title: Withdrawal from chronic ethanol liquid diet rep4

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

data_processing:
About 100,000,000 raw reads were obtained per sequenced sample and following sequence quality control using FASTQC (v. 0.11.4) and processing, reads were aligned to the reference Rattus Norvegicus Rnor 6.0 genome from NCBI (release 106), using STAR (v. 2.5.2a).
Gene counts were generated from uniquely aligned reads using FeatureCounts (v. 1.5.0), which counts mapped reads for exon features, then sums to gene-level. These have been included as Processed Data.
Raw counts were imported into R (v. 3.3.3) for statistical analysis. A total of 18,118 genes were kept for differential expression (DE) analysis. Following surrogate variable analysis, we used limma-voom to calculate a one-way ANOVA across all 3 treatments.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: counts

organism: Rattus norvegicus

source_name: Hippocampus tissue

extract_protocol:
Brains were collected for the dissection of Hippocampus. Followed by total RNA extraction using the miRNEasy protocol, which was used for RNA-sequencing (paired-end) using the Illumina platform. cDNA fragments were 80bp to 500bp, with an average length of 250bp.
RNA integrity numbers (RIN) for each RNA sample were determined using an Agilent Tapestation and were all above 8.0. Illumina True-Seq Stranded libraries were prepared and quantitated by qPCR. Reads were 100nt in length.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand, whereas Read 2 aligns to the SENSE strand.  The libraries were quantitated by qPCR and sequenced on 11 lanes (8 lanes on one flowcell, 3 lanes on another flowcell) for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.  Adaptors have been trimmed from the 3'-end of the reads.

treatment_protocol: Adult Sprague-Dawley male rats received control (C) or chronic ethanol (9% v/v) Lieber-DeCarli diets for 15 or 16 days. Chronic ethanol fed rats were withdrawn for 0 h (Chronic Ethanol) and 24 h (Withdrawal), as described by us (Pandey et al., 2008, Journal of Neuroscience 28 (14), 3729-3737).

tag: animal id

tag: strain/wt

value: Sprague Dawley/WT

value: Withdrawal


title: Withdrawal from chronic ethanol liquid diet rep6

status: Public on Jun 15 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: Withdrawal from chronic ethanol liquid diet rep5


title: SH82K33 HCC-827 Exo-RNA

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: HCC-827 cells (with a deletion in exon 19) were purchased from the American Type Culture Collection (Manassas, VA, USA) .

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

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

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

organism: Homo sapiens

source_name: primary lung cancer cell line

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

extract_protocol: Exosomes were obtained from the culture supernatant of these cells by a centrifugal ultrafiltration-based method. Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) from  isolated exosomes.

tag: tissue

value: primary lung cancer cell line

tag: cell line


title: SH82K33 PC9 Exo-RNA

description: PC9 cells (with a deletion in exon 19) were obtained from Immuno-Biological Laboratories (Gunma, Japan).


title: infected alveolar macrophages rep3

city: Freiburg

first: Sebastian

last: Baasch

address: Breisacher Str.

department: Institute for Immunodeficiency; Center for Chronic Immunodeficiency

country: Germany

institute: University Medical Center

data_processing:
De-multiplexing: Illumina bcl2fastq
Trimming: Cutadapt
Read count: STAR (V2.5.2b)
Quality control reads: FASTQC
Alignment: STAR (V2.5.2b)
Differentially expressed genes: DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tabular file of normalized_reads in control, bystanding and CMV-infected alveolar macrophages

molecule: polyA RNA

organism: Mus musculus

source_name: alveolar macrophage

extract_protocol:
Total RNA, obtained with QIAGEN microkit, was subjected to library synthesis.
After the QC procedures, total mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Mice were intranasally infected with a murine cytomegalovirus strain, which expresses a GFP cassette preceeded by a loxP sequence flanked STOP codon. 3 days after infection the mice were sacrificed and control, non-infected bystanding and infected alveolar macrophages were sorted from lung homogenates. Subsequently the alveolar macrophages were washed and lysed in RNA lysis buffer.

tag: strain

tag: genotype

value: CD11ccre ROSA26tomatoflox

value: lung

tag: cell type

value: alveolar macrophage

tag: condition

value: infected with CMV


title: NORMAL1

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

country: China

institute: Tongji University

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Genome_build: mm9
Supplementary_files_format_and_content: processed data file is a xls file contains the fpkm

source_name: skin

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: Bleomycin (BLM, Thermo Fisher Scientific, USA) was diluted in phosphate buffered saline (PBS, Sangon Biotech, China) at a concentration of 1 mg/mL and sterilized by filtration. To establish the murine fibrosis model, 100µL BLM solution were subcutaneously injected into the shaved backs (1 cm2) of mice for 28 days using a 27-gauge needle.BLM-induced SSc mice were randomly divided into 2 groups treated with PBS (100µL) or BMSC derived exosome. (15μg/100μL).

value: PBS


title: SH82K33 AZD-827 Exo-RNA

description: Osimertinib-resistant HCC827 (AZD-827) cells were established using a stepwise method.


title: Withdrawal from chronic ethanol liquid diet rep2


title: Chronic Ethanol liquid diet rep6

value: Chronic Ethanol


title: Withdrawal from chronic ethanol liquid diet rep1


title: infected alveolar macrophages rep1


title: bystanding alveolar macrophages rep2

value: bystanding


title: T24-CBX7-2

city: shanghai

first: HUANG

middle: ZHENG

state: shanghai

address: hongkou district

institute: shanghai jiaotong university

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Data filtering steps:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: T24 bladder cancer cell line

growth_protocol: RPMI + 10% FCS

extract_protocol:
total RNA was extracted using Trizol following the manufacturing protocol
Synthesis Reaction Buffer andRandom Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic， Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: bladder cancer cell line


title: Chronic Ethanol liquid diet rep5


title: Chronic Ethanol liquid diet rep4


title: T24-CBX7-1


title: T24-CON-2


title: bystanding alveolar macrophages rep1


title: T24-CON-1


title: Chronic Ethanol liquid diet rep1


title: Withdrawal from chronic ethanol liquid diet rep3


title: Chronic Ethanol liquid diet rep2


title: Chronic Ethanol liquid diet rep3


title: control alveolar macrophages rep2

description: control AM2

value: uninfected - control


title: control alveolar macrophages rep3

description: control AM3


title: Control liquid diet rep6

value: Control


title: WGBS H9 a5i/L/A

city: St Louis

first: Thorold

last: Theunissen

state: MO

address: 4515 McKinley Ave, Room 3313

department: Developmental Biology

institute: Washington Unversity School of Medicine

library_source: genomic

data_processing:
MethylC-Seq data were trimmed of adapters using Cutadapt version 1.2.1 (Martin, 2011), and aligned to the human genome hg38 with Bismark version 0.22.3 (https://academic.oup.com/bioinformatics/article/27/11/1571/216956).
The aligned reads were further processed with MethPipe (Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics), and % DNA methylation levels of CpGs on imprinted regions were compiled with the roimethstats function from MethPipe.
The genome-wide average % DNA methylation of CpGs was compiled on 1 kB sliding windows (offset 500 bp).
Genome_build: hg38
Supplementary_files_format_and_content: DNA methylation levels in the format generated by MethPipe, chr, position, strand, CpG, fraction of methylation, number of reads

molecule: genomic DNA

source_name: Naïve hESC

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Whole Genome Bisulfite conversions were performed with 200 ng of gDNA using the EZ DNA Methylation-Gold, 50rxn (Fisher-part#50444294) kit.
WGBS Libraries were created using the Accel-NGS Methyl-Seq DNA Library Kit - 24 rxns (Swift Biosciences-part#30024) and Accel-NGS Methyl-Seq Dual Indexing Kit - 96rxns (Swift Biosciences-part#38096). The libraries were pooled and sequenced on 0.240 of an NovaSeq S4 flow cell (300 XP; targeting 30x wgbs coverage/120Gb per sample) at the Genome Technology Access Center at Washington University School of Medicine in St. Louis.

value: Naive hESC

tag: culture condition

value: Alternative naive condition:a5i/L/A

tag: passage


title: bystanding alveolar macrophages rep3


title: WGBS H9 AXGYU

value: Alternative naive condition:AXGYU


title: Control liquid diet rep5


title: WGBS H9 5i/L/A


title: infected alveolar macrophages rep2


title: control alveolar macrophages rep1

description: control AM1


title: Control liquid diet rep3


title: Control liquid diet rep4


title: WGBS H9 mTeSR1

source_name: Primed hESC

value: Primed hESC


title: lungSA.2

city: PHILADELPHIA PA

first: Jun

last: Gui

state: PA

address: 380 S UNIVERSITY AVE HILL 345

department: School of Veterinary Medicine

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Gene sets from microarray data were analyzed for overlap with curated data sets (C5, H) in MSigDB
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: Lung tissues

growth_protocol: 6-8 weeks old Ifnar1+/+ (‘‘WT’’) and Ifnar1S526A mice (‘‘SA’’) littermates were maintained in a specific pathogen-free facility in accordance with American Association for Laboratory Animal Science guidelines. All mice were of C57Bl/6 background.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: 100 μl B16F10 tumor conditioned medium were intravenously injected into mice three times a week for three weeks.  After that, mice were euthanized and lung tissues were collected for RNA extraction.

tag: background strain

value: SA (Ifnar1S526A)

value: B16F10 tumor conditioned medium treated (3 times a week for 3 weeks)


title: Control liquid diet rep2

value: Sprague Dawley/WT


title: lungSA.1


title: day 100 gut organoid

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

description: WTC11 human induced pluripotent stem cells (iPSCs) genetically modified with fast green fluorescent calcium indicator GCaMP6f.

