title: RNAseq Invitro Ad GFP sample2


title: H3K27me3_CORT_2_15w

status: Public on Sep 03 2021

type: SRA

city: Barcelona

first: Mar

last: Gonzalez-Ramirez

address: C/ Dr Aiguader 88

country: Spain

institute: Center for Genomic Regulation (CRG)

library_source: genomic

data_processing:
RNA-seq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ChIP-seq analysis: Alignment: Sequence reads of the samples with spike-in were mapped to a synthetic genome containing the mouse and the fruit fly chromosomes (mm9+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bedgraph: Genome-wide ChIP-seq/RNA-seq.
Supplementary_files_format_and_content: *.bed: ChIP-seq peaks.
Supplementary_files_format_and_content: *.txt: Output files DESeq2 and DiffBind:
Supplementary_files_format_and_content: CORT-VEH_5W_results.txt: DESeq2 differential analysis
Supplementary_files_format_and_content: CORT-VEH_15W_results.txt: DESeq2 differential analysis
Supplementary_files_format_and_content: mouse_FPKMs.txt: FPKMs
Supplementary_files_format_and_content: H3K27ac_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27ac_CORT15_2-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27ac_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27ac_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27ac_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27me3_CORT15-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K27me3_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_CORT15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K27me3_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_CORT5-VEH5_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K4me3_CORT15-VEH15_DPeaks_results.txt: DiffBind differential analysis
Supplementary_files_format_and_content: H3K4me3_Peaks_CORT5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_CORT15_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_VEH5_results.txt: DiffBind differential analysis vs. Input
Supplementary_files_format_and_content: H3K4me3_Peaks_VEH15_results.txt: DiffBind differential analysis vs. Input

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
For RNAseq: RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen).
For ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013).
Libraries were prepared according to Illumina instructions.

treatment_protocol: CORT mice were treated with corticosterone as described in PMID: 31117053.

tag: tissue

value: visceral adipose tissue

tag: status

value: CS (recovery)

tag: chip antibody

value: H3K27me3 (Millipore #07–449)

tag: drosophila spike-in

value: YES


city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
Nnat+/-p female PVN chow Diet, Sample 11
SLX-13087_pvn_raw_count.tsv

library_source: transcriptomic

data_processing:
STAR 2.5.0a was used to map the fastq reads to the mouse GRCm38 genome and the gene-level count was also performed using the same software
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count in text delimited format

molecule: total RNA

source_name: PVN

extract_protocol:
Fresh frozen brains were collected from Nnat+/+ and Nnat+/-p male mice between 13 and 14 weeks of age. Coronal sections of 20-μm thickness were prepared on a cryostat (Bright OTF5000 cryostat) and mounted on RNase-free membrane-coated glass slides (Superfrost Plus, Thermo Fisher Scientific). Brain sections were fixed in 95% ethanol (30 seconds) and rehydrated in an ethanol series (75% ethanol, 50% ethanol) prior to staining with cresyl violet (Ambion). Sections were then dehydrated in another ethanol series of 50%, 75%, 95%, and 100% ethanol and left to air dry prior to laser capture. PVN and ARC, were then dissected using a PALM Microbeam Laser Capture Microdissection System (Zeiss) on a ×5 objective as previously described [18]. Briefly, tissues were captured on AdhesiveCap Clear PCR tubes (Zeiss) and stored in 80μl of QIAzol (QIAGEN) on dry ice prior to RNA extraction. Laser capture and subsequent cDNA library preparation were performed. RNA from laser-captured nuclei was extracted using the miRNeasy Micro RNA Extraction Kit (QIAGEN). Quality and quantity of the samples were then checked on an Agilent 2100 Bioanalyzer using Agilent RNA 600 pico and/or nano chips, with a typical sample RNA concentration in the range of 1 to 5 ng/μl.
RNA libraries were prepared for sequencing using Takara Clontech Smartseq Pico Input V2 reagents according to manufacturer's instruction

tag: strain

tag: genotype

value: Nnat+/-p

value: PVN

tag: Sex

value: female

tag: diet

value: chow

tag: age

value: adult

tag: weight (g)


title: H3K27me3_VEH_2_5w

value: VEH (active)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B2b_030620

city: Bethesda

first: Chao-Jung

last: Wu

state: MD

address: 9000 Rockville Pike

country: USA

institute: NIH

data_processing:
Paired-end data were processed as single-end for alignment and quantification. Cutadapt v3.4 was used to extract the first 75 bp of the read 1 (command line options -j 0 -l 75)
Single-end and processed paired-end data were quality filtered and adapter trimmed using trimgalore v0.6.6 using "-j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC" command line options.
Reads were aligned to CP052845.1 reference genome using bwa mem v0.7.17 with default parameters.
CDS mapping reads were counted using htseq v0.11.4 with "--stranded reverse" and "--mode union" arguments (comand line options -i locus_tag -t CDS -f bam -s reverse -m union)
Genome_build: CP052845.1
Supplementary_files_format_and_content: htseq-count tab-delimited file includes CDS locus tag and counts.

organism: Bordetella hinzii

source_name: Liquid culture (LB broth)

growth_protocol: Single colony was inoculated into 10 ml LB broth in a 50 ml falcon tube, and incubated overnight at 37 ℃ with 220 rpm shaking. Overnight culture was diluted to OD600 = 0.01 in 15 ml LB broth in a vented 50 ml falcon tube and grown at 37℃ with 220 rpm shaking. After 4 or 10 hours, the bacterial culture was mixed with 2 volumes of RNAprotect prior to RNA extraction.

