title: E74_ACTCGCTA

status: Public on Jan 31 2021

type: SRA

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Bulk-RNA Seq

library_source: transcriptomic

data_processing:
Single-Cell RNA Dataset : Chromium barcodes were used for demultiplexing and FASTQ files were generated using the Cellranger(Zheng et al. 2017) mkfastq pipeline. Alignment, filtering and UMI counting were performed using cellranger count. To improve detection of microglia, due to their low RNA content, cellranger reanalyse was used with the --force-cells option set at the inflection point when number of barcodes is plotted against the number of UMIs. Cells were manually filtered such that barcodes containing at least 10 counts corresponding to Cx3cr1, P2ry12 or Fcrls genes were classified as microglia, resulting in a total of 991 cells from the 4 FACS-sorted microglial populations.
Bulk RNA Dataset : Sequencing reads for the murine microglia dataset were sample demultiplexed with Je demultiplex from the JE suite using sequence barcodes in Supplementary table 11. Short sequence unique molecular identifiers (UMIs) from read pair 1 of the demultiplexed sample sequencing reads were discarded from both sequencing read pairs with Prinseq (minimum length 9). Remaining UMIs were clipped with Je clip and added to the sequencing read header to allow UMI deduplication post read mapping. Demultiplexed UMI tagged sequencing reads were filter-trimmed with Trimmomatic and aligned to the mouse genome (GENCODE's GRCm38 primary assembly annotation version vM15) using STAR(only sequencing reads from pair 2 were used for transcript quantification). Read deduplication based on UMIs was performed with Je MarkDupes and transcript read counts calculated with featureCounts. For the in vitro bulk sequencing dataset, demultiplexing was performed as we recently described (Grubman, A. et al. A CX3CR1 Reporter hESC Line Facilitates Integrative Analysis of In-Vitro-Derived Microglia and Improved Microglia Identity upon Neuron-Glia Co-culture. Stem Cell Reports (2020) doi:10.1016/j.stemcr.2020.04.007.) . In short, we used in-house pipelines including a fork of sabre tools (https://github.com/serine/sabre), and demultiplexed UMI-tagged sequencing reads were aligned to the human genome (Ensembl GRCh38 primary assembly) using RNAsik
Genome_build: GRCm38

molecule: total RNA

organism: Mus musculus

source_name: Microglia

extract_protocol: Libraries were made by individual first strand synthesis which add the index sequences indicated above.500pg of each total RNA sample was used as starting material except for a few samples where the entire RNA provided was used.  An iPSC control was also processed with each set using a separate index.  Following first strand synthesis cDNA of each set was pooled for subsequent processing.2.Final libraries were QC’d by Qubit, Bioanalyzer and qPCR.Thelibrary poolswere with mean size of ~350bp at a concentration of 4.8nM, 6.1nM, 4.8nM and 5.0nM respectively.3.For all four pools, following denaturation 2.2pM of library pool was clustered on a high output NextSeq runbased upon previous results with this type of sample.4.Clustering was within theoptimal rangefor all runsat 210k/mm2, 190k/mm2, 218k/mm2 and 190k/mm2 separably(optimal 170-230k/mm2).  This resulted in 545.7million, 492.1million, 564.9million and 493.7million readable clustersaccordingly.  Clusters passing filter wasas expected for NextSeq (significantly lower than HiSeq)with 81%, 82%, 71% and 86% (expected >70%). Percentage of reads >Q30 was also very good for all sets with Set1 94% >Q30 for R1 and71% >Q30 for R2; Set2 95% >Q30 for R1 and 66% >Q30 for R2; Set3 90% >Q30 for R1 and 70% >Q30 for R2; Set4 94% >Q30 for R1 and 73% >Q30 for R2(expected >80% for R1 and >60% for R2). This resulted in 442.8million, 405.6 million, 399.5 million and 423.6 millionfinal filtered reads respectively. 5.Library is designed so custom R1 primer reads directly into index followed by 10bp UMI.  6.R2 primer reads into RNA in the sense direction and will be best for transcript identification.7.Data is provided as 2matching Fastq files for R1 and R2.

tag: tissue

value: Microglia


title: E77_GCTCATGA

description: Bulk-RNA Seq


title: E70_AGGCAGAA

description: Bulk-RNA Seq


title: E60_CGTACTAG

description: Bulk-RNA Seq


title: E58.2_TGCAGCTA

description: Bulk-RNA Seq


title: E68.1_TCGACGTC

description: Bulk-RNA Seq


title: E38_GGAGCTAC

description: Bulk-RNA Seq


title: E64_TACGCTGC

description: Bulk-RNA Seq


title: E31_AGGCAGAA

description: Bulk-RNA Seq


title: E34_AGGCAGAA

description: Bulk-RNA Seq


title: E42_TAGGCATG

description: Bulk-RNA Seq


title: E20.1_GCTCATGA

description: Bulk-RNA Seq


title: E17_ACTGAGCG

description: Bulk-RNA Seq


title: 68_TAAGGCGA

description: Bulk-RNA Seq


title: 63_CGGAGCCT

description: Bulk-RNA Seq


title: 60_ATCTCAGG

description: Bulk-RNA Seq


title: 66_TACGCTGC

description: Bulk-RNA Seq


title: 79_TAGCGCTC

description: Bulk-RNA Seq


title: 57_GTAGAGGA

description: Bulk-RNA Seq


title: 59_ATGCGCAG

description: Bulk-RNA Seq


title: 67_CGATCAGT

description: Bulk-RNA Seq


title: 52_CTCTCTAC

description: Bulk-RNA Seq


title: 51_TCCTGAGC

description: Bulk-RNA Seq


title: 50_CGTACTAG

description: Bulk-RNA Seq


title: 53_TGCAGCTA

description: Bulk-RNA Seq


title: 49_AGGCAGAA

description: Bulk-RNA Seq


title: 55_GCGTAGTA

description: Bulk-RNA Seq


title: 48E_ATCTCAGG

description: Bulk-RNA Seq


title: 47E_CGAGGCTG

description: Bulk-RNA Seq


title: 46_TAAGGCGA

description: Bulk-RNA Seq


title: 36E_TCGACGTC

description: Bulk-RNA Seq


title: 40_TAAGGCGA

description: Bulk-RNA Seq


title: 39_CGTACTAG

description: Bulk-RNA Seq


title: 30_TCGACGTC

description: Bulk-RNA Seq


title: 34_ACTCGCTA

description: Bulk-RNA Seq


title: 37E_ATGCGCAG

description: Bulk-RNA Seq


title: 35E_ATGCGCAG

description: Bulk-RNA Seq


title: 29_GGACTCCT

description: Bulk-RNA Seq


title: 28_ACTCGCTA

description: Bulk-RNA Seq


title: 56_CGGAGCCT

description: Bulk-RNA Seq


title: 27_CTCTCTAC

description: Bulk-RNA Seq


title: 26E_TGCAGCTA

description: Bulk-RNA Seq


title: 19E_TAGGCATG

description: Bulk-RNA Seq


title: 24_ATCTCAGG

description: Bulk-RNA Seq


title: 21_CGTACTAG

description: Bulk-RNA Seq


title: 25_TACGCTGC

description: Bulk-RNA Seq


title: 13_TAAGGCGA

description: Bulk-RNA Seq


title: 14_CGATCAGT

description: Bulk-RNA Seq


title: 18E_CGATCAGT

description: Bulk-RNA Seq


title: 15_AAGAGGCA

description: Bulk-RNA Seq


title: 10_CCTAAGAC

description: Bulk-RNA Seq


title: 12_GTAGAGGA

description: Bulk-RNA Seq


title: 9R_TAGGCATG

description: Bulk-RNA Seq


title: 9_CGGAGCCT

description: Bulk-RNA Seq


title: 11E_GGACTCCT

description: Bulk-RNA Seq


title: 8R_GCGTAGTA

description: Bulk-RNA Seq


title: 45E_TAGCGCTC

description: Bulk-RNA Seq


title: 8_GCTCATGA

description: Bulk-RNA Seq


title: 7R_GGAGCTAC

description: Bulk-RNA Seq


title: 7_CGAGGCTG

description: Bulk-RNA Seq


title: 6_CCTAAGAC

description: Bulk-RNA Seq


title: 3R_CGAGGCTG

description: Bulk-RNA Seq


title: 4_GTAGAGGA

description: Bulk-RNA Seq


title: 3_TCCTGAGC

description: Bulk-RNA Seq


title: 4R_ACTGAGCG

description: Bulk-RNA Seq


title: 5R_AAGAGGCA

description: Bulk-RNA Seq


title: 6R_CCTAAGAC

description: Bulk-RNA Seq


title: 2R_GGACTCCT

description: Bulk-RNA Seq


title: 1R_TCCTGAGC

description: Bulk-RNA Seq


title: 4-microADme

description: 10x Single Cell

source_name: Microglia AD Methoxy Positive

extract_protocol: 5,000 microglia from each population (including XO4+ and XO4- microglia, 6m, 9m, 12m and 24m CX3CR1GFP microglia) were sorted into DMEM/F12 media (supplemented with 5% (v/v) FBS, 50 U/ml Penicillin and 50 µg/ml Streptomycin), centrifuged at 12,000 xg for 2 min at 4°C and resuspended in 35μl of PBS containing 0.04% (w/v) BSA (0.22 µm filtered). The samples were then diluted with nuclease-free water in accordance to 10X single cell protocol guidelines to achieve a target cell recovery of approximately 800 cells/sample (for 6m WT, 24m WT, 6m XO4- and 6m XO4+ dataset), and target recovery of 10,000 cells per sample (age dataset 6m, 9m, 12m WT microglia). Single cell capture, RNA-seq library construction and sequencing were carried out at Micromon, Monash University using the 10X Genomics Chromium system (10X Genomics). Library construction was performed by poly-A selection from total RNA using 10X Chromium controller with Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics, #PN-120237). Sequencing was performed on one High-Output lane of an Illumina NextSeq 550 (Illumina, California, USA) in paired-read 150 bp format. Chromium barcodes were used for demultiplexing and FASTQ files were generated using the Cellranger mkfastq pipeline. Alignment, filtering and UMI counting were performed using cellranger count. To improve detection of microglia, due to their low RNA content, cellranger reanalyse was used with the --force-cells option set at the inflection point when number of barcodes is plotted against the number of UMIs. Cells were manually filtered such that barcodes containing at least 10 counts corresponding to Cx3cr1, P2ry12 or Fcrls genes were classified as microglia, resulting in a total of 991 cells from the 4 FACS-sorted microglial populations.