data_processing:
Demultiplex with CellRanger v3.0.2.
Align with CellRanger v3.0.2.
Count transcripts with CellRanger v3.0.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.mtx: Matrix Market Format
Supplementary_files_format_and_content: *barcodes.tsv: Tab-separated text file includes barcodes.
Supplementary_files_format_and_content: *genes.tsv: Tab-separated text file includes genes.

source_name: iPSC-derived gut organoid

growth_protocol: Spheroids were maintained in rotary suspension culture at a density of 65 spheroids/mL in 6-well low attachment tissue culture plates. On day 7 of the differentiation protocol, 2 days after tissue aggregation, medium was changed to epicardial-permissive medium (Advanced DMEM/F12 (Gibco) with 100μM L-Ascorbic Acid (Sigma)) and refreshed every 3 days thereafter.

extract_protocol:
Multilineage and gut organoids at day 100 of culture were washed in PBS and dissociated by successive 20 min incubations in 0.25% trypsin at 37oC (maximum of 5 incubations) until complete dissociation to single cells. 10,000 cells in PBS supplemented with 0.08% FBS were prepared for sequencing by droplet encapsulation using the Chromium Controller and library preparation with the 10x Genomics Single Cell 3’ v2 Library and Gel Bead Kit (10x Genomics).
Chromium Controller and library preparation with the 10x Genomics Single Cell 3’ v2 Library and Gel Bead Kit (10x Genomics).
Libraries were sequenced using the NovaSeq S4 (Illumina) to a minimum depth of 50,000 mean reads per cell.

value: iPSC-derived organoid

tag: time point

value: Day 100


title: Control liquid diet rep1


title: lungwt.1

value: wild-type


title: WGBS H9 AXGY

value: Alternative naive condition:AXGY


title: lungwt.2


title: SCAF1714_2_1

status: Public on Jun 14 2021

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description: scRNA-seq

data_processing:
Fastq demultiplexing with cellranger v4.0.0  (bcl2fastq_version: 2.20.0.422)
Read alignment and single cell data parsing with cellranger v4.0.0 (STAR version: 2.5.1b)
Genome_build: mm10 (refdata-gex-mm10-2020-A for GEX)
Supplementary_files_format_and_content: 10x Genomics filtered h5 files

source_name: Entinostat

growth_protocol: samples were isolated by CD45+ enrichment from tumor single cell suspensions

extract_protocol:
Miltenyi CD45 Kit
libraries were constructed according to 10X Genomics user guide (Chromium 5’ v1.0)

treatment_protocol: PBS, Entinostat, NHS-IL12, Entinostat + NHS-IL12, Entinostat + NHS-IL12 from CD8 depleted mice

value: Balb/c

value: WT

tag: cell source

value: tumor CD45+ cells


title: BoC209 C4

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For  adapter sequence trimming in FASTQ files, fastp version 0.20.0 was used.
Cleaned read sequences were aligned with STAR version 2.7.3a.
Read assignment for exonic regions was performed with subread featureCounts version 2.0.0.
Fragment counts were generated with UMI-tools version 1.0.0.
Genome_build: GRCh37 and GRCm38
Supplementary_files_format_and_content: Raw fragment count data in tabular text file format.

organism:
Homo sapiens
Mus musculus

source_name: human colorectal tumor tissue, mouse stroma (PDX)

growth_protocol: Three 1-3 mm tumor pieces of early passage xenograft tumor soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.

extract_protocol:
Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).
Sequencing libraries have been prepared with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina following the manufacturer's handbook.

treatment_protocol: Nude mice were treated with cetuximab (Merck Serono) by intra peritoneal (i.p.) injection twice per week and dosed at 25mg/kg, treatment was initiated when tumor size reached approx. 100-200 mm³

value: cetuximab secondary resistant tumors following cetuximab treatment


title: SCAF1715_3_1

description: scRNA-seq


title: SCAF1713_1_1

description: scRNA-seq

source_name: PBS


title: BoC209 C5


title: SCAF1716_4_1

description: scRNA-seq

source_name: Entinostat + NHS-IL12


title: BoC237 C1


title: BoC237 C2


title: BoC237 5dC1

value: 5 d cetuximab


title: BoC32 C16


title: BoC69 C9


title: BoC106 C8


title: BoC237 C5


title: BoC69 C10


title: BoC209 C6


title: BoC237 K1

value: control


title: BoC71 F5 C6


title: BoC71 C1


title: day 100 multilineage organoid

source_name: iPSC-derived multilineage organoid


title: BoC10 C14


title: BoC106 C6


title: BoC106 C2


title: BoC106 5dC1


title: BoC35 C1


title: BoC35 5dC1


title: BoC71 5dC1


title: SCAF1717_5_1

description: scRNA-seq

source_name: Entinostat + NHS-IL12 (CD8-depleted)

value: WT with CD8 depletion


title: BoC69 C7


title: BoC71 C4


title: BoC60 C5


title: BoC60 5dC2


title: BoC71 C3


title: BoC69 C5


title: BoC32 C6


title: BoC32 5dC1


title: BoC209 5dC1


title: BoC32 C2


title: BoC10 C4


title: BoC20 5dC1


title: BoC10F 5dC1


title: BoC20 C9


title: BoC32 C5


title: 9_1_box3

city: Stanford

first: Robert

middle: Raymond

last: Butler

address: 3172 Porter Dr., MC 5475

department: Neurology & Neurological Sciences

institute: Stanford University School of Medicine

data_processing:
RNA-seq reads were trimmed with fastp 0.20.0 using -3, -5, and -l20 settings and trimming for custom sequencing adapters.
Transcriptional abundance was calculated from Rnor version 6 with salmon 0.12.0 with recommended settings (--seqBias --gcBias --validateMappings -l A) for paired reads and collapsed to gene counts using tximport.
Genome_build: Rnor version 6.0, release 96
Supplementary_files_format_and_content: Raw feature count expression matrix for all samples submitted

source_name: ventral tegmental area

extract_protocol:
Total RNA was isolated from 30 μl of lysate using TRIzol LS reagent (Life technologies, 10296028). Lysate volume was adjusted to 100 μl and 300 μl Trizol LS (3X volume) reagent was added. Then sample was incubated for 5 min at room temperature and 80 μl (1/5 volume) of chloroform was added following by shaking for 15 sec, incubation for 10 min room temperature and centrifugation for 15 min at 14,000 × rpm at 4°C. The aqueous phase containing the RNA was transferred to a new tube, 200 μl (1X volume) of isopropanol (VWR, 87000–048) was added to the aqueous phase and mixed well by inverting several times following by incubation for 10 min at room temperature and centrifugation for 25 min at 14,000 × rpm at 4°C. Total RNA precipitate formed a white gel-like pellet at the bottom of the tube. The pellet was washed with 1 ml of 75% ethanol and centrifuged for 5 min at 7500 × rpm at 4°C. The pellet was washed one more time in 1 ml of 100% ethanol and centrifuged again at the same settings. The RNA pellet was dried for 10 min at room temperature and resuspended in 30 μl of RNase-free water. The RNA sample was cleaned with RNeasy MinElute Cleanup Kit (Qiagen, 74204).
Total RNAs extracted from each sample were sent to University of Minnesota Genomic Center for library preparation and RNA-seq with standard QC metrics (RNA quantity > 1 µg, RIN > 9.0, OD260/280 > 1.9 ), NovaSeq S2 2x50bp, > 32M PE reads per library.

treatment_protocol: For sensitization, F1 males (n=5-6/group) and females (n=7/group) were randomly assigned the to three groups and tested in early adulthood (~250 g). The first group received 0.1 mg/kg of NIC (base), the second group received 0.4 mg/kg of NIC (base) and the third group received SAL (1.0 ml/kg). F1 rats were daily administered either NIC or SAL for 4 days. On days 1 and 4, rats were placed in an open field immediately after the injection and their locomotion measured for 2 hours. Rats were then left undisturbed in their home cages for 2 weeks. On day 19, all F1 rats were administered one injection of NIC (0.4 mg/kg, IP, base), immediately placed in the open fields and their locomotion measured for two hours. For the SST transcriptomic analysis F1 males (n=16) and females (n=16) were divided in 2 groups. In the first group (n=8) rats were exposed to 0.4 mg/kg of NIC (base) every day for 4 days. In the second group (n=8) rats were exposed to SAL (1.0 ml/kg) every day for 4 days. Brain tissues (~20mg) from Nac, Nash and VTA regions were harvested on day 17.