extract_protocol:
Total RNA was extracted using MagMAX Viral/Pathogen kit with additional DNase I treatment step on a KingFisher instrument (Thermo-Fisher).
Total RNA samples underwent rRNA depletion using NEBNext rRNA Depletion kit (Bacteria) (E7850). RNA-Seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760).

tag: isolate

tag: growth time


title: Nnat+/-p female PVN chow Diet, Sample 9

description:
Nnat+/-p female PVN chow Diet, Sample 9
SLX-13087_pvn_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G1_030320


title: RNAseq Invitro Ad GFP sample1

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

data_processing:
Raw reads were assessed for quality, adaptor content and duplication rates with FastQC 0.11.8,
Reads were trimmed by Cutadapt 1.18
Reads  were terminally aligned to the Ensemble mouse genome version mm10 (GRCm38) by HISAT2 2.1.0. for RNAseq or by Picard 2.18.15 for ATACseq
For ATACseq, regions of open chromatin were identified by MACS2 2.1.2 while HOMER was used for peak annotation. Differentially peaks near the Transcriptional Start Site (TSS ± 500 bp) were identified using DESeq2 3.6 (p < 0.01).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files include normalized RPKM values. ATACseq:  Bigwig files

source_name: Primary myoblasts

growth_protocol: Cells were cultured on collagen-coated dishes with HAM’s F10 medium (Gibco), 20% Fetal Bovine Serum (FBS), 1:10000 Fibroblast Growth Factor (FGF) and 1% penicillin/streptomycin and kept in an incubator (37ºC, 5% CO2)

extract_protocol: Total RNA was isolated from cultured satellite cells with the RNeasy Micro kit (QIAGEN) with on-column DNA digestion

treatment_protocol: Cells were harvested from culture

tag: cell type

value: Satellite cell-derived primary myoblasts cultured in proliferative conditions

value: young (2-4 months old)

tag: muscle state

value: resting non-injured muscle

tag: treatment

value: Adenovirus GFP 72h


title: RNAseq Invitro Ad GFP sample3


title: H3K27me3_CORT_1_15w


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B2b_030320


title: AD2669_KIF_3m: Hippocampal sample from App-NL-F mouse

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

description: Mouse hippocampal sample - App-NL-F_3m

data_processing:
FastQ files were aligned against the GRCm38/mm10 and GENCODE vM15 genome annotations using the STAR software v2.3.0e and the following parameter values: outFilterMismatchNoverLmax=0.05; outFilterMatchNmin=25.  MAPT, PSEN1, and APP humanized and/or mutated sequences were included according to the genotype of the mouse model analyzed.
Aligned BAM files were sorted and indexed using sambamba v0.7.1
RPKM estimations per isoforms were computed with the R package casper which were then aggregated at the gene level (Ensembl)
RPKM matrix was log2-transformed and quantile normalized
Differential expression was performed with the R package limma
Genome_build: GRCm38/mm10 and GENCODE vM15. MAPT, PSEN1, and APP humanized and/or mutated sequences were included according to the genotype of the mouse model analyzed.
Supplementary_files_format_and_content: RPKM estimations per gene (Ensembl) as computed by the casper R package

molecule: polyA RNA

source_name: Hippocampal sample from App-NL-F mouse

growth_protocol: Mice were maintained under standard housing conditions on a 12hr light/dark cycle, with water and food ad libitum.

extract_protocol:
Total RNA was extracted from mouse hippocampal samples using a RNeasy Mini kit (Qiagen), according to the manufacturer’s protocol and were sent for whole transcriptome sequencing at the Centro Nacional de Análisis Genómico (CNAG-CRG). Total RNA was assayed for quantity and quality using Qubit RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
The RNA-Seq libraries were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina Platforms (Roche-Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The first strand cDNA was synthesized using random priming. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double-stranded cDNA was 3’adenylated and Illumina indexed adapters (Illumina) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.
Each library was paired-end sequenced using TruSeq SBS Kit v4-HS, with a read length of 2x76bp. On average, we generated 53 million paired-end reads for each of the 48 samples of AppNL-F, AppNL-G-F, and WT mice in a fraction of a sequencing lane on HiSeq2000 (Illumina, Inc) following the manufacturer’s protocol. Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.64) and followed by generation of FASTQ sequence files by CASAVA.

treatment_protocol: Untreated mice.

tag: sample id

tag: processing batch

value: App-NL-F

tag: condition

value: hippocampus


title: AD2671_KIF_18m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_18m

tag: tissue


title: AD2668_wt_18m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_18m

source_name: Hippocampal sample from WT mouse

value: WT


title: Nnat+/-p female PVN chow Diet, Sample 8

description:
Nnat+/-p female PVN chow Diet, Sample 8
SLX-13087_pvn_raw_count.tsv


title: H3K27me3_CORT_1_5w

value: visceral adipose tissue

tag: status

value: CS (active)

tag: chip antibody


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_030420


title: H3K27ac_VEH_2_15w

value: VEH (recovery)

value: H3K27ac (Millipore #07-360)

tag: drosophila spike-in


description:
Wild-type female PVN chow Diet, Sample 5
SLX-13087_pvn_raw_count.tsv

tag: strain

tag: genotype

value: Wild-type


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B2b_030420


title: H3K27ac_VEH_1_15w

value: YES


title: Nnat+/-p female PVN chow Diet, Sample 7

description:
Nnat+/-p female PVN chow Diet, Sample 7
SLX-13087_pvn_raw_count.tsv

value: Nnat+/-p

value: PVN

tag: Sex

value: female

tag: diet


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_030620


description:
Wild-type female PVN chow Diet, Sample 3
SLX-13087_pvn_raw_count.tsv

value: chow

tag: age

value: adult

tag: weight (g)


title: H3K27ac_VEH_2_5w

value: VEH (active)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1b_030420

tag: isolate

tag: growth time


title: H3K27me3_CORT_2_5w

value: H3K27me3 (Millipore #07–449)


title: Nnat+/-p female PVN chow Diet, Sample 6

description:
Nnat+/-p female PVN chow Diet, Sample 6
SLX-13087_pvn_raw_count.tsv


description:
Wild-type female PVN chow Diet, Sample 2
SLX-13087_pvn_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G1_030420


title: AD2670_KIF_9m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_9m


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_030320


description:
Wild-type female PVN chow Diet, Sample 4
SLX-13087_pvn_raw_count.tsv