value: Cortex


title: 1E_GCGTAGTA

description: Bulk-RNA Seq


title: 10R_CTCTCTAC

description: Bulk-RNA Seq


title: 1-microWT

description: 10x Single Cell

source_name: Microglia 6M WT


title: WT-12m

description: 10x Single Cell

source_name: Microglia 12M WT


title: 2-microO

description: 10x Single Cell

source_name: Microglia 24M WT


title: 2_ACTGAGCG

description: Bulk-RNA Seq


title: WT-6m

description: 10x Single Cell


title: WT-9m

description: 10x Single Cell

source_name: Microglia 9M WT


title: 3-microAD

description: 10x Single Cell

source_name: Microglia AD Methoxy Negative


title: C5M2

city: Houston

first: Ali

last: Jalali

state: Texas

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

data_processing:
fastq files were aligned to mouse transcriptome using the mm10 index (GRCm38) provided in Rsubread package and default "align" command parameters
mapped read counts were obtained using the Rsubread "featureCounts" commnad with parameters "isPairedEnd=True" and "requireBothEndsMapped=True"
Entrez genes with 0 read counts across all samples were eliminated from the matrix table
Genome_build: mm10, provided by Rsubread package
Supplementary_files_format_and_content: comma-delimited text file that contains a matrix table with raw gene counts for every Entrez gene and every sample

source_name: glioma tumor

extract_protocol:
GFP-positive glioma tumor was dissected from adult mouse brain shortly after sacrifice under a fluorescence dissection microscope. Tissue was then subjected to Qiagen RNeasy Mini kit to purify RNA for sequencing.
RNA libraries were prepared for sequencing using 1 microgram of total RNA and standard Illumina protocols

tag: strain

tag: tumor

tag: Sex

value: M

value: glioma tumor


title: C5M5


title: C5M1


title: C5M3


title: C5M4


title: C5F8

value: F


title: C5F7


title: C5F5


title: C5F4


title: C5F6


title: C3M6


title: C5F1


title: C3M4


title: C5F3


title: C3M5


title: C5F2


title: C3M3


title: C3F5


title: C3F6


title: C3F2


title: C3F4


title: C3M1


title: H. pseudoburtonii YPD + 1M NaCl 30 min #2

city: Seoul

first: Dong Wook

last: Lee

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang university

description:
TN1806R0601--GTGAAACG
Hp_30min_2
EXP:KJS14_Nacl_30min_2:FPKM

data_processing:
Illumina Casava 1.8.2 software used for basecalling
The quality check were performed using the Fastqc tool (v 0.11.8)
Clean reads were mapped into the draft genome of Hyphopichia burtnoii and Hyphopichia pseudoburtnoii using Tophat (v 2.1.1)
The gene expression levels were then estimated using Cufflinks (v 2.2.1) based on the gene annotations.
Genome_build: Reference sequences of H. burtnoii (GCA_001661395.1) and H. pseudoburtnoii (GCA_003856775.1)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Hyphopichia pseudoburtonii

source_name: H. pseudoburtonii YPD + 1M NaCl 30 min

growth_protocol: WT H. burtonii and H. pseudoburtonii were inoculated at OD600 = 0.6 to 2.0 in YPD broth

extract_protocol:
total RNA was extracted be de novo RNA preparation method, we are going to publish this protocol
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After reached OD600 = 2.0, harvest 0 min samples, add same volume of YPD+2M NaCl broth to YPD broth. Aftef 5, 15, 30 min later, harvest each samples

tag: isolation source

value: Nuruk

tag: mutant status

value: WT

tag: treatment

value: YPD + 1M NaCl 30 min


title: C3F3


title: H. pseudoburtonii YPD + 1M NaCl 15 min #2

description:
TN1806R0599--CCGTCCCG
Hp_15min_2
EXP:KJS14_Nacl_15min_2:FPKM

source_name: H. pseudoburtonii YPD + 1M NaCl 15 min

value: YPD + 1M NaCl 15 min


title: C3F1


title: C5M6


title: H. pseudoburtonii YPD + 1M NaCl 15 min #1

description:
TN1806R0598--ATGTCAGA
Hp_15min_1
EXP:KJS14_Nacl_15min_1:FPKM


title: H. pseudoburtonii YPD + 1M NaCl 30 min #1

description:
TN1806R0600--GTCCGCAC
Hp_30min_1
EXP:KJS14_Nacl_30min_1:FPKM


title: C3M2


title: H. pseudoburtonii YPD + 1M NaCl 0 min #1

description:
TN1806R0594--GGCTACAT
Hp_0min_1
EXP:KJS14_Nacl_0min_1:FPKM

source_name: H. pseudoburtonii YPD + 1M NaCl 0 min

value: YPD + 1M NaCl 0 min


title: H. pseudoburtonii YPD + 1M NaCl 5 min #2

description:
TN1806R0597--AGTTCCGT
Hp_5min_2
EXP:KJS14_Nacl_5min_2:FPKM

source_name: H. pseudoburtonii YPD + 1M NaCl 5 min

value: YPD + 1M NaCl 5 min


title: H. pseudoburtonii YPD + 1M NaCl 0 min #2

description:
TN1806R0595--CTTGTAAT
Hp_0min_2
EXP:KJS14_Nacl_0min_2:FPKM


title: p53-T0_WT

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

country: China

institute: Xiamen University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 v2.2.5 and using samtools v1.7 to sorting bam
peaks were called using MACS2 version 2.1.2 with the following setting: band width = 300 model fold = [5, 50] pvalue cutoff = 1.00e-03
Genome_build: mm10

molecule: genomic DNA

source_name: back skin

growth_protocol: the skin isolate from 8-10 weeks mouse

extract_protocol:
Lysates were clarified from sonicated nuclei and p53-DNA  histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: treat by radition with 5Gy

value: back skin

value: ionizing radiation

tag: genotype

value: Wild type

tag: chip antibody


title: H3K4me3-6h_WT


title: p53-T0_K17KO


title: p53-6h_K17KO


title: H3K4me3-T0_WT


title: p53-6h_WT


title: GC092444: Retina Mfp2 KO rep 3

city: Leuven

first: Myriam

last: Baes

state: Belgium

address: Herestraat 49, ON II, mailbox 823

department: Department of Pharmaceutical and Pharmacological Sciences

country: Belgium

institute: KU Leuven

data_processing:
The libraries were sequenced on a HiSeq4000 instrument (Illumina). Single-end reads of 50 base pairs were produced with a minimum of 1 million reads per sample.
Quality control of raw reads was performed with FastQC v0.11.7, available online at:  http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Adapters were filtered with ea-utils fastq-mcf v1.05 (Erik Aronesty (2011), ea-utils: “Command-line tools for processing biological sequencing data”; https://github.com/ExpressionAnalysis/ea-utils).
Splice-aware alignment was performed with HiSAT2 against the mouse reference genome mm10. Reads mapping to multiple loci in the reference  genome were discarded.
Resulting BAM files were handled with Samtools v1.5 (Li et al, Bioinformatics,2009).
Quantification of reads per gene was performed with HT-seq Count v2.7.14, using Ensembl78 annotation.
Further biostatistical analyses were performed using the R-based software package BIOMEX (Taverna et al, Nucleic Acids Res, 2020)
Genome_build: mm10
Supplementary_files_format_and_content: COUNT file with absolute gene count per sample
Supplementary_files_format_and_content: CSV file with matrix of absolute gene counts per sample

source_name: Neural retina

extract_protocol:
Retinas were isolated, snap-frozen in liquid nitrogen and stored at -80°C until use. The snap-frozen neural retinas were first homogenized in Trizol, with subsequent RNA extraction using the PureLink RNA Mini Kit, including on-column DNase treatment.
The sequence libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen), according to the manufacturer’s protocol. Samples were indexed to allow for multiplexing. Library quality and size range were assessed with the DNA 1000 kit (Agilent Technologies), using a Bioanalyzer (Agilent Technologies).

value: Neural retina

tag: age

value: 3w (post natal day 21)


title: GC092443: Retina Mfp2 KO rep 2


title: GC092441: Retina Mfp2 KO rep 1


title: GC092449: Retina control rep 3


title: GC092450: Retina control rep 4


title: GC092446: Retina control rep 1


title: GC092445: Retina Mfp2 KO rep 4


title: pWAT T cells S196A biological replicate 3 technical replicate 2

city: New York

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

data_processing:
Basecalls performed using Illumina software
FastQ files were adapter and base quality trimmed using TrimGalore! v0.6.6 with the --paired flag
Expression quantification was performed using Kallisto v0.46.2 with kallisto quant and the --bias flag to generate the processed data file for each sample
Transcript to gene expression conversion for downstream analysis was performed using a custom Python/Pandas script which sums the raw counts for each transcript into their respective gene count.
Differential Expression analysis: Low expression gene filtering was performed using edgeR v3.2.2 (filterByExpr), library size normalization was performed using edgeR v3.2.2 (calcNormFactors), DGE list was generated for each comparison using edgeR v3.2.2 (exactTest - classic mode)
Genome_build: GRCm38.96
Supplementary_files_format_and_content: A tabular file for each of the samples, measuring transcript expression in raw counts and TPM (*_abundance.tsv)
A matrix file containing expression in raw counts and TPM for all the samples (All_samples_counts_tpm_transcript_level.tsv.gz)

source_name: Perigonadal white adipose tissue

extract_protocol:
Aortas were collected, embedded in OCT and CD68+ cells were collected by laser capture microdissection. Aortas, and pWAT were collected, digested and FBC, FB and T cells were sorted by flow cytometry. pWAT FBC and FB RNA were extracted  using RNeasy micro kit (Qiagen). pWAT T cells, plaque CD68+ and T cells were extracted with PicoPure RNA isolation kit (Thermo Fisher scientific). Clontech SMARTer Stranded Total RNA Seq Kit - Pico Input was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Clontech SMARTer Stranded Total RNA Seq Kit - Pico Input protocols

value: C57Bl6 ; LDLR-/-

value: Perigonadal white adipose tissue

tag: cell type

value: pWAT T cells

tag: experiment design

value: Bone marrow transplant

value: PGK1-CRE; LXRa S196A FL/FL


title: pWAT T cells S196A biological replicate 3 technical replicate 1


title: pWAT T cells S196A biological replicate 2 technical replicate 2


title: GC092448: Retina control rep 2


title: pWAT T cells S196A biological replicate 1 technical replicate 2


title: pWAT T cells S196A biological replicate 2 technical replicate 1


title: pWAT T cells WT biological replicate 3 technical replicate 2

value: PGK1-CRE; LXRa WT FL/FL


title: pWAT T cells S196A biological replicate 1 technical replicate 1


title: pWAT T cells WT biological replicate 3 technical replicate 1


title: pWAT T cells WT biological replicate 1 technical replicate 2


title: pWAT T cells WT biological replicate 2 technical replicate 1


title: T2 MuSCs

city: Créteil

first: Léo

last: Machado

state: Ile-De-France

address: 8 rue du Général Sarrail, Equipe 10 - Inserm U955

country: France

institute: INSERM

description:
SmartSeq2 single-cell RNA-seq time-course
single_cell_muscs_time_course.rds

data_processing:
For bulk RNA-seq: data processing pipeline Sequana version 0.9.19
For 10X genomics: data processing pipeline Cell Ranger version 3.0.2
For Smart-Seq2: data processing pipeline using Star version 2.4.0, cutadapt version 1.11, featureCounts version 1.4.5-p3
Differential expression for bulk RNA-seq using DESeq2 version 1.18.1
Data analysis for Smart-Seq2 using Scater version 1.8.4 and Slingshot version 1.4
Data analysis for 10X genomics using Seurat version 3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Liver_Nuclear_Atlas.rds: R object, processed Seurat object
Supplementary_files_format_and_content: Muscle_Nuclear_Atlas.rds: R object, processed Seurat object
Supplementary_files_format_and_content: single_cell_muscs_time_course.rds: R object, processed SCE object
Supplementary_files_format_and_content: bulk_muscs_time_course.csv: Table, DESeq2 output