value: saline

tag: Sex

value: F

tag: prep batch

value: J


title: 9_3_box3

source_name: nucleus accumbens shell


title: BoC10 C2


title: 9_2_box3

source_name: nucleus accumbens core


title: 8_1_box3

value: nicotine


title: 8_2_box3


title: BoC69 C6


title: 7_3_box3


title: 8_3_box3


title: 7_1_box3


title: 6_2_box3

value: I


title: 6_1_box3


title: 5_3_box3


title: 5_1_box3


title: BoC10 F C3


title: 4_2_box3

value: H


title: 4_3_box3


title: 4_1_box3


title: 7_2_box3


title: 3_1_box3

value: L


title: 3_3_box3


title: 15_2_box3

value: K


title: 16_3_box3


title: 2_3_box3

value: G


title: 3_2_box3


title: 14_3_box3


title: 5_2_box3


title: 16_1_box3


title: 14_1_box3


title: 15_1_box3


title: 2_2_box3


title: 13_1_box3


title: 6_3_box3


title: 15_3_box3


title: 2_1_box3


title: 12_3_box3


title: 12_2_box3


title: 13_3_box3


title: 12_1_box3


title: 14_2_box3


title: 11_2_box3


title: 11_3_box3


title: 10_3_box3


title: 11_1_box3


title: 10_2_box3


title: 16_2_box3


title: 1_2_box3


title: 1_3_box3


title: 13_2_box3


title: 10_1_box3


title: 9_1_box1

value: M


title: 8_3_box1

value: C


title: 7_3_box1


title: 8_1_box1


title: BoC20 C1


title: 5_2_box1

value: B


title: 5_3_box1


title: 1_1_box3


title: 5_1_R2_box1


title: 4_2_box1

value: A


title: 9_3_box1


title: 2_3_box1


title: 9_2_box1


title: 8_2_box1


title: 7_2_box1


title: 6_1_box1


title: 4_1_box1


title: 4_3_box1


title: 7_1_box1


title: 5_1_R1_box1


title: 16_3_box1

value: D


title: 15_3_box1


title: 16_1_box1


title: 3_3_box1


title: 3_2_box1


title: 15_2_box1


title: 14_1_box1


title: 14_2_box1


title: 2_1_box1


title: 13_2_box1


title: 6_3_box1


title: 12_1_box1


title: 2_2_box1


title: 12_2_box1


title: 16_2_box1


title: 13_1_box1


title: 6_2_box1


title: 13_3_box1


title: 14_3_box1


title: 11_3_box1


title: 15_1_box1


title: 10_3_box1


title: 11_1_box1


title: 11_2_box1


title: 10_2_box1


title: 10_1_box1


title: 1_3_box1


title: 1_2_box1


title: 1_1_box1


title: 15_3_box2

source_name: nash

treatment_protocol: For self-administration, F1 males were administered NIC (0.4 mg/kg, IP; n=6) and SAL (1.0 ml/kg, n=6) every day for a total of 4 days.  Starting from day 7, NIC (n=4) and SAL (n=4) exposed rats received additional NIC injection intravenously every day (30µg/kg/infusion of NIC base = ~1.8 mg/kg) for 6 days. Therefore, the NIC self-administering rats were exposed to 6 (days) X 10 (infusions) = 60 infusions. This is roughly equivalent to what the passively administered rats received: 4 (days) X 0.4 mg/kg = 1.6 mg/kg. At each day SA test was performed by counting active lever presses for both NIC injected group and SAL control (2 NIC and 2 SAL exposed rats which did not receive additional IV NIC injections). For SA transcriptomic analysis brain tissues (~20mg) from Nac, Nash and VTA regions were harvested on day 15.

value: sal


title: 16_3_box2


title: 16_1_box2

source_name: vta


title: 16_2_box2

source_name: nac


title: 12_3_box1


title: 13_3_box2


title: 15_1_box2


title: 11_3_box2


title: 11_2_box2


title: 13_2_box2


title: 4_1_box2

value: nic


title: 13_1_box2


title: 2_1_box2


title: 4_2_box2


title: 2_3_box2

value: E


title: 1_3_box2


title: 2_2_box2


title: 3_2_box2


title: Testis_RNA_Th3

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto mm10 assembly of mouse genome using Hisat2 aligner (v2.1.0).
StringTie (v1.3.5) was used to generate assembled transcripts for each condition, and to calculate the transcript abundance.
Differential gene expression was assessed using the R package DESeq2 (v1.25.0).
To identify transcripts that were differentially expressed between thiacloprid and control-derived samples, we first selected the cases for which we obtained normalized count values greater than the 50th centile of all values in at least one condition, and we then filtered the transcripts for which there was a more than a 1.5-fold difference between the thia-  and control-derived samples. The false-discovery rate (FDR) threshold was set at 5%. Genes with higher FDR were not considered as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing gene and transcript counts, gtf file containing transcriptome from stringtie, csv files containing gene expression from DESeq2.

source_name: Testis

growth_protocol: Pregnant, outbred, Swiss (RjOrl), female mice were treated with thiaclopride during embryonic development. New-borns were grown until 35 days-old.

extract_protocol:
Testes stored at -80°C from 35-day-old mice from the control group and from the 6 mg/kg/day treatment group were used for RNA extraction. Extraction was performed using RNeasy Plus Mini Kit (QIAGEN®). Approximately 30 mg of each testis was used.
A strand-specific library preparation protocol (NEBNext Ultra II Directional RNA Library) for RNA sequencing was performed in the lab according the protocol provided by manufacture by using 1µg of total RNA.

treatment_protocol: Pregnant mice were treated with thia by administering the compound down the esophagus and into the stomach by using a gavage needle from the embryonic day E6.5 until E15.5. Thia was suspended in olive oil; the control mice received only oil.

value: Swiss

value: testis

tag: age

value: 35 days

tag: thiaclopride dose

value: 6 mg/kg body weight/day


title: 1_1_box2


title: 1_2_box2


title: Testis_RNA_Th2


title: Testis_RNA_C3

value: 0 mg/kg body weight/day


title: 15_2_box2


title: 4_3_box2

value: F


title: 3_3_box2


title: PRG5-905_9 multifocal biopsy from thymic lymphoma

city: La Jolla

first: Don

middle: W.

last: Cleveland

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

description: multifocal biopsy from thymic lymphoma

data_processing:
Basecalls performed using CASAVA version 1.8
reads trimmed with fastp
reads aligned to transcriptome with STAR version 2.7.2b
gene-level summaries obtained with RSEM version 1.1.17
Genome_build: mm10
Supplementary_files_format_and_content: raw count file

extract_protocol:
Thymic tissues were snap frozen in liquid nitrogen and stored in -80. Biopsies were taken from frozen tissues placed on -80 chilled metallic stage and processed for DNA+RNA extraction using AllPrep DNA/RNA mini kit (Qiagn)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6 x 129S4Sv/Jae

value: Thymic lymphoma

value: p53+/-; Plk4(Col1a1); rtTA(Rosa); centrin-GFP(Rosa)

value: 2-week doxycycline starting 30 days of age

tag: gender

value: Female


title: Testis_RNA_C1


title: 11_1_box2

value: G


title: PRG5-908_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma

tag: treatment

value: Male


title: PRG5-908_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma

tag: tissue


title: PRG5-905_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-908_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-903_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-899_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma

value: p53-/-; Plk4(Col1a1); rtTA(Rosa); centrin-GFP(Rosa)


title: PRG5-905_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-905_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-899_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-903_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: 3_1_box2

value: B


title: PRG5-899_2 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-903_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-899_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: Testis_RNA_Th1


title: PRG5-894_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-899_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-894_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-903_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: Testis_RNA_C2


title: PRG5-908_9 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-894_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-884_6 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-884_8 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-884_2 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-894_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-884_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-881_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-881_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-881_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-881_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-870_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-869_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-870_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-870_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-862_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-870_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-869_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-862_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-862_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-862_9 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-857_9 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-325_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-202_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-857_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-857_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-869_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-624 control healthy thymic tissue

description: control healthy thymic tissue

value: Normal thymus

value: p53+/+; Plk4(Col1a1); rtTA(Rosa); centrin-GFP(Rosa)


title: PRG5-202_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-869_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-980 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-857_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-615 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-819 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-120 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-978 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-325_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-325_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-787 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-663 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-325_1 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-202_5 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-653 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-202_3 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-961 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-553 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-497 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-862_7 multifocal biopsy from thymic lymphoma

description: multifocal biopsy from thymic lymphoma


title: PRG5-562 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-818 control healthy thymic tissue

description: control healthy thymic tissue


title: PRG5-643 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-659 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-637 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: C. albicans cells - Fluconazole 3 Hour - rep 2

first: Ryan

middle: Patrick

last: Dohn

address: 5841 S. Maryland Ave.

department: Department of Medicine

institute: University of Chicago

description: Cells diluted 20 hours prior to experiment

data_processing:
A Snakemake protocol called dropRunner was used to create an expression matrix corresponding to the UMI of each gene in a cell. https://github.com/aselewa/dropseqRunner
STARsolo (STAR 2.7.0a) was used for sequence alignment to the respective yeast genomes
Genome_build: sacCer3_s288c (S. cerevisiae); A21-s02-m09-r10 (C. albicans)
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every cell, cell barcode file, and gene id file.

organism: Candida albicans

source_name: C. albicans cells

growth_protocol: Yeast cells were grown in suspension in rich YEPD media over night and diluted 4 hours prior to experiment to obtain log phase growth.

extract_protocol:
Cells encapsulation into nL droplets using a microfluidic device along with oligo poly-dT beads and zymolyase containing lysis buffer. Cells were then incubated at 37°C for 15-25 minutes for lysis. mRNA was captured by the poly-dT oligo beads.
Reverse tracnription to cDNA was performed using a template switch oligo. Beads then underwent exonuclease treatment and PCR amplification. A Illumina Nextera (cat#FC-131-1096) was used with 500-600 pg cDNA for construction of sequencing libraries.

treatment_protocol: Heat Shock Cells incubated in 42°C thermomixer for 20 minutes prior to microfluidic encapsulation.