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1b_030620


title: AD2667_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m


description:
Wild-type female PVN chow Diet, Sample 1
SLX-13087_pvn_raw_count.tsv


title: AD2665_KIF_18m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_18m


title: H3K27ac_CORT_1_15w

value: CS (recovery)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1b_030320


title: AD2664_KIF_9m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_9m

value: App-NL-F


title: sgPC-5-1

city: Chicago

first: Simon

last: Schwoerer

address: 900 E 57th St

institute: University of Chicago

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Adapter sequences were trimmed with 'Trimmomatic' and validated read pairs were aligned to the mouse genome with 'STAR' with default parameters.
Uniquely aligned reads were used to count gene features with 'featureCounts'.
Normalization and differential expression was determined using the 'DESeq2' package.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text of normalized RPKM values per gene

source_name: NIH-3T3 cells

growth_protocol: NIH-3T3 cells (ATCC CRL-1658) growingn in DMEM containing 10% FBS and 1% P/S were infected with lentivirus to express R26 sg1, PC sg2, PC sg5 and Cas9.  Infected cells were selected with 2 ug/mL Puromycin. Polycolonal cells were used fro experiments.

extract_protocol:
RNA was isolated from cells using Trizol reagent
Libraries were prepared from poly-A+ RNA with the NEBNext Ultra RNA library prep kit.

treatment_protocol: Cells were seeded at 0.25e6 cells per mL in DMEM containing 10% FBS and 1% P/S.  The next day cells were washed with PBS, and treatment media (DMEM without L-glutamine, supplemented with 0.2 mM L-glutamine, 10% dialyzed FBS and 1% P/S) was added. Cells were cultured in treatment media for 48h.

value: NIH/Swiss

tag: cell line

tag: medium

value: 0.2 mM glutamine

tag: group

value: PC-ko


title: AD2662_wt_18m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_18m

tag: sample id

tag: processing batch

value: WT

value: hippocampus


title: H3K27ac_CORT_2_15w

tag: tissue

value: visceral adipose tissue

value: H3K27ac (Millipore #07-360)


title: sgPC-2-2


title: AD2666_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

tag: condition


title: H3K27ac_CORT_1_5w

tag: status

value: CS (active)

tag: chip antibody

value: YES


title: AD2663_KIF_3m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_3m


title: AD2660_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1a_030320


title: AD2661_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m


title: sgR26-1-2

tag: strain

value: control


title: sgPC-5-2


title: RNAseq_VEH_5_15w

value: VEH (recovery)

tag: drosophila spike-in

value: NO


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h2B3_020420.2


title: H3K27ac_CORT_2_5w


title: H3K27ac_VEH_1_5w


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h2B3_020420.3


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1a_030620


title: RNAseq_VEH_2_15w


title: AD2659_KIF_18m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_18m

tag: genotype


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1B1a_030420


title: sgPC-2-1


title: AD2658_KIF_9m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_9m


title: RNAseq_VEH_3_15w


title: RNAseq_VEH_1_15w


title: RNAseq_VEH_5_5w


title: X10w_1_input

city: Baltimore

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner.
Reads counts were calculated for each sample.
Differential expression of genes were computed between control samples and noise exposed samples (6h and 24h post noise).
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: *.TPM.txt: Tab-delimited text files include counts per million reads (TPM) for each sample.

extract_protocol:
RNA was extracted from whole cochlear samples (input) and following immunoprecipitation using an HA antibody (IP) to enrich for outer hair cell transcripts or supporting cell transcripts following the protocol outlined in Sanz et al., 2009.
RNA-seq libraries were prepared in biological triplicates using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer's instructions.

tag: cell type

value: Whole cochlea

value: 10 weeks

tag: treatment

tag: antibody


title: sgR26-1-1


title: RNAseq_VEH_4_15w


title: X10w_4_input

tag: age


title: AD2656_wt_18m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_18m


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h1G2_020420.2

tag: isolate

tag: growth time


title: AD2655_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h2B3_020420.3


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h1G2_020420.3


title: RNAseq_VEH_4_5w

value: VEH (active)


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h1G2_020420.1


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h2B3_020420.1


title: AD2653_KIF_18m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_18m


title: X10w_4_IP

value: Supporting cells (enriched)

value: HA antibody


title: AD2652_KIF_9m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_9m

value: App-NL-F


title: AD2651_KIF_3m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_3m


title: RNA-Seq of Bordetella hinzii isolates, sample: 8h2B3_020420.1


title: XN6h_2_IP

value: 105dB SPL noise for 2h

tag: time point

value: 6h following noise exposure


title: AD2650_wt_18m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_18m

value: WT


title: XN6h_4_input


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h2B3_020420.2


title: X10w_1_IP


title: AD2649_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m

value: hippocampus


title: XN6h_4_IP


title: AD2657_KIF_3m: Hippocampal sample from App-NL-F mouse

description: Mouse hippocampal sample - App-NL-F_3m


title: XN24h_3_input

value: 24h following noise exposure


title: XN24h_3_IP


title: RNAseq_VEH_3_5w

value: visceral adipose tissue


title: RNAseq_VEH_2_5w


title: AD2648_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m


title: AD2647_KI_9m: Hippocampal sample from App-NL-G-F mouse

description: Mouse hippocampal sample - App-NL-G-F_9m

value: App-NL-G-F


title: AD2654_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_020420.2


title: XN24h_2_IP


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_020420.1


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1G2_020420.3


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1G2_020420.2


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G2_020420.3


title: XN24h_1_input


title: RNAseq_CORT_2_15w

value: CS (recovery)


