1 cells using the RNeasy Mini kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked with 4200 TapeStation .
RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina

tag: cell line

value: FAT1 CR

tag: passages


title: Donor2_MIX_H2


title: Donor2_MIX_H12


title: Day0-2

source_name: human ESC-MSCs, IFN-gamma nontreated, replicate 2


title: Day1-2

source_name: human ESC-MSCs, IFN-gamma treated for 1day, replicate 2


title: Donor2_MIX_H4


title: Day0-1

source_name: human ESC-MSCs, IFN-gamma nontreated, replicate 1


title: Donor2_MIX_H11


title: Donor2_MIX_G9


title: Donor2_MIX_H1


title: Donor2_MIX_G8


title: Donor2_MIX_G6


title: Donor2_MIX_G4


title: Donor2_MIX_G3


title: MCF-7 parental rep1

value: parental


title: Donor2_MIX_G12


title: Donor2_MIX_G2


title: Donor2_MIX_H5


title: Donor2_MIX_G10


title: Donor2_MIX_G1


title: Donor2_MIX_H3


title: Donor2_MIX_F7


title: Donor2_MIX_F9


title: Donor2_MIX_F8


title: EpiLCs, CHIR and PD treated

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: treated for 24 hours

hyb_protocol: Following fragmentation, hybridization to the Mouse Gene 2.0 ST array (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The data were summarized with Plier16 algorithm implemented in GeneSpring GX 12.6.1 software (Agilent Technologies).

source_name: EpiLCs treated with CHIR99021 and PD0325901

label_protocol: GeneChip WT PLUS Reagent kit was used according to Affymetrix protocol.

growth_protocol: mESCs were cultured in N2B27 containing LIF and BMP4. EpiLCs were cultured in N2B27 supplemented with 20 ng/ml ActivinA and 12 ng/ml bFGF

extract_protocol: Total RNAs were extracted using Qiagen RNeasy kit according to the manufacturer’s protocol. On-column DNase digestion was performed.

treatment_protocol: mESCs and EpiLCs were treated with 3 μM CHIR99021 or 3μM CHIR99021 with 1μM PD0325901 for 24 hours