source_name: Skeletal muscle stem cells

extract_protocol:
For single-nuclei: Single-cell Gel Bead-In-EMulsions (GEMs) were generated using a Chromium Controller  instrument (10x Genomics).           For bulk RNA-seq : Quick RNA FFPE kit (Zymo, R1008) following instructions (without tissue digestion step)  For smart-seq2 single-cell RNA-seq: Pax7-nGFP cells were sorted single-cell by FACS in 96 well plates (4titude, 4ti-0960). Each well contained 2.5 µl PKD buffer (Qiagen, 1034963)  supplemented with 1:16 proteinase K (Qiagen, 19131). Prior to RNA separation, plates were  decrosslinked for 1 h at 56 °C. RNA separation was performed on a Hamilton STAR  according to the G&T-seq protocol (Macaulay et al., 2015) .
For single-nuclei: Sequencing libraries were prepared using Chromium Single Cell  3’ Reagent Kits (10x Genomics, 1000074), according to the manufacturer’s instructions. For bulk RNA-seq: Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input  Mammalian following the manufacturer’s instructions (Clontech, 635005). for smart-seq2 single-cell: cDNA libraries were generated based on the Smart-seq2 protocol (Picelli et al., 2014).
For single-nuclei: Libraries were then sequenced by pair with a  HighOutput flowcel using an Illumina Nextseq 500 with the following mode: 26 base-pairs  (bp) (10X Index + UMI), 8 bp (i7 Index) and 57 bp (Read 2). For bulk RNA-seq2: Sequencing was performed with the Illumina HiSeq 2500  system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven  indexing cycles, to obtain 65 bp single-end reads. Sequencing data were processed with  Illumina Pipeline software (Casava version 1.9). For smart-seq2 single-cell RNA-seq: 384 single-cell libraries were pooled  together and sequenced single-end 50 bp on a single lane of a HiSeq4000 (Illumina).

treatment_protocol: For muscle injury: Bacl2, for liver injury: Ccl4, for fixation: PFA, for dissociation: collagenase/dispase

tag: tissue treatment

value: Injured

tag: preparation method

value: Single-cell

tag: fixation status

value: Fixed


title: T4 MuSCs


title: H. pseudoburtonii YPD + 1M NaCl 5 min #1

description:
TN1806R0596--AGTCAACA
Hp_5min_1
EXP:KJS14_Nacl_5min_1:FPKM

value: Nuruk

value: WT


title: pWAT T cells WT biological replicate 1 technical replicate 1


title: T0 MuSCs

value: Intact


title: pWAT FB S196A biological replicate 4 technical replicate 2

value: pWAT FB


title: pWAT FB S196A biological replicate 4 technical replicate 1


title: pWAT FB S196A biological replicate 3 technical replicate 2


title: pWAT FB S196A biological replicate 2 technical replicate 2


title: pWAT FB S196A biological replicate 1 technical replicate 2


title: pWAT FB WT biological replicate 4 technical replicate 1


title: pWAT FB WT biological replicate 2 technical replicate 2


title: pWAT FB WT biological replicate 3 technical replicate 1


title: pWAT FB WT biological replicate 2 technical replicate 1


title: pWAT T cells WT biological replicate 2 technical replicate 2


title: pWAT FBC S196A biological replicate 4 technical replicate 1

value: pWAT FBC


title: pWAT FB WT biological replicate 1 technical replicate 1


title: pWAT FB WT biological replicate 1 technical replicate 2


title: pWAT FBC S196A biological replicate 3 technical replicate 2


title: pWAT FBC S196A biological replicate 3 technical replicate 1


title: pWAT FBC S196A biological replicate 2 technical replicate 1


title: pWAT FBC S196A biological replicate 1 technical replicate 2


title: pWAT FBC WT biological replicate 3 technical replicate 2


title: pWAT FBC S196A biological replicate 2 technical replicate 2


title: pWAT FBC WT biological replicate 4 technical replicate 1


title: pWAT FBC WT biological replicate 4 technical replicate 2


title: pWAT FB S196A biological replicate 3 technical replicate 1


title: pWAT FBC WT biological replicate 2 technical replicate 2


title: pWAT FBC WT biological replicate 3 technical replicate 1


title: pWAT FB S196A biological replicate 1 technical replicate 1


title: pWAT FB WT biological replicate 4 technical replicate 2


title: pWAT FB S196A biological replicate 2 technical replicate 1


title: pWAT FBC WT biological replicate 1 technical replicate 1


title: pWAT FBC WT biological replicate 1 technical replicate 2


title: Plaque T cells S196A biological replicate 3 technical replicate 2

source_name: Atherosclerotic plaque

value: Atherosclerotic plaque

value: Plaque T cells


title: pWAT FBC WT biological replicate 2 technical replicate 1


title: Plaque T cells S196A biological replicate 2 technical replicate 2


title: pWAT FBC S196A biological replicate 4 technical replicate 2


title: Plaque T cells S196A biological replicate 2 technical replicate 1


title: Plaque T cells WT biological replicate 3 technical replicate 2


title: Plaque T cells WT biological replicate 2 technical replicate 1


title: Plaque T cells WT biological replicate 2 technical replicate 2


title: Plaque T cells S196A biological replicate 1 technical replicate 1


title: Plaque T cells S196A biological replicate 1 technical replicate 2


title: pWAT FBC S196A biological replicate 1 technical replicate 1


title: Plaque T cells WT biological replicate 1 technical replicate 1


title: pWAT FB WT biological replicate 3 technical replicate 2


title: CAA-3

city: Bloemfontein

first: Carolina

middle: H

last: Pohl

state: Free State

address: 205 Nelson Mandela avenue, Park West

department: Department of Microbial, Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

description:
processed data file:
Supplementary Table S2

data_processing:
Base calling by Illumina Nextseq 500 RTA v2
fastq files (150 bp; paired-end) were analysed for quality by FastQC (v0.11.5; Andrews, 2010)
low-quality reads and bases were discarded using PRINSEQ-lite (v0.20.4; Schmieder & Edwards, 2011) with -min_len 20 -ns_max_n 0 -min_qual_mean 20 -trim_qual_right 30 -trim_qual_type min -trim_qual_rule lt -trim_qual_window 5 -trim_qual_step 3
Alignment to Candida albicans SC5314 genome (assembly 21; The Candida Genome Database; Skrzypek et al., 2017) using TopHat2 fr-secondstrand (Dutton et al., 2016)
BAM files sorted and indexed with SAMtools (Li et al., 2009)
Gene expression count tables created with BEDTools multicov command (Quinlan et al., 2010)
Differential expression analysis done with DESeq2 (Love et al., 2014)
Genome_build: Candida albicans SC5314 genome (assembly 21; The Candida Genome Database; Skrzypek et al., 2017)
Supplementary_files_format_and_content: xlsx file containing assembly 21 identifier, systematic name, log2fold change and padj value. In addition, normalised gene counts are given. Data is filtered according to padj value (padj < 0,05) in sheet2 and log2fold change <-1 and >1 in sheet 3

organism: Candida albicans

source_name: In vitro single species biofilm

growth_protocol: 24 h cultures (Yeast nitrogen base for C. albicans @ 30°C; Luria-Bertani for P. aeruginosa @ 37°C) were washed with phosphate buffered saline (3X) and diluted (1x10^6 cells/mL for C. albicans; OD600 of 0,05 for P. aeruginosa) in 20 mL sterile RPMI-1640 medium and incubated for 6 hours @ 37°C.

extract_protocol:
Supernatant was removed and cells were scraped off and suspended in RNAlater. Samples were stored @ -80°C until extraction. Total RNA was extracted using Rneasy protect Mini kit (Qiagen) and quality control was done using NanoDrop ND1000, Qubit RNA HS Assay Kit and Agilent Bioanalyzer XP Kit. A total of 1 µg RNA was treated with Illumina Ribo-Zero rRNA removal kit to remove rRNA
indexed libraries were prepared using the ScriptSeqTM v2 RNA-Seq Library Preparation Kit and ScriptSeqTM Index PCR Primers – Set 1 (Illumina). The sizes of the libraries were profiled with the Bioanalyzer High Sensitivity Assay Kit (Agilent) and quantified (Qubit HS DNA Assay Kit). Samples were diluted and a 1 % Phix control library (Illumina) was spiked into samples. Sequencing was completed on the Nextseq 500 (Illumina) using Nextseq 500 High Output (150 cycle) Kits which yielded paired-end reads

treatment_protocol: 100 µM arachidonic acid or equivalent ethanol control (0,076 % ethanol) were added to RPMI-1640 medium with cells prior to incubation

tag: constituants

value: yeast

tag: strains

value: C. albicans + 100 µM arachidonic acid

tag: amount of biofilms pooled per sample

value: 5 X 20 mL petri dish (90 mm)

tag: biofilm age

value: 6 hours


title: CAA-2


title: D21_Control_3

city: Oxford

first: Shoumo

last: Bhattacharya

address: Roosevelt Drive

department: RDM Cardiovascular Medicine

country: United Kingdom

institute: Wellcome Centre For Human Genetics, University of Oxford

data_processing:
Basecalling was performed directly on the HiSeq 4000 run and bclToFastq v2.20.0 was used to generate fastq files
Reads were trimmed for adapter sequence using skewer
Reads were mapped to mouse reference genome using HISAT2 v2.0.4
Duplicate reads were removed using Picard tools
Counts for individual Ensembl gene features were summarised using featureCounts (multi-mapping reads excluded)
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file of gene counts

source_name: Murine Heart

extract_protocol:
RNA from mouse hearts was extracted using RNeasy Mini Kit (Qiagen, Cat#74104) following the manufacturer’s instructions..
Purification of mRNA, generation of double stranded cDNA and library construction were performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with minor modifications to manufacturer specifications

treatment_protocol: EAM mice were immunized on day 0 and day 7 by injection of 200 μl SCFA+peptide/PBS emulsion (100 μg peptide) + PTX on day 0. Control mice received 200ul of SCFA+PBS on D0 and D7 + PTX on day 0.

tag: strain

value: Balb/c

value: wild type

value: Control

tag: time

value: Day 21

tag: tissue

value: Heart


title: D21_Control_4


title: D21_Myocarditis_4

value: EAM


title: D21_Myocarditis_2


title: Plaque T cells S196A biological replicate 3 technical replicate 1

value: C57Bl6 ; LDLR-/-

value: Bone marrow transplant

value: PGK1-CRE; LXRa S196A FL/FL


title: CET-3

description:
processed data file:
Supplementary Table S1
Supplementary Table S2

value: C. albicans + 0,076 % ethanol


title: CAA-1


title: D21_Myocarditis_1


title: D21_Control_1


title: D15_Myocarditis_4

value: Day 15


title: CET-2


title: D21_Control_2


title: Plaque T cells WT biological replicate 3 technical replicate 1

value: Atherosclerotic plaque

value: PGK1-CRE; LXRa WT FL/FL


title: Plaque T cells WT biological replicate 1 technical replicate 2

value: Plaque T cells


title: D15_Myocarditis_2


title: D21_Myocarditis_3


title: D15_Myocarditis_1


title: M0 strain vs Tn38 strain Replicate 1

type: RNA

city: Marseille cedex 20

first: Gauthier

last: Dangla-Pélissier

state: PACA

address: 31 chemin Joseph Aiguier

department: IMM

institute: CNRS

description: Biological replicate 1 of 2. PAPI-1 induced transference vs Control strain

hyb_protocol: 300 ng of Cy3-labelled and of Cy-5 labelled cDNA mixtures were hybridized for 17 hr at 65°C according to Agilent protocols on the MGPA DNA Chips.