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G2_020420.2


title: RNAseq_VEH_1_5w


title: XN24h_1_IP


title: AD2644_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m


title: NN6h_3_input

source_name: PrestinCre/+;RiboTagHA/+

value: PrestinCre/+;RiboTagHA/+


title: XN6h_2_input


title: RNAseq_CORT_2_5w

value: CS (active)


title: RNAseq_CORT_3_15w

value: NO


title: AD2643_wt_6m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_6m


title: RNAseq_CORT_4_15w


title: AD2645_KI_3m: Hippocampal sample from App-NL-G-F mouse

description: Mouse hippocampal sample - App-NL-G-F_3m


title: RNA-Seq of Bordetella hinzii isolates, sample: 2h2B3_020420.2


title: RNAseq_CORT_5_15w


title: NN6h_2_input

value: Whole cochlea


title: RNA-Seq of Bordetella hinzii isolates, sample: 6h1G2_020420.1


title: RNAseq_CORT_1_15w


title: 12 hours (10_12.1)

city: Rome

first: Giscard

middle: Humberto Oliveira

last: Lima

address: Piazza Lauro de Bosis, 15

country: Italy

institute: University of Rome Foro Italico

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole human genome using STAR 2.5.3 with default parameters
Gene counts, were obtained by an annotation model based on RefSeq Transcripts (release 96) and normalized by Fragments Per Kilobase Million (FPKM) and by adding 0.0001 to all read counts, to allow statistical testing.
Differential gene expression was determined by Partek Gene Set Analysis (GSA) using default settings.
Genome_build: Human Genome GRCh37 reference (hg19)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Healthy male

extract_protocol:
Whole blood samples were collected and stored tubes and K2EDTA tubes at 4C, then incubated at room temperture for 1 hour. After storage, samples were extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard MGI DNBSEQ-G400RS  protocols; DNBSEQ-G400RS sequencer.

value: Whole blood

tag: Sex

value: male

tag: group

value: EDTA

tag: time

value: short-term storage (12 hours)


title: AD2641_KI_9m: Hippocampal sample from App-NL-G-F mouse

tag: sample id

tag: processing batch

tag: tissue


title: RNA-Seq of Bordetella hinzii isolates, sample: 2h2B3_020420.1


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h1G2_020420.1


title: RNA-Seq of Bordetella hinzii isolates, sample: 2h1G2_020420.3


title: NN6h_1_input

value: 10 weeks


title: RNAseq_CORT_5_5w

tag: status


title: 12 hours (9_12.1)


title: XN24h_2_input

value: 105dB SPL noise for 2h


title: AD2640_KI_6m: Hippocampal sample from App-NL-G-F mouse

description: Mouse hippocampal sample - App-NL-G-F_6m

tag: condition


title: RNA-Seq of Bordetella hinzii isolates, sample: 4h2B3_020420.3


title: 48 hours (6_48.1)

value: short-term storage (48 hours)


title: RNAseq_CORT_3_5w

tag: drosophila spike-in


title: RNA-Seq of Bordetella hinzii isolates, sample: 2h2B3_020420.3


title: AD2646_KI_6m: Hippocampal sample from App-NL-G-F mouse

tag: genotype


title: NN6h_2_IP

tag: cell type

value: Outer Hair cells (enriched)

value: 6h following noise exposure

value: HA antibody


title: RNAseq_CORT_1_5w

value: visceral adipose tissue


title: AD2642_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

value: WT

value: hippocampus


title: NN6h_1_IP

value: PrestinCre/+;RiboTagHA/+

tag: treatment


title: RNAseq_CORT_4_5w

value: CS (active)


title: 48 hours (8_48.1)


title: NN6h_3_IP

tag: antibody


title: AD2639_KI_3m: Hippocampal sample from App-NL-G-F mouse

value: App-NL-G-F

tag: age


title: AD2637_wt_6m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_6m


title: RNA-Seq of Bordetella hinzii isolates, sample: 12h2B3_020420.2

tag: isolate


title: 48 hours (9_48.1)


title: RNA-Seq of Bordetella hinzii isolates, sample: 2h1G2_020420.2

tag: growth time


title: AD2638_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m


title: AD2636_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m


title: 6 hours (10_6.1)

value: short-term storage (6 hours)


title: RNA-Seq of Bordetella hinzii isolates, sample: 2h1G2_020420.1


title: RNA-Seq of Bordetella hinzii isolates, sample: 12h2B3_020420.3


title: N10w_3_IP


title: 6 hours (8_6.1)

value: Whole blood


title: RNA-Seq of Bordetella hinzii isolates, sample: 12h2B3_020420.1


title: 24 hours (9_24.1)

value: male

value: short-term storage (24 hours)