value: EpiLCs induced from EB3 mESCs

tag: treatment


title: Donor2_MIX_F6


title: mESCs, CHIR treated

description: treated for 24 hours

source_name: mESCs treated with CHIR99021

value: EB3 mESCs


title: Donor2_MIX_F5


title: EpiLCs, non-treated

description: non-treated

source_name: non-treated EpiLCs

value: non-treated


title: Donor2_MIX_F11


title: Donor2_MIX_F4


title: Donor2_MIX_E8


title: Donor2_MIX_G5


title: EpiLCs, CHIR treated

description: treated for 24 hours

source_name: EpiLCs treated with CHIR99021


title: mESCs, CHIR and PD treated

description: treated for 24 hours

source_name: mESCs treated with CHIR99021 and PD0325901


title: Donor2_MIX_E7


title: Donor2_MIX_E10


title: Donor2_MIX_E5


title: Donor2_MIX_E12


title: Donor2_MIX_E4


title: mESCs, non-treated

description: non-treated

source_name: non-treated mESCs


title: Donor2_MIX_E1


title: Donor2_MIX_D9


title: Donor2_MIX_D7


title: Donor2_MIX_D5


title: Donor2_MIX_D6


title: Donor2_MIX_D4


title: Donor2_MIX_D8


title: Donor2_MIX_D10


title: Donor2_MIX_D1


title: Donor2_MIX_D11


title: Donor2_MIX_C9


title: Donor2_MIX_C8


title: Donor2_MIX_E6


title: Donor2_MIX_C7


title: Donor2_MIX_C6


title: Donor2_MIX_B9


title: Donor2_MIX_C4


title: Donor2_MIX_B7


title: Donor2_MIX_B3


title: Donor2_MIX_B6


title: Donor2_MIX_B2


title: Donor2_MIX_B8


title: Donor2_MIX_B5


title: Donor2_MIX_C5


title: Donor2_MIX_A7


title: Donor2_MIX_A9


title: Donor2_MIX_B12


title: Donor2_MIX_B11


title: Donor2_MIX_A6


title: Donor2_MIX_A4


title: Donor2_MIX_A11


title: Donor2_MIX_A10


title: Donor2_MEP_H8

value: MEP


title: Donor2_MEP_H5


title: Donor2_MEP_H2


title: Donor2_MEP_H7


title: Donor2_MEP_G5


title: Donor2_MEP_G4


title: Donor2_MEP_G9


title: Donor2_MEP_H10


title: Donor2_MEP_G6


title: Donor2_MEP_G2


title: Donor2_MEP_G3


title: Donor2_MEP_G12


title: Donor2_MIX_A8


title: Donor2_MEP_G11


title: Donor2_MEP_F9


title: Donor2_MIX_B1


title: Donor2_MEP_F7


title: Donor2_MEP_G10


title: Donor2_MEP_G1


title: Donor2_MEP_F8


title: Donor2_MEP_F12


title: Donor2_MEP_F6


title: Donor2_MEP_F2


title: Donor2_MEP_F4


title: Donor2_MEP_F5


title: Donor2_MEP_F3


title: Donor2_MEP_E8


title: Donor2_MEP_E7


title: Donor2_MEP_G8


title: Donor2_MEP_E5


title: Donor2_MEP_E9


title: Donor2_MEP_F10


title: Donor2_MEP_F11


title: Donor2_MEP_H12


title: Donor2_MEP_E4


title: Donor2_MEP_E11


title: Donor2_MEP_D9


title: Donor2_MEP_E1


title: Donor2_MEP_E10


title: Donor2_MEP_D5


title: Donor2_MEP_D6


title: Donor2_MEP_D1


title: Donor2_MEP_D8


title: Donor2_MEP_D11


title: Donor2_MEP_D7


title: Donor2_MEP_C8


title: Donor2_MEP_D4


title: Donor2_MEP_D12


title: Donor2_MEP_C7


title: Donor2_MEP_C10


title: Donor2_MEP_C6


title: Donor2_MEP_C3


title: Donor2_MEP_C1


title: Donor2_MEP_B8


title: Donor2_MEP_B9


title: Donor2_MEP_B7


title: Donor2_MEP_E3


title: Donor2_MEP_B3


title: Donor2_MEP_B6


title: Donor2_MEP_B5


title: Donor2_MEP_B4


title: Donor2_MEP_B2


title: Donor2_MEP_C11


title: Donor2_MEP_B12


title: Donor2_MEP_B11


title: Donor2_MEP_B10


title: Donor2_MEP_B1


title: Donor2_MEP_A8


title: Donor2_MEP_A9


title: Donor2_MEP_A7


title: Donor2_MEP_C12


title: Donor2_MEP_C5


title: Donor2_MEP_A2


title: Donor2_MEP_A6


title: Donor2_MEP_A4


title: Donor2_MEP_A12


title: Donor2_MEP_A5


title: Donor2_MEP_A11


title: Donor2_MEP_A3


title: Donor2_MEP_A10


title: Donor1_MKP_C4

value: MKP

value: Donor 1


title: Donor1_MKP_B8


title: Donor1_MKP_C3


title: Donor1_MKP_B9


title: Donor1_MKP_B4


title: Donor1_MKP_B7


title: Donor1_MKP_B5


title: Donor1_MKP_B10


title: Donor1_MKP_A9


title: Donor1_MKP_B6


title: Donor1_MEP_H4


title: Donor1_MKP_A11


title: Donor1_MEP_H2


title: Donor1_MEP_H10


title: Donor1_MKP_A6


title: Donor1_MEP_H7


title: Donor1_MEP_G9


title: Donor1_MEP_H1


title: Donor1_MKP_A10


title: Donor1_MEP_H9


title: Donor1_MKP_A5


title: Donor1_MEP_H8


title: Donor1_MKP_A4


title: Donor1_MEP_G5


title: Donor1_MKP_A8


title: Donor1_MEP_G7


title: Donor1_MEP_H3


title: Donor1_MEP_G8


title: Donor2_MEP_A1


title: Donor1_MKP_A7


title: Donor1_MEP_G3


title: Donor1_MEP_G2


title: Donor1_MEP_G11


title: Donor1_MEP_F8


title: Donor1_MEP_G10


title: Donor1_MEP_G1


title: Donor1_MEP_G12


title: Donor1_MEP_F9


title: Donor1_MEP_F7


title: Donor1_MEP_F6


title: Donor1_MEP_F4


title: Donor1_MEP_F2


title: Donor1_MEP_E6


title: Donor1_MEP_E4


title: Donor1_MEP_E8


title: Donor1_MEP_F10


title: Donor1_MEP_F1


title: Donor1_MEP_F3


title: Donor1_MEP_E3


title: Donor1_MEP_F11


title: Donor1_MEP_E9


title: Donor1_MEP_E10


title: Donor1_MEP_D9


title: Donor1_MEP_E12


title: Donor1_MEP_D7


title: Donor1_MEP_D8


title: Donor1_MEP_E2


title: Donor1_MEP_E1


title: Donor1_MEP_E11


title: Donor1_MEP_D5


title: Donor1_MEP_D10


title: Donor1_MEP_D11


title: Donor1_MEP_D1


title: Donor1_MEP_C8


title: Donor1_MEP_C5


title: Donor1_MEP_D3


title: Donor1_MEP_D4


title: Donor1_MEP_F12


title: Donor1_MEP_C3


title: Donor1_MEP_C2


title: Donor1_MEP_E5


title: Donor1_MEP_C11


title: Donor1_MEP_B3


title: Donor1_MEP_B7


title: Donor1_MEP_B9


title: Donor1_MEP_B4


title: Donor1_MEP_B11


title: Donor1_MEP_B10


title: Donor1_MEP_B1


title: Donor1_MEP_A7


title: Donor1_MEP_A6


title: Donor1_MEP_A11


title: Donor1_MEP_A3


title: Donor1_MEP_A10


title: Donor1_MEP_A9


title: Donor1_MEP_A4


title: Donor1_ERP_H9

value: ERP


title: Donor1_MEP_A1


title: Donor1_ERP_H7


title: Donor1_ERP_H12


title: Donor1_MEP_C6


title: Donor1_ERP_H11


title: Donor1_MEP_C10


title: Donor1_MEP_B6


title: Donor1_ERP_G7


title: Donor1_ERP_G9


title: Donor1_ERP_G6


title: Donor1_ERP_G8


title: Donor1_ERP_H10


title: Donor1_ERP_G10


title: Donor1_ERP_G1


title: Donor1_ERP_F8


title: Donor1_ERP_F6


title: Donor1_ERP_G3


title: Donor1_MEP_A8


title: Donor1_ERP_G12


title: Donor1_ERP_F7


title: Donor1_ERP_E7


title: Donor1_ERP_E9


title: Donor1_ERP_E8


title: Donor1_ERP_F4


title: Donor1_ERP_F2


title: Donor1_ERP_F1


title: Donor1_ERP_F3


title: Donor1_ERP_E3


title: Donor1_ERP_E2


title: Donor1_ERP_E6


title: Donor1_ERP_E4


title: Donor1_ERP_E12


title: Donor1_ERP_E11


title: Donor1_ERP_E10


title: Donor1_ERP_G2


title: Donor1_ERP_E1


title: Donor1_ERP_D5


title: Donor1_ERP_D6


title: Donor1_ERP_F12


title: Donor1_ERP_D9


title: Donor1_ERP_C7


title: Donor1_ERP_D1


title: Donor1_ERP_D3


title: Donor1_ERP_D11


title: Donor1_ERP_C6


title: Donor1_ERP_E5


title: Donor1_ERP_D7


title: Donor1_ERP_D12


title: Donor1_ERP_D2


title: Donor1_ERP_C5


title: Donor1_ERP_D10


title: Donor1_ERP_C2


title: Donor1_ERP_C11


title: Donor1_ERP_C3


title: Donor1_ERP_C10


title: Donor1_ERP_B5


title: Donor1_ERP_B9


title: Donor1_ERP_B8


title: Donor1_ERP_B7


title: Donor1_ERP_B6


title: Donor1_ERP_D8


title: Donor1_ERP_C9


title: Donor1_ERP_B2


title: Donor1_ERP_B12


title: Donor1_ERP_C8


title: Donor1_ERP_B11


title: Donor1_ERP_B10


title: Donor1_ERP_C12


title: Donor1_ERP_A8


title: Donor1_ERP_A9


title: Donor1_ERP_C1


title: Donor1_ERP_A2


title: Donor1_ERP_A7


title: Donor1_ERP_A3


title: Donor1_ERP_A6


title: Donor1_CMP_H5

value: CMP


title: Donor1_CMP_H4


title: Donor1_CMP_H3


title: Donor1_CMP_H8


title: Donor1_ERP_A12


title: Donor1_CMP_H7


title: Donor1_CMP_H12


title: Donor1_CMP_G7


title: Donor1_CMP_H10


title: Donor1_CMP_G8


title: Donor1_CMP_G6


title: Donor1_CMP_G5


title: Donor1_ERP_B1


title: Donor1_CMP_G1


title: Donor1_CMP_G2


title: Donor1_CMP_G4


title: Donor1_CMP_F9


title: Donor1_ERP_B3


title: Donor1_ERP_A11


title: Donor1_CMP_F6


title: Donor1_ERP_A1


title: Donor1_CMP_F8


title: Donor1_CMP_F4


title: Donor1_CMP_F3


title: Donor1_CMP_F2


title: Donor1_CMP_F12


title: Donor1_CMP_F5


title: Donor1_CMP_F7


title: Donor1_CMP_F10


title: Donor1_CMP_F1


title: Donor1_CMP_H11


title: Donor1_CMP_E8


title: Donor1_CMP_E7


title: Donor1_CMP_F11


title: Donor1_CMP_E5


title: Donor1_CMP_G3


title: Donor1_CMP_E2


title: Donor1_CMP_E12


title: Donor1_CMP_E4


title: Donor1_CMP_E1


title: Donor1_CMP_D8


title: Donor1_CMP_D6


title: Donor1_CMP_D4


title: Donor1_CMP_D11


title: Donor1_CMP_D10


title: Donor1_CMP_D2


title: Donor1_CMP_C7


title: Donor1_CMP_D1


title: Donor1_CMP_D9


title: Donor1_CMP_D3


title: Donor1_CMP_C8


title: Donor1_CMP_E6


title: Donor1_CMP_C5


title: Donor1_CMP_C12


title: Donor1_CMP_C6


title: Donor1_CMP_A12


title: Donor1_CMP_B12


title: Donor1_CMP_C10


title: Donor1_CMP_A1


title: Donor1_CMP_B1


title: Donor1_CMP_C11


title: Donor1_CMP_C1


title: Donor1_CMP_D12


title: Ovariectomized_Female_estradiol_cocaine_134

city: Farmington

first: Richard

middle: E

last: Mains

state: CT

address: 263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.

department: Neuroscience

institute: University of Connecticut Health Center

description:
OEC 126, 128, 134, 136, 140
134-OEC

data_processing:
Base calling and quality scores using RTA 2.1.3 from NextSeq control software 1.3.0.23
Reads were aligned to mm10 using Bowtie v. 2.1.0.0 and Samools v. 0.1.19.0
Exon-exon splice junctions were identified using Tophat v. 2.0.9
Transcriptome assembly and quantification of expression was performed with Cufflinks v. 2.2.0
Differential expression analyzed using Cuffdiff v. 2.2.0, DESeq2 and Limma
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: Ovariectomized female, estradiol, cocaine

growth_protocol: all animals handled for 3 days before experiment

extract_protocol:
Left and right nucleus accumbens punches were extracted in Trizol and processed as per manufacturer's instructions
AmpliSeq™ Library PLUS; RNASeq samples were barcoded and all run in a single lane with 9.4 + 4.7 million reads per sample.

treatment_protocol: cocaine was administered 10 mg/kg/d on treatment days 1 and 7; and 20 mg/kg/d for days 2-6.