value: 15 microg/mL Fluconazole

value: 3 Hour


title: PRG5-387 control healthy thymic tissue

description: control healthy thymic tissue


title: C. albicans cells - Fluconazole 1.5 Hour - rep 2

value: 1.5 Hour


title: PRG5-490 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-280 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: C. albicans cells - 20 minute Lysis - rep 2

value: untreated


title: C. albicans cells - Fluconazole Control - rep 2


title: PRG5-309 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: C. albicans cells - Fluconazole 3 Hour - rep 1


title: PRG5-328 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-98 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: C. albicans cells - Fluconazole Control - rep 1


title: PRG5-157 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-266 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: C. albicans cells - 15 minute Lysis - rep 2


title: PRG5-25 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: PRG5-24 single biopsy from thymic lymphoma

description: single biopsy from thymic lymphoma


title: HTO_rep2_library

city: Marseille

first: Mathis

last: Nozais

address: 27bd Lei Roure

institute: CRCM

description: Anti-CD45 and CMH I  antibody tagged with hashtag oligonucleotide

data_processing:
Reads from replicate1 and 2 mRNA libraries were mapped to mm10  transcripts and cells using CellRanger software (v3.0.1), giving for both replicate an mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz and mRNA_matrix.mtx.gz files.
Reads from our two HTO libraries were processed with CITE-seq-count (v1.4.3), giving for both sample an HTO_barcodes.tsv.gz, HTO_features.tsv.gz and HTO_matrix.mtx.gz files
Reads from ADT library were  also processed with CITE-seq-count (only for our second replicate), giving ADT_barcodes.tsv.gz, ADT_features.tsv.gz and ADT_matrix.mtz.gz
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files

source_name: Thymus and spleen

extract_protocol:
10x Genomics Chromium Single-Cell 3’ v2 protocol
10x Genomics Chromium Single-Cell 5’ v2 protocol

tag: library

value: HTO


title: mRNA_rep2_library

value: mRNA


title: HTO_rep1_library


title: gWAT - HighFat - FHL2KO4 [MB_32_S26]

city: Amsterdam

first: Carlie

last: de Vries

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam University Medical Center

data_processing:
Reads were subjected to quality control (FastQC, dupRadar, Picard Tools), trimmed using Trimmomatic v0.32 (Bolger, Lohse and Usadel, 2014) and aligned to the genomes using HISAT2 (v2.1.0) (Sirén, Välimäki and Mäkinen, 2014).
Counts were obtained using HTSeq (v0.11.0) using the corresponding GTFs (Anders, Pyl and Huber, 2014).
Differential expression was assessed using an empirical Bayes moderated t-test within limma’s linear model framework including the precision weights estimated by voom (Smyth, 2005; Law et al., 2014).
Genes were re-annotated using biomaRt using the Ensembl genome databases.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files contain raw counts of sequencing reads for each ENSEMBL transcript.

source_name: gWAT - HighFat - FHL2KO

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
Libraries were generated using the Kapa mRNA Hyperprep kit (Roche).

treatment_protocol: Mice were subjected to 8 weeks of high fat diet and terminated for organ isolation.

tag: strain backgroudn

tag: genotype/variation

value: 21 weeks

value: High Fat Diet

value: Gonadal White Adipose Tissue


title: gWAT - HighFat - WT4 [MB_28_S21]

source_name: gWAT - HighFat - WT

value: WT


title: BoC69 5dC1

value: 5 d cetuximab


title: gWAT - HighFat - WT3 [MB_27_S20]


title: gWAT - HighFat - FHL2KO3 [MB_31_S25]


title: gWAT - HighFat - FHL2KO1 [MB_29_S22]


title: mRNA_rep1_library


title: BoC71 K2

value: control


title: gWAT - HighFat - WT1 [MB_25_S18]


title: BoC60 K5


title: d0 Epcam+CD31/34/45-

city: Los Angeles

first: ting

last: Xie

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

data_processing:
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) with default parameters, using a custom mm10 transcriptome reference from GENCODE M9 annotation, containing all protein coding and long non-coding RNA genes. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 1.3.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns." "The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) with default parameters, using a custom mm10 transcriptome reference from GENCODE M9 annotation, containing all protein coding and long non-coding RNA genes. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 1.3.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include gene expression for each cell with or without normalization.

source_name: Epcam+CD31/34/45- cells from normal mouse

extract_protocol:
Fluorescence- activated cell sorting (FACS) experiments were performed using fresh lung preparations. Mouse lung homogenates for single-cell flow cytometry were prepared as previously described (PMID 27400124). Briefly, fresh mouse lungs were perfused with 10 ml PBS, elastase (4 U/ml; Worthington Biochemical Corporation) were injected through the trachea to inflate the lung and dissociate epithelial cells. After that, samples were cut into approximately 1-mm3 pieces and digested with DNase I (100 U/ml; Sigma). Single cell homogenates were collected after passing through cell strainers and centrifugation. Flow cytometry was used to sort Epcam+, CD31-, CD34-, and CD45- MCs. Primary antibodies to CD31, CD34, and CD45, and secondary antibody anti-streptavidin were all from eBioscience (San Diego, CA). Mouse anti-EpCAM (G8.8, catalog 118215) were from BioLegend (San Diego, CA). 7-AAD was from BD Biosciences (San Diego, CA). Singlet discrimination was sequentially performed using plots for forward scatter (FSC-A versus FSC-H) and side scatter (SSC-W versus SSC-H). Dead cells were excluded by scatter characteristics and viability stains. All FACS experiments were performed on an Aria III sorter (BD Immunocytometry Systems, San Jose, CA) at the Cedars-Sinai Medical Center Shared FACS Facility and FACS data were analyzed using FlowJo software (TreeStar, Ashland, OR).
Single-cell RNA-seq libraries were prepared per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). After RT, GEMs were harvested and the cDNAs were amplified, cleaned up with SPRIselect Reagent Kit.  Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2), to obtain a sequencing depth of 100K~200K reads per cell.
10X single cell RNA-seq

tag: strain

value: mouse lung

tag: cell type

value: Epcam+CD31/34/45- Epithelial Cells


title: Heart - HighFat - FHL2KO3 [MB_23_S16]

source_name: Heart - HighFat - FHL2KO

value: Heart


title: Heart - HighFat - FHL2KO2 [MB_22_S15]


title: BoC32 K2

source_name: human colorectal tumor tissue, mouse stroma (PDX)


title: ADT_rep2_library

description: Antibody against cell ssurface proteins  tagged with hashtag oligonucleotide

value: ADT


title: Heart - HighFat - FHL2KO1 [MB_21_S14]


title: BoC20 K3


title: BoC209 K2


title: Heart - HighFat - WT3 [MB_19_S11]

source_name: Heart - HighFat - WT


title: Heart - HighFat - WT2 [MB_18_S10]


title: Heart - HighFat - WT1 [MB_17_S9]


title: BoC10 K14


title: BoC106 K1


title: Heart - HighFat - FHL2KO4 [MB_24_S17]


title: BoC69 K2


title: WWA

city: Guangzhou

first: Yue

last: Li

address: #111 Liuhua Road

institute: Department of Intensive Care Unit, General Hospital of Southern Theatre Command of PLA

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 33bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Blood

growth_protocol: serum collected from patients and exosome were isolated

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: heat stroke

tag: sample type

value: serum exosome

tag: condition

value: heat stroke


title: T602


title: 3489_PBMC

first: Rekha

last: Dhanwani

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Do not have consent from patient to submit raw data

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Peripheral Blood

growth_protocol: Frozen PBMCs were thawed,stained for T cell surface and memory markers, and sorted in Trizol.

extract_protocol:
100,000 PBMCs, CD4 and CD8 memory T cells were sorted and collected in Trizol in a 1.5 ml tube. Tubes were vortexed, spun and stored at -80C until processed. RNA was extracted using RNA microRNA kit (Qiagen) on a Qiacube.
Purified total RNA was amplified following the smart-seq2 protocol. cDNA was purified using AMPure XP beads, and barcoded Illumina sequencing libraries were generated, loaded and sequenced on the Illumina sequencing platform HiSeq 2500.

treatment_protocol: No treatment

value: PBMC

value: M


title: 3323_PBMC


title: 3331_PBMC


title: BoC35 K3


title: 3352_PBMC


title: T1


title: 2991_PBMC

value: F


title: 3203_PBMC


title: NC2

value: healthy control


title: NC1


title: 2981_PBMC


title: Heart - HighFat - WT4 [MB_20_S13]


title: HJY


title: FYW


title: TP53TP1-3

city: wuhan

first: Baiyang

last: Chen

address: donghu road 169

institute: wuhan university

data_processing:
Illumina HiSeq XTen sequencer was used.
Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Genome_build: Homo_sapiens GRCh38.p10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Huh7 cells

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen), and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: Huh7 cells were transfected with TP53TG1 overexpressed plasmid and control plasmid respectively. Three replicates each.