title: N10w_2_input

value: Whole cochlea


title: AD2635_KI_9m: Hippocampal sample from App-NL-G-F mouse


title: N10w_1_IP

value: 10 weeks


title: N10w_2_IP


title: AD2634_KI_6m: Hippocampal sample from App-NL-G-F mouse


title: NN24h_3_input

value: 105dB SPL noise for 2h

tag: time point

value: 24h following noise exposure


title: 12 hours (8_12.1)

tag: Sex

value: EDTA

value: short-term storage (12 hours)


title: AD2630_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m


title: NN24h_3_IP

value: Outer Hair cells (enriched)

value: HA antibody


title: 48 hours (10_48.1)

tag: group

value: short-term storage (48 hours)


title: 24 hours (6_24.1)

tag: time


title: N10w_1_input


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_020420.3


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_020420.2


title: RNA-Seq of Bordetella hinzii isolates, sample: 12h1G2_020420.2


title: N10w_3_input


title: 24 hours (8_24.1)


title: AD2632_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m

tag: sample id

value: WT

value: hippocampus


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_020420.1


title: AD2633_KI_3m: Hippocampal sample from App-NL-G-F mouse

tag: processing batch


title: AD2631_wt_6m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_6m

tag: tissue


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G2_020420.3


title: RNA-Seq of Bordetella hinzii isolates, sample: 12h1G2_020420.3


title: NN24h_2_input

value: PrestinCre/+;RiboTagHA/+


title: AD2629_KI_9m: Hippocampal sample from App-NL-G-F mouse

value: App-NL-G-F


title: 6 hours (9_6.1)

value: short-term storage (6 hours)


title: AD2627_KI_3m: Hippocampal sample from App-NL-G-F mouse


title: 6 hours (6_6.1)

value: Whole blood


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G2_020420.2


title: 12 hours (6_12.1)

value: male


title: 24 hours (10_24.1)

value: short-term storage (24 hours)


title: NN24h_2_IP


title: S12_EDTA

data_processing:
DNBSEQ-G400 sequencer  built-in software (UI software) was used for base calling sequenced read
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole human genome using STAR 2.5.3 with default parameters
Gene counts, were obtained by an annotation model based on RefSeq Transcripts (release 96) and normalized by Fragments Per Kilobase Million (FPKM) and by adding 0.0001 to all read counts, to allow statistical testing.
Differential gene expression was determined by Partek Gene Set Analysis (GSA) using default settings.
Genome_build: Human Genome GRCh37 reference (hg19)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Whole blood samples were collected and stored (−80°C) into Tempus™ tubes and K2EDTA tubes. After storage, Tempus™ and K2EDTA tubes were thawed at room temperature. Blood was transferred from K2EDTA tubes into new Tempus™ tube, and then extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard MGI DNBSEQ-G400RS  protocols; DNBSEQ-G400RS sequencer.

value: long-term storage


title: S12_Tempus

value: Tempus


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h8B1_112019


title: S10_Tempus


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h8B1_111819


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h7B1_112019


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G2_020420.1


title: NN24h_1_input

value: Whole cochlea

value: 10 weeks

value: 105dB SPL noise for 2h


title: S10_EDTA

value: EDTA


title: AD2625_wt_6m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_6m


title: S7_Tempus


title: NN24h_1_IP

value: Outer Hair cells (enriched)

value: 24h following noise exposure


title: RNA-Seq of Bordetella hinzii isolates, sample: 12h1G2_020420.1


title: NLGF747: Hippocampal sample from AppNL-G-F penbu treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Penbu

extract_protocol:
Total RNA was extracted from mouse hippocampal samples using a RNeasy Mini kit (Qiagen), according to the manufacturer’s protocol and were sent for whole transcriptome sequencing at the Centro Nacional de Análisis Genómico (CNAG-CRG). Total RNA was assayed for quantity and quality using Qubit RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
The RNA-Seq libraries were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina Platforms (Roche-Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The first strand cDNA was synthesized using random priming. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double-stranded cDNA was 3’adenylated and Illumina indexed adapters (Illumina) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.
Each library was paired-end sequenced using TruSeq SBS Kit v4-HS, with a read length of 2x76bp. On average, we generated 39 million paired-end reads for each of the 32 AppNL-G-F and WT mice in a fraction of a sequencing lane on HiSeq2000 (Illumina, Inc) following the manufacturer’s protocol. Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.64) and followed by generation of FASTQ sequence files by CASAVA.

treatment_protocol: During the treatment period, AppNL-G-F mice received a daily intraperitoneal injection of the indicated drugs for 4 weeks. Etodolac (50 mg/kg), dexketoprofen (15 mg/kg), fenoprofen (50 mg/kg) and bendroflumethiazide (20 mg/kg) were dissolved in a mixture of 5%Tween-80 (Sigma-Aldrich), 25% propylene glycol (Sigma-Aldrich), 25% Poly(ethylene glycol) (Sigma-Aldrich) and 45% phosphate buffered saline (PBS). Penbutolol (20 mg/kg) and pargyline (20 mg/kg) were dissolved in PBS (veh.2). The drug doses were chosen according to previous publications on these compounds or on similar compounds76-81. Groups of Appwt/wt and AppNL-G-F mice were also treated with the vehicles.

