title: les4-mutant-1


title: les4-mutant-2

status: Public on May 12 2021

type: SRA

city: zheng zhou

first: xiaohuan

last: mu

address: zhengzhou long zi hu

country: China

institute: Henan Agricultural University

library_source: transcriptomic

data_processing:
Clean reads were derived after removal of low quality regions and adapter sequences from raw reads. Then clean reads were aligned to the maize reference genome (B73 RefGen_v4, available online: https://www.maizegdb.org/assembly/) using HISAT2
Aligned reads from HISAT2 mapping were subjected to String Tie for DeNovo Transcript assembly
The expression of each gene was normalized to fragments per kilobase of transcript per million reads (FPKM) to compare among different samples. The R package “DESeq2” were used to identify differentially expressed genes with fold changes (FC) above 2 and False Discovery Rate (FDR) lower than 0.05
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: FPKMs

molecule: total RNA

organism: Zea mays

extract_protocol:
Total RNA was extracted from sample using the Trizol reagent
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s manual and index codes were added to attribute sequences to each sample

tag: genotype

tag: tissue

value: leaf


title: Fb242_fibroblast

type: genomic

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Hybridization is done at 48°C for 16 hours in hybridisation chamber.

scan_protocol: Chips are scanned in the iScan from illumina (setting Infinium LCG).

data_processing:
All genomic DNAs were assayed on Illumina HumanOmni2.5-8M bead chip arrays to feature 2372784 single nucleotide polymorphism (SNP) markers for each DNA sample. Samples with low genotyping rate (<95%) were removed. SNPs that have a call rate lower than 0.95 were removed.  PLINK 1.07 and GCTA analysis tools were used for data QC and processing. Genetic relationship matrix (GRM) between pairs of individuals were estimated in our samples. “snpStats” (Bioconductor) was used as statistical tool for SNP association studies.
SNP Name, Sample ID, Allele 1 Forward, Allele 2 Forward, Allele 1 Top, Allele 2 Top, Allele 1 AB, Allele2 AB, GC Score, X, Y.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: foreskin-derived dermal fibroblasts

label_protocol: ddCTP and GTP are labelled with biotin and ddATP and TTP with DNP (Dinitrophenol). The nucleotides are then stained with Fluorescent streptavidin and anti-DNP Ab.

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

tag: ancestry

value: African

tag: gender

value: male

value: foreskin-derived dermal fibroblasts


title: les4-wt-3


title: oxaliplatin rep3

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

description: mRNA

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Genome_build: NA
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include reads count values for each Sample.

organism: Rattus norvegicus

source_name: dorsal root ganglion

extract_protocol:
Rats DRGs were flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGIseq500 RNA library kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Dorsal root ganglion

tag: treatment

value: Oxaliplatin


title: oxaliplatin rep4

description: mRNA


title: Fb239_fibroblast


title: oxaliplatin rep2

description: mRNA


title: les4-wt-2


title: Fb237_fibroblast


title: Sample-111 (Total Bulk RNA-seq)

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

country: USA

institute: University of California Irvine

data_processing:
Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
Genome_build: hg38
Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.

source_name: AD brain

extract_protocol:
Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq

tag: age

tag: Sex

value: M

tag: pmi

tag: diagnosis

value: AD

tag: brain region

value: CB

tag: isolation

value: total RNA isolation


title: Sample-110 (Total Bulk RNA-seq)


title: les4-wt-1


title: oxaliplatin rep1

description: mRNA


title: Sample-114 (Total Bulk RNA-seq)


title: Sample-109 (Total Bulk RNA-seq)

value: F


title: Fb236_fibroblast


title: Fb235_fibroblast


title: Late_Entry_Vector

city: Berkeley

first: Tina

middle: Lynn

last: Sing

state: California

address: Barker Hall, Rm 616, University of California, Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
cDNA inserted into pDONR222 via Gateway cloning
Sample 15

data_processing:
Library strategy: DNA-Seq
Sequencing reads were aligned to the SK1 genome using HISAT2
Transcripts per million reads (TPM) were calculated with STRINGTIE
Genome_build: SK1 genome from Saccharomyces Genome Resequencing Project (Sanger Institute)
Supplementary_files_format_and_content: Tab-delimited text output files from STRINGTIE include TPM values for each gene

organism: Escherichia coli

growth_protocol: All cells were grown in the indicated liquid media. E. coli were grown at 37˚C and S. cerevisiae were grown at 30˚C. G418 was added to all S. cerevisiae cultures to maintain plasmid selection.

extract_protocol:
mRNA and plasmid extracts were all performed using standard techniques.
mRNA was isolated with Oligo(dT)25 Dynabeads (Ambion) and libraries were preparerd with the NEXTFLEX Rapid Directional RNA-seq Kit (PerkinElmer). cDNA sequencing libraries were prepared with the NEXTFLEX Rapid DNA-seq Kit (PerkinElmer).
mRNA-seq (Samples 1-10) and DNA-seq (Samples 11-175)

treatment_protocol: cDNA libraries were induced by growing S. cerevisiae in media containing galactose (YPGR) or uninduced by growing in media containing glucose (YPD).

tag: strain

value: DHalpha + pDONR222-<Late cDNA library>

tag: meiotic cdna library

value: Late Meiosis

tag: growth condition

value: LB + Kanomycin


title: Fb234_fibroblast


title: paclitaxel rep3

description: mRNA

value: Paclitaxel


title: MeiosisII_Entry_Vector

description:
cDNA inserted into pDONR222 via Gateway cloning
Sample 14

value: DHalpha + pDONR222-<Meiosis II cDNA library>

value: Meiosis II


title: Sample-11 (Total Bulk RNA-seq)

value: FC


title: Sample-108 (Total Bulk RNA-seq)


title: Sample-107 (Total Bulk RNA-seq)


title: MeiosisI_Entry_Vector

description:
cDNA inserted into pDONR222 via Gateway cloning
Sample 13

value: DHalpha + pDONR222-<Meiosis I cDNA library>

value: Meiosis I


title: Early_Entry_Vector

description:
cDNA inserted into pDONR222 via Gateway cloning
Sample 12

value: DHalpha + pDONR222-<Early cDNA library>

value: Early Meiosis


title: Sample-106 (Total Bulk RNA-seq)


title: Fb227_fibroblast

value: African

value: male

value: foreskin-derived dermal fibroblasts


title: Sample-105 (Total Bulk RNA-seq)

value: M

value: AD

value: CB


title: Starvation_Entry_Vector

description:
cDNA inserted into pDONR222 via Gateway cloning
Sample 11

value: DHalpha + pDONR222-<Starvation cDNA library>

value: Starvation


title: paclitaxel rep1

description: mRNA

value: Dorsal root ganglion


title: Fb226_fibroblast


title: negative + ethanol, sample1

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: Human GRCh38
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

source_name: placenta

growth_protocol: he HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated by using Trizol reagent and RNeasy Micro Kit
Library preparation was done according to Illumina TruSeq® Stranded mRNA kit protocol.

treatment_protocol: The transfection with siRNA was done either with 30 nM siRNA pair or 30 nM siRNA universal negative control and using approximately 100 000 cells and duoble transfection. The first transfection was done in suspension and the second transfection in adherent cells. After 24 hours of second transfection, negP4 and CPPED1P4 cells were treated with 100 ng of P4 that had been dissolved in 0.1 % EtOH. negEtOH and CPPED1EtOH cells were treated only with 0.1% EtOH.

tag: cell line

value: placenta

tag: rna interference

value: non-targeting siRNA

value: ethanol


title: paclitaxel rep2

description: mRNA

value: Paclitaxel


title: Sample-103 (Total Bulk RNA-seq)

value: F

value: total RNA isolation


title: Vehicle rep3

description: mRNA

value: Vehicle


title: chloramine 2

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_005966.1
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

organism: Acinetobacter baylyi

source_name: Acinetobacter bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains A.baylyi ADP1 were cultured in triplicate in 10 mL 10 mg/L chloramine or 10 mg/L free chlorine , at 25 °C, without shaking

tag: agent

value: chloramine


title: Fb225_fibroblast

value: African


title: Vehicle rep2

description: mRNA


title: chloramine 3


title: Fb223_fibroblast

value: male


title: paclitaxel rep4

description: mRNA


title: Sample-102 (Total Bulk RNA-seq)


title: Fb220_fibroblast

value: Caucasian

value: foreskin-derived dermal fibroblasts


title: Vehicle rep1

description: mRNA


title: chloramine 1


title: Fb230_fibroblast


title: Sample-100 (Total Bulk RNA-seq)

source_name: Control brain

value: M

value: Control

value: FC


title: free chlorine 2

value: free chlorine


title: Repeat-tagged lacZ-α Illumina Sequencing

city: Marburg

first: Lennart

last: Randau

state: Hessen

address: Karl-von-Frisch-Str. 4

department: Biology

country: Germany

institute: Phillips-Universität Marburg

description: small RNA

data_processing:
removal of sequences of low quality (quality score limit, 0.05; maximum number of ambiguities 2)
trimming of adapter sequences
filtering by length (15-nt cutoff)
The trimmed sequences were mapped to the reference genome of Bl21 (DE3) and the sequence of the target plasmid using default settings.
Genome_build: E.coli reference genome (CP001509)  pETDuet1_sfGFP_Repeat  pBAD_sfGFP_Repeat  pBAD_lacZ_Repeat
Supplementary_files_format_and_content: The processed data files are in .wig (wiggle) format. They contain the mapping graphs of the three samples which were created from the coverage plots of the generated read track files.

source_name: Repeat-tagged lacZ-α

growth_protocol: Cells were grown in LB medium to logarithmic phase

extract_protocol:
The treated RNA was afterwards purified by EtOH precipitation including 1 % (v/v) glycogen.
cDNA libraries were created with the NEBNext® Multiplex Small RNA Library Pret Set for Illumunia according to the manufacturer’s instructions. 100 ng of input RNA was used and amplified cDNA libraries were separated by native PAGE for size selection of 120-250 bp. The selected sizes were extracted from the gel and EtOH precipitated Illumina HiSeq 2500 sequencing were performed at the Max-Planck Genome Centre, Cologne, according to their protocol.