tag: cell line

value: Hepatocellular carcinoma cell line

value: TP53TG1 overexpressing


title: 2638_PBMC


title: 1455_PK_PBMC


title: C. albicans cells - Fluconazole 1.5 Hour - rep 1

city: Chicago

value: 15 microg/mL Fluconazole

tag: time point

value: 1.5 Hour


title: 1067_PK_PBMC


title: 2748_PBMC


title: 3509_PBMC


title: TP53TP1-1


title: NC3

value: Control


title: WFH


title: NC2


title: 1064_PK_PBMC


title: 3328_PBMC


title: NC1


title: 2766_PBMC


title: SLEWSN

city: Beijing

first: Xuan

last: Zhang

address: dongdan

institute: Peking union medical college hospital

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Transcripts predicted with coding potential by CNCI (Coding-Non-Coding-Index) (v2) ，CPC (Coding Potential ，Calculator) (0.9-r2)，Pfam Scan (v1.3) and PhyloCSF(v20121028)  were filtered out, and those without coding potential were our candidate set of lncRNAs.
Phast (v1.3) is a software package contains much of statistical programs, most used in phylogenetic analysis (Siepel, et al. 2005), and phastCons is a conservation scoring and identificating program of conserved elements. We used phyloFit to compute phylogenetic models for conserved and non-conserved regions among species and then gave the model and HMM transition parameters to phyloP to compute a set of conservation scores of lncRNA and coding genes.
Genome_build: GRCH28
Supplementary_files_format_and_content: tab-delimited text files include FPKM, raw counts values for each Sample

source_name: neutrophil_new onset treatment-naïve SLE patients

growth_protocol: No in vitro culture

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Patients of Systematic Lupus Erythematosus

value: Female

value: blood

value: neutrophil


title: 2953_PK_PBMC


title: S219

tag: Sex


title: S212


title: 2705_PBMC


title: S204


title: 2610_PBMC


title: 2750_PBMC


title: S205

value: Male


title: TP53TP1-2


title: S194


title: 2457_PK_PBMC


title: NC3


title: 2606_PBMC


title: C103

source_name: neutrophil_healthy control

value: Healthy Control


title: C104


title: 1479_PK_PBMC


title: C102


title: 1477_PK_PBMC


title: C101


title: 2763_PBMC


title: C48


title: 1430_PBMC


title: C38


title: 1423_PBMC


title: MSC_2_Zymosan_FK

city: Brno

first: Marco

last: De Zuani

address: Pekarska, 53

department: CTM

country: Czech Republic

institute: FNUSA - ICRC

data_processing:
Transcript abundaces were estimated using kallisto and mapped reads were summarized to genes unsing Tximport.
Datasets were filtered for low count reads (<10), normalized using a TMM-approach and transformed to logCPM
Genome_build: Ensembl GRCh38.p12
Supplementary_files_format_and_content: For each file, matrix table of Tximport outputs for every gene including raw count values prior to data filtration and normalization

source_name: adipose-derived mesencymal stromal cells

extract_protocol:
Total RNA was isolated by column separation using a RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), according to manufacturer’s protocol. RNA quality was assessed with Bioanalyzer2100 RNA Nano 6000 chips (Agilent technologies, Santa Clara, California, USA) and samples with RIN > 9 were used for sequencing.
An Illumina sequencing library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, MA, USA) following manufacturer’s protocols.

treatment_protocol: human AT-MSCs from three different donors were stimulated with either 10 μg/mL zymosan, 10 μg/mL zymosan + 200 ng/mL FK506 or left untreated.

value: Zymosan 10ug/mL + FK506 200ng/mL


title: 1421_PBMC


title: 1416_PBMC


title: MSC_1_Zymosan_FK

value: adipose-derived mesencymal stromal cells


title: MSC_3_Zymosan

value: Zymosan 10ug/mL


title: 1414_PBMC

value: PBMC

value: M


title: MSC_2_Zymosan


title: 1077_PK_PBMC


title: MSC_3_Zymosan_FK


title: 1066_PK_PBMC


title: 3487_PBMC

value: F


title: MSC_2_NT

value: untreated


title: MSC_1_Zymosan


title: 3035_PK_PBMC


title: 3498_PBMC


title: 2933_PK_PBMC


title: MSC_3_NT


title: 1429_PBMC


title: MSC_1_NT


title: 2862_PBMC


title: 2797_PBMC


title: 2852_PBMC


title: 2788_PBMC


title: 2781_PBMC


title: Creinhardtii_Y4

city: Montreal

first: Elise

last: Morel

state: QC

address: 2900, boul. Édouard-Montpetit

department: Chemistry

country: Canada

institute: Univeristy of Montreal

data_processing:
Filtering quality and adapter trimming were carried out with Trim Galore! (Version 0.3.7) using  the following configurations; --phred33 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -a2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -r1 21 -r2 21
Reads were aligned to the C. reinhardtii genome v5.3 assembly using TopHat2 (v2.0.14) with --max-intron-length 28000 --min-intron-length 30 -G C_236_gene_exons.gff3. Approximately 45 million reads were mapped for each sample (around 82% of raw data) with concordant pair alignment accounting for 85% of the total mapped reads in each sample.
Samtools (v1.2) was used to sort and index output files from TopHat2 (.bam files)
The number of reads (i.e. raw counts) per gene were determined using the Python package HTSequensing (v0.6.1) the following configurations;-r name  -m union -f bam -s no --type=exon --idattr=Parent
GeneBody coverage python script (RSeQC) (v2.4) was used to calculate the number of reads for each nucleotide position and to generate a plot illustrating the coverage profile along the gene using -r C_236_gene_exons.gff3.bed.
Genome_build: C_236_gene_exons.gff3 (C. reinhardtii genome v5.3 assembly)
Supplementary_files_format_and_content: tab-delimited text files include raw count values (i.e. number of reads mapped) for all samples and genes

organism: Chlamydomonas reinhardtii

source_name: whole organism

growth_protocol: The wild-type strain CC-125 (aka 137c, Chlamydomonas resource center) was cultured in 4×diluted TAP at 20°C under conditions of 12 h light/12 h dark (60 mmol s-1 m-2) using orbital shaking (100 rpm), until algae reached their mid-exponential growth phase. Cells were then washed (3×) by pelleting them by centrifugation (2000xg for 3 min) then resuspending them in an exposure medium (see below) that contained no metal.

extract_protocol:
Frozen cell pellets were thawed and immediately resuspended in freshly prepared lysis buffer (0.3 M NaCl, 5.0 mM EDTA, 50 mM Tris-HCl (pH 8.0), 2.0% (w/v) SDS, 3.3 U mL‑1 proteinase K) where they were incubated at 37°C for 15 min with orbital shaking (300 rpm). Total RNA was isolated by extracting the sample 3x with phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.8), followed by 1x with chloroform:isoamyl alcohol (24:1). At each step, samples were centrifuged (12000xg, 10 min, 4°C) and supernatants were transferred into new tubes. Total RNA was precipitated from the final aqueous phase by isopropanol, then washed with 75% ethanol. After a final centrifugation, the pellet was resuspended in 20-30 µL of nuclease-free water.
DNase treatment, polyA RNA selection, library preparation (NEB/KAPA mRNA stranded library preparation) and Illumina sequencing were carried out at the Genome Quebec facilities (www.gqinnovationcenter.com). Two lanes on a HiSeq 4000 were used for the paired-end sequencing (2 × 100 base pairs) of 25 samples (5 replicates for each treatment: Ce; Tm; Y; Mix; Controls).

treatment_protocol: The concentrated cell suspension was then diluted to 6.5-10 x 104 cells mL-1 (i.e. 0.15 cm2.mL-1) in an exposure solution containing the appropriate metal concentration. Culture densities and cell surface areas were measured using a Multisizer 3 particle counter (50 µm aperture; Beckman Coulter). Cells were exposed for 2 h to 0.5 µM of Ce, Tm, Y or their equimolar mixture (Mix) in 10.0 mM NaHEPES (pH buffered at 7.0 in a solution also containing 10.0 µM Ca(NO3)2). The exposure duration and concentration were selected to minimize physicochemical modifications to the exposure medium, while maximizing genomic response. Following the 2 h exposure, cells were pelleted from 200 mL of the exposure solution by centrifugation (2000×g, 2 min, 4°C). Cell pellets were resuspended in 1 mL nuclease-free water before being transferred into 1.5 mL microtubes where cells were again pelleted by centrifugation. Cell pellets were frozen on dry ice and stored at −80 °C.

tag: taxonomy

value: Plantae, Chlorophyceae (unicellular microalgae)

value: wild-type strain, CC-125

tag: developmental stage

value: mid-exponential growth phase

tag: exposure medium

tag: cell surface concentration during exposure


title: Creinhardtii_Tm2

value: 10.0 mM NaHEPES (pH buffered at 7.0 in a solution also containing 10.0 µM Ca(NO3)2)