tag: biological replicate

tag: vehicle

value: AppNL-G-F

value: Penbu treated


title: AD2624_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

value: WT

tag: condition

value: hippocampus


title: AD2628_KI_6m: Hippocampal sample from App-NL-G-F mouse

tag: genotype

value: App-NL-G-F


title: AD2626_wt_9m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_9m


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h7B1_111919


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h8B1_111919


title: NLGF579: Hippocampal sample from AppNL-G-F etodolac treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Etodolac

value: Etodolac treated


title: S7_EDTA

value: Whole blood


title: S6_Tempus

value: male


title: NLGF757: Hippocampal sample from AppNL-G-F not-treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Not.treated

value: Not-treated


title: NLGF714: Hippocampal sample from AppNL-G-F dexketo treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Dexketo

value: Dexketo treated


title: S6_EDTA

value: long-term storage


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h5G1a_112019


title: S5_EDTA


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h7B1_111819


title: NLGF489: Hippocampal sample from AppNL-G-F bendro treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Bendro

value: Bendro treated


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h5G1a_111919


title: WT394: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT


title: S3_Tempus

value: Tempus


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51784_112019

tag: strain


title: scRNAseq of root tips growing with nitrate

city: Guangzhou

first: Li

middle: Xu

last: Hui

state: Guangdong

address: #10 Shiliugang

country: China

institute: Guangdong Academy of Science

data_processing:
The raw reads were aligned to the B73 reference genome, and gene expression was quantified using the Cell Ranger pipelines (v3.1, 10× Genomics).
Genome_build: Zea_mays.B73_RefGen_v4.42
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and ervey cell or sample

organism: Zea mays

source_name: root tips growning with nitrate

extract_protocol:
primary roots were sampled and cut into small pieces of approximately 0.5mm and then digested in protoplasting solution (1.25% cellulase R10, 0.3% macerozyme R10, 400 mM mannitol, 20 mM 4-morpholineethanesulfonic acid, 20 mM KCl, 10 mM CaCl2 and 0.1% BSA).
RNA library were perpared with the Chromium Single Cell 3’ Reagent Kit v3 according to the manufacturer's protocol.

treatment_protocol: Twenty sterilized B73 seeds (sterilized with 1% sodium hypochlorite) were placed on germination paper, which was soaked in nutrient solution (nitrate+) with 4 mM Ca(NO3)2, 0.75 mM K2SO4, 0.65 mM MgSO4, 0.1 mM KCl, 0.25 mM KH2PO4, 0.01 mM H3BO3, 0.001 mM MnSO4, 0.0001 mM CuSO4, 0.001 mM ZnSO4, 0.000001 mM (NH4)6Mo7O24, and 0.1 mM FeNa-EDTA . Then, the germination papers were rolled and placed vertically in a sealed plastic bag. The paper roll was incubated at 25?/22? with an 8h light/16h dark cycle for 4 days. For nitrate deficiency treatment (nitrate-), the Ca(NO3)2 in nutrient solution had been replaced by an equal concentration of CaCl2.

value: 2cm root tips

value: four days after germination

tag: treatment

value: with nitrate


title: NLGF746: Hippocampal sample from AppNL-G-F penbu treated mouse


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51783_112019


title: WT297: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT


title: S3_EDTA

value: EDTA


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h5G1a_111819


title: S1_Tempus


title: NLGF530: Hippocampal sample from AppNL-G-F etodolac treated mouse

value: AppNL-G-F


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51784_111819


title: NLGF379: Hippocampal sample from AppNL-G-F not-treated mouse


title: S5_Tempus


title: scRNAseq of root tips growing without nitrate

source_name: root tips growning without nitrate

value: without nitrate


title: WT333: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT

value: WT


title: S1_EDTA


title: NLGF756: Hippocampal sample from AppNL-G-F not-treated mouse

value: hippocampus


title: PPMV

city: Toronto

first: Yasaman

last: Aghazadeh

state: ON

address: 101, College St

country: Canada

institute: McEwen Stem Cell Institute

description: Unspliced RNA

data_processing:
Considering that any ambiguously assigned reads (e.g. for homologous genes) are removed from the data and do not contribute towards UMI counts and are not in the final read matrix, we removed the INS-IGF2 entries from the human GTF file to unmask the INS transcripts.
The UMIs were generated using cellranger (v3.1). A custom reference was used. To create a reference for multiple species, we used the mkref command with multiple FASTA and GTF files for mm10, Ratus6.0.98 and GRCh38. The single-nuclei RNA-seq assay captures unspliced pre-mRNA as well as mature mRNA. However, after alignment, cellranger count only counts reads aligned to exons. Since the pre-mRNA will generate intronic reads, it may be useful to count these reads as well. As recommended by 10xGenomics, we created three custom “pre-mRNA” GTF files, listing each gene transcript locus as an exon, in order to count intronic reads.   Considering that any ambiguously assigned reads (e.g. for homologous genes) are removed from the data and don’t go towards UMI counts and are not in the final read matrix, we removed the INS-IGF2 entries from the human GTF file to unmask the INS transcripts.
The distribution of total features detected in each reference genome per cell were analyzed to determine thresholds for assigning species identity (data not shown). Nuclei were assigned as either originating from human, mouse or rat if the feature count from the respective genome was over 1000, 300, or 200 features. 5421 human, 2862 mouse, and 334 rat cells were identified. 3333 nuclei had feature counts below the threshold for all three organisms and were omitted. One cell passed the threshold for both the human and rat genome and was omitted
Counts were normalized (method = “LogNormalize”, scale.factor = 10 000) before scaling (ScaleData) to regress the influence from variable UMIs.
Genome_build: mm10 (mus musculus), Ratus6.0.98 (rattus norvegicus) and GRCh38 (homo sapiens)
Supplementary_files_format_and_content: CSV

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

source_name: Human embryonic stem cells differentiated to pancreatic progenitors, co-transplanted with rat adipose derived microvessels to mice.

growth_protocol: hESCs were cultured on mouse embrynic fibroblasts, using hES media and rock inhibitor.