treatment_protocol: RNA samples were treated with DNase I to remove potential DNA contamination. Fragmentation was achieved by addition of a ZnCl2 fragmentation buffer (final concentration: 10 mM Tris-HCl pH 6.8, 10 mM ZnCl2) and heating for 10 min at 95°C. Fragmentation was immediately stopped by putting the sample on ice and addition of 2µl 500 mM Na2-EDTA pH 8. The fragmented RNA was separated by denaturating Urea-PAGE and extracted from the gel. Fragmentation by bivalent metal ions presumably results in 2ʹ,3ʹ-cyclic phosphate and 5ʹ-OH RNA termini (Forconi & Herschlag, 2009), so fragments were first dephosphorylated (for 2ʹ,3ʹ-cyclic phosphate curation) and subsequently phosphorylated (for 5ʹ-OH curation) with T4 PNK. 15 µl of fragmented RNA was mixed with 6 µl of 5x dephosphorylation buffer (500 mM Tris-HCl pH 6.5, 500 MgAc, 25 mM β-mercaptoethanol) and 1 µl T4 PNK (Ambion) in a total volume of 30 µl and incubation for 6 h at 37 °C for dephosphorylation. For phosphorylation, 1 mM ATP and 1 µl T4 PNK were added and the mixture was further incubated for 1 h at 37 °C.

tag: promoter

value: pBAD

tag: library source

value: transcriptome


title: Fb219_fibroblast

tag: ancestry

tag: tissue


title: Vehicle rep4

description: mRNA

value: Dorsal root ganglion

tag: treatment


title: Sample-10 (Total Bulk RNA-seq)

tag: age

value: AD


title: Fb218_fibroblast

tag: gender


title: Repeat-tagged sfgfp Illumina Sequencing

description: small RNA

source_name: Repeat-tagged sfgfp


title: Sample-104 (Total Bulk RNA-seq)

tag: Sex

tag: pmi

value: CB


title: Fb217_fibroblast


title: control3

value: control


title: Sample-1 (Total Bulk RNA-seq)

tag: diagnosis

tag: brain region

value: total RNA isolation


title: gRNAscr_2_INPUT

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end FastQ files were trimmed for adapters and quality scores using TrimGalore v0.6.4_dev, default parameters, with --paired enabled.
Alignments to the mm10 genome were performed using bowtie2 v2.3.4.1.
Peak calling for each sample was performed with the macs2 v2.2.7.1 callpeak function (--g mm --nomodel --extsize 204 --SPMR) using anti-FLAG as treatment and input as control parameters per each sample.
Genome_build: mm10
Supplementary_files_format_and_content: NarrowPeak files according ENCODE specifications with the following columns: chromosome, chromosome start position, chromosome end position, name, score, strand, signalValue, pValue, qValue, point-source called for this peak.

organism: Mus musculus

source_name: NIH-3T3 cells

growth_protocol: NIH-3T3 cells (ATCC) were thawed and maintained in DMEM medium (Gibco) supplemented with 10% Premium Fetal Bovine Serum (Wisent) and 1X Penicillin-Streptomycin-Glutamine (Gibco). Cells were grown in a humidified incubator of 5% carbon dioxide at 37⁰C and cultured in 100mmx20mm tissue culture dishes (Corning) and harvested or passaged by trypsinization (Gibco) upon reaching 80-90% confluency.

extract_protocol:
150mm tissue culture dishes containing 90% confluent NIH-3T3 cells from each experimental condition were cross-linked and immunoprecipitated with the Active Motif ChIP-IT High Sensitivity Kit according to manufacturers instructions and using Sigma M2 ANTI-FLAG antibody (F1804). Samples were sonicated on the Bioruptor (Diagenode) in 1.5 mL Eppendorf tubes at high power for three 10-minute cycles of 30 seconds on and 30 seconds off, replacing warmed water with ice-cold water and minimal ice between each cycle. 1% of sonicated chromatin was purified according to ChIP-IT Kit protocol and quantified by NanoDrop. 30 µg input chromatin was used for immunoprecipitation.
Fragmented DNA from 12 samples (three replicates each of gRNAscr anti-FLAG, gRNA3 anti-FLAG, gRNAscr input, and gRNA3 input) was quantified using 2100 Bioanalyzer (Agilent Technologies). Libraries were generated robotically with the maximum volume provided by the client of fragmented DNA (range 100-300 bp) using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs), as per the manufacturer’s recommendations. Adapters and PCR primers were purchased from Integrated DNA Technologies (IDT). Size selection was carried out using SparQ beads (Qiagen) prior to PCR amplification (12 cycles). Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Lentiviral particles derived from plasmids for dCas9 (pLV hUbC-dCas9-T2A-GFP, Addgene #53191), gRNA (pLenti-puro backbone), Cre recombinase (pLenti6/V5-DEST backbone) were incubated sequentially with 80,000 NIH-3T3 cells plated 24 hours before. For dCas9 gRNA3/gRNAscr cells, dCas9 expressing cells were first isolated by flow cytometry (GFP positive) and, after expansion and incubation with gRNA virus, selected with 10 µg/mL puromycin.

tag: chip antibody

value: dCas9 & gRNAscr (lentiviral)


title: free chlorine 3

tag: strain


title: gRNAscr_3_INPUT


title: free chlorine 1


title: Fb216_fibroblast


title: Sample-96 (snATAC-seq)

description:
snATAC-seq_filtered_feature_bc_matrix.h5
snATAC-seq_cell_meta.csv

extract_protocol:
Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq

tag: isolation

value: unbiased total nuclei isolation


title: gRNAscr_1_INPUT

tag: cell line


title: Fb214_fibroblast


title: control1


title: gRNAscr_3_ANTI_FLAG

value: FLAG (SIGMA M2)


title: Fb213_fibroblast

value: male


title: control2


title: Sample-43 (snATAC-seq)

value: F


title: Sample-101 (Total Bulk RNA-seq)


title: gRNAscr_2_ANTI_FLAG


title: 1048_F: Adipose RNA-seq

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description: High-plane of nutrition

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

molecule: polyA RNA

organism: Bos taurus

source_name: Adipose

growth_protocol: Angus X Holstein-Friesian heifer calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-21 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.2 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from adipose samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks.

tag: diet

value: High

value: Adipose

tag: breed

value: Holstein-Friesian X Angus


title: Fb212_fibroblast

value: African

value: foreskin-derived dermal fibroblasts


title: Sample-100 (snATAC-seq)

value: M

value: Control

value: FC


title: 2537_F: Adipose RNA-seq

description: Moderate-plane of nutrition

value: Moderate


title: gRNAscr_1_ANTI_FLAG


title: Sample-90 (snATAC-seq)


title: 2535_F: Adipose RNA-seq

description: High-plane of nutrition


title: 2532_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: gRNA3_3_INPUT

value: dCas9 & gRNA3 (lentiviral)


title: Fb210_fibroblast


title: gRNA3_2_INPUT


title: Fb209_fibroblast

value: Caucasian


title: Sample-82 (snATAC-seq)


title: Sample-66 (snATAC-seq)


title: Sample-58 (snATAC-seq)


title: Sample-45 (snATAC-seq)

value: AD


title: Fb207_fibroblast


title: 2528_F: Adipose RNA-seq

description: High-plane of nutrition


title: 2346_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: gRNA3_3_ANTI_FLAG


title: 2120_F: Adipose RNA-seq

description: High-plane of nutrition


title: gRNA3_1_INPUT


title: Sample-52 (snATAC-seq)


title: 1707_F: Adipose RNA-seq

description: High-plane of nutrition


title: Fb205_fibroblast


title: gRNA3_2_ANTI_FLAG


title: gRNA3_1_ANTI_FLAG


title: Fb211_fibroblast


title: Fb204_fibroblast


title: Sample-46 (snATAC-seq)


title: 1690_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: Sample-47 (snATAC-seq)


title: PShigh, VDJ

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Partek
Trim tags, Align to STAR - 2.7.3a, Deduplicate UMIs, Filter Barcodes -> Single Cell Counts
Filter Total reads: (Min: 1,766, Max: 150,213)  Expressed genes: (Min: 500, Max: 4,000)  Mitochondrial reads percent: (Min: 0%, Max: 15.00%)
Normalize CPM (counts per million)  Add: 1.0  Log: 2.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
Nick Ceglia
Filtered gene expression matrices were generated using 10X CellRanger (version 3.1.0).
Paired single-cell VDJ sequences and annotations were generated using 10X Cellranger VDJ (version 4.0.0) and high confidence sequences were mapped to gene expression barcodes.
Feature barcode matrices were generated for each sample with five mouse using antibody barcode patterns from TotalSeq.
Mouse specific barcodes were demultiplexed by HTO using Seurat (version 3.1).
Genome_build: Ensembl mm10
Supplementary_files_format_and_content: _matrix.mtx mtx (matrix market format) Gene by Cell Count Matrix
Supplementary_files_format_and_content: _genes.tsv tsv Ensembl Transcript Ids and Gene Symbols
Supplementary_files_format_and_content: _barcodes.tsv tsv Filtered Cell Barcodes
Supplementary_files_format_and_content: _filtered_contig_annotations.csv csv Barcoded VDJ sequences and annotation data
Supplementary_files_format_and_content: _demultiplexed_barcodes.csv csv Cell barcode to mouse by HTO

source_name: Sorted CD8 T cells from peritoneal cavity

growth_protocol: Sorted in vivo CD8 TIL

extract_protocol:
The single cell suspension was loaded onto a Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, and cDNA amplification.
Library preparation of 10,000 cells proceeded using the Chromium Single Cell 5’ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 16 cycles and 11-50ng of the material was used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 or NextSeq 500 in a 26bp or 28bp/91bp paired end run using the NovaSeq 6000 S1 or S2 Reagent Kit (100 cycles) or NextSeq 500/550 High Output Kit v2.5 (150 cycles) (Illumina). An average of 256 million paired reads was generated per sample.
scRNA/TCR sequencing with feature barcoding

treatment_protocol: Mice were treated with anti-Tim-4 and anti-PD-1 on days 7 and 10 after tumor challenge

tag: cd8 t cell subset

value: PShigh


title: 1689_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: PSlow, VDJ

value: PSlow


title: Sample-40 (snATAC-seq)