value: nucleus accumbens

tag: strain

tag: Sex

value: female


title: Ovariectomized_Female_estradiol_saline_132

description:
OES 122, 124, 130, 132, 138
132-OES

source_name: Ovariectomized female, estradiol, saline


title: Ovariectomized_Female_estradiol_saline_138

description:
OES 122, 124, 130, 132, 138
138-OES


title: Ovariectomized_Female_estradiol_saline_130

description:
OES 122, 124, 130, 132, 138
130-OES


title: Ovariectomized_Female_estradiol_cocaine_136

description:
OEC 126, 128, 134, 136, 140
136-OEC


title: Ovariectomized_Female_estradiol_cocaine_126

description:
OEC 126, 128, 134, 136, 140
126-OEC


title: Ovariectomized_Female_estradiol_cocaine_128

description:
OEC 126, 128, 134, 136, 140
128-OEC


title: Ovariectomized_Female_estradiol_cocaine_140

description:
OEC 126, 128, 134, 136, 140
140-OEC


title: Ovariectomized_Female_estradiol_saline_122

description:
OES 122, 124, 130, 132, 138
122-OES


title: Ovariectomized_Female_placebo_cocaine_133

description:
OPC 125, 127, 133, 135, 139
133-OPC

source_name: Ovariectomized female, placebo, cocaine


title: Ovariectomized_Female_placebo_cocaine_139

description:
OPC 125, 127, 133, 135, 139
139-OPC


title: Ovariectomized_Female_placebo_cocaine_127

description:
OPC 125, 127, 133, 135, 139
127-OPC


title: Donor1_CMP_E3


title: Ovariectomized_Female_placebo_cocaine_135

description:
OPC 125, 127, 133, 135, 139
135-OPC


title: Ovariectomized_Female_estradiol_saline_124

description:
OES 122, 124, 130, 132, 138
124-OES


title: Ovariectomized_Female_placebo_cocaine_125

description:
OPC 125, 127, 133, 135, 139
125-OPC


title: Ovariectomized_Female_placebo_saline_137

description:
OPS 121, 123, 129, 131, 137
137-OPS

source_name: Ovariectomized female, placebo, saline


title: Ovariectomized_Female_placebo_saline_121

description:
OPS 121, 123, 129, 131, 137
121-OPS


title: Ovariectomized_Female_placebo_saline_131

description:
OPS 121, 123, 129, 131, 137
131-OPS


title: Female_cocaine_79

description:
FC 70, 71, 72, 79, 80
79-FC

source_name: Female cocaine


title: Female_cocaine_72

description:
FC 70, 71, 72, 79, 80
72-FC


title: Female_cocaine_71

description:
FC 70, 71, 72, 79, 80
71-FC


title: Female_saline_78

description:
FS 64, 65, 66, 77, 78
78-FS

source_name: Female saline


title: Female_saline_77

description:
FS 64, 65, 66, 77, 78
77-FS


title: Donor1_CMP_D7

source_name: CD34+ selected PBSC


title: Female_saline_66

description:
FS 64, 65, 66, 77, 78
66-FS


title: Ovariectomized_Female_placebo_saline_129

description:
OPS 121, 123, 129, 131, 137
129-OPS


title: Male_cocaine_69

description:
MC 67, 68, 69, 75, 76
69-MS

source_name: Male cocaine

value: male


title: Female_saline_64

description:
FS 64, 65, 66, 77, 78
64-FS


title: Female_saline_65

description:
FS 64, 65, 66, 77, 78
65-FS


title: Male_cocaine_67

description:
MC 67, 68, 69, 75, 76
67-MC


title: Male_saline_74

description:
MS 61, 62, 63, 73, 74
74-MS

source_name: Male saline


title: Male_cocaine_68

description:
MC 67, 68, 69, 75, 76
68-MC


title: Male_cocaine_76

description:
MC 67, 68, 69, 75, 76
76-MC


title: Ovariectomized_Female_placebo_saline_123

description:
OPS 121, 123, 129, 131, 137
123-OPS


title: Male_saline_63

description:
MS 61, 62, 63, 73, 74
63-MS


title: Female_cocaine_80

description:
FC 70, 71, 72, 79, 80
80-FC


title: Male_saline_62

description:
MS 61, 62, 63, 73, 74
62-MS


title: Male_saline_73

description:
MS 61, 62, 63, 73, 74
73-MS


title: Female_cocaine_70

description:
FC 70, 71, 72, 79, 80
70-FC


title: Male_saline_61

description:
MS 61, 62, 63, 73, 74
61-MS


title: Male_cocaine_75

description:
MC 67, 68, 69, 75, 76
75-MC


title: HG3-M2

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

data_processing:
Sample data was demultiplexed and raw sequence files generated using bcl2fastq2 app in Illumina’s cloud application, Basespace.
SureCell RNA Single-Cell application to extract the cell barcodes and the Unique Molecular Identifiers (UMIs). The raw sequence files were aligned to the hg19 human reference genome and gene expression was quantified.
A knee plot of the genic UMIs per cell barcode was used to set thresholds for cells for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: umicount table with genes as columns and cell barcodes as rows

source_name: serous epithelial ovarian cancer

growth_protocol: Pathological discard tissue, from women who were scheduled for surgery to evaluate a suspicious pelvic mass, primary tumor and metastatic lesions (when available), were obtained at time of surgery and frozen for later analysis. Tissue was minced and frozen in 40% FBS, 40% RPMI and 20% DMSO.

extract_protocol:
Thawed tissue samples were digested and dissociated into single-cell suspensions using Miltenyi’s gentleMACS Octo dissociator and tumor dissociation kit following manufacturer’s instructions. Single cells were collected by straining digested tissue through a MACS Smart strainer (70um), washed, then layered over a Ficoll gradient to remove red blood cells and debris.  To enrich the tumor cell fraction for live cells, dead cells were excluded using Dead Cell Removal kit and MS columns (Miltenyi Biotec) and remaining viable cells were prepared for scRNA-seq.
Using the BioRad droplet digital SEQ Single-cell Isolator and the Illumina SureCell Whole Transcriptome Analysis 3’ library prep kit, scRNA-seq was performed on isolated cells from ovarian tumor tissue samples following the manufacturer’s instructions. Briefly single-cells were encapsulated, lysed then barcoded within each droplet.  Following first and second strand cDNA synthesis, Illumina’s Nextera technology was used to generate a library for NGS. Final libraries were assessed and quantified using a High Sensitivity DNA chip and a 2100 BioAnalyzer (Agilent Technologies) prior to sequencing on a NexSeq 500 high output flow cell.

tag: sample id

tag: diagnosis

value: HGSOC

tag: site

value: Metastatic

tag: subject id


title: HG4-P3

value: Primary


title: HG4-P2


title: HG2F-M


title: LG2-P

value: LGSOC


title: HG2F-P


title: HG1-P


title: HG4-P1


title: HG4-P4


title: LG2-M


title: HG3-P


title: HG1-M


title: LG1-P


title: NM1

value: Normal

value: Normal Ovary


title: HG3-M1


title: PN1-P

value: Peritonal


title: NA1-P

value: Neo adjuvant


title: siNCOR2_2_shARfl_Rep_3

first: Myles

last: Brown

address: 450 Brookline Ave., D730

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Differential gene expression was determined using the Visualization Pipeline for RNA-seq (https://bitbucket.org/cfce/viper/) and DEseq {Anders, 2010 #64}
Genome_build: hg19
Supplementary_files_format_and_content: Differential expression tables produced by Deseq

growth_protocol: LNCaP95 cells maintained in phenol red-free RPMI 1640 medium with supplemented 10% charcoal/dextran-treated FBS, 1% L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
TRIzol (Thermo Fisher Scientific) and Direct-zol RNA Mini Prep Plus (Zymo Research)
Generated by the Center for Functional Cancer Epigenetics at the Dana Farber Cancer Institute using 1 ug total RNA and the Illumina TruSeq stranded mRNA sample kit. Libraries were sequenced on the Illumina NextSeq 500 platform

treatment_protocol: Cells transiently transfected with siRNA targeting Nuclear Co-Repressors NCOR1, NCOR2, or NRIP1 for 24h.

tag: transfection

value: shARfl

tag: batch date (d.m.y)


title: siNRIP1_2_shARfl_Rep_3


title: siNRIP1_1_shARfl_Rep_2


title: siNRIP1_2_shARfl_Rep_1


title: siNRIP1_2_shARfl_Rep_2


title: siNRIP1_1_shARfl_Rep_3


title: siNCOR2_2_shARfl_Rep_1


title: siNRIP1_1_shARfl_Rep_1


title: siNCOR2_1_shARfl_Rep_3


title: siNCOR2_1_shARfl_Rep_2


title: siNCOR2_2_shARfl_Rep_2


title: BN1-P

value: Benign


title: siCtrl_2_shARfl_Rep_3


title: siCtrl_2_shARfl_Rep_1


title: siNCOR1_2_shARfl_Rep_3


title: siNCOR1_2_shARfl_Rep_1


title: siNCOR1_1_shARfl_Rep_1


title: siNRIP1_2_shARv7_Rep_1


title: siNRIP1_2_shARv7_Rep_2


title: siNRIP1_1_shARv7_Rep_3


title: siNCOR2_1_shARfl_Rep_1


title: siCtrl_2_shARfl_Rep_2


title: siNCOR1_2_shARfl_Rep_2


title: siNCOR1_1_shARfl_Rep_2


title: siCtrl_1_shARfl_Rep_3


title: siNCOR1_1_shARfl_Rep_3


title: siNRIP1_2_shARv7_Rep_3


title: siCtrl_1_shARfl_Rep_2


title: siCtrl_1_shARfl_Rep_1


title: siNCOR2_2_shARv7_Rep_3


title: siNRIP1_1_shARv7_Rep_2


title: siNRIP1_1_shARv7_Rep_1


title: siNCOR2_2_shARv7_Rep_2


title: siNCOR2_2_shARv7_Rep_1


title: siNCOR2_1_shARv7_Rep_1


title: siNCOR1_2_shARv7_Rep_2


title: siNCOR1_2_shARv7_Rep_3


title: siNCOR1_2_shARv7_Rep_1


title: siNCOR2_1_shARv7_Rep_2


title: siNCOR1_1_shARv7_Rep_3


title: siNCOR2_1_shARv7_Rep_3


title: siCtrl_2_shARv7_Rep_3


title: siNCOR1_1_shARv7_Rep_1


title: siNCOR1_1_shARv7_Rep_2


title: siCtrl_2_shARv7_Rep_2


title: siCtrl_1_shARv7_Rep_3


title: siCtrl_2_shARv7_Rep_1


title: siNRIP1_2_shGFP_Rep_3

value: shGFP


title: siCtrl_1_shARv7_Rep_2


title: siNRIP1_2_shGFP_Rep_1


title: siCtrl_1_shARv7_Rep_1


title: siNRIP1_2_shGFP_Rep_2


title: siNCOR1_2_shGFP_Rep_1


title: siNCOR1_2_shGFP_Rep_2


title: siNCOR1_1_shGFP_Rep_3


title: siNCOR2_2_shGFP_Rep_2


title: siNCOR2_2_shGFP_Rep_1


title: siNRIP1_1_shGFP_Rep_2


title: siNCOR1_1_shGFP_Rep_2


title: siCtrl_1_shGFP_Rep_3


title: siCtrl_2_shGFP_Rep_3


title: siNCOR1_2_shGFP_Rep_3


title: siNCOR1_1_shGFP_Rep_1


title: siNCOR2_1_shGFP_Rep_1


title: siCtrl_2_shGFP_Rep_1


title: siCtrl_2_shGFP_Rep_2


title: siNCOR2_1_shGFP_Rep_2


title: siNCOR2_1_shGFP_Rep_3


title: siNRIP1_1_shGFP_Rep_3


title: siCtrl_1_shGFP_Rep_1


title: siNRIP1_1_shGFP_Rep_1


title: VU40T_DAC_Para

city: Birmingham

first: Malgorzata

last: Wiench

address: 5 Mill Pool Way

department: School of Dentistry

country: United Kingdom

institute: University of Birmingham

data_processing:
Quantification was performed using Salmon, according to the DESeq2 guidelines [PMID: 28263959]
salmon quant --seqBias --numBiasSamples 2000000 --gcBias --biasSpeedSamp 10 -I GRCh37_index -l IU
Differential expression analysis was performed using DESeq2 using default parameters and the Ensembl gene models.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with one tab per DESeq2 comparison