extract_protocol:
Cells were embedded in hydrogels and transplanted in the mice. Hydrogels were reteieved adter 100 days and snap frozen. Nuceli was isolated as per 10X genomic published protocols. Details can be found : https://support.10xgenomics.com/isolation-of-nuclei
The Unique Molecular ID (UMI) were generated using Cellranger (v3.1). A custom reference for multiple species was made using the mkref command with FASTA and GTF files for mm10, Ratus6.0.98 and GRCh38. Single nuclei reads were mapped to this custom reference genome using Cellranger.  The sNuc-Seq assay captured unspliced pre-mRNA as well as mature mRNA. However, after alignment, Cellranger only counted reads aligned to exons. A three custom “pre-mRNA” GTF file was created listing each gene transcript locus as an exon, in order to count intronic reads.

treatment_protocol: hESC were differentiated to PP through a 4 step process, using "Nostro protocol" Derails published at: Korytnikov R, Nostro MC, Methods, 2016, DOI: 0.1016/j.ymeth.2015.10.017.

tag: cell type

value: Cells differentiated in vivo from PP (transplanted, human source), microvascular cells (transplanted, rat source) and cells infilterated from the mouse.

value: Host mice is Scid Beige


title: NLGF469: Hippocampal sample from AppNL-G-F dexketo treated mouse


title: HK1 DMSO treated (control)

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

state: Singapore

address: Centre for Translational Medicine,14 Medical Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
HK1-DMSO
This sample represents two replicates of HK1. Each SRR contains raw data for one replicate.

data_processing:
Mappping and statistic analysis by Juicer v.1.5.7
Genome_build: hg19
Supplementary_files_format_and_content: A highly compressed binary file that provides rapid random access to the matrices.It bin the reads which mapping quality over 30 at 9 base-pair-delimited resolutions: 2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K. It can be visualized in the Juicebox.

source_name: HK1 cell line

extract_protocol:
The clinical samples were collected by needle biopsy in a 1.5µL microtube from different sites; liver, pelvic and posterier nasal space using a needle size of 16/18G
Biopsy samples were falsh frozen in liquid nitogen follwod by pulverization using pre-cooled mortar and pestle. Biop-C library was generated using the Arima-HiC kit.

value: nasopharyngeal cancer

tag: gender

value: Male


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51784_111919


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51783_111919


title: HK1 THZ1 treated

description:
HK1-THZ1
This sample represents two replicates of HK1. Each SRR contains raw data for one replicate.


title: Normal cell line

description:
NP-69
This sample represents two replicates of HK1. Each SRR contains raw data for one replicate.

source_name: NP-69 cell line

value: Nasopharyngeal Epithelial Cell Line


title: NLGF471: Hippocampal sample from AppNL-G-F bendro treated mouse


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51783_111819


title: Mouse_FACT_H3K27ac_thickness_with_5um_rep2_mm10

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
Library strategy: FACT-seq
Adaptors were trimmed.
All reads were aligned to hg38/mm10 using bowtie2 with the following parameters "--end-to-end --very-sensitive -I 10 -X 700"
The aligned BAM files were sorted and filtered with alignment quality of >Q2 using samtools v.1.9.
The bigwig files were generated from BAM files using deeptools with the parameters "bamCoverage –normalizeUsing CPM".
H3K27me3 peaks were called using SICER with following parameters ‘gap size = 600 bp and window size = 200 bp’.
H3K27ac peaks were called using SICER with following parameters ‘gap size = 400 bp and window size = 200 bp.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: bigwig and peaks.txt files

source_name: Mouse kidney 8 weeks

growth_protocol: GM12878 cells were grown in RPMI 1640 (Gibco, 31870-025), 2 mM L-glutamine (Gibco, 25030-024), 15% fetal bovine serum (Gibco, 10270-106) and 1% Pen/Strep (Gibco, 15140-122).

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

value: FVBN

value: kidney

value: FFPE


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51730_111919


title: NPC clinical sample_Replicate1

source_name: NPC clinical sample

value: not provided


title: NPC clinical sample_Replicate2


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1d_112019

tag: isolate


title: NPC cell line

description: This sample represents two replicates of HK1. Each SRR contains raw data for one replicate.

growth_protocol: HK1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 media (Hyclone) supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS; Hyclone) and 1% penicillin/streptomycin (Hyclone) in an incubator at 5% CO2 and 37°C.

tag: age


title: NLGF404: Hippocampal sample from AppNL-G-F penbu treated mouse

value: Penbu treated


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51730_111819

tag: growth time


title: Mouse_FACT_H3K27ac_thickness_with_7um_rep1_mm10


title: WT296: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT

value: Not-treated


title: Mouse_FACT_H3K27ac_thickness_with_7um_rep2_mm10


title: NPC clinical sample_3

source_name: posterior nasal space


title: Mouse_FACT_H3K27ac_thickness_with_5um_rep1_mm10


title: Mouse_FACT_H3K27ac_thickness_with_10um_rep2_mm10


title: Mouse_FACT_H3K27ac_thickness_with_10um_rep1_mm10


title: RNA-Seq of Bordetella hinzii isolates, sample: 10hATCC51730_112019


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1d_111919


title: WT322: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT


title: NLGF377: Hippocampal sample from AppNL-G-F not-treated mouse


title: NPC clinical sample_2

source_name: Pelvic


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1d_111819


title: NLGF520: Hippocampal sample from AppNL-G-F not-treated mouse


title: Mouse_FACT_liver_rep2_mm10

source_name: Mouse liver 8 weeks

value: liver


title: NLGF521: Hippocampal sample from AppNL-G-F etodolac treated mouse

value: Etodolac treated


title: NPC clinical sample_1

source_name: Liver


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1a_111919

source_name: Liquid culture (LB broth)