value: unbiased total nuclei isolation


title: 1531_F: Adipose RNA-seq

description: High-plane of nutrition


title: Fb208_fibroblast

value: male


title: Fb201_fibroblast


title: Sample-37 (snATAC-seq)

value: F


title: 1395_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: Pslow, HTO


title: Fb206_fibroblast


title: Fb200_fibroblast


title: SD rep2

city: San Francisco

first: Nicholas

last: Gentry

institute: UCSF

data_processing:
Salmon: Extraction, mapping, counting
DESeq2: DEG calling
Genome_build: mm10
Supplementary_files_format_and_content: Txt files with raw salmon processed read counts for every gene and sample

source_name: Hippocampus

extract_protocol:
Translating Ribosome Affinity Purification
mRNA polyA enrichment

treatment_protocol: Sleep deprivation

value: Hippocampus

value: 4 months


title: Sample-33 (snATAC-seq)


title: Fb197_fibroblast


title: Sample-27 (snATAC-seq)


title: SD rep1


title: Fb196_fibroblast


title: 1388_F: Adipose RNA-seq

description: High-plane of nutrition

value: High

value: Adipose

value: Holstein-Friesian X Angus


title: Sample-22 (snATAC-seq)

value: M


title: 1360_F: Adipose RNA-seq

description: High-plane of nutrition


title: Sample-50 (snATAC-seq)


title: Control rep2


title: Fb195_fibroblast

value: foreskin-derived dermal fibroblasts


title: Fb202_fibroblast


title: 1089_F: Adipose RNA-seq

description: High-plane of nutrition


title: Control rep1


title: Sample-19 (snATAC-seq)

value: FC


title: Fb194_fibroblast


title: Pshigh, HTO


title: 1082_F: Adipose RNA-seq

description: Moderate-plane of nutrition

value: Moderate


title: Sample-17 (snATAC-seq)


title: Fb193_fibroblast


title: 1057_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: Sample-101 (snATAC-seq)

value: Control


title: 1392_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: Fb192_fibroblast

value: Caucasian


title: Sample-96 (snRNA-seq)

description:
snRNA-seq_filtered_feature_bc_matrix.h5
snRNA-seq_cell_meta.csv

molecule: nuclear RNA

extract_protocol:
Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq


title: 1050_F: Adipose RNA-seq

description: High-plane of nutrition


title: Fb191_fibroblast

value: African


title: 991_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: Fb190_fibroblast


title: day13_Tumor_CD8_right_7_1

city: Noda City Chiba

first: Mikiya

last: Tsunoda

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo university of science

data_processing:
Library strategy: TCR-seq
Adapter trimming and quality filtering of sequencing data were performed by using Cutadapt-3.2 and PRINSEQ-0.20.4. Sequencing data were processed by MiXCR-3.0.5.
In MiXCR, Filtered reads were aligned to reference mouse TCR V/D/J sequences registered in the international ImMunoGeneTics information system: -starting-material=rna, -5-end=no-v-primers-, -3-end=c-primers, -adapters=no-adapters, vParameters.geneFeatureToAlign=VTranscript, -vjAlignmentOrder=JThenV, then identical sequences were assembled and grouped in clones with PCR and sequencing error correlation with the following parameters: -badQualityThreshold=15, –separateByV=true, –separateByJ=true, -only-productive=true, –region-of-interest=CDR3.
The Variable (V) and Joining (J) segment of TCRs were represented in IMGT gene nomenclature. List of final clones were analyzed by VDJtools-1.2.1. Then, the sequencing reads of sample was normalized to the six times of cell count in each sample by “DownSample” command of VDJtools. T-cell clones were determined as TCR reads with the same TCR V segment, J segment and CDR3 nucleotide sequence.
Genome_build: IMGT reference sequences of mouse TRB
Supplementary_files_format_and_content: text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

source_name: tumor on day 13 after innoculation of LLC

growth_protocol: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the bilateral backs of C57BL/6 mice.

extract_protocol:
Tumor was divided into two and treated individually. Each tumor was cut into small fragments and digested for 45 minutes at 37°C with 0.1% collagenase (FUJIFILM Wako, Osaka, Japan). The cells were then subjected to 40% Percoll PLUS (Cytiva, Marlborough, MA) and leukocytes were recovered from the cell pellet. ACK buffer was added to the cells for lysing of red blood cells. The extracted dLN was cut into small fragments and mashed using a cell strainer.
The cell number was determined using Flow-Count fluorospheres (Beckman Coulter, San Diego, CA) and a CytoFLEX S flow cytometer (Beckman Coulter). Cells were then stained with a mix of Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioXcell) and fluorophore-conjugated anti-mouse mAbs as indicated in Table S1.
After T cells were enriched magnetically, CD8+ T cells, CD4+ T cells, CD8+ CD44hi T cells or CD4+ CD44hi T cells were sorted using FACS Aria II or Aria III (BD Biosciences, San Jose, CA). Nonviable cells and IVS-CD45.2 positive cells were excluded from the sorting gate based on forward and side scatter profiles and propidium iodide staining. Purity of sorted cells was always over 95%.
TCR libraries were prepared on purified T cells lysed in lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, and 10 mM EDTA]. PolyA RNAs were isolated according to a previous report with some modifications (GSE110711).To perform reverse transcription and template-swiching, beads were then suspended in 10 µL of RT mix [1× First Strand buffer (Thermo Fisher Scientific), 1 mM dNTP, 2.5 mM DTT (Thermo Fisher Scientific), 1 M betaine (Sigma-Aldrich), 9 mM MgCl2, 1 U/µL RNaseIn Plus Rnase Inhibitor (Promega), 10 U/µL Superscript II (Thermo Fisher Scientific), and 1µM of i5-TSO], and incubated for 60 min at 42ºC and immediately cooled on ice. Beads were washed once with with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0).
To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. Beads with containing cDNA was resuspended with the 25 µL of first PCR mixture [0.4 µM of primers (i5, Trac_ex, and Trbc_ex), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, #KK2602)], and the thermal cycling was performed as following condition: denaturation at 95°C for 3 min, 5 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 65°C and extension for 30 sec at 72°C, followed by a final extension at 72°C for 2 min.
Then, 2.5 µL of first PCR product was mixed with the 22.5 µl of second PCR mixture [0.35 µM of primers (i5_2nd, i7-BC_mTrac, and i7-BC_mTrbc), and 1x KAPA Hifi Hotstart ReadyMix], and the thermal cycling was performed under the same condition as first PCR. The second-PCR products were purified by an Agencort AM Pure XP kit (Bexkman-Coulter, CA, #A63881) at a 0.7:1 ratio of beads to sample, and eluted with 20 µL of Tris-HCl (pH 8.0).
To amplify TCR library and add adaptor sequence for next generation sequencer, the third PCR was performed as follows. 5µL of purified second PCR product was mixed with the 20 µl of third PCR mixture [0.4 µM of primers (i5-BC and i7-BC), and 1x KAPA Hifi Hotstart ReadyMix (KAPA Biosystems, Wilmington, MA, USA, #KK2602)], and the thermal cycling was performed under the same condition as first PCR, excepted for the number of cycles (23 cycles). The third-PCR products were purified as second PCR. The products were pooled and then purified and subjected to dual size selection using ProNex size-selective purification system (Promega) and eluted with 25 μL of Tris-HCl (pH 8.5). Final TCR libraries, whose lengths were about 600 base pairs were sequenced using an Illumina Novaseq 6000 S4 flowcell (67 bp read 1 and 140 bp read 2) (Illumina, USA). Only read2 contained the sequence regarding the definition of T cell clones.

tag: cell type

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD4- CD8+ T cells

value: 8 weeks

value: female

tag: tumour cell line

value: Lewis lung carcinoma

tag: organ

value: tumor


title: Sample-82 (snRNA-seq)

value: unbiased total nuclei isolation


title: 986_F: Adipose RNA-seq

description: High-plane of nutrition

tag: tissue


title: day13_Tumor_CD8_right_8_1

tag: age


title: Sample-90 (snRNA-seq)

value: F


title: day13_Tumor_CD8_right_7_2


title: Sample-66 (snRNA-seq)


title: 981_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: day13_Tumor_CD8_right_6_2


title: day13_Tumor_CD8_right_8_2


title: Sample-58 (snRNA-seq)


title: 975_F: Adipose RNA-seq

description: Moderate-plane of nutrition


title: Fb188_fibroblast

tag: ancestry

tag: gender

value: male


title: Sample-52 (snRNA-seq)

tag: Sex

tag: pmi


title: day13_Tumor_CD8_right_6_1


title: AB5075 cspC::tn

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen CLC Genomics Workbench (version 20) as paired-end reads for analysis and adapter indices trimmed
Reads corresponding to ribosomal RNA were filtered out and removed
Gene expression values were calculated using the Expression Browser tool
Differential expression between wildtype parental strain and cspC transposon mutant strain was generated using the Differential Expression in Two Groups tool
Fold change comparisons were exported in excel format
Genome_build: The Genbank genome file used as reference was accession CP008706.1
Supplementary_files_format_and_content: Differential expression is presented as fold-change of expression in cspC transposon mutant relative to wildtype parental strain, along with the read counts for each sample, in excel format.

organism: Acinetobacter baumannii

source_name: bacterial cells

growth_protocol: Overnight A. baumannii cultures were used to inoculate fresh LB broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh LB medium at OD600 0.05. After 3 hours of growth, 5 mL of cells were harvested for RNA isolation.

extract_protocol:
Total bacterial RNA was isolated utilizing an RNeasy Kit (Qiagen) and contaminating DNA was removed by treatment with TURBO DNA-free kit (Ambion). Samples with a RIN of >9.9 measured by Agilent 2100 Bioanalyzer system and corresponding RNA 6000 Nano kit (Agilent) were used in this study. Ribosomal RNA was removed using a Ribo-Zero Kit for Gram-negative Bacteria (Illumina) and MICROBExpress Bacterial mRNA enrichment kit (Agilent).
Library construction was performed using the TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.

treatment_protocol: Samples were stored at -80°C prior to RNA extraction.