scan_protocol: DNA-Chip were scanned by Axon 4500 fluorescence reader. Fluorescence intensity were then extracted by the Genepix software after global fluorescence intensity normalisation.

data_processing: Data were further treated with R (http://cran.r-project.org/) using LIMMA package from Bioconductor (http://www.bioconductor.org/). Intra-array normalization has been performed using local Lowess (Loess) regression method with “Normexp” background noise correction, whereas inter–array normalization has been performed using a quantile method. Genes differentially expressed have been extracted using LIMMA package using linear regression (lmFit), Bayesian models (eBayes) and Benjamini-Hochberg multiple-test correction (BH). We considered significant in the different replicates for a p-value<0.05. .

organism: Pseudomonas aeruginosa

source_name: M0 strain replicate 1

label_protocol: 500 ng of RNA were further processed for double Cy3/Cy5 labelling using the ChipShot Direct Labeling and Clean-Up System kits (Promega). Briefly, 500 ng of RNA was first hybridized with hexameric primers. Then dNTPs (330 nM each) were added together with 1 mM of Cy3 or Cy5 (Amersham) and 200 units of ChipShot Reverse transcriptase. The mixture was incubated 2 h at 42°C and the reaction stopped by a 15 min incubation at 37°C with RNAse. Unincorporated nucleotides were removed by using the Chip-Shot Direct Labeling and Clean-Up System (Promega). Dye incorporation rates were measured using a Nanodrop® ND-1000 spectrophotometer (Nanodrop technologies Wilmington, DE).

growth_protocol: The bacteria were grown under agitation at 37°C

extract_protocol: The samples were quickly processed to prepare RNA using the PureYield RNA Midiprep System (Promega), cleaned up and concentrated using the RNeasy Micro Kit (Qiagen). Yield, purity and integrity of RNA were checked by the Experion automated electrophoresis system (Bio-Rad) and the absence of DNA contamination was verified by PCR.

treatment_protocol: The bacteria were harvested during the beginning of the stationary phase (7 h; 3.4 unit of OD600), by centrifugation at 4°C.

tag: genetic background

tag: growth

value: 7 h of growth in LB medium

source_name: Tn38 strain replicate 1


title: D15_Control_3

tag: genotype

tag: treatment


title: M0 strain vs Tn38 strain Replicate 2

description: Biological replicate 2 of 2. PAPI-1 induced transference vs Control strain

source_name: M0 strain replicate 2

source_name: Tn38 strain replicate 2


title: D15_Control_1


title: CET-1

value: yeast

value: 5 X 20 mL petri dish (90 mm)


title: Agelaia_Worker

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

data_processing:
Trinity used to assemble a de novo transcriptome
RSEM used to calculate normalised gene counts per Trinity transcript
Supplementary_files_format_and_content: Trinity fasta transcriptome files (.fnn) and tab-delimited RSEM files for each queen/worker which include TPM/FPKM and expected count for each sample.

organism: Agelaia cajennensis

source_name: Whole brain

extract_protocol:
All wasps were collected directly from their nests during the daytime, placed immediately into RNAlater (Ambion, Invitrogen) and stored at -20°C until further use. Total RNA was extracted using the RNeasy Universal Plus Mini kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: caste

value: Worker

value: whole brain


title: D10_Myocarditis_4

value: Balb/c

value: wild type

value: Day 10


title: D10_Myocarditis_3

value: EAM

value: Heart


title: D15_Myocarditis_3


title: Queen2_PaccQ2

organism: Polybia quadricincta

value: Queen


title: Agelaia_Queen


title: D10_Control_4

value: Control


title: Metapolybia_Queen

organism: Metapolybia cingulata


title: D10_Control_3


title: D10_Control_2


title: Metapolybia_Worker


title: HSISS4 CovR D53E RNAseq

city: Louvain-La-Neuve

first: Adrien

last: Knoops

address: Croix du sud 4-5, bte L7.07.06

department: LIBST

institute: UCLouvain

data_processing:
Sequenced mRNAs or smRNAs generated several millions reads that were mapped on the WT S. salivarius chromosome and processed on the galaxy server (use.galaxy.org) using Bowtie2 algorithm to yield BAM files containing the read coordinates and Featurecount to count the number of reads per coding sequence (CDS). The dataset was exported into an excel file for further analyses. First, the dataset was standardized to CDS-mapped reads per million overall reads. Then, we estimated a ratio of CDS-mapped reads in mutants vs WT.
Genome_build: Streptococcus salivarius HSISS4: CP013216
Supplementary_files_format_and_content: the xls files reporting RNAseq were generated via the galaxy server (use.galaxy.org).The sheet is organized in columns as follows:
Supplementary_files_format_and_content: column 1 : product accession of gene associated
Supplementary_files_format_and_content: column 2 : locus tag of gene
Supplementary_files_format_and_content: column 3 : position of gene start
Supplementary_files_format_and_content: column 4 : position of gene end
Supplementary_files_format_and_content: column 5 : strand orientation
Supplementary_files_format_and_content: column 6 : product length of protein associated
Supplementary_files_format_and_content: column 7 : Symbol of gene
Supplementary_files_format_and_content: column 8 : Name of gene
Supplementary_files_format_and_content: column 9 : COG assignation function
Supplementary_files_format_and_content: column 10 : Gene previously described as belonging to the ComR regulon (Mignolet, 2018)
Supplementary_files_format_and_content: column 11 : Gene previously described as belonging to the ComX regulon (Mignolet, 2018)
Supplementary_files_format_and_content: column 12 : Total number of reads for WT
Supplementary_files_format_and_content: column 13 : Total number of reads for T287A
Supplementary_files_format_and_content: column 14 : Total number of reads for D53E
Supplementary_files_format_and_content: column 15 : Normalized number of reads for WT
Supplementary_files_format_and_content: column 16 : Normalized number of reads for T287A
Supplementary_files_format_and_content: column 17 : Normalized number of reads for D53E
Supplementary_files_format_and_content: column 18 : Ratio of normalized abundance of reads per CDS in T287A mutant versus WT background
Supplementary_files_format_and_content: column 19 :  Ratio of normalized abundance of reads per CDS in D53E mutant versus WT background

organism: Streptococcus salivarius

source_name: Streptococcus salivarius HSISS4 CovR D53E

growth_protocol: Streptococcus salivarius and derivatives were grown at 37°C in chemically defined medium supplemented with glucose (CDMG) without shaking

extract_protocol: [Library construction details not provided]

value: CovR D53E

tag: medium

value: CDM+glucose


title: M0 strain vs M0∆tprA strain Replicate 2

description: Biological replicate 2 of 3. PAPI-1 induced transference vs PAPI-1 inactivated transference strain.

hyb_protocol: 300 ng of Cy3-labelled and of Cy-5 labelled cDNA mixtures were hybridized for 17 h at 65°C according to Agilent protocols on the MGPA DNA Chips.

source_name: M0-59060-stop strain replicate 2


title: D10_Myocarditis_1


title: M0 strain vs M0∆tprA strain Replicate 3

description: Biological replicate 3 of 3. PAPI-1 induced transference vs PAPI-1 inactivated transference strain.

source_name: M0 strain replicate 3


title: M0 strain vs M0∆tprA strain Replicate 1

description: Biological replicate 1 of 3. PAPI-1 induced transference vs PAPI-1 inactivated transference strain.

source_name: M0-59060-stop strain replicate 1


title: D10_Control_1


title: D15_Control_4

value: Day 15


title: HSISS4 CovR T287A RNAseq

source_name: Streptococcus salivarius HSISS4 CovR T287A

value: CovR T287A


title: HSISS4 CovR WT RNAseq

source_name: Streptococcus salivarius HSISS4 CovR WT

value: CovR WT


title: CD31_EC_LT

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

data_processing:
Base calling: Basecalling was carried out with Illlumina RTA software, version 2.4.11 or 2.7.7
Base calling, demultiplexing: Demultiplexing was carried out with Illlumina Bcl2fastq software, version 2.20.0
Sequence alignment: Sequence alignment was performed with CellRanger version 2.0.1.
Expression matrix generation: Expression matrix was generated with CellRanger version 2.0.1. and subdivided by sample using Seurat3
Genome_build: mm10
Supplementary_files_format_and_content: filtered_gene_bc_matrices.tar.gz: CellRanger Out folder with aggregated and normaliised data from all samples
Supplementary_files_format_and_content: UMIcounts.Rdata: Rdata file of sparse matrix with UMI counts for single cells from all samples
Supplementary_files_format_and_content: UMIcountNT.Rdata: Rdata file of sparse matrix with UMI counts for single cells from naïve mammary gland (no tumour) sample
Supplementary_files_format_and_content: UMIcountsST.Rdata: Rdata file of sparse matrix with UMI counts for single cells from small tumour sample
Supplementary_files_format_and_content: UMIcountsLT.Rdata: Rdata file of sparse matrix with UMI counts for single cells from large tumour sample

source_name: Mammary gland

extract_protocol:
Cells were dirtectly FACS sorted into 0.04% BSA in PBS
Chromium Single Cell 3' Reagent Kit (v3 Chemistry) was used in order to generate  indexed 3ʹ Gene Expression libraries

tag: age

value: 8-12 weeks old

tag: Stage

value: Large EO771 mammary tumour


title: D15_Control_2


title: CD31_EC_ST

value: Small EO771 mammary tumour


title: CD31_EC_NT

value: Naïve mammary gland


title: Worker1_PaccW1

value: Worker

value: whole brain


title: D10_Myocarditis_2

value: Balb/c

value: wild type


title: Sorted GFP negative cells from MPNST_E

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Short reads were aligned using STAR 2.4.2.8 by default setting
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: MPNST tumor cells

extract_protocol:
Fresh allograft MPNST were dissociated using gentleMACS Octo Dissociator (Miltenyi Biotec) with 1g/ml collagenase. Wildtype cell and dead cells were removed by FACS gating. GFP+ and GFP- cells were collected into L15 media and total RNA were extracted by Qiagen RNeasy extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Sorted MPNST tumor cells

tag: cell population

value: GFP-


title: Sorted GFP positive cells from MPNST_D

value: GFP+


title: Sorted GFP negative cells from MPNST_D


title: p53 ChIP, mES, Nutlin

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

data_processing:
Base calling: RTA 1.12.4.2 and sequencing chemistry: Illumina TruSeq 3.0. All raw files were generated using this method.
Alignment: Illumina Casava 1.8.2. All processed data files were generated using this method.
Processed files are peak files. Peak calling was performed using MACS (version 1.4.1 2011_06_27; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05)
Genome_build: mm9

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Life Technologies)

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
NEB ChIP-seq prep kit

treatment_protocol: Cells were treated with 20 mM Nutlin for 8 hours.

tag: sample type

value: cell culture

tag: passages

value: less than 20

value: C57BL/6X129Sv mix

tag: antibody

tag: antibody vendor/catalog/lot

value: Santa Cruz/sc-1312/K1907


title: Input, mES, Nutlin

tag: strain


title: Sorted GFP positive cells from MPNST_E


title: Sorted GFP negative cells from MPNST_C


title: Sorted GFP positive cells from MPNST_B


title: Sorted GFP positive cells from MPNST_C


title: Sorted GFP positive cells from MPNST_A


title: Sorted GFP negative cells from MPNST_B


title: SAMPLE 8_control

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent G5761A Scanner

data_processing: Genespring 14.9, Normalization: Shift to 75 percentile

label_protocol: Agilent low-Input QuickAmp Labeling Kit

extract_protocol: Trizol for RNA isolation

value: fibroblast

value: transfected with control oligonucleotides


title: Sorted GFP negative cells from MPNST_A


title: SAMPLE 7_miR-127-3p

value: transfected with miR-127-3p mimic oligonucleotides


title: SAMPLE 3_control

value: transfected with control or miR-127-3p mimic oligonucleotides


title: Lac vs. reference stationary phase_3

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1.