title: Creinhardtii_Tm4


title: Creinhardtii_Tm1


title: 2635_PBMC

tag: gender


title: Creinhardtii_Tm3


title: Creinhardtii_Y5


title: 2396_PBMC


title: 1595_PK_PBMC


title: 1576_PK_PBMC


title: Creinhardtii_Y2


title: 1434_PK_PBMC


title: Creinhardtii_Y3


title: Creinhardtii_Y1


title: 3509_CD8

value: CD8 memory


title: 3489_CD8


title: Creinhardtii_Tm5


title: 3331_CD8


title: 3352_CD8


title: Creinhardtii_YCeTm4


title: Creinhardtii_YCeTm1


title: 3323_CD8


title: Creinhardtii_YCeTm3


title: Creinhardtii_Ctl5


title: Creinhardtii_Ctl4


title: Creinhardtii_Ctl3


title: 2981_CD8


title: Creinhardtii_Ctl2


title: 2748_CD8


title: 2638_CD8


title: Creinhardtii_Ce5


title: 1455_PK_1


title: Creinhardtii_YCeTm5


title: Creinhardtii_Ce3


title: 1064_PK_2


title: Creinhardtii_Ctl1


title: 1067_PK_2


title: 2838_CD8


title: 1404PK_CD8_Park1


title: 3328_CD8


title: 2953_PK_1


title: Creinhardtii_Ce1


title: Creinhardtii_Ce2


title: 2766_CD8


title: 3203_CD8


title: Creinhardtii_YCeTm2


title: 2750_CD8


title: 2991_CD8


title: 10492 DHS-seq KO Act B cell

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
ChIP-seq and DHS-seq: Sequence reads that passed the Illumina quality filtering were considered for alignment. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 12.5 (ref. 18). The Pax5 Bio-ChIP-seq data generated with FO B cells stimulated with anti-CD40 plus IL-4 for 2 days were trimmed to 36-mers and aligned as single end sequences, to make them comparable to the already published mature B cell ChIP-seq data (GSM932925-GSM932931). Peaks were called using the MACS program version 1.3.6.1 (ref. 21) with default parameters, a read length of 36 or 76, a mature B cell input14 and a genome size of 2.654.911.517 bp (mm9). For the analysis of DHS data, the read shifting model building was turned off. Peaks were further filtered for P values of < 10-10. ATAC-seq: The sequence data were down-sampled to 20.040.789 reads (corresponding to the sample size of the mature B cell experiment; GSM932925-GSM932931), and peaks were called with MACS_1.3.6.1, using only the first read of each fragment, and the sequencing data of mature B cells (GSM2058441) as input.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.6.1p1 (ref. 28) with the overlap resolution mode set to ‘union’. The datasets were grouped according to genotype and type of stimulation and were analyzed using the R package DESeq2 version 1.8.2 (ref. 29). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Variance stabilizing transformations were computed with the blind option set to ‘FALSE’. Variance stabilized counts were transformed from log2 to log10 scale for the scatterplots shown in Supplementary Figs. 4f, 6a and 8a. The default DESeq2 pair-wise setup (model design formula: “~ genotype”; Wald test) was used for comparison of the RNA-seq data of knockout (Cd23-Cre Pax5fl/–) versus control (Cd23-Cre Pax5fl/+) activated B cells stimulated for 2 days with anti-CD40 and IL4. Untreated and 1-hour anti-IgM-stimulated knockout and control lymph node B (LN B) cells were analyzed, considering the main effects of the genotype (I, II) and time (III, IV) as well as their ‘interaction’ effect, which quantifies if the time effect differs across genotype (model design formula: “~ genotype + time + genotype:time”; Wald tests). If not mentioned otherwise, genes with an adjusted P value < 0.05 and an absolute fold change > 3 as well as a mean TPM (averaged within conditions) > 5 were called as significantly expressed. Immunoglobulin and T cell receptor genes were filtered from the list of significantly expressed genes, but were included in the TPM calculations.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million after extension to 150 base pairs (.density_150.rpm.bw); text tab delim = TPM values in ASCII text format tab delimited

source_name: stimulated B cell

extract_protocol: About 1-5 ng of cDNA, (Bio-)ChIP-precipitated DNA or DHS-enriched DNA were used as starting material for generating sequencing libraries with the NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module, as described17. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England BioLabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer's guidelines

tag: genotype

value: Cd23-Cre Pax5(F/-)

tag: cell preparation

value: 2-day anti-CD40 IL-4 stimulation

tag: cell sorting strategy

value: CD43 depletion MACS sort


title: 10491 DHS-seq Act B cell

value: Cd23-Cre Pax5(F/+)


title: 9769 RNA-seq KO Act B cell

description: SuperScript® VILO™ cDNA Synthesis, Udgase treated


title: Creinhardtii_Ce4


title: 9767 RNA-seq KO Act B cell


title: 2705_CD8


title: 2610_CD8


title: 9766 RNA-seq Act B cell


title: 9768 RNA-seq Act B cell


title: 9596 H3K4me2 Act B cell

tag: chip antibody

value: H3K4me2 Ab (Upstate 07-030)


title: 2457_PK_1


title: 2606PK_CD8_Park1


title: 1479_PK_1


title: 9597 H3K4me2 KO Act B cell

tag: strain


title: 2763_CD4

tag: cell type


title: 9593 Pax5 Bio-ChIP-seq

description: B-cells were plated at a density of 5 × 105 cells/ml in IMDM medium supplemented with 10% FCS, 1 mM glutamine, 50 µM β-mercaptoethanol, anti-CD40 antibody and IL-4 for 2d

value: Streptavidin


title: 1423PK_CD8_Park1


title: 1429PK_CD8_Park1


title: 1421PK_CD8_Park1


title: 1414PK_CD8_Park1


title: 1416PK_CD8_Park1


title: 1413PK_CD8_Park1


title: 1403PK_CD8_Park1


title: HEK293 si-Hsp70L1_si-Pelo Thapsigargin rep1

city: Lexington

first: Jae Seok

last: YOON

state: MA

address: 44 Hartwell Avenue

department: CFFT Lab

institute: Cystic Fibrosis Foundation

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina NCS software (2.2.0)
3' adaptor sequence of each read was trimmed by FastX-toolkit.
Reads mapped to four rRNA sequences (RNA5S1, RNA5-8SN5, RNA18SN5, and RNA28SN5) by HISAT2 (2.0.3) were eliminated.
The remaining reads were aligned to the transcript variant with the longest coding sequence (CDS) of each human gene using HISAT2 (2.0.3).
Multi-mapped reads were discarded, and only reads with the size ranging from 18 to 34 nt were utilized.
Genome_build: hg38
Supplementary_files_format_and_content: Text file; Column-1: 5'end position of read on Xbp1 (nt), Column-2: Read count, and Column-3: Read per million total reads (RPM).

source_name: HEK293 cells

extract_protocol:
RNase I footprinting, ribosome pelleting, TRIZOL extraction of riboseom-protected mRNA fragments
Preadenylated linker ligation, reverse transcription, cDNA circularization, rRNA depeletion, PCR amplification

tag: si-rna knockdown

value: si-Hsp70L1 and si-Pelo

tag: treatment

value: Thapsigargin for 4 h


title: HEK293 si-Hsp70L1_si-Pelo Thapsigargin rep2


title: Doxorubicin-resistant cells, biological rep 2

city: Ottawa

first: Julie

last: St-Pierre

state: Ontario

address: 451 Smyth Road

department: Department of Biochemistry, Microbiology and Immunology

institute: University of Ottawa

description: MCF-7 derived cell line, resistant to doxorubicin and cultured with 98.1 nM doxorubicin (constant dose)

hyb_protocol: Hybridization was performed Genome Quebec using the GeneChip Hybridization, Wash, and Stain Kit from Thermo Fisher

scan_protocol: Scans were performed by Genome Quebec using a HiSeq 2000 from Illumina

data_processing:
Data were analyzed using Affymetrix Gene Expression and Transcriptome Analysis Console software, using default parameters.
RMA

label: biotin

source_name: Doxorubicin-resistant MCF-7 cells + Doxorubicin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Cells were obtained from Amadeo Parissenti (PMID 18980695) and cultured as described using high-glucose Dulbecco's Modified Eagle's Medium (DMEM, Wisent #319-005-CL), 10% FBS, and penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol: RNA extraction was performed using BioRad Aurum RNA column extraction kit with DNAse step, per manufacturer's instructions

treatment_protocol: Control cells were maintained in 0.1% DMSO, DoxR cells were maintained in 98.1 nM doxorubicin, and EpiR cells were maintained in 852 nM epirubicin at all times

tag: cell line (origin)

value: MCF-7 Breast Cancer

tag: drug

value: Doxorubicin (98.1 nM)


title: 1477_PK_1

value: M


title: HEK293 si-Pelo Thapsigargin rep2

value: si-Pelo


title: HEK293 si-Pelo Thapsigargin rep1


title: 3498_CD8


title: 1430PK_CD8_Park1


title: Epirubicin-resistant cells, biological rep 2

description: MCF-7 derived cell line, resistant to epirubicin and cultured with 852 nM epirubicin (constant dose)

source_name: Epirubicin-resistant MCF-7 cells + Epirubicin

value: Epirubicin (852 nM)


title: Control cells, biological rep 2

description: MCF-7 derived cell line, sensitive to chemotherapy and cultured with 0.1% DMSO

source_name: MCF-7 cells + DMSO


title: 1066_PK_2


title: Doxorubicin-resistant cells, biological rep 3


title: HEK293 si-Hsp70L1 Thapsigargin rep2


title: 3035_PK_1


title: HEK293 si-Hsp70L1 Thapsigargin rep1


title: Control cells, biological rep 3


title: 2933_PK_1

value: F


title: Epirubicin-resistant cells, biological rep 3


title: 2885_PK_1


title: HEK293 si-Control Thapsigargin rep2

value: si-Control


title: Doxorubicin-resistant cells, biological rep 1


title: Control cells, biological rep 1


title: HEK293 si-Hsp70L1_si-Pelo DMSO rep2

value: DMSO for 4 h


title: 2862_CD8

value: CD8 memory


title: Epirubicin-resistant cells, biological rep 1


title: HEK293 si-Hsp70L1_si-Pelo DMSO rep1


title: 1077_PK_2


title: 2852_CD8


title: 2797_CD8


title: HEK293 si-Pelo DMSO rep1


title: 3487_CD8


title: 2788_CD8


title: HEK293 si-Hsp70L1 DMSO rep2


title: 2781_CD8


title: 2396PK_CD8_Park1


title: HEK293 si-Control Thapsigargin rep1


title: HEK293 si-Control DMSO rep2


title: 2635PK_CD8_Park1


title: 2791_CD8


title: 1576_PK_1


title: HEK293 si-Hsp70L1 DMSO rep1


title: HEK293 si-Control DMSO rep1


title: 1434_PK_1


title: 1595_PK_1


title: Unstimulated_migrated_LC

city: Southampton

first: James

middle: David

last: Davies

state: Hampshire

address: LE57, Lab and Pathology block, Tremona Road

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

description:
single cell RNA
human skin primary unstimulated migrated LCs

data_processing:
Samples were de-multiplexed with bcl2fastq tool from Illumina
Reads were  aligned to human_hg19 reference genome using STAR
Genome_build: hg19
Supplementary_files_format_and_content: read count

source_name: Epidermis

growth_protocol: Migrated LC were extracted from 48 hour culture of epidermis sheets. LCs were enriched using FACS (CD1a+, CD207+, HLADR+). TNF-stimulated LCs were stimulated with TNF𝛼 (25ng/ml) for 24 hours.