tag: genotype

value: cspC transposon mutant

tag: growth medium

value: LB

tag: growth conditions

value: exponential growth, 3h, 37°C


title: day13_Tumor_CD8_right_5_2

tag: strain


title: 911_F: Adipose RNA-seq

description: Moderate-plane of nutrition

value: Adipose

value: Holstein-Friesian X Angus


title: day13_Tumor_CD8_right_5_1


title: AB5075 wildtype

value: Wildtype


title: Sample-47 (snRNA-seq)

value: M

tag: diagnosis

value: AD

tag: brain region

value: FC

tag: isolation


title: 553_F: Adipose RNA-seq

description: High-plane of nutrition

tag: diet

value: High

tag: breed


title: day13_Tumor_CD8_left_8_2

tag: cell type

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD4- CD8+ T cells

value: 8 weeks

tag: tumour cell line


title: Sample-50 (snRNA-seq)


title: 3622_F: Adipose RNA-seq

description: Moderate-plane of nutrition

value: Moderate

tag: tissue


title: AB5075 Biofilm

data_processing:
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen CLC Genomics Workbench (version 20) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Gene expression values were calculated using the Expression Browser tool
Differential expression between biofilm and planktonic samples were generated for each strain and timepoint individually using the Differential Expression in Two Groups tool
Fold change comparisons were exported in excel format
Genome_build: The Genbank genome file used as reference was accession CP008706.1
Supplementary_files_format_and_content: Differential expression in biofilm populations relative to their planktonic counterpart are presented as fold-change values in excel format. Read counts (uniquely mapped and total mapped) for all samples, and expression values (TPM) for biofilm sample are also reported.

growth_protocol: Overnight A. baumannii cultures were used to inoculate fresh LB broth at an optical density (OD600) of 0.5 in 96-well microtiter plates, in biological triplicate. Test cultures were grown for 24 h at 37°C in a static incubator prior to collection. To collect planktonic samples, 75 μL of supernatant was removed from the top of each well, and those for like strains were pooled. Samples were immediately combined with 5 mL of ice-cold PBS, and pelleted by refrigerated centrifugation for subsequent RNA isolation. For biofilm samples, the remaining supernatant was removed and biofilm containing wells were washed three times with 200 μL of ice-cold PBS. Ice-cold PBS was added a final time, pipetted vigorously to disrupt biofilm cells, and like strains were pooled. Samples were then immediately combined with an additional 5 mL of ice-cold PBS and pelleted by refrigerated centrifugation for subsequent RNA isolation.

value: Static biofilm, 24 h, 37 degreeC


title: Fb189_fibroblast

value: African

value: foreskin-derived dermal fibroblasts


title: Sample-46 (snRNA-seq)

tag: age

value: unbiased total nuclei isolation


title: day13_Tumor_CD8_left_8_1

value: female

value: Lewis lung carcinoma

tag: organ

value: tumor


title: 3148_F: Adipose RNA-seq

description: High-plane of nutrition

value: Adipose


title: 3620_F: Adipose RNA-seq

description: High-plane of nutrition

value: Holstein-Friesian X Angus


title: Sample-45 (snRNA-seq)

value: F


title: lin3-3: C. linearis stage B3 plant 3

city: Philadelphia

first: Lauren

middle: Jeane

last: Frazee

state: PA

institute: Temple University

data_processing:
We sequenced the libraries on an Illumina HiSeq 2500 platform with 125 bp paired end reads, at the Genome Innovation Center, McGill University, Montreal, Canada.
Raw read quality was verified with FastQC [v0.11.9].
We aligned the raw transcriptome sequences to the C. rattanii genome using the STAR 2-pass method [v2.7.3a].
RNA-seq reads from each sample that aligned to annotated gene models were summarized in R [v3.6.2] with the “featureCounts” function in the “Rsubread” package [v2.0.1].
Genome_build: Collinsia rattanii de novo high quality genome sequence as described in Frazee et al. 2021 in G3 journal and stored on figshare (file name = rattanii_manual_breaks_bamfilt.final.fasta).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

organism: Collinsia rattanii

source_name: floral bud (pre-anthesis)

growth_protocol: Plants were germinated at the University of Tennessee-Knoxville, following conditions in Hazzouri et al. (2013) and subsequently shipped to University of California-Riverside, where they were grown to flowering and buds were collected.

extract_protocol:
We extracted RNA from each bud, using Qiagen RNeasy Plant Mini Kits (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol.
We used an NEBNext Ultra Directional RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

tag: bud stage

value: C. linearis plant 3

value: floral bud (pre-anthesis)


title: Sample-43 (snRNA-seq)

tag: Sex

value: AD

value: FC


title: day13_Tumor_CD8_left_7_1

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD4- CD8+ T cells


title: day13_Tumor_CD8_left_7_2

value: 8 weeks


title: 2570_F: Adipose RNA-seq

description: High-plane of nutrition

value: High


title: lin3-2: C. linearis stage B3 plant 2

value: C. linearis plant 2


title: day13_Tumor_CD8_left_6_2


title: lin3-1: C. linearis stage B3 plant 1

value: C. linearis plant 1


title: 2551_F: Adipose RNA-seq

description: Moderate-plane of nutrition

value: Moderate


title: Sample-37 (snRNA-seq)

tag: pmi

value: unbiased total nuclei isolation


title: day13_Tumor_CD8_left_6_1

value: female


title: Sample-33 (snRNA-seq)

value: M


title: day13_Tumor_CD8_left_5_2

value: Lewis lung carcinoma

value: tumor


title: AB5075 Planktonic

tag: genotype

value: Wildtype

value: LB

value: Static planktonic, 24 h, 37degreeC


title: M_Obp50cBCD_5_J3_S53

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

data_processing:
Raw reads were merged across lanes using a custom UNIX shell script.
Adapter trimming, detection of abnormal polynucleotide sequences, filtering for low quality (Q<20) and short (<35nt) sequence reads and generation of basic sequence quality metrics were performed using the AfterQC pipeline.
Detection of rRNA contamination was performed using the bbduk command from the BBTools package and consolidated rRNA sequences from the SILVA database.
High quality sequence reads were aligned to Drosophila melanogaster reference genome using the allele-aware GSNAP aligner available within the GMAP package.
SAM files were converted to BAM, sorted and indexed using the samtools package.
Sorted and indexed BAM files were used for counting of meta-features (exons) using the featurecounts command within the Subread package.
Uniquely mapped alignments were consolidated at the gene level to produce raw counts.
Genome_build: Release 6.13
Supplementary_files_format_and_content: Tab-delimited text files include raw count values for one sample
Supplementary_files_format_and_content: Matrix table in tab-delimited text file contains raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: whole flies

extract_protocol:
We collected replicates of 30 adult mated flies, sexes separately, of up to two lines per genotype between 8:00 am and 11:00 am and flash froze them on dry ice in 2 mL tough microtubes (Thermofisher, Waltham, MA). Total RNA was extracted using a modified version of the RNAeasy plus mini kit (Qiagen, Hilden, Germany) protocol. Four 2.4 mm metal beads (Thermofisher) were added to each sample tube and the flies were homogenized in a bead mill (Thermofisher) for 2 minutes at 5m/s, after which the RNA was eluted with a total of 30 μL H2O.
We used the NuQuant +UDI, Drosophila AnyDeplete kit (Tecan, Männedorf, Switzerland) to deplete ribosomal RNA and prepare bar-coded cDNA libraries for sequencing after 17 cycles of amplification. We used the Qubit 1X HS dsDNA HS kit (Thermofisher) to quantify the libraries and high sensitivity D1000 screentape (Agilent, Santa Clara, CA) to check the quality of size selection. We then normalized the libraries to 5nM concentration and pooled them in order to get a final equimolar concentration of 3nM.

value: Male

tag: line


title: Sample-27 (snRNA-seq)

value: AD


title: lin2-2: C. linearis stage B2 plant 2

value: floral bud (pre-anthesis)


title: lin2-1: C. linearis stage B2 plant 1


title: F_Obp50Pos_8_J2_S52

value: Female


title: Sample-22 (snRNA-seq)

value: FC


title: lin1-3: C. linearis stage B1 plant 3

value: C. linearis plant 3


title: Sample-19 (snRNA-seq)

value: F


title: day13_Tumor_CD8_left_5_1

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD4- CD8+ T cells

value: 8 weeks


title: day13_Tumor_CD4_right_8_2

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD8- CD4+ T cells


title: M_Obp50b_4_J1_S51


title: Sample-17 (snRNA-seq)

value: unbiased total nuclei isolation


title: F_Obp50a_11_84_S36


title: day13_Tumor_CD4_right_8_1

value: female


title: F_Obp50a_11_83_S35


title: day13_Tumor_CD4_right_7_2

value: Lewis lung carcinoma


title: Sample-101 (snRNA-seq)

description: Due to low quality, this sample was not part of analysis.

value: Control


title: lin1-1: C. linearis stage B1 plant 1

value: C. linearis plant 1


title: day13_Tumor_CD4_right_7_1

value: tumor


title: rat3-3: C. rattanii stage B3 plant 3

value: C. rattanii plant 3


title: lin2-3: C. linearis stage B2 plant 3


title: M_Obp50a_11_81_S33

value: Male


title: day13_Tumor_CD4_right_6_2


title: rat3-2: C. rattanii stage B3 plant 2

value: C. rattanii plant 2


title: CO

city: Sydney

first: Anai

last: Gonzalez-Cordero

state: NSW

address: 214 Hawkesbury Road, Westmead

institute: Children’s Medical Research Institute and University of Sydney

data_processing:
The Cell Ranger (2.0.1 software) count module was used to align sequence reads from scRNA-seq experiment to the GRCh38 human reference genome and to generate the cell-by-gene count matrix.
Genes and cells were filtered retaining those that are expressed in at least three cells and those that have at least 500 genes detected. Cells were further filtered by removing (i) those that have over 10 percent mitochondrial genes in all detected genes and (ii) predicted doublets using DoubletFinder (Version 2.0.3) with an expected rate of 2.5% (according to 10X Genomics guidelines).
Genome_build: GRCh38 human reference genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Human induced pluripotent stem cell

extract_protocol:
Organoids were dissociated and subset of cell suspension was stained with 0.4% Trypan Blue (Gibco) and assessed for viability and concentration using Countess II Automated Cell Counter (Invitrogen).  Single cell suspensions were passed through 40µm cell strainer (Corning) and concentration was adjusted to 1000 cells/µL. Suspension were loaded in single-cell-B Chip (10X Genomics) for target output of 10,000 cells per sample. Single-cell droplet capture was performed on the Chromium Controller (10X Genomics).
Library preparation was performed in accordance with the Single-Cell 3’ v3 protocol.