growth_protocol: DMEM with 1% Penicillin/Streptomycin, 4mM L-glutamine, 10% FBS, 1X non-essential amino acids, 1mM sodium pyruvate.

extract_protocol:
RNA was extracted from cells using RNeasy Mini Kit (Qiagen) following the manufactorers guidelines and including the DNase I digestion step (RNase-Free DNase set, Qiagen).
For each sample three biological replicates were pooled to make a library using the TruSeq Stranded mRNA Library Prep kit following the manufacturers protocol

treatment_protocol: VU40T head and neck squamous cell carcinoma cells were treated with 500nM 5-aza-2'deoxycytidine (DAC) and/or 132.3μM Paracetamol (acetaminophen) for 96h before collection. The media were changed after the first 48h and fresh drugs were added.

value: 500nM 5-aza-2'-deoxycytidine (DAC) + 132.3μM Paracetamol (Para)


title: VU40T_Para

source_name: VU40T head and neck squamous cell carcinoma

value: 132.3μM Paracetamol (Para)


title: siNCOR2_2_shGFP_Rep_3


title: siCtrl_1_shGFP_Rep_2


title: VU40T_Control

description:
Ctrl_vs_PARA_diff_expr.xlsx
Ctrl_vs_DAC_diff_expr.xlsx
Ctrl_vs_PARA_DAC_diff_expr.xlsx

value: No treatment control


title: VU40T_DAC

value: 500nM 5-aza-2'-deoxycytidine (DAC)


title: K13 IL-10 12h rep1

first: W. K. Eddie

last: Ip

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

data_processing:
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality regions by btrim.  The trimmed reads were mapped to mouse genome (GRCm38) by tophat2.  After the counts are collected, the differential expression analysis was done by DEseq2, which calculated the fold changes and adjusted p-values.
Genome_build: GRCm38

source_name: Il10-/- BMDMs

growth_protocol: To grow bone-marrow derived macrophages (BMDMs), bone marrow cells were flushed from femur and tibia bones of IL-10-deficient mice strain in C57BL/6 background (Il10-/- C57BL/6) between 6 and 12 weeks of age, and were grown at 37°C in a humidified incubator in RPMI-1640 medium containing L-glutamine, 10% FCS and 30% L929 supernatant (i.e. BMDM growth media) for 7-8 days.

extract_protocol:
RNA were extracted using RNaesy Kit (Qiagen) followed by RNA clear up with on-column DNase digestion.
cDNA library was prepared using TruSeq Chemistry (Illumina).

treatment_protocol: The RNA seq analysis was performed separately in two groups of samples. Group 1: BMDMs were stimulated for 3 h without (control samples C1 and C2) or with 100 ng/ml of lipopolysaccharide (LPS)(sampels C3 and C4), 100 ng/ml of IL-10 (samples D1 and D2) or both (sampels D3 and D4). Group 2: BMDMs were stimulated without (control samples K1 and K2) or with 100 ng/ml of LPS (for 6 h: samples K3 and K4; for 12 h: samples K9 and K10), 100 ng/ml of IL-10 (for 6 h: samples K7 and K8; for 12 h: sampels K13 and K14) or both (for 6 h: sampels K5 and K6; for 12 h: samples K11 and K12).

tag: cell type

value: Bone marrow-derived macrophages

value: Primary cell culture


title: K12 LPS+IL-10 12h rep2

value: LPS+IL-10 12h


title: K14 IL-10 12h rep2


title: K11 LPS+IL-10 12h rep1


title: K5 LPS+IL-10 6h rep1

value: LPS+IL-10 6h


title: K6 LPS+IL-10 6h rep2


title: K7 IL-10 6h rep1


title: K9 LPS 12h rep1

value: LPS 12h


title: K10 LPS 12h rep2


title: Melanoma

first: Burak

last: Dura

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

data_processing:
Base calling, alignment, filtering and generation of gene expression matrices are all performed according to the protocols described in Macosko et al. Cell 2015
Genome_build: hg19, mm10
Supplementary_files_format_and_content: tab limited text files include transcript counts for each gene for individual cells

source_name: subcutaneously injected tumor

extract_protocol: mRNA captured on barcoded beads were reverse transcribed and amplified using half a PCR reaction. Tagmentation and final library preparation was performed using Illumina Nextera XT Kit (FC-131-1024) according to manufacturer's protocol.


title: K3 LPS 6h rep1

value: LPS 6h


title: K8 IL-10 6h rep2


title: K4 LPS 6h rep2


title: fourN_CPC

city: San Diego

first: Oscar

last: Echeagaray

state: CA

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

data_processing:
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 2.0; 98 bp Read1, 8 bp i7 Index, and 26 bp Read2).  Reads were aligned to the Mus musculus genome.
1036 diploid and 628 tetraploid freshly isolated CPC samples were recovered. Cells with less than 1000 genes or more than 10% of mitochondrial gene UMI count were filtered out and genes detected less than in three cells were filtered out. Altogether, 1664 cells and 15579 genes were kept for downstream analysis using Seurat R Package (v2.3.4).
Sequenced reads were aligned to the mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: values of digital expression matrix; rows are genes; columns are cells with cell barcode

source_name: CPC

extract_protocol:
Adult c-Kit+ CPCs were isolated and expanded as previously described. Twelve-week-old FVB female mice were heparinized and anesthetized by ketamine-xylazine solution. Hearts were removed from the chest cavity and perfused on a Langendorff system at 1mL/min flow rate at 37ºC with perfusion buffer (NaCl, KCl, KH2PO4, Na2HPO4, MgSO4•7H2O, NaHCO3, KHCO3 HEPES, Taurine, Glucose, and BDM) for blood removal, and tissue was subsequently digested for 10-15 minutes with Liberase DH digestion buffer (Roche 05401089001, 5 mg/mL in perfusion buffer). Heart was collected in STOP buffer (10% Bovine calf serum, 12.5 µM CaCl2), minced into 1 mm3 and dissociated through pipetting. The non-myocyte population was separated through serial cell straining (100µm, 40µm, and 30µm pore size), followed by centrifugation at ~300 rfc for 10 minutes. Lin-cKit+ CPCs were obtained by immunomagnetic sorting with Lineage depletion kit and CD117-conjugated Microbeads (Miltenyi Biotech 130-048-102). Fresh isolated CPCs were separated for immediate single-cell RNA-Seq analysis or cultured in growth medium ((Dulbecco's modified Eagle's medium, 10% embryonic stem cells FBS, 1% insulin-transferrin-selenium, leukemia inhibitory factor [10 ng/ml], basic fibroblast growth factor [10 ng/ml], epidermal growth factor [20 ng/ml], L-glutamine [0.07mg/mL], 1% penicillin-streptomycin-glutamine, 0.1% gentamicin, 2% B27 supplement, 1% N2 supplement). Cells were plated on a pre-coated (0.1% porcine gelatin) cell culture-grade dish. Adherent cultures were expanded and passaged five times when 40% confluency was reached and used for single-cell RNA-seq.
The Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3' Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V2 User Guide.

value: FVB

tag: age

value: Twelve-week-old

value: female

value: cardiac progenitor cells (CPCs)

tag: ploidy

value: Tetraploid


title: D4 LPS+IL-10 3h rep2

value: LPS+IL-10 3h


title: twoN_CPC

value: Diploid


title: D3 LPS+IL-10 3h rep1


title: K1 Control rep1

value: control


title: C3 LPS 3h rep1

value: LPS 3h


title: C4 LPS 3h rep2


title: D1 IL-10 3h rep1


title: D2 IL-10 3h rep2


title: C1 Control rep1


title: C2 Control rep2


title: 1984_BM_fl

city: San Francisco

first: Candice

last: Herber

address: 1550 4th Street

institute: UCSF

data_processing:
illumina Casava1.8 software used for producing FastQ files.
RNA-seq data processing were performed in the Galaxy platforms version 1.6.2 (https://usegalaxy.org/)
Run quality was checked by FastQC (tool version 0.11.5)
Removed low quality end sequences using Trim Galore! read trimmer (tool version 1.14)
Aligned to the mouse mm10 genome sequence in Galaxy using Tophat v2.1.0 (with default setting)
Read counting was done by featureCounts version 1.6.0 using the mm10 genes reference.
Read count normalization and differential expression between samples were done by DESeq2 (Tool version DESeq2 v1.18.1)
Genome_build: Mouse Dec. 2011 (GRCm38/mm10) (mm10)
Supplementary_files_format_and_content: Raw counts: tabular txt, Normalized Counts: tabular txt

source_name: Whole bone marrow

extract_protocol:
Total RNA extracted in Trizol reagent and purified by Direct-zol spin columns (Zymo Research)
Ovation Trio RNA-Seq System (NuGEN) was used to generate the cDNA library for sequencing on an Illumina HiSeq 4000 by using standard protocol.