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconductor – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Clostridioides difficile 630

source_name: Clostridioides difficile 630∆erm at stationary phase grown in casamino acids medium supplemented with 0.5 g/L L-lactate

label_protocol: RNA samples were labelled with Cy3 (L-lactate supplementation) and Cy5 (no supplementation) using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: The C. difficile 630∆erm strain (DSM28645) (Hussain, HA, 2005) obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany) was grown anaerobically at 37 °C in a defined medium containing 10 g/L casamino acids (Cartman and Minton, 2010; Neumann-Schaal et al. 2015) and supplemented with 0.5 g/L L-lactate.

extract_protocol: Bacterial RNA was extracted using the Qiagen RNeasy Kit Mini (Qiagen, Hilden, Germany) according to manufacturer’s instructions with minor modifications. Briefly, pellets from a 45 mL culture were resolved in 200 µl TE buffer and 15 mg/ml lysozyme, incubated for 30 min at room temperature and vigorously mixed every 2 min for 10 sec for enzymatically disruption of cells. Approximately 700 µL of RLT buffer and one spatula of glass beads were added and mixed vigorously for 3 min for mechanical disruption of cells. Samples were centrifuged (3 min, 10.000 rpm) and supernatant was mixed with 470 µL of 100% ethanol. Afterwards, RNA purification was carried out using the Qiagen RNeasy Kit protocol. DNA contaminating the RNA samples was removed using RNase-free DNase I twice (Qiagen, Hilden, Germany). The RNA was further assessed by analysis on the Bioanalyzer 2100 (Agilent, Santa Clara, CA) and RNA 6000 Nano Reagents (Agilent, Santa Clara, CA). According to the amount of RNA extracted and its quality (RINs>8), the best samples per time point were used for transcriptomic analysis.

treatment_protocol: Samples were taken in the exponential growth (at 1/2 ODmax) and at the beginning of the stationary phase (ODmax).

tag: genotype/variation

value: <delta>erm

tag: supplementation

value: 0.5 g/L L-lactate

tag: growth phase

value: Stationary

source_name: Clostridioides difficile 630∆erm at stationary phase grown in casamino acids medium (reference)


title: Lac vs. reference stationary phase_1


title: Lac vs. reference stationary phase_4


title: SAMPLE 1_control


title: SAMPLE 4_miR-127-3p


title: SAMPLE 2_miR-127-3p


title: SAMPLE 6_control


title: Lac vs. reference exponential phase_2

source_name: Clostridioides difficile 630∆erm at exponential phase grown in casamino acids medium supplemented with 0.5 g/L L-lactate

value: Exponential

source_name: Clostridioides difficile 630∆erm at exponential phase grown in casamino acids medium (reference)


title: Lac vs. reference stationary phase_2


title: SAMPLE 5_miR-127-3p


title: Lac vs. reference exponential phase_3


title: Lac vs. reference exponential phase_4


title: Lac vs. reference exponential phase_1


title: STRAIN_MMTV_Neu_2T3_GRUBBS

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Untreated MMTV-Neu+/- tumor RNA versus whole mouse reference RNA

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Whole Mouse Reference RNA-2009

growth_protocol: described in He et al., 2004. BioTechniques, Vol. 37:464-468

extract_protocol: Qiagen Rneasy Kit

tag: reference

value: Whole Mouse Reference

label: Qiagen Rneasy Kit

source_name: Untreated MMTV-Neu+/- tumor RNA

extract_protocol: total RNA

tag: tumor

value: Mouse tumor derived RNA

value: MMTV-Neu+/-


title: STRAIN_MMTV_Neu_p53het_1T3_GRUBBS

description: Untreated MMTV-Neu+/- TP53+/- tumor RNA versus whole mouse reference RNA

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

treatment_protocol: described in He et al., 2004. BioTechniques, Vol. 37:464-468

source_name: Untreated MMTV-Neu+/- TP53+/- tumor RNA

value: MMTV-Neu+/- TP53+/-


title: STRAIN_MMTV_Neu_p53het_15T4_GRUBBS

growth_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: STRAIN_MMTV_Neu_9T3_GRUBBS

treatment_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: STRAIN_MMTV_Neu_p53het_1T1_GRUBBS


title: STRAIN_MMTV_Neu_4T2_GRUBBS


title: STRAIN_MMTV_Neu_13T1_GRUBBS


title: STRAIN_MMTV_Neu_p53het_6T2_GRUBBS


title: STRAIN_MMTV_Neu_15T1_GRUBBS


title: STRAIN_MMTV_Neu_p53het_24T1_GRUBBS


title: STRAIN_MMTV_Neu_12T1_GRUBBS


title: MMTV_ErbB2_Project-0131_4-T5_Grubbs

description: DMBA treated MMTV-Neu+/- tumor RNA versus whole mouse reference RNA

source_name: DMBA treated MMTV-Neu+/- tumor RNA


title: MMTV_ErbB2_Project-0131_9-T2_Grubbs


title: Cultured bovine granulosa cells under control conditions rep 1

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

description: C1_(BovGene-1_0-st).rma-gene-full-Signal

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the Expression Console (Version V1.3.1.187, Affymetrix) using the RMA method for normalization. Further comparative analysis was done with the Transcriptome Analysis Console 3.0 (Affymetrix).

label: Biotin

organism: Bos taurus

source_name: Cultured bovine granulosa cells, control conditions

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

extract_protocol: Total RNA was isolated with the Nucleo Spin® RNA II Kit according to the manufacturer’s instructions and quantified with a NanoDrop1000 Spectrophotometer (Thermo Scientific, Bonn, Germany). The cDNA was prepared by using the SensiFAST cDNA Synthesis Kit from 200ng RNA as per the manufacturer's protocol.

treatment_protocol: Bovine ovaries were collected from slaughter house material. Granulosa cells were collected from small to medium follicles (2-6mm diameter) with a syringe with an 18 gauge needle in PBS that contained antibiotics. Routinely, 1.25x10e5 viable cells were seeded on 24-well collagen R coated plates in basal α-MEM supplemented with 25ng/ml IGF-I, 20 ng/ml FSH and 2 μM androstenedione. Conditioned media were replaced with fresh media including all respective supplements every other day. Oleic acid (400μM) was added with the first change of media (i.e. after 2 days in culture).

value: Cultured bovine ovarian granulosa cells

tag: gender

value: Female

tag: treatment

value: Control


title: T60 MuSCs [Bulk]

description:
Bulk RNA-seq time-course
bulk_muscs_time_course.csv

source_name: Skeletal muscle stem cells

tag: tissue treatment

value: Dissociated

tag: preparation method

value: Bulk

tag: fixation status

value: Fixed


title: MMTV_ErbB2_Project-0131_17-T7_Grubbs


title: T90 MuSCs [Bulk]


title: Cultured bovine granulosa cells under control conditions rep 2

description: C2_(BovGene-1_0-st).rma-gene-full-Signal

tag: cell type


title: T120 MuSCs [Bulk]


title: T30 MuSCs [Bulk]


title: Cultured bovine granulosa cells treated with oleic acid rep 4

description: OA4_(BovGene-1_0-st).rma-gene-full-Signal

source_name: Cultured bovine granulosa cells, oleic acid treated

value: Oleic acid


title: TaDaG2-MRG15_n2

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

data_processing:
Library strategy: DamID-seq
FASTQ files were processed using damidseq_pipeline, default options.
Peaks were called on the averaged binding track via a three-state hidden markov model using hmm.peak.caller (https://github.com/owenjm/hmm.peak.caller)
Genome_build: DmBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised log2(Dam-fusion/Dam) enrichment.  MRG15 bound peaks are provided in GFF format. The files MRG15-vs-Dam.average.gatc.bedgraph and MRG15-vs-Dam.peaks.gff include data from all samples.

organism: Drosophila melanogaster

source_name: dissected 3rd instar larval brain

extract_protocol:
Larval brains were dissected in PBS, and processed for DamID-seq as previously described (Marshall et al., 2016; Marshall and Brand, 2017) with the following modifications. Briefly, DNA was extracted using a Quick-DNA Miniprep plus kit (Zymo), digested with DpnI (NEB) overnight and cleaned-up with a PCR purification kit (Machery-Nagel), DamID adaptors were ligated, digested with DpnII (NEB) for 2 hours, and amplified via PCR using MyTaq DNA polymerase (Bioline).
2 µg DNA was sonicated in a Bioruptor Plus (Diagenode). DamID adaptors were removed by AlwI digestion, and 500 ng of the resulting fragments end-repaired with a mix of enzymes (T4 DNA ligase (NEB) + Klenow Fragment (NEB) + T4 polynucleotide kinase (NEB)), A-tailed with Klenow 3’ to 5’ exo- (NEB), ligated to Illumina Truseq LT adaptors using Quick Ligase enzyme (NEB) and amplified via PCR with NEBNext Hi-fidelity enzyme (NEB).

tag: tissue

value: brain

tag: developmental stage

value: 3rd instar larvae

tag: construct


title: Cultured bovine granulosa cells under control conditions rep 4

description: C4_(BovGene-1_0-st).rma-gene-full-Signal


title: Cultured bovine granulosa cells treated with oleic acid rep 2

description: OA2_(BovGene-1_0-st).rma-gene-full-Signal


title: Cultured bovine granulosa cells treated with oleic acid rep 3

description: OA3_(BovGene-1_0-st).rma-gene-full-Signal


title: TaDaG2-MRG15_n1


title: MMTV_ErbB2_Project-0131_15-T1_Grubbs


title: Cultured bovine granulosa cells treated with oleic acid rep 1

description: OA1_(BovGene-1_0-st).rma-gene-full-Signal


title: T15 MuSCs [Bulk]


title: Cultured bovine granulosa cells under control conditions rep 3

description: C3_(BovGene-1_0-st).rma-gene-full-Signal


title: MMTV_ErbB2_p53_Project-5811_9-T3_Grubbs

description: DMBA-treated MMTV-Neu+/- TP53+/- tumor RNA versus whole mouse reference RNA


title: Spheroid ring, technical rep 1

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description:
Gene expression data from cornified-like, spheroid-derived  keratinocyte ring
71-1_(HuGene-2_0-st).rma-gene-full-Signal

hyb_protocol: Amplified and labeled samples were hybridized to GeneChip HuGene 2.0 ST Arrays (Affymetrix) for 16 h at 45°C using a GeneChip Hybridization Oven 640 and a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).  Hybridized arrays were washed and stained using GeneChip Fluidics Stations 450 (Affymetrix).

scan_protocol: Arrays were then scanned using a GeneChip Scanner 3000 7G system and computer workstation equipped with GeneChip Command Console 4.0 software (Affymetrix).