value: Cortical brain organoid


title: F_Obp50Pos_8_71_S39

value: Female


title: lin1-2: C. linearis stage B1 plant 2

value: C. linearis plant 2

value: floral bud (pre-anthesis)


title: day13_Tumor_CD4_right_5_1


title: M_Obp50Pos_8_70_S38


title: ATAC-seq_MCF7_2

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

data_processing:
Reads from RNA-seq experiments were aligned to genome build hg19 using STAR. All ATAC-Seq data sets were trimmed and aligned to genome build hg19 genome using Bowtie2.
Duplicate reads of RNA-seq and ATAC-seq data were removed with SAMtools.
The mRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff. MACS2 was used to identify regions of ATAC-seq peaks.
The top 10000 ATAC-seq peaks were used for known motif enrichment analysis, which were performed using HOMER (v4.9).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig (bw) files were generated using deepTools.

source_name: parental MCF7

growth_protocol: The MCF7 and doxorubicin-resistant MCF7 (MCF7-DR) cell lines originally obtained from the Cell Bank of the Type Culture Collection of the Chinese Academy of Sciences Committee (Shanghai, China), were kindly provided by the key laboratory of breast cancer in Shanghai, Fudan University. All cells were cultured in DMEM medium (KEL Biotech, China), supplemented with 2 mM L-Glutamine (Gibco, USA), 10% fetal bovine serum (KEL Biotech, China), 0.1 M sodium pyruvate (Gibco, USA), 50 units/mL penicillin and 50 µg/mL streptomycin (Sigma-Aldrich, USA). The MCF7 and MCF7-DR cells were grown in 10-cm culture dishes at 37 °C in a humidified 5% CO2 atmosphere, and the medium was renewed every 2-3 days.

extract_protocol:
Total RNA was isolated from samples using TRIzol Reagent (Invitrogen, USA) and purified using RNeasy Mini Kit (QIAGEN, Germany). Agilent Bioanalyzer 2100 was used to assess RNA integrity.
The RNA‐seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions. PE150 sequencing was performed on the Illumina HiSeq X Ten platform (Novogene Biotech, China). The ATAC-seq libraries were prepared using a total of 50,000 fresh cells were washed twice with 100 μl of cold PBS (KEL Biotech, China) and resuspended in 100 μl of lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 0.1% IGEPAL CA-630 (Sigma-Aldrich) and 3 mM MgCl2] for 10 min on ice to prepare the nuclei. Immediately after lysis, the suspension of nuclei was spun at 500 g at 4°C for 5 min to remove the supernatant. Nuclei were then incubated with the 50 μl of Tn5 transposition reaction mix (DIATRE Biotech, China) at 37 °C for 30 min. The stop buffer was then added directly into the reaction to end the tagmentation. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Germany). PCR was performed to amplify the library for 12 cycles. Libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers.

treatment_protocol: The parental MCF7 cells were grown in a drug-free medium, resistant-derived cells were maintained in doxorubicin hydrochloride (MedChem Express, USA) at a concentration of 1 μM.

tag: treatment

value: untreated

tag: cell line


title: ATAC-seq_MCF7-DR_2

source_name: doxorubicin-resistant MCF7 (MCF7-DR)

value: treated with 1 μM doxorubicin hydrochloride


title: rat3-1: C. rattanii stage B3 plant 1

value: C. rattanii plant 1


title: F_Obp50d_7_67_S36


title: M_Obp50d_7_66_S35


title: rat1-3: C. rattanii stage B1 plant 3


title: day13_Tumor_CD4_right_5_2

tag: strain

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD8- CD4+ T cells

value: 8 weeks


title: rat2-2: C. rattanii stage B2 plant 2


title: M_Obp50Pos_8_69_S37


title: rat2-3: C. rattanii stage B2 plant 3


title: day13_Tumor_CD4_right_6_1

value: female


title: day13_Tumor_CD4_left_8_1

value: Lewis lung carcinoma


title: ATAC-seq_MCF7_1


title: RNA-seq_MCF7-DR_2


title: day13_Tumor_CD4_left_7_2


title: rat1-2: C. rattanii stage B1 plant 2


title: ATAC-seq_MCF7-DR_1


title: M_Obp50d_7_65_S34


title: Sample-100 (snRNA-seq)

value: M

tag: diagnosis

value: Control

tag: brain region

value: FC

value: unbiased total nuclei isolation


title: M_Obp50a_11_82_S34

value: Male


title: F_Obp50d_7_64_S44


title: day13_Tumor_CD4_left_8_2

value: tumor


title: RNA-seq_MCF7-DR_1


title: day13_Tumor_CD4_left_7_1


title: rat2-1: C. rattanii stage B2 plant 1


title: F_Obp50c_6_64_S33


title: T48Sm-2

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

data_processing:
sequenced using Illumina HiSeq2500 of Gene Denovo Biotechnology Co.
The short reads sequence alignment tool Bowtie2 (version 2.2.8) was used to map read sequences to the ribosomal RNA (rRNA) database, and the mapped reads were removed.
For each transcribed region, use StringTie software to calculate the FPKM (number of fragments per thousand base pairs of transcribed fragments per thousand base pairs) value to quantify its expression abundance and variation.
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample …

organism: Oncorhynchus mykiss

source_name: Spleen

extract_protocol:
According to the manufacturer's protocol, total RNA from the spleen of rainbow trout was extracted using the Trizol kit (Invitrogen, Carlsbad, California, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The experimental and control groups were treated with IHNV and PBS for 48 hours, respectively.

value: spleen

value: at 48 hours post-infection

tag: infection

value: IHNV for 48 hours


title: RNA-seq_MCF7_1


title: F_Obp50b_4_63_S43

value: Female


title: day13_Tumor_CD4_left_6_1


title: day13_Tumor_CD4_left_6_2


title: Cells from normal adjacent tissue

first: Chunbo

last: Li

address: 419 FangXie Road, Shanghai

department: Department of Obstetrics and Gynecology

institute: Obstetrics and Gynecology Hospital of Fudan University

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as macrophage,endothelial cell,epithelial cell,fibroblast,smooth muscle cell and Endostromal cells.
We constructed single-cell trajectory of epithelial cell and endothelial cell by using reversed graph embedding method implemented in R Monocle package (version 2.6.3)
Genome_build: hsa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: normal adjacent tissue

extract_protocol: Libraries were constructed using the Single Cell 3’ Library Kit V2 (10× Genomics).

value: normal adjacent tissue

tag: disease state

value: cervical cancer


title: T48Sm-1


title: F_Obp50a_1_62_S42


title: Cells from cervical cancer tissue

source_name: cervical cancer tissue

value: cervical cancer tissue


title: C48Sm-2

value: PBS for 48 hours


title: Activated CD4+ with 50 uM prog 24 hrs Donor 8

city: Linköping

first: Sandra

last: Hellberg

address: Universitetssjukhuset

country: Sweden

institute: Linköping University

data_processing:
Per-cycle base call (BCL) files were demultiplexed and converted to FASTQ using bcl2fastq v2.19.1.403 from the CASAVA software suite (Illumina
The FASTQ files were processed with TrimGalore! to remove adapter contamination and trimming of low-quality regions.
Paired-end reads were aligned and mapped to the Ensemble human reference genome GRCh37 (Genome Reference Consortium Human Build 37) using STAR (version 2.5.3.a).
Gene read counts were generated using StringTie (version 1.3.3).
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 8

extract_protocol:
Cells were lysed in RLT Plus Buffer with the addition of beta-mercaptoethanol according to the instructions provided by the manufacturer. Homogenization and disruption was made using syringe and needle. Lysates were stored at -80 degrees until extraction. RNA was extracted using the Allprep DNA/RNA mini kit from Qiagen. RNA was eluted with 30 µl of RNase-free water.
Libraries were constructed with TruSeq Stranded mRNA (Illumina, San Diego, CA, USA)

value: blood

tag: cell type

tag: gender


title: C48Sm-1

tag: tissue


title: day13_Tumor_CD4_left_5_1

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ter119), TCRBetaplus and CD8- CD4+ T cells

tag: age

value: 8 weeks

value: female

tag: tumour cell line


title: RNA-seq_MCF7_2

value: untreated


title: Activated CD4+_24hrs_Donor 8

source_name: Activated CD4+ T cells, 24 hrs, donor 8


title: C48Sm-3


title: day13_dLN_CD8_right_8_1

source_name: tumor draining lymph node on day 13 after innoculation of LLC

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ly6G), TCRBetaplus, and CD4- CD8+ CD44hi T cells

value: Lewis lung carcinoma

tag: organ

value: tumor draining lymph node


title: day13_dLN_CD8_right_6_1

tag: Sex


title: rat1-1: C. rattanii stage B1 plant 1

tag: bud stage

value: C. rattanii plant 1

value: floral bud (pre-anthesis)


title: day13_Tumor_CD4_left_5_2

value: tumor


title: day13_dLN_CD8_right_7_1


title: M_Obp50c_6_62_S23

value: Male

tag: genotype


title: Activated CD4+ with 50 uM prog 6 hrs Donor 8

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 8


title: Ventral foregut mesoderm 27_12_rep3

city: Ithaca

first: Emily

middle: C

last: Funk

address: 215 Tower Rd

department: Ecology and Evolutionary Biology

institute: Cornell University

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 12

data_processing:
Trimmomatic (version 0.38) was used to remove adaptor sequences and low quality regions from the reads
Reads were aligned to the Amia calva genome using STAR aligner (version 2.6) and reads counts per genes were quantified using STAR quant mode
Differential expression bewteen dorsal and ventral tissues was analyzed by building generalized linear models in edgeR carried out in R (version 3.6.0). Low expressed genes were filtered, and only genes expressed at minimum of 1 counts per million (cpm) in at least half of the samples or expressed at minimum of 0.5 cpm in at least three quarters of samples.
Genome_build: Amia calva (Braasch pers. comm.; to be published)
Supplementary_files_format_and_content: tab-delimited text file includes counts per million for each sample

organism: Amia calva

source_name: ventral foregut mesoderm

growth_protocol: Recently fertilized bowfin eggs were collected from nests in Oneida Lake NY during May of 2018. Eggs were reared at 12.8 degrees Celsius in water collected from Oneida Lake in the animal care facility at Cornell University. Bowfin embryos were sampled just before gas bladder budding, at budding, and during outgrowth at Ballard (1986) stages 24, 25, and 27 respectively.