value: CD-1; 129P2 mixed

tag: tissue

value: Whole bone marrow

tag: genotype


title: 1810_BM_KO

value: Esr1flox/flox; Nkx2-1Cre Tg/+


title: K2 Control rep2

value: Bone marrow-derived macrophages

value: Primary cell culture


title: 1811_BM_KO


title: DMC-POPS3_S9_L005_R1_001

city: La Jolla

first: David

middle: Mario

last: Cauvi

state: California

address: 9500 Gilman Dr.

department: Surgery

institute: University of California, San Diego

description: POPS replicate 3

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) using the STAR v2.5.1a aligner.
Read quantification was performed with RSEM v1.3.0 and GENCODE annotation (Mus_musculus.GRCm38.68.gtf). The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis.
Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing corrections using a moderated t-statistic in Limma.
Functional enrichment of the differentially expressed genes was performed using the Bioconductor GSVA package for implementing GSEA, Signaling Pathway Impact Analysis with the Bioconductor package SPIA and overrepresentation analysis in WebGestalt.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

source_name: CD-1 mice intraperitoneally injected for 1 hour with POPS liposomes

extract_protocol:
Peritoneal cells were harvested by lavage 1 hour after the PBS or liposome injection, and processed for total RNA isolation using RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA)
RNA sequencing libraries were then generated from 1 µg of RNA using the TruSeq® Stranded Total RNA Library Prep Gold Sample Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS (400 µl; control, CTL), POPC liposomes (400 µg at 1 mg/ml) or POPS liposomes (400 µg at 1 mg/ml) were injected in the peritoneal cavity of CD-1 mice.

value: Peritoneal cells

value: CD-1 (Crl:CD1 (ICR))

value: 9 weeks


title: DMC-POPC1_S4_L005_R1_001

description: POPC replicate 1

source_name: CD-1 mice intraperitoneally injected for 1 hour with POPC liposomes


title: DMC-POPC2_S5_L005_R1_001

description: POPC replicate 2


title: DMC-POPC3_S6_L005_R1_001

description: POPC replicate 3


title: 1818_BM-fl


title: DMC-POPS2_S8_L005_R1_001

description: POPS replicate 2


title: DMC-CTL3_S3_L005_R1_001

description: Control replicate 3

source_name: CD-1 mice intraperitoneally injected for 1 hour with PBS


title: DMC-POPS1_S7_L005_R1_001

description: POPS replicate 1


title: 1807_BM_fl


title: DMC-CTL2_S2_L005_R1_001

description: Control replicate 2


title: 1815_BM_fl


title: DMC-CTL1_S1_L005_R1_001

description: Control replicate 1


title: 2mmTassel_wildtype_rep1

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence, then mapped to ZmB73v3 whole genome using Tophat v2.1.1
Differentially expressed genes were identified using Cuffdiff v2.2.1
Genome_build: ZmB73v3.31

organism: Zea mays

source_name: 2-3mm maize B73 field-grown wildtype tassels

growth_protocol: 2-3mm maize B73 field-grown tassels

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Stranded Illumina RNA sequencing libraries were generated using the TruSeqv3 kit (Illumina)

treatment_protocol: 2-3mm maize B73 field-grown (five plants per sample) were harvested

tag: background

value: wildtype


title: 2mmTassel_wildtype_rep2


title: 2mmTassel_re2mut_rep3

source_name: 2-3mm maize B73 field-grown rel2-ref mutant tassels

value: rel2-ref mutant


title: 2mmTassel_re2mut_rep2


title: 1985_BM_KO


title: 2mmTassel_re2mut_rep1


title: 1825_BM_KO


title: rna_KO2_rep1

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

description: mRNA-seq

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

source_name: rna KO2

extract_protocol:
Truseq stranded mRNA library prep
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)
Ribosome profiling&mRNA-seq

tag: genetic background

tag: cell line

tag: extracted molecule

value: total RNA


title: rna_WT_rep1

description: mRNA-seq

source_name: rna WT


title: rna_KO1_rep2

description: mRNA-seq

source_name: rna KO1


title: rna_WT_rep2

description: mRNA-seq


title: rna_KO2_rep2

description: mRNA-seq


title: ribo_KO2_rep2

description: Ribosome Profiling

source_name: ribo KO2

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)
Ribosome profiling&mRNA-seq


title: ribo_KO1_rep2

description: Ribosome Profiling

source_name: ribo KO1


title: ribo_KO1_rep1

description: Ribosome Profiling


title: ribo_KO2_rep1

description: Ribosome Profiling


title: 2mmTassel_wildtype_rep3

tag: treatment


title: ribo_WT

description: Ribosome Profiling

source_name: ribo WT

value: WT


title: HG001_DrsaI_Comp_TotRNA_R2

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

country: France

institute: CNRS

description:
comp2_S22
norm,C2

data_processing:
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2
Genome_build: GCA_001900185.1
Supplementary_files_format_and_content: Tables obtained by DEseq2 reporting the Fold Changes, p-values and p-adj-values

organism: Staphylococcus aureus

growth_protocol: Bacteria were grown in Brain Heart Infusion (BHI) medium until late exponential phase of growth (6h). Erythromycin at 10 ug/ml final concentration was added to the medium for plasmid selection.

extract_protocol:
Bacterial lysis was performed with FastPrep and the RNA purification followed strictly the procedure described for the FastRNA Pro Blue Kit (MP Biomedicals).
DNase I (0.1 U/ml) treatment was performed 1h at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. RNAs were treated to deplete abundant rRNAs, and the cDNA libraries were performed using the ScriptSeq complete kit (bacteria) from Illumina. The libraries were sequenced using Illumina MiSeq with a V3 Reagent kit (Illumina), which preserves the information about the orientation of the transcripts and produces reads of 150 nts, which map on the complementary strand. Each RNA-seq was performed in triplicates.

tag: strain background

tag: genotype/variation

value: {delta}rsaI mutant complemented with a plasmid expressing RsaI

tag: growth phase

value: late exponential phase of growth (6h)


title: HG001_DrsaI_Comp_TotRNA_R1

description:
comp1_S19
norm,C1


title: HG001_DrsaI_TotRNA_R2

description:
delta2_S21
norm,D2

value: {delta}rsaI mutant


title: HG001_TotRNA_R3

description:
WT3_S23
norm,W3

value: wild type


title: HG001_DrsaI_Comp_TotRNA_R3

description:
comp3_S25
norm,C3


title: HG001_DrsaI_TotRNA_R1

description:
delta1_S18
norm,D1


title: HG001_DrsaI_TotRNA_R3

description:
delta3_S24
norm,D3


title: HG001_TotRNA_R2

description:
WT2_S20
norm,W2


title: Wild type line #5

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Adaptors and low quality nucleotides were removed from raw sequencing paired-end reads by Trim_Galore.
Bowtie was used to map clean reads to mm9 reference genome.
Multi-mapped reads and duplicated reads were further removed using samtools.
Peak calling was performed by using MACS1.4
Genome_build: mm9
Supplementary_files_format_and_content: bed format files for peaks called in WT and DA samples.

source_name: embryonic stem cells

growth_protocol: embryonic stem cells were passaged in LIF containing embryonic stem cells media (10% FBS)

extract_protocol:
Genomic DNA was extracted with Qiagen Dneasy Blood & Tissue kit according to the manufacturer's protocol.
100 ng genomic DNA extracted from ES cells were fragmented in 50 μL Tagmentation buffer at 55°C. Fragmented DNA was purified by Zymo DNA clean&concentrator Kit (Zymo Research, Tustin, CA). Then, the selective 5hmC chemical labeling was performed in 25 μL glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing above fragmented DNA, 100 μM N3-UDP-Glc, 1 μM β-GT, and incubated at 37°C for 2 hr. After purified in 45 μL ddH2O, 1.5 μL DBCO-PEG4-Biotin (Click Chemistry Tools, 4.5 mM stored in DMSO) was added and incubated at 37°C for 2 hr. The biotin labeled DNA was pulled down by 5 µL C1 Streptavidin beads (Life Technologies, Carlsbad, CA) for 15 min at room temperature. Next, the captured DNA fragments were subjected to 13 cycles of PCR amplification using Nextera DNA sample preparation kit (Illumina, San Diego, CA). The resulting amplified product was purified by 1.0X AMPure XP beads. Input library was made by direct PCR from fragmented DNA without chemical labeling and capture. The libraries were quantified by a Qubit fluorometer (Life Technologies) and sequenced on an Illumina HiSEQ2500 sequencer with paired-end 40-bp reads.