extract_protocol: cDNA libraries were  tagmented and PCR-amplified (Nextera tagmentation kit, Illumina)

treatment_protocol: Highly purified (CD1a+, CD207+, HLA-DR+) single human LCs were co-encapsulated with genetically-encoded beads (Drop-seq). Monodisperse droplets at 1 nl in size were generated using the microfluidic devices fabricated in the Centre for Hybrid Biodevices, University of Southampton. Following encapsulation, approximately 400 unstimulated and TNF-stimulated LC STAMPS (beads exposed to a single cell) were taken further for library prep. The resulting libraries were run on a shared NextSeq run (1.5x105 reads for maximal coverage) at the Wessex Investigational Sciences Hub laboratory, University of Southampton, to obtain single cell sequencing data.

tag: condition

value: Unstimulated

value: Langerhans cells


title: 1431PK_CD8_Park1


title: Cardiac Endothelial cells_Tcruzi2

city: Boston

first: Mercio

last: Perrin

address: 150 Harisson Avenue

institute: Tufts University

data_processing:
Illumina bcl2fastq v1.8.4 for basecalling
Sequenced reads were mapped to mm10 genome using tophat v2.0.10 with paramters -p12 and aligned reads were output in BAM format.
The FPKM values and differentiate expression analyses were prformed using cuffdiff v2.1.1 using the BAM files from tophat alignment
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, and log2 fold change and p- & q-vlaue from differential expression analysis

source_name: Cardiac Endothelial cells_Tcruzi

extract_protocol:
The mRNA was isolated using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Confluent mouse cardiax endothelial cells were treather with vehicle (PBS) or with T.cruzi trypomastigotes (Colombiana strain) for 3h

tag: Sex

value: Female

value: T.cruzi trypomastigotes, MOI 1, 3h

value: Mouse Cardiac Endothealial cells


title: Cardiac Endothelial cells_Tcruzi1


title: Cardiac Endothelial cells_Veh2

source_name: Cardiac Endothelial cells_Veh

value: Veh (PBS)


title: Sldmr6-1.2-Xg_rep4

city: Berkeley

first: Daniela

middle: Paula

last: de Toledo Thomazella

address: 2151 Berkeley Way

department: PMB/IGI

institute: UC Berkeley

description:
BSDT_counts.txt
BSDT001N2

data_processing:
Illumina bcl2fastq v2.20.0 was used for basecalling.
Illumina adapters and low-quality reads were removed from the sequenced libraries using Trim Galore v0.6.4.
The filtered reads were aligned to the reference genome (SL 4.0) using STAR v2.6.1c.
The featureCounts function (v 1.6.3) from the subread package was used to count reads that mapped to protein-coding genes.
Genome_build: SL 4.0/ITAG 4.0
Supplementary_files_format_and_content: BSDT_counts.txt: Tab-delimited text file including read counts per gene for each sample.

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Wild type and mutant (Sldmr6-1.1 and Sldmr6-1.2) plants were grown on soil (Miracle-Gro Supersoil Potting Soil) in a growth chamber at 25°C under a 16h light/8h dark photoperiod. The experiment was performed with six-week-old plants.

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma, STRN250).
RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA library prep kit (Illumina 20020594).

treatment_protocol: Four individual plants of each genotype (wild type, Sldmr6-1.1 and Sldmr6-1.2 mutants) were used for RNA sequencing. Two leaves from each plant were syringe-infiltrated with a mock solution (10 mM MgCl2) or with a X. gardneri strain 153 suspension (OD600=0.25). Samples were harvested six hours after infiltration.

tag: cultivar

tag: age

value: 6 weeks

tag: tissue

value: Leaf

value: Xanthomonas gardneri

tag: time after treatment


title: 1426PK_CD8_Park1

tag: gender


title: 1422PK_CD8_Park1


title: Sldmr6-1.2-Xg_rep3

description:
BSDT_counts.txt
BSDT001M2

tag: genotype


title: Sldmr6-1.2-Xg_rep2

description:
BSDT_counts.txt
BSDT001L2


title: Cardiac Endothelial cells_Veh1


title: HEK293 si-Pelo DMSO rep2


title: Sldmr6-1.2-Xg_rep1

description:
BSDT_counts.txt
BSDT001K2


title: 66360 miRNA-seq KO LN B cells

description: small RNA

data_processing:
Adaptor clipping, sequence alignment against the mouse genome (mm10) and read counting of small-RNA-library reads was performed by applying the nextflow pipline available at https://gitlab.com/tburk/smallRNA-meth, described in PMID: 29481550, with maxMultialign set to 1000. Annotations were derived from miRBase v22 (PMID: 30423142). Only mature miRNAs (defined by predominance in > 50 % of all samples) were considered for analysis of differential expression by DESeq2 version 1.18.1 (PMID: 25516281).
Genome_build: mm9
Supplementary_files_format_and_content: text tab delim

source_name: lymph node mature B cell

extract_protocol:
total RNA was harvested using Trizol reagent followed by size selection for small RNAs using the mime-seq protocol from Alberti C. et al. (2018)
After reverse transcription of small RNAs into cDNA, the KAPA Real Time Library Amplification Kit, TruSeq Universal Adapter and Index reverse primers (Solexa) were used to amplify cDNA libraries

value: Cd23-Cre Pax5(F/-)

tag: cell preparation

value: CD23+ MACS sort


title: TNF-stimulated_migrated_LC

description:
single cell RNA
human skin primary TNF-stimulated migratory LCs

value: TNF-stimulated


title: 1415PK_CD8_Park1


title: 3509_CD4

value: CD4 memory


title: 66359 miRNA-seq KO LN B cells

description: small RNA

tag: cell sorting strategy


title: 66358 miRNA-seq LN B cells

description: small RNA

value: Cd23-Cre Pax5(F/+)


title: Sldmr6-1.1-Xg_rep4

description:
BSDT_counts.txt
BSDT001V2


title: Sldmr6-1.2-mock_rep1

description:
BSDT_counts.txt
BSDT001G2

value: Mock


title: Sldmr6-1.2-mock_rep3

description:
BSDT_counts.txt
BSDT001I2


title: Sldmr6-1.2-mock_rep2

description:
BSDT_counts.txt
BSDT001H2


title: 3352_CD4

value: M


title: 66357 miRNA-seq LN B cells

description: small RNA


title: Sldmr6-1.1-Xg_rep3

description:
BSDT_counts.txt
BSDT001U2


title: 61910 miRNA-seq KO splenic FO B cells

description: small RNA

source_name: splenic mature B cell


title: 61908 miRNA-seq KO splenic FO B cells

description: small RNA


title: 3489_CD4

source_name: Peripheral Blood


title: 61906 miRNA-seq splenic FO B cells

description: small RNA


title: Sldmr6-1.1-mock_rep4

description:
BSDT_counts.txt
BSDT001R2


title: Sldmr6-1.2-mock_rep4

description:
BSDT_counts.txt
BSDT001J2


title: 61904 miRNA-seq splenic FO B cells

description: small RNA


title: 2991_CD4

value: F


title: 2981_CD4


title: Sldmr6-1.1-mock_rep3

description:
BSDT_counts.txt
BSDT001Q2


title: shPHF8 rep2 RNA-seq

city: Barcelona

first: Simona

last: Iacobucci

state: Spain

address: Travessera de Gracias

department: Department of Molecular Genomics

country: Spain

institute: IBMB-CSIC

data_processing:
Alignment was performed using HISAT2
Assignment of aligned reads to genes using HTSeq
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Bed files contain genomic coordinates. BigWig files contain the information for displaying graphs.

source_name: Astrocytes

growth_protocol: NSCs were cultured in a poly-D-lysine (5 mg/ml, 2 hours at 37°C) and laminin (5 mg/ml, 4 hours at 37°C) pre-coated dishes growing with a media comprising equal parts DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing penicillin/streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential amino acids (0.1 mM), sodium pyruvate (1 mM), Hepes (5 mM), heparin (2 mg/l), bovine serum albumin (25 mg/l) and -mercaptoethanol (0.01 mM). We added fresh recombinant human EGF (R&D Systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final, respectively. For NSCs differentiation into astrocytes, the medium was replaced by the differentiation medium containing DMEM/F-12, 5% N2, Glutamax, and 10% FBS; fresh differentiation medium was supplied every 2 days.

extract_protocol:
For RNA-seq, RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Human/Mouse/Rat Kit (ref. RS-122-2201/2, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA was used for ribosomal RNA depletion RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina High HiSeq 2500)

treatment_protocol: Astrocytes were infected with lentivirus expressing shRNA control (shctr rep1, shctr rep2) or shRNA specific for PHF8 (shPHF8 rep1, shPHF8 rep2)

tag: Stage

value: Astrocytes differentiated from NSCs


title: 2748_CD4

city: La Jolla


title: shPHF8 rep1 RNA-seq

tag: strain


title: Sldmr6-1.1-mock_rep1

description:
BSDT_counts.txt
BSDT001O2


title: DCIS_tumor_rep3

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

institute: Osaka Prefecture University

description: RNA from biopsy specimens

hyb_protocol: Fifteen ug of cRNA were subjected to fragmentation using the 3' fragmentation buffer hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis Console® using RMA as a summerization algorithm.

source_name: Tumorous region, MI-FTC, FFPE

label_protocol: Biotinylated cRNA were prepared usibg the GeneChip® WT Pico Reagent Kit from 100 ng total RNA (GeneChip® WT Pico Reagent Kit User Manual, Affymetrix).

extract_protocol: Total RNA was isolated using RNAiso reagent (Takara-bio, Kusatsu, Japan).