data_processing: Following completion of array scans, probe cell intensity (CEL) files were imported into Expression Console Software (Affymetrix) and processed at the gene-level using Affymetrix’s HuGene-2_0-st library file and Robust Multichip Analysis (RMA) algorithm to generate CHP files. After confirming data quality within Expression Console, CHP files containing log2 expression signals for each probe were then imported into Transcriptome Analysis Console Software version 3.0.0.466 (Affymetrix) to analyze cell type specific transcriptional responses using one-way between-subject analysis of variance.

label: biotin

organism: Homo sapiens

source_name: Neonatal human foreskin epidermis

label_protocol: Microarray experiments were performed using Affymetrix’s platform. Total RNA samples were amplified and biotinylated using GeneChip WT PLUS Reagent Kit (Affymetrix), according to the manufacturer’s protocol.

growth_protocol: Primary normal human keratinocytes (NHKc) were isolated from neonatal foreskin and cultured in keratinocyte serum-free medium (KSFM) supplemented with 20 ng/mL EGF, 10 ng/mL FGF, 0.4% bovine serum albumin, and 4μg/mL insulin. NHKc were seeded into a 96-well round-bottom plate coated with a polymerized mixture of agarose (0.05%) using the same media. The formed spheroids were maintained for at least 24 h in suspension prior to harvest. Multicellular suspension spheroids were subsequently plated into 2-D monolayer culture until they formed cornified-like rings. Same media was also used in this last step.

extract_protocol: Total RNA was isolated from cells using the All Prep DNA/RNA Mini Kit (QIAGEN) according to the manufacturer’s protocol. RNA quality was assessed using an Agilent 2100 Bioanalyzer. RNA integrity numbers (RIN) ranged from 9.0 to 9.1.

treatment_protocol: Multicellular normal human keratinocyte suspension spheroid culturess were plated into uncoated 2-D polystyrene monolayer cell culture dishes and fed KSFM-sc every 2 days until all cells proliferated out of the spheroid and a cornified-like spheroid-ring formed. Corresponding mass cultured kerationcytes were maintained in KSFM-sc until later needed for experimentation.

value: neonatal foreskin epidermis

value: Spheroid-derived adherent human keratinocytes


title: Mass culture, technical rep 1

description:
Gene expression data from normal keratinocyte mass culture
69-1_(HuGene-2_0-st).rma-gene-full-Signal

value: Primary Normal human keratinocytes


title: Mass culture, technical rep 2

description:
Gene expression data from normal keratinocyte mass culture
69-2_(HuGene-2_0-st).rma-gene-full-Signal


title: Spheroid ring, technical rep 2

description:
Gene expression data from cornified-like, spheroid-derived  keratinocyte ring
71-2_(HuGene-2_0-st).rma-gene-full-Signal


title: Spheroid ring, technical rep 3

description:
Gene expression data from cornified-like, spheroid-derived  keratinocyte ring
71-3_(HuGene-2_0-st).rma-gene-full-Signal


title: T0 MuSCs [Bulk]

value: Intact


title: Mass culture, technical rep 3

description:
Gene expression data from normal keratinocyte mass culture
69-3_(HuGene-2_0-st).rma-gene-full-Signal


title: MMTV_ErbB2_p53_Project-0131_10-T11_Grubbs

value: Whole Mouse Reference

source_name: DMBA-treated MMTV-Neu+/- TP53+/- tumor RNA

extract_protocol: Total RNA


title: MMTV_ErbB2_p53_Project-5811_3-T2_Grubbs

value: Mouse tumor derived RNA


title: MMTV_ErbB2_Project-0131_4-T4_Grubbs

description: DMBA treated MMTV-Neu+/- tumor RNA versus whole mouse reference RNA

value: MMTV-Neu+/-


title: TaDaG2-Dam_n2


title: Control rep2

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1)
Remaining reads were further filtered for low complexity with reaper (v. 15-065)
Reads were aligned to the Drosophila melanogaster.BDGP6.92 genome using STAR (v. 2.5.3a)
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1)
Genome_build: Drosophila melanogaster Ensembl release 92, BDGP6
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package

source_name: Antenna

growth_protocol: Flies were maintained at 25ºC in 12 h light:12 h dark conditions, except where noted. D. melanogaster strains were maintained on a standard wheat flour-yeast-  fruit-juice medium.

extract_protocol:
The antennae from 2-5 day old flies were harvested via snap-freezing in a mini-sieve. Total RNA was extracted using a standard TRIzol/chloroform protocol.
From 100 ng total RNA, mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module. RNA-seq libraries were then prepared from the mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: For each pair of biological replicates, 350 females control (peb-Gal4,UAS-Dcr2/+;UAS-E93KK108140/+) and E93RNAi (peb-Gal4,UAS-Dcr2/+;VIE-260B/+) were grown under identical conditions.

value: Antenna

value: No


title: E93RNAi rep1

value: Yes


title: E93RNAi rep2


title: Plaque CD68+ WT biological replicate 2

first: Michael

last: Garabedian

institute: NYU School of Medicine

data_processing:
Basecalls performed using Illumina software
FastQ files were adapter and base quality trimmed using TrimGalore! v0.6.6 with the --paired flag
Expression quantification was performed using Kallisto v0.46.2 with kallisto quant and the --bias flag to generate the processed data file for each sample
Transcript to gene expression conversion for downstream analysis was performed using a custom Python/Pandas script which sums the raw counts for each transcript into their respective gene count.
Differential Expression analysis: Low expression gene filtering was performed using edgeR v3.2.2 (filterByExpr), library size normalization was performed using edgeR v3.2.2 (calcNormFactors), DGE list was generated for each comparison using edgeR v3.2.2 (exactTest - classic mode)
Genome_build: GRCm38.96
Supplementary_files_format_and_content: A tabular file for each of the samples, measuring transcript expression in raw counts and TPM (*_abundance.tsv)
A matrix file containing expression in raw counts and TPM for all the samples (All_samples_counts_tpm_transcript_level.tsv.gz)

source_name: Atherosclerotic plaque

extract_protocol:
Aortas were collected, embedded in OCT and CD68+ cells were collected by laser capture microdissection. Aortas, and pWAT were collected, digested and FBC, FB and T cells were sorted by flow cytometry. pWAT FBC and FB RNA were extracted  using RNeasy micro kit (Qiagen). pWAT T cells, plaque CD68+ and T cells were extracted with PicoPure RNA isolation kit (Thermo Fisher scientific). Clontech SMARTer Stranded Total RNA Seq Kit - Pico Input was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Clontech SMARTer Stranded Total RNA Seq Kit - Pico Input protocols

value: C57Bl6 ; LDLR-/-

value: Atherosclerotic plaque

value: Plaque CD68+

tag: experiment design

value: Bone marrow transplant

tag: genotype

value: PGK1-CRE; LXRa WT FL/FL


title: Plaque CD68+ WT biological replicate 1

tag: strain


title: C1_Kidney_Saline

city: Birmingham

first: Colin

middle: Robert

last: Reily

state: Alabama

department: Medicine

institute: University of Alabama at Birmingham

description: Control

data_processing:
Mapping sequence reads to the mouse reference genome using CLC genomics workbench
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Gene expression between specified groups was performed using DESeq2
Mus musculus GRCm38 reference genome used via ENSEMBL, using the STAR aligner v.2.5.2b.
Genome_build: GRCm38

source_name: Kidney

extract_protocol:
Half a kidney was harvest in RNAlater, and stored at -80C. Samples were shipped to GeneWhiz for RNA extraction and RNA-Seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tail vein i.v. of saline or immune complexes were administered 3 times over a 7 day period.

tag: Sex

value: female

value: Kidney

value: Saline


title: Control rep3


title: Plaque CD68+ S196A biological replicate 2

value: PGK1-CRE; LXRa S196A FL/FL


title: CIC1_Kidney_Immune Complex

description: Disease

value: Immune Complex


title: CIC2_Kidney_Immune Complex

description: Disease


title: C2_Kidney_Saline

description: Control


title: E93RNAi rep3


title: Control rep1


title: Mouse peritoneal macrophage infected with L.donovani parasites (A2 passage)

city: Kolkata

first: Nahid

last: Ali

state: West Bengal

address: 4, Raja Subodh Chandra Mallick Rd, Poddar Nagar, Jadavpur,

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
The generated data was aligned to the ucsc_mm10 and TriTrypDB-28_LdonovaniBPK282A1 genome using TopHat, Subread-featurecounts and edgeR.
Genome_build: ucsc_mm10, TriTrypDB-28_LdonovaniBPK282A1

source_name: Mouse peritoneal macrophage infected with L. donovani parasites (A2 passage)

extract_protocol:
Using the standard Trizol Method
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophage


title: Mouse peritoneal macrophage infected with L.donovani parasites (A25 passage)

source_name: Mouse peritoneal macrophage infected with L. donovani parasites (A25 passage)


title: Control Mouse peritoneal macrophage

source_name: Control Mouse peritoneal macrophage


title: liver_chow_wk12_m42

city: Lübeck

first: Henriette

last: Kirchner

address: Ratzeburger Allee 160

department: Institute for Human Genetics

institute: University of Lübeck

description: Gene expression data from mouse liver fed a chow diet for 12 weeks

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Clariom D assay, mouse. Clariom D assays, mouse were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Clariom D assays, mouse were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data analysis was performed with the Transcriptome Analysis Console software (version 4.0.2.15) with the analysis type 'Expression (Gene + Exon)'. As summarization method 'Gene + Exon - SST-RMA' was used for signal normalization. ANOVA method 'ebayes' was used for comparison. A probe set was considered expressed if at least 50% of the detection above background (DABG) values were below the DABG threshold.

source_name: liver of mice with chow feeding for 12 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Expression Analysis Technical Manual, 2017, Affymetrix).

extract_protocol: RNA was isolated from snap-frozen liver using the miRNeasy mini kit (Qiagen, Germany) according to the manufacturer’s instructions blinded.

value: liver

tag: age

value: 12 weeks

tag: condition

value: chow diet


title: liver_chow_wk1_m10

description: Gene expression data from mouse liver fed a chow diet for 1 week

source_name: liver of mice with chow feeding for 1 week

value: 1 week


title: liver_chow_wk1_m6


title: liver_HFD_wk1_m51

description: Gene expression data from mouse liver fed a high-fat diet for 1 week

source_name: liver of mice with HFD feeding for 1 week

value: high-fat diet


title: NTLPER200: Peruvian, NTL, Patient, 200

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 200,Age: 42,Gender: Male,HBV: Positive,mtDNA haplotypes: D

hyb_protocol: 5.5 μg of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the limma software standard pipeline (R package) and normalized using Robust Multichip Average (RMA) algorithm.

source_name: Peruvian patient with hepatocellular carcinoma (HCC)

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA, according to the standard Affymetrix protocol (Manual Target Prepartion for GeneChip Whole Transcription Expression Array, 20013, Affymetrix).

extract_protocol: Total RNA was extracted using TRI Reagent® (Sigma-Aldrich), according to the manufacturer's instructions.

treatment_protocol: Sampling protocol: About 50 mg of HCC, as well as NTL from tumor-free margins of the resected surgical pieces, were harvested, flash-frozen in liquid nitrogen, and kept at -150°C for long-term storage.