value: ESC

tag: flag tag

value: C-terminal FLAG tag on TET1


title: D2018A input

value: TET1 mutation, D2018A


title: Wild type input


title: D2018A line #7


title: rna_KO1_rep1

description: mRNA-seq


title: Wild type line #2


title: Blood_Platelets_Vumc-bact-PLTEcoliO18-4

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

institute: VU University Medical Center

description:
Vumc-bact-PLTEcoliO18-4
VumcbactPLTEcoliO18-TR2032
processed data file: allSamples_readCounts_ISreads.txt

data_processing:
Single-end 100 bp reads were subjected to pre-alignment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: allSamples_readCounts_ISreads.txt: Samples in the tab-delimited text file were processed according to the described protocol and data of all samples was merged in a comprehensive read count matrix.

source_name: Thrombocytes

growth_protocol: Washed platelets were resuspended in SPP+ buffer and kept on a see-saw shaker for one hour before starting the experiments.

extract_protocol:
Whole blood was collected in citrate-coated BD Vacutainer tubes. Platelet rich plasma (PRP) was prepared using centrifugation at 150 x g for 15 minutes. PRP was applied to an Optiprep density gradient and spun at 350 x g for 15 minutes to decrease the leukocyte number of the suspension. After harvesting the platelet layer, cells were washed with HEPES-Tyrode buffer (10 mM HEPES, 137 mM NaCl, 2.8 mM KCl, 1 mM MgCl2,12 mM NaHCO3, 0.4 mM Na2HPO4, 5.5 mM glucose, and 0.35% bovine serum albumin [BSA]). Centrifugation was performed without break, and before every centrifugation step 400 nM prostaglandin I2 (PGI2) was added to prevent platelet activation. Incubation of washed platelets with bacteria was followed by centrifugation of the samples at 500 x g for 10 minutes. The pellets were used for RNA isolation with a standard phenol-chloroform procedure. Briefly, centrifuged cells were resuspended in 500 µl Trizol reagent, and added to Phase lock tubes together with chloroform. The RNA pellet was air-dried and resuspended in 40 µl RNase-free water. RNA quality and quantity were measured using Bioanalyzer 2100 with RNA 6000 Picochip.
100-500 pg of platelet total RNA diluted in nuclease-free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturer's protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the TruSeq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or TruSeq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity were measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations (12-19 samples per HiSeq lane) and submitted for 100 bp Single Read sequencing on the HiSeq 2500 platform (Illumina).

treatment_protocol: Two different strains of E. coli bacteria were used: the non-pathogenic E. coli K12 C600 and the uropathogenic E. coli O18:K1. The bacteria were grown in lysogeny broth at 37°C and 160 rpm until they reached an OD600 nm of 0.5-0.9. The cells were pelleted by centrifugation at 18 000 x g for 10 minutes and washed with SSP+ buffer. After washing, the platelet pellet was resuspended in SSP+ and used for in vitro exposure to the bacteria on a 1:1 platelet-bacteria ratio. Platelet-bacteria samples were incubated on a see-saw shaker (10 rpm) for 3 hours.

tag: disease status

value: Healthy

value: Platelets

tag: condition

value: E. coli O18

tag: individual id


title: Blood_Platelets_Vumc-bact-PLTEcoliO18-3

description:
Vumc-bact-PLTEcoliO18-3
Vumc-bactPLTEcoliO18TR2016
processed data file: allSamples_readCounts_ISreads.txt

tag: cell type


title: Wildtype_mESC_HiC_Biological_Rep2

city: Cambridge

first: Abbie

last: Groff

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8.  The reads were mapped to the mm9 mouse reference genome. There was a high correlation among the Hi-C biological replicates, indicating the high quality and reproducibility of the datasets. Therefore, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset, and used the pooled datasets for all subsequent analyses.
Genome_build: mm9

source_name: Mouse Embryonic Stem Cells

extract_protocol: Hi-C libraries were generated with an in-situ Hi-C protocol (Beleghzal et al, 2016), using the HindIII restriction enzyme.  Briefly, ~25 million cells were crosslinked with 1 % formaldehyde for 10 minutes at room temperature. After quenching the formaldehyde with glycine, the nuclei were isolated, and the DNA was digested with HindIII, end-labelled with biotin-14-dCTP, and in-dilution ligation was performed. Following phenol-chloroform extraction, the biotin was removed from non-ligated ends, and the DNA was sheared by using a Covaris S220 instrument. After A-tailing and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Hi-C libraries were prepared in two biological replicates from mESC.


title: Wildtype_mESC_HiC_Biological_Rep1


title: D2018A line #8


title: Blood_Platelets_Vumc-bact-PLTEcoliO18-2

description:
Vumc-bact-PLTEcoliO18-2
Vumc-bactPLTEcoliO18-TR2024
processed data file: allSamples_readCounts_ISreads.txt


title: Blood_Platelets_Vumc-bact-PLTEcoliK12-2

description:
Vumc-bact-PLTEcoliK12-2
Vumc-bactPLTEcoliK12-TR2017
processed data file: allSamples_readCounts_ISreads.txt

value: E. coli K12


title: PerilKO_mESC_HiC_Biological_Rep2

value: PerilKO


title: Blood_Platelets_Vumc-bact-PLTEcoliK12-4

description:
Vumc-bact-PLTEcoliK12-4
Vumc-bactPLTEcoliK12-TR2033
processed data file: allSamples_readCounts_ISreads.txt


title: Blood_Platelets_Vumc-bact-PLTEcoliO18-1

description:
Vumc-bact-PLTEcoliO18-1
Vumc-bactPLTEcoliO18-TR2008
processed data file: allSamples_readCounts_ISreads.txt


title: Blood_Platelets_Vumc-bact-PLTEcoliK12-3

description:
Vumc-bact-PLTEcoliK12-3
Vumc-bactPLTEcoliK12-TR2025
processed data file: allSamples_readCounts_ISreads.txt


title: Blood_Platelets_Vumc-bact-PLTEcoliK12-1

description:
Vumc-bact-PLTEcoliK12-1
Vumc-bactPLTEcoliK12-TR2009
processed data file: allSamples_readCounts_ISreads.txt


title: HG001_TotRNA_R1

description:
WT1_S17
norm,W1


title: Blood_Platelets_Vumc-bact-contrPLT-4

description:
Vumc-bact-contrPLT-4
Vumc-bactcontrPLT-TR2031
processed data file: allSamples_readCounts_ISreads.txt

value: Control


title: Blood_Platelets_Vumc-bact-contrPLT-3

description:
Vumc-bact-contrPLT-3
VUMC-bactcontrPLT-TR2015
processed data file: allSamples_readCounts_ISreads.txt


title: MYOD1 ChIPseq

city: MILL VALLEY

first: Brian

middle: A

last: Hodge

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

data_processing:
FastQ Groomer was used to convert raw Fastq reads into Fastq-sanger format, and then Trimmomatic was ued to cut adapter and illumina-specific sequences from the reads.
Trimmed reads were aligned to the mm10 genome (provided by UCSC database) with the bowtie2 package.
Samtools was utilized to convert between sam format to bam format.
bamToBed was utilized to convert the reads to Bed format.
no input sample (normalization was done with background filtering with stringent settings)
Genome_build: mm10 UCSC

source_name: Gastrocnemius muscle

extract_protocol:
Approximately 800 mg of adult skeletal gastrocnemius muscle was homogenized in cell lysis buffer (10mM HEPES, pH7.5, 10mM MgCl2, 60mM KCl, 300mM sucrose, 0.1mM EDTA, pH8.0, 0.1% Triton X-100, 1mM DTT, protease inhibitors) containing 1% formaldehyde. Cross-linking was stopped after 30 minutes by adding glycine to a final concentration of 0.125M. Nuclei and muscle fibers were separated by centrifugation at 25g for 5 minutes. The supernatant was collected, and nuclei were spun down by centrifugation at 800 g for 5 minutes and re-suspended in 350 µl of RIPA buffer (20mM Tris, pH8.0, 2mM EDTA, pH8.0, 0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 140mM NaCl). The nuclei preparation was sonicated to shear the DNA to 150-600 bp and then centrifuged at 14,000 g for 15 minutes. The supernatant was collected and pre-cleared with protein A/G slurry at 4ºC for 1 hr.  Protein A/G beads were removed by centrifugation and supernatant was split into two equal parts, which will be mixed with either MYOD1 Ab or pre-immune serum and incubated overnight at 4ºC. The immune-complex was incubated with protein A/G beads slurry for 4 hours and the beads will be washed with RIPA buffer 5 times and TE buffer twice. DNA was then eluted twice with 250 µl of elution buffer (1% SDS and 0.1M NaHCO3) for 20 minutes and supernatant was collected after 5 minutes centrifugation at high speed. Twenty-five microliters of 4M NaCl was mixed with the 500µl of elute and incubated at 65ºC overnight. Then 10µl of 0.5M EDTA, 20µl of 1M Tris pH 6.5 and 2µl 10mg/ml proteinase K was added to each sample and incubated at 55ºC for 1.5 hr. DNA was recovered by using PCR purification kit (Qiagen).
ChIP DNA samples from the MYOD1 antibody were prepared for Solexa sequencing according to the Illumina protocol using methods described in Cao et al., (Dev. Cell, 2010) with DNA fragments ranging in size from 150 to 600 bp.