tag: individual

value: DCIS patient 3

value: Mammary gland

tag: tissue region

value: tumor

value: female


title: shctr rep2 RNA-seq


title: WT-Xg_rep4

description:
BSDT001F2
BSDT_counts.txt

value: Wild-type

tag: treatment


title: Sldmr6-1.1-mock_rep2

description:
BSDT_counts.txt
BSDT001P2

value: 6 weeks


title: 2638_CD4

tag: cell type


title: Sldmr6-1.1-Xg_rep1

description:
BSDT_counts.txt
BSDT001S2

value: Leaf


title: 3203_CD4


title: DCIS_normal_rep3

description: RNA from biopsy specimens

source_name: Non-tumorous region, MI-FTC, FFPE

value: normal


title: DCIS_tumor_rep2

description: RNA from biopsy specimens

value: DCIS patient 2


title: MeNQ 3000 mg/L, Rep4

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: An Agilent Technologies (Agilent Technologies, Santa Clara, CA, USA) single color custom 8 x 60K microarray format (Amadid #: 063815) was used for all investigations.  A completely randomized design was utilized for microarray hybridizations where each individual D. pulex sample was selected at random (using a random number generator) for hybridization onto individual microarrays.  The Agilent Low Input Hybridization Kit (one color) was used for microarray hybridizations following manufacturer’s recommendations.  A total of 24 microarrays were hybridized which included four replicates for all MeNQ exposures including the control (0 mg/L), 174, 346, 709, 1385, and 2286 mg/L exposure treatments.

scan_protocol: An Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C) was used to scan microarray images at 2 μm resolution.  Data were extracted from microarray images using Agilent Feature Extraction software, version 10.7.3.1.

data_processing: Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX 14.9 (Agilent Technologies).  GeneSpring was also utilized for the expression analysis where a one-way ANOVA was conducted (p = 0.01) including Benjamini-Hochberg multiple-tests corrections.  Post-hoc tests were also conducted where the SNK test was utilized to determine which transcripts had significant differential expression relative to the 0 mg/L control.

organism: Daphnia pulex

source_name: whole animal

label_protocol: The Agilent Low Input Quick Amp Labeling Kit (one color) protocol was followed using 65 ng of total RNA as starting material from each biological sample.

growth_protocol: Daphnia pulex were obtained from in-house cultures (originally purchased from EC Testing) and reared in accordance with guidance in Laird et al. (2015).  REFERENCE:  Laird JG, Kennedy AJ, Melby NL, Gong P.  2015. Development of a Chronic Toxicity Testing Method for Daphnia pulex, US Army, Engineer Research and Development Center Report.  ERDC/EL SR-15-5. pp 1-25.

extract_protocol: The D. pulex samples were flash frozen in liquid nitrogen and stored at -80°C until RNA extractions were conducted.  Frozen samples were homogenized using disposable mortar and pellet pestles for each sample (Kimble Kontes, Vineland, NJ).  Total RNA isolation and on-column DNase digestion was conducted using the Qiagen RNeasy Mini Kit (Qiagen, Germantown, MD) following manufacturer’s recommendations.  RNA quantity was assessed using a NanoDrop One Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA) and final quality was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) where electrophoresis gels were visually inspected for degradation prior to use in downstream applications.

treatment_protocol: MeNQ (CAS Number 4245-76-5) was obtained from a commercial vendor (TCI America, product number M0749).  According to manufacturer specifications, this MeNQ was 98% pure and was hydrated (25% of mass as water) for safety purposes. MeNQ was used as received from the vendor for preparation of exposure solutions. Water used for preparation of stock solutions and for the control exposures was tap water (City of Vicksburg, MS, municipal source) dechlorinated using carbon filtration for all toxicity bioassays. For the D. pulex bioassay, standard synthetic freshwater bioassay medium (moderately hard reconstituted water) was used (USEPA 2002).  Bioassays were conducted at a target temperature of 25 °C for 11 d as this period was required to acquire 3 broods. Exposures were performed in 50 mL beakers with a test solution volume of 40 mL. One test animal was exposed in each beaker, and 10 replicate beakers were tested per treatment. The daily feeding ration mixture consisting of half Raphidocelis subcapitata and half yeast, cereal leaves, and trout chow fish food. Complete water renewals were conducted three times a week on Mondays, Wednesdays and Fridays.  The reproductive output was quantified as the total number of neonates produced in three broods per parental adult that survived to assay completion.  D. pulex were exposed to MeNQ at control (0 mg/L), 174, 346, 709, 1385, and 2286 mg/L (measured concentrations) as juveniles through three-broods of reproduction.   The reproduction assays included 20 animals exposed individually per treatment.  The animals remaining at the termination of the assay were randomly assigned to a set of 4 replicate groups of animals per treatment to serve as treatment replicates in the transcriptomic-expression experimental design (6 treatments x 4 replicates).  REFERENCE:  U.S. Environmental Protection Agency (2002) Methods for measuring the acute toxicity of effluents and receiving waters to freshwater and marine organisms. EPA-821-R-02-012, 5th ed. Office of Water, Washington, DC.

value: adult


title: DCIS_normal_rep1

description: RNA from biopsy specimens

value: DCIS patient 1


title: shctr rep1 RNA-seq


title: DCIS_normal_rep2

description: RNA from biopsy specimens


title: DCIS_tumor_rep1

description: RNA from biopsy specimens


title: WT-Xg_rep3

description:
BSDT001E2
BSDT_counts.txt

value: Xanthomonas gardneri


title: WT-Xg_rep2

description:
BSDT001D2
BSDT_counts.txt


title: 2838_CD4

value: CD4 memory


title: Sldmr6-1.1-Xg_rep2

description:
BSDT_counts.txt
BSDT001T2


title: Input PHF8

data_processing:
Read quality check was performed using FASTQ
Reads were mapped to the Mus musculus genome mm10 with Bowtie2
Peak calling was performed using MACS, using an effective genome size of 1870000000.0 and a p-value of 0,001 for PHF8 ChIP-seq
Genome_build: mm10
Supplementary_files_format_and_content: Bed files contain genomic coordinates of called peaks. Wig and bigWig files contain the information for displaying graphs.

extract_protocol:
For ChIp-seq lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the NEBNext® Ultra DNA Library Prep for Illumina® kit (ref. E7370) according to the manufacturer's protocol.

tag: chip antibody

value: WT


title: 1455_PK_CD4

value: M


title: WT-Xg_rep1

description:
BSDT001C2
BSDT_counts.txt


title: WT-mock_rep3

description:
BSDT001A2
BSDT_counts.txt

value: Mock


title: LN9-1358IR

city: Palo Alto

first: Nathan

middle: Edward

last: Reticker-Flynn

address: 3373 Hillview Ave

department: Pathology

institute: Stanford University

data_processing:
Raw sequencing reads were filtered and adapters trimmed using Trimmomatic v0.36. Quality was assessed using FastQC v0.11.3.
Transcript abundance was quantified using Salmon v0.7.2 in quasi-mapping mode and using the sequence, GC, and position bias correction parameters.Mitochondrial reads were removed and TPM values were re-normalized following their removal.
Differential expression analysis was performed using DESeq2.
Genome_build: GRCm38 GENCODE release M11
Supplementary_files_format_and_content: tab-delimeted files contain TPM values for each sample generated by Salmon, renormalized after removal of "mt-" transcripts.

source_name: melanoma

growth_protocol: All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin

extract_protocol:
Cell lines were trypsinized, washed with complete serum, centrifuged, and washed with PBS. Following washing cell pellets were frozen at -80C. After thawing, cells were resuspended in buffer RLT and lysed using QiaShredders. Extraction was performed using the Qiagen RNEasy Plus mini kit according to the manufacturer's protocol.
Library construction was performed by Centrillion Genomic Services using the Illumina TruSeq RNA Sample Prep Kit

tag: generation


title: LN9-1315BL


title: 3328_CD4

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

extract_protocol:
100,000 PBMCs, CD4 and CD8 memory T cells were sorted and collected in Trizol in a 1.5 ml tube. Tubes were vortexed, spun and stored at -80C until processed. RNA was extracted using RNA microRNA kit (Qiagen) on a Qiacube.
Purified total RNA was amplified following the smart-seq2 protocol. cDNA was purified using AMPure XP beads, and barcoded Illumina sequencing libraries were generated, loaded and sequenced on the Illumina sequencing platform HiSeq 2500.


title: 1064_PK_CD4


title: PHF8 ChIP-seq

value: Astrocytes differentiated from NSCs

value: PHF8 (Abcam ab36068)


title: WT-mock_rep4

description:
BSDT001B2
BSDT_counts.txt


title: 1404PK_CD4_Park1

value: F


title: MeNQ 0 mg/L, Rep3


title: 1067_PK_CD4


title: MeNQ 187.5 mg/L, Rep4


title: MeNQ 375 mg/L, Rep4


title: MeNQ 1500 mg/L, Rep4


title: WT-mock_rep2

description:
BSDT001Z1
BSDT_counts.txt


title: 2953_PK_CD4


title: LN8-1194BR


title: LN8-1205BL


title: 2766_CD4


title: WT-mock_rep1

description:
BSDT001Y1
BSDT_counts.txt


title: MeNQ 375 mg/L, Rep3


title: LN8-1198AR


title: 2750_CD4


title: LN7-1120BL


title: 2705_CD4


title: LN7-1112AR


title: LN7-1134BL


title: 2610_CD4


title: MeNQ 375 mg/L, Rep2


title: 2606PK_CD4_Park1


title: 2763_CD8


title: LN6-991AL


title: LN6-944AL


title: MeNQ 187.5 mg/L, Rep3


title: MeNQ 750 mg/L, Rep4


title: MeNQ 375 mg/L, Rep1


title: MeNQ 0 mg/L, Rep2