extract_protocol:
Using a cryostat (Leica CM 1950), embedded bowfin embryos were sectioned transversely at 15 µm from the anterior to posterior ends of the gas bladder bud and mounted on polyethylene naphthalate (PEN) membrane slides.From each transverse section, the dorsal and ventral regions of the foregut endoderm and mesoderm were excised using the Zeiss Palm Microbeam LCM System at the Cornell University Biotechnology Resource Center. LCM was completed in 2 hours or less for each slide to minimize RNA degradation in the samples. Immediately following LCM, we stabilized the RNA with buffer RLT with β-Mercaptoethanol (Qiagen RNeasy Micro) and homogenized the sample by vortexing for 2 minutes. RNA extraction was performed using the Qiagen RNeasy Micro Kit. RNA amplification and cDNA reverse transcription was completed using the NuGEN Ovation RNA-seq System V2.
We used NEBNext Ultra II DNA Library Prep Kit to prepare cDNA libraries for sequencing. All libraries were quality checked on a Tape Station by the Cornell BRC Genomics Facility and showed a single peak of between 170 and 240 base pairs.

tag: developmental stage

value: Ballard stage 27

value: ventral foregut

tag: tissue type

value: mesoderm


title: Activated CD4+_6hrs_Donor 8

source_name: Activated CD4+ T cells, 6 hrs, donor 8

tag: treatment


title: T48Sm-3

value: spleen

value: at 48 hours post-infection

value: IHNV for 48 hours


title: F_Obp50c_6_63_S24

value: Female

tag: line


title: M_Obp50b_4_59_S21


title: day13_dLN_CD8_right_5_1

tag: strain

value: 8 weeks


title: Ventral foregut endoderm 27_11_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 11

source_name: ventral foregut endoderm

value: endoderm


title: F_Obp50cBCD_5_58_S48


title: Activated CD4+_24hrs_Donor 7

source_name: Activated CD4+ T cells, 24 hrs, donor 7

value: blood

value: female


title: F_Obp50a_1_61_S41


title: M_Obp50c_6_61_S22


title: Activated CD4+ with 50 uM prog 24 hrs Donor 7

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 7


title: day13_dLN_CD8_left_8_1

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ly6G), TCRBetaplus, and CD4- CD8+ CD44hi T cells

value: Lewis lung carcinoma


title: M_Obp50cBCD_5_57_S47


title: Activated CD4+_6hrs_Donor 7

source_name: Activated CD4+ T cells, 6 hrs, donor 7


title: Activated CD4+ with 50 uM prog 24 hrs Donor 6

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 6


title: F_Obp50b_4_54_S31

source_name: whole flies


title: Dorsal foregut endoderm 27_9_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 9

source_name: dorsal foregut endoderm

value: dorsal foregut and gas bladder


title: Ventral foregut mesoderm 27_7_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 7


title: day13_dLN_CD8_left_5_1

value: tumor draining lymph node


title: F_Obp50cBCD_5_55_S45


title: day13_dLN_CD8_left_6_1


title: Dorsal foregut mesoderm 27_8_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 8

source_name: dorsal foregut mesoderm


title: Ventral foregut endoderm 27_6_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 6


title: Activated CD4+_24hrs_Donor 6

source_name: Activated CD4+ T cells, 24 hrs, donor 6


title: M_Obp50a_1_50_S30


title: day13_dLN_CD4_right_8_1

value: Intravenous staining-negative, lineage-negative (CD11b, B220, NK1.1 and Ly6G), TCRBetaplus, and CD8- CD4+ CD44hi T cells


title: day13_dLN_CD8_left_7_1


title: M_Obp50a_1_49_S29

value: Male


title: Dorsal foregut mesoderm 27_5_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 5

value: Ballard stage 27


title: day13_dLN_CD4_right_7_1


title: Activated CD4+ with 50 uM prog 6 hrs Donor 6

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 6


title: M_Obp50c_24_44_S16


title: Dorsal foregut mesoderm 27_10_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 10


title: day13_dLN_CD4_right_6_1


title: Ventral foregut mesoderm 27_4_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 4

value: ventral foregut


title: M_Obp50c_24_43_S15


title: Activated CD4+_6hrs_Donor 6

source_name: Activated CD4+ T cells, 6 hrs, donor 6


title: F_Obp50c_24_42_S14


title: Activated CD4+ with 50 uM prog 6 hrs Donor 7

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 7


title: Activated CD4+ with 50 uM prog 24 hrs Donor 5

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 5


title: Ventral foregut endoderm 27_3_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 3


title: day13_dLN_CD4_right_5_1

source_name: tumor draining lymph node on day 13 after innoculation of LLC


title: day13_dLN_CD4_left_8_1


title: F_Obp50c_24_41_S13


title: day13_dLN_CD4_left_7_1


title: Dorsal foregut endoderm 27_2_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 2


title: Activated CD4+ with 50 uM prog 6 hrs Donor 5

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 5


title: Dorsal foregut endoderm 27_1_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 1


title: M_Obp50b_19_36_S28


title: day13_dLN_CD4_left_6_1


title: M_Obp50b_19_35_S27


title: day13_dLN_CD4_left_5_1


title: Activated CD4+_24hrs_Donor 5

source_name: Activated CD4+ T cells, 24 hrs, donor 5


title: Ventral foregut mesoderm 25_42_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 42

source_name: ventral foregut mesoderm

value: Ballard stage 25

value: mesoderm


title: Ventral foregut endoderm 25_36_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 36

source_name: ventral foregut endoderm


title: Activated CD4+ with 50 uM prog 24 hrs Donor 4

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 4


title: Activated CD4+_24hrs_Donor 4

source_name: Activated CD4+ T cells, 24 hrs, donor 4


title: Dorsal foregut mesoderm 25_35_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 35


title: Chronic-2-scRNA

first: Jia

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: Bladder mucosal layer of 8-weeks old C57BL/6 mice treated with 4 round CPP for 11 days

extract_protocol:
The mucosal layer was torn from mice bladder and dissociated immediately.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: bladder

value: 8-weeks old

value: wild type


title: F_Obp50b_19_33_S25

value: Female


title: Chronic-1-scRNA


title: Dorsal foregut endoderm 25_34_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 34

value: endoderm


title: Activated CD4+_6hrs_Donor 5

source_name: Activated CD4+ T cells, 6 hrs, donor 5

value: blood


title: Activated CD4+ with 50 uM prog 6 hrs Donor 4

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 4

value: female


title: M_Obp50cBCD_21_28_S12

source_name: whole flies


title: Ventral foregut mesoderm 25_33_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 33


title: Acute-2-scRNA

source_name: Bladder mucosal layer of 8-weeks old C57BL/6 mice treated with CPP for 48 hours


title: Acute-1-scRNA


title: Dorsal foregut mesoderm 25_31_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 31

source_name: dorsal foregut mesoderm


title: Healthy-2-scRNA

source_name: Bladder mucosal layer of 8-weeks old C57BL/6 mice


title: F_Obp50b_19_34_S26


title: Ventral foregut endoderm 25_32_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 32


title: Activated CD4+_6hrs_Donor 4

source_name: Activated CD4+ T cells, 6 hrs, donor 4


title: F_Obp50cBCD_21_26_S43


title: Unactivated CD4+ 6 hrs_Donor 4

source_name: Unactivated CD4+ T cells, 6 hrs, donor 4


title: F_Obp50cBCD_21_25_S42


title: M_Obp50NegBCD_26_24_S41


title: Healthy-1-scRNA


title: APOEr_3

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: Michigan

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

description:
gene_count_matrix_kemp_APOEr.txt
S6

data_processing:
Sample reads were aligned with HISAT2 v2.2.0
Conversion of the aligned files to BAM format was done with SAMtools v1.10
Gene assembly and quantification was done with Stringtie 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: in vitro pancreatic tumor cells

growth_protocol: 7940b KPC tumor cells were maintained in DMEM with 10% FBS and 1% pen/strep

extract_protocol:
Cells were lysed in RLT buffer and RNA was extracted with Qiagen RNeasy Plus Mini Kit
Library was constructed using standard Illumina protocols

treatment_protocol: 7940b KPC cells were treated with vehicle or 0.3ug/mL murine recombinant ApoE for 48 hours

value: KPC

value: APOEr


title: Unactivated CD4+ 24 hrs_Donor 4

source_name: Unactivated CD4+ T cells, 24 hrs, donor 4


title: Activated CD4+_24hrs_Donor 3

source_name: Activated CD4+ T cells, 24 hrs, donor 3


title: Ventral foregut mesoderm 25_28_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 28


title: Dorsal foregut endoderm 25_29_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 29

source_name: dorsal foregut endoderm

value: dorsal foregut and gas bladder


title: M_Obp50NegBCD_26_23_S40


title: M_Obp50cBCD_21_27_S44


title: Ventral foregut endoderm 25_27_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 27

value: ventral foregut endoderm


title: APOEr_2

description:
gene_count_matrix_kemp_APOEr.txt
S5


title: Unactivated CD4+ 24 hrs_Donor 3

source_name: Unactivated CD4+ T cells, 24 hrs, donor 3


title: M_Obp50NegBCD_27_22_S39


title: APOEr_1

description:
gene_count_matrix_kemp_APOEr.txt
S4


title: Dorsal foregut mesoderm 25_26_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 26


title: Activated CD4+ with 50 uM prog 6 hrs Donor 3

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 1


title: vehicle_3

description:
gene_count_matrix_kemp_APOEr.txt
S3

value: vehicle


title: M_Obp50NegBCD_27_21_S38

value: Male


title: Activated CD4+ with 50 uM prog 24 hrs Donor 3

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 3


title: F_Obp50NegBCD_27_20_S37


title: F_Obp50NegBCD_27_19_S11


title: vehicle_1

description:
gene_count_matrix_kemp_APOEr.txt
S1


title: Unactivated CD4+ 6 hrs_Donor 3

source_name: Unactivated CD4+ T cells, 6 hrs, donor 3


title: Ventral foregut mesoderm 24_24_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 24

source_name: ventral foregut mesoderm

value: Ballard stage 24


title: PFC_Zbtb16_WT5

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M17). Uniquely mapped reads were quantified using HTSeq v0.9.1 suite using protein coding genes by gene.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Input tables are included as tab separated files.