tag: patient diagnosis

value: hepatocellular carcinoma (HCC)

value: Non-tumor liver

tag: subject id

value: Patient 200

value: Male

tag: hbv status

value: Positive

tag: mtdna haplotype

value: D


title: NTLPER201: Peruvian, NTL, Patient, 201

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 201,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D

value: Patient 201

tag: gender

value: Negative


title: Plaque CD68+ S196A biological replicate 1

city: New York

address: 550 First Avenue

value: C57Bl6 ; LDLR-/-

value: Atherosclerotic plaque

value: Plaque CD68+

value: Bone marrow transplant


title: liver_chow_wk12_m47

value: liver


title: NTLPER193: Peruvian, NTL, Patient, 193

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 193,Age: 13,Gender: Male,HBV: Negative,mtDNA haplotypes: A

value: Patient 193

value: A


title: NTLPER192: Peruvian, NTL, Patient, 192

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 192,Age: 33,Gender: Male,HBV: Positive,mtDNA haplotypes: B

value: Patient 192

value: B


title: liver_HFD_wk12_m91

description: Gene expression data from mouse liver fed a high-fat diet for 12 weeks

source_name: liver of mice with HFD feeding for 12 weeks

value: 12 weeks

value: high-fat diet


title: NTLPER188: Peruvian, NTL, Patient, 188

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 188,Age: 94,Gender: Female,HBV: Negative,mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Non-tumor liver

value: Patient 188

value: Female


title: liver_chow_wk12_m45

value: chow diet


title: liver_HFD_wk1_m60

value: 1 week


title: liver_chow_wk12_m46


title: NTLPER190: Peruvian, NTL, Patient, 190

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 190,Age: 46,Gender: Female,HBV: Positive,mtDNA haplotypes: A

value: Patient 190

value: Positive


title: liver_chow_wk1_m3


title: liver_HFD_wk12_m100


title: liver_HFD_wk12_m99


title: NTLPER116: Peruvian, NTL, Patient, 116

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 116,Age: 77,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: Patient 116

value: Male

value: Negative


title: liver_chow_wk12_m41

value: liver


title: liver_HFD_wk1_m55


title: liver_chow_wk1_m7


title: liver_chow_wk1_m5


title: NTLPER100: Peruvian, NTL, Patient, 100

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 100,Age: 44,Gender: Female,HBV: Positive,mtDNA haplotypes: B

value: Patient 100


title: NTLPER191: Peruvian, NTL, Patient, 191

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 191,Age: 67,Gender: Male,HBV: Negative,mtDNA haplotypes: A

value: Patient 191

value: A


title: NTLPER173: Peruvian, NTL, Patient, 173

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 173,Age: 53,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: Patient 173

value: B


title: NTLPER121: Peruvian, NTL, Patient, 121

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 121,Age: 82,Gender: Female,HBV: Negative,mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Patient 121


title: liver_HFD_wk1_m54

value: high-fat diet


title: liver_HFD_wk12_m95

value: 12 weeks


title: liver_HFD_wk12_m96


title: NTLPER117: Peruvian, NTL, Patient, 117

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 117,Age: 44,Gender: Female,HBV: Negative,mtDNA haplotypes: B

value: Non-tumor liver

value: Patient 117

value: Female


title: NTLPER095: Peruvian, NTL, Patient, 095

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 095,Age: 30,Gender: Male,HBV: Positive,mtDNA haplotypes: A

value: Patient 095

value: Positive


title: NTLPER092: Peruvian, NTL, Patient, 092

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 092,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D

value: Patient 092

value: Male

value: D


title: liver_chow_wk1_m4

description: Gene expression data from mouse liver fed a chow diet for 1 week

value: liver

value: 1 week

value: chow diet


title: NTLPER090: Peruvian, NTL, Patient, 090

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 090,Age: 28 Gender: Male,HBV: Positive,mtDNA haplotypes: A

value: Patient 090

value: A


title: liver_HFD_wk1_m52

description: Gene expression data from mouse liver fed a high-fat diet for 1 week


title: NTLPER088: Peruvian, NTL, Patient, 088

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 088,Age: 67,Gender: Male,HBV: Positive,mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Patient 088

value: B


title: liver_chow_wk1_m2


title: liver_HFD_wk12_m92

value: 12 weeks

value: high-fat diet


title: NTLPER070: Peruvian, NTL, Patient, 070

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 070, Age: 64, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Non-tumor liver

value: Patient 070


title: NTLPER054: Peruvian, NTL, Patient, 054

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 054, Age: 46, Gender: Female, HBV: Positive, mtDNA haplotypes: D

value: Patient 054

value: Female


title: NTLPER047: Peruvian, NTL, Patient, 047

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 047, Age: 78, Gender: Female, HBV: Positive, mtDNA haplotypes: C

value: Patient 047

value: Positive

value: C


title: NTLPER068: Peruvian, NTL, Patient, 068

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 068, Age: 44, Gender: Female, HBV: Positive, mtDNA haplotypes: B

value: Patient 068


title: NTLPER026: Peruvian, NTL, Patient, 026

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 026, Age: 36, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 026

value: Male


title: liver_HFD_wk1_m59

value: liver

value: 1 week


title: liver_HFD_wk12_m94

description: Gene expression data from mouse liver fed a high-fat diet for 12 weeks


title: NTLPER016: Peruvian, NTL, Patient, 016

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 016, Age: 74, Gender: Female, HBV: Positive, mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Patient 016


title: Enrichment PCR libarary for S4_min_D6 group1

city: Stony Brook

first: Robert

middle: Scott

last: Powers

address: 100 Nicolls Rd

department: Pathology

institute: Stony Brook University

description:
amplicon cDNA was generated via enrichment PCR and used to identify sgRNAs in single cells
S4_filtered_barcodes.tsv.gz
S4_filtered_features.tsv.gz
S4_filtered_matrix.mtx.gz
S4_raw_barcodes.tsv.gz
S4_raw_features.tsv.gz
S4_raw_matrix.mtx.gz
S4_protospacer_calls_per_cell.csv

data_processing:
cellranger mkfastq: Generating FASTQs with cellranger mkfastq, done by Novogene
cellranger count (Feature Barcode Analysis): The FASTQ files of 10X scRNA expression library and its corresponding enrichment PCR library of each sample were aligned to GRCh38-3.0.0 human genome assemble and CRISPR feature reference using the count pipeline of Cell Ranger software (version 3.0.1, 10X Genomics by following the manual of Feature Barcoding Analysis of 10X Genomics.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Feature barcode matrix table with raw counts of each gene in the individual cells
Supplementary_files_format_and_content: CSV files containing sgRNA identity information for the individual cells

source_name: MCF10A cells

extract_protocol: Singe cell transcriptomes (Gene expression libraries) were prepared according to 10X Genomics' protocol.Briefly, cells  were harvested and captured using one lane of a 10X Chromium device per sample using 10X V2 Single Cell 3′- Solution reagents (10X Genomics). Approximately 16,000 cells were loaded into 10X Chromium chips and 5,000 - 9,000 cells were captured per lane for each condition. Around 10 ng of full-length cDNA out of downstream shearing and library pre steps were hold for sgRNA-enrichment PCR to prepare enrichment libraries. Gene expression Libraries and enrichment libraries were mixed at ratio of 25:1, and sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

value: Non tumorigenic mammary epithelial cells

tag: treatment

value: Combinatorial CROPseq cell library cultured in minimal medium at Day 6

tag: molecule

value: PCR amplicon (Enrichment library)


title: Enrichment PCR libarary for S4_min_D6 group3

tag: cell type


title: Enrichment PCR libarary for S4_min_D6 group2


title: Enrichment PCR libarary for S4_min_D6 group4


title: liver_HFD_wk12_m98

tag: tissue

value: 12 weeks

value: high-fat diet


title: NTLPER025: Peruvian, NTL, Patient, 025

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 025, Age: 15, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Non-tumor liver

value: Patient 025

value: B


title: liver_HFD_wk1_m56


title: liver_chow_wk12_m48

description: Gene expression data from mouse liver fed a chow diet for 12 weeks

value: chow diet


title: liver_chow_wk12_m43


title: 10X gene expression library (S4_min_D6)

description:
10X gene expression library
S4_filtered_barcodes.tsv.gz
S4_filtered_features.tsv.gz
S4_filtered_matrix.mtx.gz
S4_raw_barcodes.tsv.gz
S4_raw_features.tsv.gz
S4_raw_matrix.mtx.gz
S4_protospacer_calls_per_cell.csv

value: single cell transcriptomes (Gene expression library)


title: NTLPER015: Peruvian, NTL, Patient, 015

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 015, Age: 32, Gender: Female, HBV: Positive, mtDNA haplotypes: B

value: Patient 015

value: Female

value: Positive


title: Enrichment PCR libarary for S3_tgf_D6 group4

description:
amplicon cDNA was generated via enrichment PCR and used to identify sgRNAs in single cells
S3_filtered_barcodes.tsv.gz
S3_filtered_features.tsv.gz
S3_filtered_matrix.mtx.gz
S3_raw_barcodes.tsv.gz
S3_raw_features.tsv.gz
S3_raw_matrix.mtx.gz
S3_protospacer_calls_per_cell.csv

value: Combinatorial CROPseq cell library cultured in TGFbeta1 supplemented medium at Day 6


title: NTLPER034: Peruvian, NTL, Patient, 034

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 034, Age: 28, Gender: Female, HBV: Positive, mtDNA haplotypes: A

value: Patient 034

value: A


title: liver_HFD_wk1_m57

value: liver

value: 1 week


title: NTLPER013: Peruvian, NTL, Patient, 013

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 013, Age: 68, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Patient 013

value: Male


title: NTLPER011: Peruvian, NTL, Patient, 011

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 011, Age: 17, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 011


title: Enrichment PCR libarary for S3_tgf_D6 group3

value: Non tumorigenic mammary epithelial cells

value: PCR amplicon (Enrichment library)


title: Enrichment PCR libarary for S3_tgf_D6 group2


title: Enrichment PCR libarary for S3_tgf_D6 group1


title: NTLPER004: Peruvian, NTL, Patient, 004

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 004, Age: 70, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Non-tumor liver

value: Patient 004

value: B


title: Enrichment PCR libarary for S2_full_D6 group4

description:
amplicon cDNA was generated via enrichment PCR and used to identify sgRNAs in single cells
S2_filtered_barcodes.tsv.gz
S2_filtered_features.tsv.gz
S2_filtered_matrix.mtx.gz
S2_raw_barcodes.tsv.gz
S2_raw_features.tsv.gz
S2_raw_matrix.mtx.gz
S2_protospacer_calls_per_cell.csv

value: Combinatorial CROPseq cell library cultured in full medium at Day 6


title: 10X gene expression library (S3_tgf_D6)

description:
10X gene expression library
S3_filtered_barcodes.tsv.gz
S3_filtered_features.tsv.gz
S3_filtered_matrix.mtx.gz
S3_raw_barcodes.tsv.gz
S3_raw_features.tsv.gz
S3_raw_matrix.mtx.gz
S3_protospacer_calls_per_cell.csv

value: single cell transcriptomes (Gene expression library)


title: Enrichment PCR libarary for S2_full_D6 group3


title: Enrichment PCR libarary for S2_full_D6 group2


title: HCCPER201: Peruvian, HCC, Patient, 201

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 201,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D

value: Patient 201

value: Negative

value: D


title: 10X gene expression library (S2_full_D6)