tag: strain

tag: Sex

value: male

tag: collection

value: 24 hour timecourse

value: Gastrocnemius muscle


title: cTfh_untreated

source_name: blood

value: untreated


title: cTfh_stimulated

value: PMA/ionomycin


title: PerilKO_mESC_HiC_Biological_Rep1


title: Tcm_stimulated


title: Tcm_untreated


title: Blood_Platelets_Vumc-bact-contrPLT-1

description:
Vumc-bact-contrPLT-1
Vumc-bact-contrPLT-TR2023
processed data file: allSamples_readCounts_ISreads.txt


title: Blood_Platelets_Vumc-bact-contrPLT-2

description:
Vumc-bact-contrPLT-2
Vumc-bactcontrPLT-TR2007
processed data file: allSamples_readCounts_ISreads.txt


title: HEK_HUVEC_K562_mix

source_name: cell lines

value: HEK293:Human embryonic kidney cells, HUVEC:Human umbilical vein endothelial cells, K562:erythroleukemic cell line

tag: passages


title: PBMC_high_rep18

city: Houston

first: Gabriel

middle: R

last: Fries

state: TX

address: 1941 East Rd

department: Psychiatry and Behavioral Sciences

institute: The University of Texas Health Science Center at Houston

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol on iScan microarray reader.

data_processing: Raw data were quantile-normalized using the Gene Expression Module v1.0 on GenomeStudio software v2011.1 (Illumina).

source_name: Peripheral blood mononuclear cells

label_protocol: RNAs were initially labeled into biotinylated cRNAs with the TargetAmp Nano Labeling Kit (Epicentre).

extract_protocol: Cells from heparine-collected peripheral blood were isolated with Ficoll-Paque® (GE Healthcare) protocol. Total RNA was isolated from isolated cells with RNeasy Plus Mini Kit (Qiagen). Quality control was performed with Agilent Bioanalyzer.

tag: anhedonia

value: high

tag: gender

tag: age

tag: race

value: Black/AA


title: PBMC_high_rep9


title: PBMC_high_rep13


title: PBMC_high_rep22


title: PBMC_high_rep15


title: PBMC_high_rep3


title: PBMC_high_rep4

value: female


title: PBMC_high_rep19


title: PBMC_low_rep10

value: low


title: PBMC_low_rep15


title: PBMC_low_rep24

value: White


title: PBMC_low_rep23


title: PBMC_high_rep20


title: PBMC_high_rep17


title: PBMC_low_rep22


title: PBMC_high_rep16


title: PBMC_high_rep21


title: PBMC_high_rep23


title: PBMC_high_rep24

value: Unknown/Not Reported


title: PBMC_high_rep2


title: PBMC_high_rep12


title: PBMC_low_rep20


title: PBMC_low_rep18


title: PBMC_low_rep19


title: PBMC_high_rep1


title: MS2-RsaI_R3

description: MS2 affinity purified RNA

data_processing:
library strategy: MS2-affinity purification coupled with RNA sequencing (MAPS)
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2. Two analysis have been done, the first including samples 1-3 (1 MS2-Contr and two MS2-RsaI) the second including the sample 1-7 (2 controls (MS2-contr-R1 and MS2-contr_R2), 3 RsaI wt (MS2-RsaI_R1, MS2-RsaI_R2 and MS2-RsaI_R3), 1 RsaI mut2 (MS2-RsaImut2) and 1 RsaI mut4 (MS2-RsaImut4)). For this analysis four categorical variable or factor are considered (MS2contr, MS2RsaIwt, MS2RsaImut2 and MS2RsaImut4). Moreover, since the MS2 purifications were done in two separate experiments (1 MS2 contr and two MS2RsaI wt in one experiment; 1 MS2 contr, 1 MS2 RsaI wt, 1 MS2RsaI mut2 and 1 MS2RsaI mut4) introducing some aleatory variables, data pairing have been performed by assigning a blocking factor (batch effect).
Genome_build: GCA_001900185.1
Supplementary_files_format_and_content: Tables obtained by DEseq2 reporting the Fold Changes, p-values and p-adj-values

extract_protocol:
Bacterial cells were resuspended in lysis Buffer (20 mM Tris-HCl pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and broken using the FastPrep apparatus. Crude extract were loaded on a MS2-MBP coated column and purified by affinity chromatography. Eluted RNA were extracted with phenol/chloroform :isoamylalcohol prior to RNAseq analysis.
DNase I (0.1 U/ml) treatment was performed 1h at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. RNAs were treated to deplete abundant rRNAs, and the cDNA libraries were performed using the ScriptSeq complete kit (bacteria) from Illumina. The libraries were sequenced using Illumina MiSeq with a V3 Reagent kit (Illumina), which preserves the information about the orientation of the transcripts and produces reads of 150 nts, which map on the complementary strand. Each RNA-seq was performed at least in duplicates.

tag: strai

value: late exponential phase of growth (6h)

value: MS2-RsaI plasmid


title: MS2-RsaI mut4

description: MS2 affinity purified RNA

source_name: MS2-RsaI mut

value: MS2-RsaI mutant


title: MS2-RsaI mut2

description: MS2 affinity purified RNA


title: PBMC_high_rep11


title: PBMC_low_rep21


title: PBMC_low_rep11

value: More than one race


title: PBMC_low_rep12


title: PBMC_high_rep10


title: PBMC_low_rep16


title: PBMC_high_rep14


title: PBMC_low_rep14


title: PBMC_high_rep7


title: PBMC_high_rep8


title: PBMC_low_rep13


title: PBMC_low_rep9


title: PBMC_high_rep6


title: PBMC_low_rep7


title: PBMC_low_rep17


title: PBMC_high_rep5


title: PBMC_low_rep8


title: PBMC_low_rep3


title: PBMC_low_rep2


title: MS2-Control_R2

description: MS2 affinity purified RNA


title: PBMC_low_rep6


title: PBMC_low_rep4


title: Species_mix_5000_single_cells

city: New Haven

organism:
Homo sapiens
Mus musculus

value: NIH3T3 mouse fibroblast, K562 erythroleukemic cell line


title: MS2-RsaI_R2

description: MS2 affinity purified RNA


title: MS2-RsaI_R1

description: MS2 affinity purified RNA


title: MS2-Control_R1

description: MS2 affinity purified RNA


title: 040916_13C

status: Public on Nov 01 2018

first: Sarah

middle: B

last: Peters

state: AL

address: 1918 University Blvd, MCLM 643

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq  software version 1.8.4 used for basecalling.
Raw sequence fastq files were trimmed using TrimGalore! version 0.4.1 with parameters --paired --trim1
STAR version 2.5.1b was used to align the trimmed fastq files to the UCSC mm10 reference genome using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Cufflinks version 2.2.1 was used to estimate transcript abundances using parameters -g -L
Genome_build: mm10
Supplementary_files_format_and_content: Excel file (tab-delimited) containing gene symbols and FPKM values for each sample

source_name: Mutant crown dental pulp

extract_protocol:
Teeth were dissected divided into roots and crowns.  Dental pulp tissue was removed and immersed in Lysis Buffer (Quiagen #1015762).  Samples were pestled to break up tissue and RNA was isolated with RNA Sample Prep Tool (Zymo Research #R2072).
RNA libraries were prepared using the Agilent SureSelect Strand-Specific mRNA protocol for Illiumina sequencing as per the manufacturer's instructions.

tag: tissue

value: postnatal dental pulp cells

value: postnatal day 7


title: 04016_10R

source_name: Mutant root dental pulp


title: 040916_6R

source_name: Control root dental pulp


title: WT_2

city: New York

last: Cantor

state: New York

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to the mm9 genome with bowtie.
FPKM values and differential expression was determined using cuffdiff.
Genome_build: mm9

source_name: pro-B cell

extract_protocol:
Pro-B cells were sorted directly into RLT (Qiagen) lysis buffer and RNA extracted with micro Rneasy columns. RNA quality and quantity was determined by a Bioanalyzer and normalized for library construction.
Libraries were prepared with the SMARTER method for low-input RNA using standard Illumni procedures.