extract_protocol:
total RNA was extracted from prefrontal cortex (PFC) of male mice at 7 weeks with the AllPrep DNA/RNA Mini Kit (#80204, Qiagen, Hilden, Germany) according to the manufacturer’s instruction. RNA integrity number (RIN) of total RNA was quantified by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Pico Kit (#5067-1513, Agilent, Santa Clara, CA).
RNA-seq was performed as a service by Macrogen Japan Corp. (Kyoto, Japan). Briefly, total RNA with RIN values of ≥8.1 were used for RNA-seq library preparation. mRNA was purified from 500 ng total RNA, and subjected to cDNA library making (fragmentation, first and second strand syntheses, adenylation, ligation and amplification) by TruSeq Stranded mRNA Library Prep (#20020594, Illumina, San Diego, CA) according to the manufacturer’s instruction. cDNA library quality was quantified by 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Library was sequenced as 101 bp paired-end on Illumina NovaSeq6000.

tag: experiment

value: Zbtb16 WT

value: prefrontal cortex (PFC)

tag: rin

tag: library type

value: Paired-End

tag: protocol

value: Protocol 1


title: F_Obp50NegBCD_26_18_S10


title: F_Obp50NegBCD_26_17_S9


title: Dorsal foregut endoderm 24_21_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 21


title: Ventral foregut endoderm 24_23_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 23

source_name: ventral foregut endoderm

value: ventral foregut


title: Activated CD4+ with 50 uM prog 6 hrs Donor 2

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 2

tag: cell type

tag: gender


title: Activated CD4+_24hrs_Donor 2

source_name: Activated CD4+ T cells, 24 hrs, donor 2

tag: tissue


title: Activated CD4+ with 50 uM prog 24 hrs Donor 2

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 2


title: Ventral foregut mesoderm 24_20_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 20

value: mesoderm


title: Dorsal foregut mesoderm 24_22_rep3

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 22

source_name: dorsal foregut mesoderm


title: PFC_Zbtb16_WT3

source_name: prefrontal cortex (PFC) of male mice at 7 weeks


title: Activated CD4+_6hrs_Donor 2

source_name: Activated CD4+ T cells, 6 hrs, donor 2


title: PFC_Zbtb16_WT4


title: M_Obp50Neg_30_8_S8

source_name: whole flies


title: Dorsal foregut endoderm 25_25_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 25

value: Ballard stage 25


title: PFC_Zbtb16_WT2


title: Activated CD4+_6hrs_Donor 3

source_name: Activated CD4+ T cells, 6 hrs, donor 3


title: Ventral foregut endoderm 24_19_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 19

value: endoderm


title: Activated CD4+ with 50 uM prog 24 hrs Donor 1

source_name: Activated CD4+ T cells+50 uM prog, 24 hrs, donor 1

value: blood


title: M_Obp50Neg_30_7_S7


title: F_Obp50Neg_30_6_S6

value: Female


title: vehicle_2

description:
gene_count_matrix_kemp_APOEr.txt
S2

source_name: in vitro pancreatic tumor cells

value: KPC


title: Activated CD4+_24hrs_Donor 1

source_name: Activated CD4+ T cells, 24 hrs, donor 1

value: female


title: Dorsal foregut mesoderm 24_18_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 18

value: dorsal foregut and gas bladder


title: PFC_Zbtb16_WT1


title: F_Obp50Neg_30_5_S5


title: PFC_Zbtb16_KO5

value: Zbtb16 KO


title: Unactivated CD4+ 24 hrs_Donor 1

source_name: Unactivated CD4+ T cells, 24 hrs, donor 1


title: M_Obp50Neg_31_4_S4


title: Ventral foregut mesoderm 24_16_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 16


title: PFC_Zbtb16_KO4


title: M_Obp50Neg_31_3_S3


title: Ventral foregut endoderm 24_15_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 15


title: F_Obp50Neg_31_2_S2


title: Activated CD4+_6hrs_Donor 1

source_name: Activated CD4+ T cells, 6 hrs, donor 1


title: PFC_Zbtb16_KO2


title: PFC_Zbtb16_KO1


title: Activated CD4+ with 50 uM prog 6 hrs Donor 1

source_name: Activated CD4+ T cells+50 uM prog, 6 hrs, donor 1


title: F_Obp50Neg_31_1_S1


title: Dorsal foregut mesoderm 24_14_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 14


title: Dorsal foregut endoderm 24_13_rep1

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 13

source_name: dorsal foregut endoderm


title: D1821622 [targeted exome sequencing]

status: Public on May 11 2021

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description: mix experiment 4 -biological replicate 1

data_processing:
Library strategy: targeted exome sequencing
Data-processing was performed according to the bcbio workflow including sequencing adaptor trimming, mapping, duplicate read marking, variant calling (using Vardict), variant annotation using VEP, dbNSFP and dbscSNV.

source_name: hESC

growth_protocol: Naive UGENT-11/60 hESCs (referred to as C12) were cultured as described previously (Warrier et al., 2017). In brief, naive hESCs were cultured on inactivated (by irradiation) Mouse Embryonic Fibroblasts (MEFs; A34180, Fisher Scientific). MEFs were seeded at a density of 200 000 cells per well of a 6-well plate in MEF media consisting of DMEM 1x (41965-039, Invitrogen) supplemented with 10% fetal calf serum, 1% L-glutamine (25030-025, Invitrogen) and 1% Penicillin/Streptomycin (15140-122, Invitrogen). Cells were allowed to attach and spread prior to use. hESC were subsequently seeded on the attached MEF. Basal naive hESC medium consisted of Knockout DMEM (10829-018, Invitrogen) containing 20% knockout serum replacement (10828-028, Invitrogen), 2mM L-glutamine, 1% Penicillin/Streptomycin, 1% non-essential amino acids (11140-050, Invitrogen), and 0.1mM β-mercapto-ethanol (31350-010, Invitrogen). This basal naive hESC medium is supplemented with 12ng/ml bFGF (100–18B, Peprotech) and 1000U recombinant human LIF (300-05, Sigma) and the small molecules 1μM PD0325903 (13034, Sanbio), 3μM CHIR99021 (1386, Axon Medchem), 10μM Forskolin (F6886, Sigma) and 50ng/ml ascorbic acid (A8960, Sigma) and used as complete media. Naive hESCs were maintained in hypoxic conditions of 5% O2 and 5% CO2 conditions at 37°C. MEF depletion in the hESC culture at passaging was done by discarding the 0.05% trypsin/EDTA (25300-054, Invitrogen) applied to the culture after an incubation of 5min at room temperature. Next, loosened hESC colonies and remaining MEF were resuspended in complete hESC media. Naive colonies were passaged as single cells at a density of 35 000 cells per well of a 6-well plate every three days and were re-plated on inactivated MEFs.

extract_protocol:
Genomic DNA extraction  Cell pellets were dissolved in 150µl PBS. Genomic DNA was subsequently extracted by QIAcube (Qiagen) using the QiaAmp Blood mini kit (250, Qiagen) consisting of AL, AE, AW1 and AW2 buffers, Qiagen protease, QIAmp mini spin columns and collection tubes. DNA extraction was conducted according to the manufacturer’s instructions. DNA concentrations were measured by using the Dropquant software of the Dropsense. Samples were diluted appropriately and used for exome sequencing, sWGS and ddPCR.
Tumor and normal DNA were profiled using the 69-gene MDG SeqCap SOLID panel (https://www.cmgg.be/nl/zorgverlener/labguide/platform-moleculaire-diagnostiek-uz-gent-mdg). This assay involves hybridization of barcoded libraries to custom oligonucleotides (Nimblegen SeqCap) designed to capture all protein-coding exons and select introns of 69 commonly implicated oncogenes, tumor suppressor genes, and members of pathways deemed actionable by targeted therapies. Barcoded sequence libraries were prepared using 100ng genomic DNA with the KAPA HyperPlus Prep Kit (Kapa Biosystems KK8504) and combined in equimolar pools.  The captured pools were subsequently sequenced on an Illumina MiSeq as paired-end 150-base pair reads, producing > 300-fold coverage per ROI.

tag: full id

value: C12 17q MonoCL N LMS - #50+4 – 30/11 – start Mixexp4

tag: vivar id

tag: cell line

tag: cell line subclass

tag: pluripotency

value: naive

tag: feederlayer

value: MEF

value: start

tag: passage


title: D1903651 [targeted exome sequencing]

description: mix experiment 5 -biological replicate 2

value: start Mix 5 MC C12 17q N LMS #54+2 #start 22/02/2019

tag: treatment


title: D1821621 [targeted exome sequencing]

value: C12 wt N MonoCL LMS - #49+4 – 30/11 – start Mixexp4


title: D1903650 [targeted exome sequencing]

value: start Mix 5 MC C12 wt N LMS #53+2 #start 22/02/2019


title: Dorsal foregut endoderm 24_17_rep2

description: Amia_CountsMatrix_logCPM_wOrthologs.txt column name: 17

tag: developmental stage

value: Ballard stage 24

tag: tissue type


title: PFC_Zbtb16_KO3

tag: experiment

tag: genotype

value: prefrontal cortex (PFC)

tag: Sex

value: Male

value: Paired-End

value: Protocol 1


title: Unactivated CD4+ 6 hrs_Donor 1

source_name: Unactivated CD4+ T cells, 6 hrs, donor 1

value: blood


title: T28_Fetal liver

type: RNA

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: Human fetal liver

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Human fetal liver

label_protocol: Manufature's protocol

growth_protocol: Primed human iPSCs were maintained in StemFiT media (Ajinomoto) supplemented with 100 ng/ml bFGF on Laminin 511 E8 fragment-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.   Other cell lines were maintained according to the manufacturer's protocols.   The RNA samples derived from normal tissues were purchased from Clontech.