description:
10X gene expression library
S2_filtered_barcodes.tsv.gz
S2_filtered_features.tsv.gz
S2_filtered_matrix.mtx.gz
S2_raw_barcodes.tsv.gz
S2_raw_features.tsv.gz
S2_raw_matrix.mtx.gz
S2_protospacer_calls_per_cell.csv


title: Enrichment PCR libarary for S2_full_D6 group1


title: Enrichment PCR libarary for S1_full_D0 group4

description:
amplicon cDNA was generated via enrichment PCR and used to identify sgRNAs in single cells
S1_filtered_barcodes.tsv.gz
S1_filtered_features.tsv.gz
S1_filtered_matrix.mtx.gz
S1_raw_barcodes.tsv.gz
S1_raw_features.tsv.gz
S1_raw_matrix.mtx.gz
S1_protospacer_calls_per_cell.csv

value: Combinatorial CROPseq cell library cultured in full medium at Day 0


title: HCCPER193: Peruvian, HCC, Patient, 193

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 193,Age: 13,Gender: Male,HBV: Negative,mtDNA haplotypes: A

value: Patient 193

value: A


title: HCCPER200: Peruvian, HCC, Patient, 200

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 200,Age: 42,Gender: Male,HBV: Positive,mtDNA haplotypes: D

value: hepatocellular carcinoma (HCC)

value: Patient 200

value: Positive


title: HCCPER192: Peruvian, HCC, Patient, 192

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 192,Age: 33,Gender: Male,HBV: Positive,mtDNA haplotypes: B

value: Patient 192

value: Male


title: HCCPER191: Peruvian, HCC, Patient, 191

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 191,Age: 67,Gender: Male,HBV: Negative,mtDNA haplotypes: A

value: Patient 191


title: Enrichment PCR libarary for S1_full_D0 group3

value: Non tumorigenic mammary epithelial cells

value: PCR amplicon (Enrichment library)


title: Enrichment PCR libarary for S1_full_D0 group1


title: Enrichment PCR libarary for S1_full_D0 group2


title: 10X gene expression library (S1_full_D0)

description:
10X gene expression library
S1_filtered_barcodes.tsv.gz
S1_filtered_features.tsv.gz
S1_filtered_matrix.mtx.gz
S1_raw_barcodes.tsv.gz
S1_raw_features.tsv.gz
S1_raw_matrix.mtx.gz
S1_protospacer_calls_per_cell.csv


title: HCCPER180: Peruvian, HCC, Patient, 180

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 180,Age: 34,Gender: Male,HBV: Positive,mtDNA haplotypes: B

value: Patient 180

value: B


title: HCCPER173: Peruvian, HCC, Patient, 173

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 173,Age: 53,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: Patient 173


title: HCCPER121: Peruvian, HCC, Patient, 121

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 121,Age: 82,Gender: Female,HBV: Negative,mtDNA haplotypes: B

value: Patient 121

value: Female


title: HCCPER188: Peruvian, HCC, Patient, 188

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 188,Age: 94,Gender: Female,HBV: Negative,mtDNA haplotypes: B

value: Patient 188

value: Negative


title: HCCPER190: Peruvian, HCC, Patient, 190

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 190,Age: 46,Gender: Female,HBV: Positive,mtDNA haplotypes: A

value: Patient 190


title: scRNA-seq dataset: SKMEL28 48hr dabrafenib-treated

first: Frank

middle: Vincent

last: Celeste

address: 101 Nicolls Road

data_processing:
For the single-cell RNA-seq datasets: *I1_001.fastq.gz: contains the 8 nt sample index, *R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt), *R2_001.fastq.gz: contains the 150 nt RNA sequence. Single Cell sequencing data were pre-processed by cellranger 3.0.1 from 10X Genomics using default settings. Downstream analysis was performed by Seurat 3.0
For the bulk RNA-seq datasets: Salmon (Release 1.2.1) was used to generate a list of genome targets (decoys) with the human genome assembly (GRCh38). Index files were generated by concatenating transcriptome (GRCh38 cDNA) and genome (GRCh38 DNA) reference files. RNA-seq reads were pseudo-aligned to the reference index with Salmon (Release 1.2.1). Gene-level counts were prepared for differential expression analysis with tximport (Release 1.14.2). Differential expression was measured using DESeq2 (Release 1.26.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets: barcodes.tsv, features.tsv, matrix.mtx
For the bulk RNA-seq datasets: .txt files containing abundance values

source_name: Cutaneous melanoma cell line

growth_protocol: Clonal SK-MEL-28 cells were cultured on TC-treated plates in MEM with 5% FBS supplemented with antibiotics and antimycotics. Cells were plated and allowed to attach 24 hours prior to drug treatment.

extract_protocol:
For the single-cell RNA-seq datasets: Cells for each sample set were pooled from three 100 mm tissue culture plates, following drug treatment for the indicated time.Cells were detached with TrypLE and a single cell suspension of viable cells was prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.  For the bulk RNA-seq datasets: Cell plating was staggered such that RNA from 3-day treated, 9-day treated, and untreated control samples was extracted from cells simultaneously, using RNeasy Mini Kit (QIAGEN) protocol and reagents.
For the single-cell RNA-seq datasets: Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.  For the bulk RNA-seq datasets: Library preparation was performed using the KAPA mRNA HyperPrep Kit. An Agilent Bioanalyzer was used to verify the RNA concentration and assess RNA sample quality.

treatment_protocol: 48 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar dabrafenib.

tag: cell line

value: dabrafenib

tag: time point

value: 48 Hour


title: scRNA-seq dataset: SKMEL28 72hr dabrafenib-treated

treatment_protocol: 72 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar dabrafenib.

value: 72 Hour


title: scRNA-seq dataset: SKMEL28 24hr dabrafenib-treated

treatment_protocol: 24 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar dabrafenib.

value: 24 Hour


title: HCCPER179: Peruvian, HCC, Patient, 179

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 179,Age: 33,Gender: Male,HBV: Positive,mtDNA haplotypes: C

value: hepatocellular carcinoma (HCC)

value: Patient 179

value: Positive

value: C


title: HCCPER116: Peruvian, HCC, Patient, 116

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 116,Age: 77,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: Patient 116

value: Male


title: HCCPER117: Peruvian, HCC, Patient, 117

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 117,Age: 44,Gender: Female,HBV: Negative,mtDNA haplotypes: B

value: Patient 117

value: B


title: HCCPER120: Peruvian, HCC, Patient, 120

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 120,Age: 20,Gender: Female,HBV: Positive,mtDNA haplotypes: B

value: Patient 120


title: scRNA-seq dataset: SKMEL28 untreated

treatment_protocol: 24 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media.

value: untreated

value: 0 Hour


title: HCCPER109: Peruvian, HCC, Patient, 109

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 109,Age: 38,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: Patient 109

value: Negative


title: scRNA-seq dataset: PC9 48hr gefitinib-treated

source_name: Lung adenocarcinoma cell line derived from metastatic site (lymph node)

growth_protocol: Clonal PC-9 cells were cultured on TC-treated plates in RPMI with 5% FBS supplemented with antibiotics and antimycotics. Cells were plated and allowed to attach 24 hours prior to drug treatment.

treatment_protocol: 48 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar gefitinib.

value: gefitinib


title: scRNA-seq dataset: PC9 72hr gefitinib-treated

treatment_protocol: 72 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar gefitinib.


title: HCCPER106: Peruvian, HCC, Patient, 106

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 106,Age: 72,Gender: Male,HBV: Positive,mtDNA haplotypes: D

value: Patient 106

value: D


title: HCCPER104: Peruvian, HCC, Patient, 104

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 104,Age: 72,Gender: Male,HBV: Positive,mtDNA haplotypes: A

value: Patient 104

value: A


title: scRNA-seq dataset: PC9 24hr gefitinib-treated

treatment_protocol: 24 hours prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar gefitinib.

value: 24 Hour


title: TaDaG2-Dam_n1

source_name: dissected 3rd instar larval brain

value: brain

tag: developmental stage

value: 3rd instar larvae

tag: construct


title: HCCPER101: Peruvian, HCC, Patient, 101

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 101,Age: 24,Gender: Male,HBV: Positive,mtDNA haplotypes: C

value: hepatocellular carcinoma (HCC)

value: Patient 101

value: Positive

value: C


title: scRNA-seq dataset: PC9 untreated


title: HCCPER099: Peruvian, HCC, Patient, 099

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 099,Age: 32,Gender: Female,HBV: Positive,mtDNA haplotypes: D

value: Patient 099

value: Female


title: HCCPER100: Peruvian, HCC, Patient, 100

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 100,Age: 44,Gender: Female,HBV: Positive,mtDNA haplotypes: B

value: Patient 100

value: B


title: NTLPER091: Peruvian, NTL, Patient, 091

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 091,Age: 65,Gender: Male,HBV: Negative,mtDNA haplotypes: A

value: Non-tumor liver

value: Patient 091

value: Male

value: Negative


title: HCCPER093: Peruvian, HCC, Patient, 093

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 093,Age: 35,Gender: Male,HBV: Negative,mtDNA haplotypes: C

value: Patient 093


title: HCCPER091: Peruvian, HCC, Patient, 091

value: A


title: H1155_PAX5_KO_3

city: Tianjin

first: Zhe

last: LIU

address: 22 Qixiangtai Road

department: Department of Immunology

institute: TIanjin Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0
FeatureCounts v1.5 and stringtie v1.3 for RNA quantification and qualification
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SCLC cell

extract_protocol:
totoal RNAs from H1155 empty-1/2/3  and H1155-PAX5.KO-1/2/3 were extracted by Trizol Reagent according to the manufacturer`s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H1155 were transfected with 305 empty or PAX5 KO lentivirus for 8h per day and change with normal medium, repeat 4 days.

value: Lung

tag: transfection

value: PAX5 KO


title: HCCPER092: Peruvian, HCC, Patient, 092

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 092,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D

value: Patient 092

value: D


title: NTLPER083: Peruvian, NTL, Patient, 083

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 083,Age: 73,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Patient 083


title: H1155_PAX5_KO_2


title: Polistes_worker_3

city: London

first: Christopher

last: Wyatt

address: Gower street

institute: UCL

data_processing:
Trinity used to assemble a de novo transcriptome
RSEM used to calculate normalised gene counts per Trinity transcript
Supplementary_files_format_and_content: Trinity fasta transcriptome files (.fnn) and tab-delimited RSEM files for each queen/worker which include TPM/FPKM and expected count for each sample.

organism: Polistes canadensis

source_name: Whole brain

extract_protocol:
All wasps were collected directly from their nests during the daytime, placed immediately into RNAlater (Ambion, Invitrogen) and stored at -20°C until further use. Total RNA was extracted using the RNeasy Universal Plus Mini kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: caste

value: Worker

value: whole brain


title: H1155_PAX5_KO_1


title: HCCPER090: Peruvian, HCC, Patient, 090

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 090,Age: 28 Gender: Male,HBV: Positive,mtDNA haplotypes: A

value: Patient 090

tag: age

value: Positive


title: Polistes_worker_1


title: HCCPER025: Peruvian, HCC, Patient, 025

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 025, Age: 15, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 025

value: B


title: HCCPER034: Peruvian, HCC, Patient, 034

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 034, Age: 28, Gender: Female, HBV: Positive, mtDNA haplotypes: A

value: Patient 034

value: Female


title: H1155_Empty_3

value: wild type