value: pro-B cell

value: 6-7 weeks

tag: hsc markers

tag: genotype/variation

value: wild type


title: Bmi1KO_2

value: Bmi1 KO


title: Bmi1KO_1


title: WT_1


title: 040916_7C

source_name: Control crown dental pulp


title: PBMC_low_rep5

value: male


title: PBMC_low_rep1


title: Input_B

first: Inna

last: Tabansky

address: 1230 York Ave, Box 275

department: Neurobiology and Behavior

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.8.2
The fastq were aligned to the mouse reference genome (version mm10) using STAR v2.3 (Dobin et al. 2013) aligner with default parameters
The alignment results were then evaluated through RNA-SeQC v1.17  (DeLuca et al., 2012) to ensure that all the samples had a consistent alignment rate, and no obvious 5’ or 3’ bias.
Aligned reads were then summarized through featureCounts (Liao et al., 2014) with the gene model from Ensemble (Mus_musculus.GRCm38.75.gtf) at gene level: specifically, the uniquely mapped reads (NH ‘tag’ in bam file) that overlapped with an exon (feature) by at least 1bp were counted and then the counts of all exons annotated to an Ensemble gene (meta features) were summed into a single number.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrix on coding ensembl genes (row) of all samples (column)

source_name: Reticular NGC neurons_input

extract_protocol:
The nucleus was dissected under a microscope on ice, 5-6 animals were pooled, and immediately subjected to Translating Ribosome Affinity purification protocol.
libraries were prepared using the SMARTer Universal Low Input RNA Library Prep Kit (Cat. Nos. 634945, 634946)

treatment_protocol: Animals (8-16 weeks old) were placed in a stereotax and injected with CAV2-EGFP virus into coordinates: -1.2 mm AP, ±1 mm ML, and 5 mm DV.

value: pooled male and female

value: 8-16 weeks

tag: injected with

value: CAV2-EGFP into thalamus

tag: molecule subtype

value: total RNA


title: Input_1


title: Bound_A

source_name: Reticular NGC neurons_bound

value: Affinity purified ribosomes from GFP-labeled cells (TRAP)


title: Bound_1


title: Species_mix_open-surface_format

extract_protocol: mRNA captured on barcoded beads were reverse transcribed and amplified using half a PCR reaction. Tagmentation and final library preparation was performed using Illumina Nextera XT Kit (FC-131-1024) according to manufacturer's protocol.


title: Input_A


title: Species_mix_closed-environment_format


title: FCRL5+.d155.r5

city: London

first: Damián

last: Perez-Mazliah

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Reads were adapter and quality trimmed using cutadapt v1.9.1 with the following non-default settings: “-a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length 30 -q 20,20”
Gene-level abundance estimates were generated from the trimmed reads using RSEM v1.2.31 running STAR v2.5.1b with default settings.  RSEM indices were built against the Mus musculus Ensembl release 89 transcriptome.
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM gene-level abundance estimates.

growth_protocol: Mice were housed at the BRF facilities of the MRC National Institute for Medical Research, Mill Hill, London

extract_protocol:
Total RNA was extracted using Ribopure kit (Ambion)
cDNA was generated from total RNA with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA). Next-generation sequencing libraries were produced with the Ovation Ultralow System V2 (Nugen)

treatment_protocol: Spleen cells were dissected, surface stained with fluorescent probes/antibodies, and flow cytometry sorted directly into Tri reagent (Ambion) (1 vol sample/ 9 vol Tri reagent)

value: Spleen

value: MSP1-specific B cell

tag: phenotype

tag: days post-infection


title: FCRL5+.d155.r3

tag: cell type


title: FCRL5+.d155.r2

tag: strain


title: FCRL5-.d155.r3


title: FCRL5-.d155.r5


title: FCRL5-.d155.r1


title: FCRL5+.d155.r4


title: FCRL5-.d155.r4


title: naive.d0.r5

value: naive


title: naive.d0.r1


title: naive.d0.r3


title: naive.d0.r4


title: MN replicate 2

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

data_processing:
Adapter contamination in the paired-end reads was removed using PEAT.
The trimmed reads were aligned to the mm10 genome with STAR.
GENCODE (version M9) was used to annotated to aid the junction read alignment in STAR the output of which was submitted to Cufflinks for de novo transcript assembly with the option ‘library type; first-strand’ to allow strand-specific alignments.
Only transcripts that were longer than 200 bp, had no overlap with any known genes, and consisted of more than one exon were regarded as novel lncRNAs.
pooled these novel lncRNAs along with all known genes annotated in GENCODE and used HTseq to calculate the read count aligned onto each transcript.
Normalized read counts by TMM (M: 30%, A: 5%)
calculated the specificity score of each transcript among the samples at different stages according to the Jensen–Shannon definition for tissue specificity scores.
Mormalized read count > 10, fold-change > 1.25 and the transcripts were split into three groups: protein coding genes, annotated lncRNAs, and novel lncRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: Paired-end, strand-specific RNA-seq Alignment reads to mouse genome not overlapping with known genes. mm10 transcriptome including novel lncRNAs and known genes. Read count of each transcript tallied by HTSeq. Normalized read counts by TMM (M:30%; A:5%). Stage-specific lncRNAs (normalized read count > 10 ,fold-change > 1.25 )   mm10 by STAR. Novel lncRNAs by cufflinks

source_name: motor neuron (MN)

growth_protocol: ESCs were cultured and differentiated into spinal MNs as previously described (Wichterle et al., 2002; Wichterle et al., 2009). Cells were trypsinized and collected for FACS at day 7 to purify GFPon neurons for strand-specific RNA-seq.

extract_protocol:
FACS sorted cells were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: motor neuron (MN)

value: Day 7

tag: genotype


title: MN replicate 1


title: IN replicate 1

source_name: interneuron (IN)

value: interneuron (IN)


title: D4 replicate 2

source_name: motor neuron progenitor (pMN)

value: motor neuron progenitor (pMN)

value: Day 4


title: Bound_B

tag: Sex


title: D4 replicate 1


title: IN replicate 2


title: FCRL5+.d155.r1


title: Wildtype_4

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
Illumina bcl2fastq v2.17 used to convert BCL to fastq
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Pancreatic islets

extract_protocol:
Islets were isolated as described above and incubated over night at 37 degree centigrade. The next day, 500 islets per genotype were picked into Trizol (Invitrogen) as one sample and kept at -80 degree centigrade until RNA extraction and sequencing. 5 different WT samples and 4 different R138X samples were analyzed. Total RNA was purified from all samples using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using MagMAX™Turbo™DNase Buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA Purification Kit (Invitrogen).
Strand-specific RNA-seq libraries were prepared using KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems). Twelve-cycle PCR was performed to amplify libraries. Sequencing was performed on Illumina HiSeq®2500 (Illumina) by multiplexed single-read run with 33 cycles.

value: Pancreatic islets

value: WT


title: Wildtype_3


title: Wildtype_2


title: SLC30A8 R138X mutation in islets_2


title: SLC30A8 R138X mutation in islets_1


title: Wildtype_5


title: SLC30A8 R138X mutation in islets_4


title: SLC30A8 R138X mutation in islets_3


title: Wildtype_1


title: naive.d0.r2


title: FCRL5-.d155.r2


title: CY75_1_CD45_CD8_3__S116_comb_BCD8

first: Orr

last: Ashenberg

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
Full-length RNAseq (SMART-Seq2) reads.
processed data file: counts.csv
processed data file: tpm.csv
processed data file: cell.annotations.csv

data_processing:
Full-length RNAseq (SMART-Seq2).
Tophat
Bowtie mapping to UCSC hg19 human transcriptome.
RSEM v1.2.8
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: cell.annotations.csv: Comma-separated cell sample annotation table; For each cell (row): cell name, sample type, cell type, treatment group, cohort, number of genes, number of reads.
Supplementary_files_format_and_content: counts.csv: Comma-separated counts table; Full-length RNAseq (SMART-Seq2); The expression levels for each gene (rows) in each single cell (column) in counts as calculated using RSEM.
Supplementary_files_format_and_content: tpm.csv: Comma-separated log-transformed transcripts per million (TPM) table; Values are provided as log2[(TPM/10) +1]; Full-length RNAseq (SMART-Seq2); The expression levels for each gene (rows) in each single cell (column) in transcripts per million (TPM) as calculated using RSEM.

source_name: melanoma tumor

extract_protocol:
Dissociated individual cells from fresh tumor resections. Isolated immune and non-immune cells by FACS based on CD45 staining.
Full-length RNAseq (SMART-Seq2) libraries sequenced with 38bp paired-end reads on an Illumina NextSeq 500.

tag: tumor-of-origin

tag: treatment-group

tag: cohort

value: Tirosh


title: CY75_1_CD45_CD8_3__S161_comb_BCD8


title: CY75_1_CD45_CD8_8__S327_comb_BCD8


title: monika_F5_S148_comb_BCD8_3


title: CY75_1_CD45_CD8_7__S283_comb_BCD8


title: CY75_1_CD45_CD8_3__S185_comb_BCD8

value: NK


title: monika_A3_S102_comb_BCD8_3


title: CY75_1_CD45_CD8_3__S175_comb_BCD8


title: CY75_1_CD45_CD8_8__S356_comb_BCD8


title: CY75_1_CD45_CD8_3__S189_comb_BCD8


title: CY75_1_CD45_CD8_3__S187_comb_BCD8


title: monika_B2_S111_comb_BCD8_3


title: CY75_1_CD45_CD8_8__S294_comb_BCD8


title: CY75_1_CD45_CD8_3__S104_comb_BCD8


title: monika_C3_S122_comb_BCD8_3


title: CY75_1_CD45_CD8_8__S378_comb_BCD8


title: CY75_1_CD45_CD8_1__S90_comb_BCD8