extract_protocol: RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Fetal tissue


title: T26_Fetal heart

description: Human fetal heart

source_name: Human fetal heart


title: T17_Spleen

description: Human spleen

source_name: Human spleen

value: Adult tissue


title: T20_Thymus

description: Human thymus

source_name: Human thymus


title: T25_Fetal brain

description: Human fetal brain

source_name: Human fetal brain


title: T22_Tonsil

description: Human tonsil

source_name: Human tonsil


title: T19_Testis

description: Human testis

source_name: Human testis


title: T16_Smooth muscle

description: Human smooth muscle

source_name: Human smooth muscle


title: T14_Skeletal muscle

description: Human skeletal muscle

source_name: Human skeletal muscle


title: T10_Pancreas

description: Human pancreas

source_name: Human pancreas


title: T24_Uterus

description: Human uterus

source_name: Human uterus


title: T23_Trachea

description: Human trachea

source_name: Human trachea


title: T11_Placenta

description: Human placenta

source_name: Human placenta


title: T27_Fetal kidney

description: Human fetal kidney

source_name: Human fetal kidney


title: T21_Thyroid

description: Human thyroid

source_name: Human thyroid


title: T5_Heart

description: Human heart

source_name: Human heart


title: T8_Lung

description: Human lung

source_name: Human lung


title: T12_Prostate

description: Human prostate

source_name: Human prostate


title: T29_Fetal Spleen

description: Human fetal Spleen

source_name: Human fetal Spleen


title: T7_Liver

description: Human liver

source_name: Human liver


title: T2_Bone marrow

description: Human bone marrow

source_name: Human bone marrow


title: T15_Small intestine

description: Human small intestine

source_name: Human small intestine


title: T13_Salivary gland

description: Human salivary gland

source_name: Human salivary gland


title: T1_Adrenal gland

description: Human adrenal gland

source_name: Human adrenal gland


title: T9_Ovary

description: Human ovary

source_name: Human ovary


title: T4_Colon

description: Human colon

source_name: Human colon


title: T6_Kidney

description: Human kidney

source_name: Human kidney


title: T3_Brain

description: Human brain

source_name: Human brain


title: C19_Astrocyte

description: human astrocytes

source_name: human astrocytes

value: Somatic cell line


title: T18_Stomach

description: Human stomach

source_name: Human stomach


title: C14_BrEC

description: human bronchial epithelial cells

source_name: human bronchial epithelial cells


title: C18_NPC

description: human neural progenitor cells

source_name: human neural progenitor cells


title: Survivor 1 (Irradiated) (E2)

city: Winston-Salem

first: J. Mark

last: Thakur

state: North Carolina

address: Medical Center Boulevard

department: Pathology-Comparative Medicine

institute: Wake Forest School of Medicine

data_processing:
Raw read quality was assessed by FASTQC analysis (Babraham Bioinformatics).
Reads with >Q20 quality score were aligned to the Ensembl Macaca mulatta genome build Mmul_1 using the STAR sequence aligner
Gene counts were extracted using feature Counts software
Differentially expressed genes (DEGs) were analyzed using limma-voom
Genome_build: Mmul_1
Supplementary_files_format_and_content: Gene counts

organism: Macaca mulatta

source_name: Lung

extract_protocol:
Total RNA was extracted from 40-80 mg frozen lung tissues from three different affected regions of the lung from eight irradiated animals (4 non-survivors and 4 survivors) and from two different randomly selected regions from three unirradiated control animals. Tissue was placed into a 1.4 mm ceramic bead tube with 1 ml QIAzol lysis reagent and homogenized using a bead mill (Bead Ruptor 24, Omni International, Kennesaw, GA). The tissue sample tube was processed on the Bead Ruptor for 1 cycle at a speed of 5.5 m/s for 20 sec; and repeated up to six times until the sample was completely homogenized. All homogenized lysates were extracted for total RNA using the RNeasy Microarray Tissue Mini kit (Qiagen, Germantown, MD). Extracted RNA was DNase-treated and purified using the RNA Clean and Concentrator-5 kit (Zymo Research, Irvine, CA), then assessed for RNA quality using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: age at irradiation (years)

value: irradiated

tag: survival status

value: survivor


title: Survivor 1 (Irradiated) (E3)


title: Survivor 4 (Irradiated) (H3)


title: C17_Ekc

description: human epidermal keratinocytes

source_name: human epidermal keratinocytes

tag: cell type


title: Survivor 2 (Irradiated) (F3)

tag: tissue


title: Survivor 3 (Irradiated) (G1)


title: Survivor 2 (Irradiated) (F2)


title: Survivor 2 (Irradiated) (F1)


title: Survivor 4 (Irradiated) (H1)


title: Survivor 3 (Irradiated) (G2)


title: C7_HepG2

value: Cancer cell line


title: Survivor 3 (Irradiated) (G3)


title: Survivor 4 (Irradiated) (H2)


title: C9_Jurkat

description: Jurkat

source_name: Jurkat


title: C12_HDF TIG120

description: TIG120 human dermal fibroblasts

source_name: TIG120 human dermal fibroblasts


title: C6_MCF7


title: C3_585A1

description: 585A1 human induced pluripotent stem cell line

value: Pluripotent stem cell line


title: C8_HeLa

description: HeLa

source_name: HeLa


title: Survivor 1 (Irradiated) (E1)


title: C15_PrEC

description: human prostate epithelial cells

source_name: human prostate epithelial cells


title: C11_DP74

description: DP74 dental pulp-derived mesenchymal stem cells


title: C16_Hepatocyte

description: human hepatocytes

source_name: human hepatocytes


title: C4_2102Ep4D3

description: 2102Ep4D3 human embryonic carcinoma cell line


title: C1_H9

description: H9 human embryonic stem cell line

source_name: H9 human embryonic stem cell line


title: C10_AdMSC

description: Adipose tissue-derived mesenchymal stem cells


title: C5_NTERA2 clone D1

description: NTERA2 (clone D1) human embryonic carcinoma cell line


title: C2_201B7

description: 201B7 human induced pluripotent stem cell line


title: Non-survivor 4 (Irradiated) (D3)

value: Non-survivor


title: Non-survivor 4 (Irradiated) (D2)


title: Non-survivor 3 (Irradiated) (C2)


title: Non-survivor 4 (Irradiated) (D1)


title: Control 3 (C3-1)

value: control


title: Control 1 (C1-1)


title: Non-survivor 2 (Irradiated) (B2)


title: Non-survivor 2 (Irradiated) (B3)


title: Non-survivor 1 (Irradiated) (A1)


title: Control 1 (C1-2)


title: Non-survivor 2 (Irradiated) (B1)


title: C13_PBMC

description: human peripheral blood mononuclear cells


title: Non-survivor 1 (Irradiated) (A2)


title: Non-survivor 3 (Irradiated) (C3)


title: Ctr_WildTypeSarA

city: Hanover

first: Liviu

last: Cengher

state: NH

address: 45 Dewey Field Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine

data_processing:
Basecalling using Illumina Native App
Reads were mapped to the S. aureus NCTC8325 genome (NC_007795.1) using CLC Genomics Workbench 11
An initial maximum P-value of 0.1 for peak calling using CLC Genomics workbench 11
Peaks were annotated using the S. aureus NCTC8325 (NC_007795.1) genome using CLC Genomics workbench 11
Genome_build: NC_007795.1
Supplementary_files_format_and_content: Peak Text Files

organism: Staphylococcus aureus

source_name: RNA from ChIP

growth_protocol: Strains with pSK236:SarA-Myc were grown at 37C to post-exponential phase (~4 hr) in TSB with 10  μg per ml of chloramphenicol

extract_protocol:
Cells were treated with 1% formaldehyde and lysed by sonication, followed by cytosolic fraction harvesting, and DNA sheering by sonication for an fragment size between 200-500 bp. Followed by extraction, decrosslinking, and purification of DNA. Three replicates were pooled for further analysis.
Libraries were prepared according to Illumina's  DNA Sample Kit. 50 ng of total DNA was used for the library preparation and the libraries were pooled at equimolarity and loaded at 2 nM for clustering.

treatment_protocol: Sheared SarA-Myc tag cross-linked protein-DNA complex was immunoprecipitated with or without an anti-Myc antibody

tag: strain

value: Control, No Pulldown


title: IL12-GEMy Cell Product

city: Bethesda

first: Rosandra

last: Kaplan

state: Maryland

address: 10 Center Drive

department: Pediatric Oncology Branch

institute: National Institute of Health

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 whole genome using STAR 2.7.3a built in Partek Flow
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Partek E/M model
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: C57BL/6 mice were injected orthotopically with 5E5 M3-9-M ffluc-mCherry rhabdomyosarcoma tumor cells in the gastrocnemius muscle of the leg.

extract_protocol:
Lungs were harvested 3 days post IL12-GEMy treatment, 15 days post primary tumor inoculation. Flash frozen lungs were homogenized in TRIzol and RNA was isolated by chloroform extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 8E6 IL12-secreting genetically engineered myeloid cells (IL12-GEMys) intravenously on day 12 post tumor inoculation.

tag: disease state

value: naive

value: Lentiviral Transduction+SCF+FLT3L+IL-6

value: Bone Marrow


title: Control 3 (C3-2)


title: Non-survivor 1 (Irradiated) (A3)


title: No Tumor No Treatment 4

source_name: Naïve_No Treatment_Lung

value: No Treatment

value: lung


title: Tumor No Treatment 4

source_name: M3-9-M Tumor-Bearing_No Treatment_Lung

value: M3-9-M Tumor-Bearing


title: Exp_SarAknockout

value: DsarA HG003

value: sarA-Myc Pulldown


title: Tumor No Treatment 3


title: Tumor+IL12-GEMy 3

source_name: M3-9-M Tumor-Bearing_IL12-GEMy_Lung


title: No Tumor No Treatment 3


title: Tumor+IL12-GEMy 4


title: No Tumor+IL12-GEMy 4


title: No Tumor+IL12-GEMy 3


title: Tumor+IL12-GEMy 2


title: Control 2 (C2-2)


title: Non-survivor 3 (Irradiated) (C1)


title: Tumor No Treatment 2


title: Control 2 (C2-1)


title: No Tumor+IL12-GEMy 2


title: No Tumor No Treatment 2


title: Tumor No Treatment 1


title: No Tumor+IL12-GEMy 1


title: No Tumor No Treatment 1

source_name: naïve_No Treatment_Lung