title: Mouse_FACT_liver_rep1_mm10


title: Mouse_FACT_H3K4me1_with_harsh_condition_mm10


title: RNA-Seq Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

city: Montreal

first: Erwin

last: Schurr

address: 1001 boulevard Decarie

institute: McGill University Health Centre

description:
Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV27.MTB.0_RNA_R1_quant.sf

data_processing:
Basecalling was done with Illumina Casava 1.8.2 and fastq files generated via bcl2fastq v2.18.
Fastq files were trimmed to remove leftover adaptor sequences and < phred 20 bases using cutadapt v2.6.
Read alignment was performed with STAR v2.7.3a and resulting alignments in transcriptomic coordinates was input to Salmon v1.1.0 for gene expression estimation.
Gene level estimated counts matrix was created in R v3.6.1, using tximport v1.12.3 with the option “lengthScaledTPM”.
Libray depth and compositional bias scaling factors were calculated via the function calcNormFactors from edgeR v3.26.8 and used by limma’s voom function (v3.40.6) to generate the normalized log2(CPM) expression matrix.
Genome_build: GRCh38.p13 (ENSEMBL v99)
Supplementary_files_format_and_content: tab-delimited text files including transcript estimated counts and TPM values for each sample.
Supplementary_files_format_and_content: tab-delimited matrix table with raw estimated gene counts for every gene and sample (lengthScaledTPM).
Supplementary_files_format_and_content: tab-delimited matrix table with normalized gene expression in log2 scale for tested genes (created with limma's voom function). Covariates not regressed out.

source_name: bronchoalveolar lavage

extract_protocol:
Cells were lysed with Trizol and kept at -80°C until extraction.  RNA isolation was performed with miRNeasy kit and RNA integrity (RIN) was assessed with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard unstrand Illumina protocols (TruSeq RNA Library Preparation Kit v2, Set A ).

treatment_protocol: Bronchoalveolar lavage samples were filtered to remove macro contaminants and alveolar macrophages (AM) cells enrich via tube adhesion method. 1 x 106 AM cells were cultured with media (not challenged) or media + Mtb (challenged) for 20h.

tag: ethnicity

value: Caucasian

tag: Sex

value: M

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

value: not detected

tag: prescription drugs

value: Descovy, Isentress

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV26.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: age

value: Atripla

value: Emtricitabine, Tenofovir_DF, Efavirenz

value: yes


title: RNA-Seq Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV26.MTB.0_RNA_R1_quant.sf

tag: Sex

tag: sexually transmitted infections


title: NLGF385: Hippocampal sample from AppNL-G-F not-treated mouse

tag: sample id

tag: biological replicate

tag: processing batch

tag: vehicle

tag: genotype

value: AppNL-G-F

tag: treatment

tag: condition

tag: tissue

value: hippocampus


title: Mouse_FACT_H3K27ac_with_harsh_condition_mm10

tag: strain

value: FVBN

value: kidney


title: RNA-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV25.MTB.0_RNA_R1_quant.sf

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1a_112019

tag: isolate

tag: growth time


title: RNA-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV25.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G3_111919


title: RNA-Seq Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV27.MTB.1_RNA_R1_quant.sf

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G1_112019


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G3_112019


title: WT321: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT

tag: sample id

tag: biological replicate

tag: processing batch

tag: vehicle

tag: genotype

value: WT

tag: treatment

tag: condition

tag: tissue


title: WT295: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT


title: NLGF494: Hippocampal sample from AppNL-G-F not-treated mouse


title: NLGF463: Hippocampal sample from AppNL-G-F dexketo treated mouse

value: Dexketo treated


title: NLGF402: Hippocampal sample from AppNL-G-F penbu treated mouse

value: Penbu treated


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G1_111919

tag: isolate

tag: growth time


title: NLGF646: Hippocampal sample from AppNL-G-F bendro treated mouse

value: Bendro treated


title: NLGF511: Hippocampal sample from AppNL-G-F etodolac treated mouse

value: Etodolac treated


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h4G1a_111819


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G1_111819


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3G3_111819


title: Patient 1 Lung Scan 26689 A8 ROI 008

type: RNA

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

hyb_protocol: Immunoflourecent tissue profiling was performed using PanCK (488) cytokeratin, CD45 (647) immune response, CD68 (568) macrophage inflammatory response, and DAPI DNA staining to enable selection of 12 regions of interest (ROIs) for targeted spatial transcriptomics using the commercial Nanostring GeoMx.

scan_protocol: Nanostring GeoMx Digital Spatial Profiling (DSP) Platform

data_processing:
Digital Count Coversion (DCC) files are generated by GeoMx NGS Pipeline. The pipeline processed reads for high quality with adapter removal resulting in trimmed reads, and the paired-end reads were merged and aligned. Then PCR duplicates were removed by matching on the Unique Molecular Index (UMI), resulting in deduplicated reads.
Biological Probe QC was performed  to exclude outlier probes.
QC was done in two steps, first Segment QC and then Biological Probe QC.  In segment QC, raw read threshold, percent aligned reads, sequence saturation and technical background were compared to an expected range to determine the overall quality of the data. We then performed Biological Probe QC to determine the thresholds for excluding outlier probes. Once all ROIs were processed, the raw counts were Q3 normalized against housekeeping genes by averaging to the geometric mean of the internal spike-in controls by which system variation was accounted for.
Normalization was done by Nanostring's software. The raw counts were Q3 normalized against housekeeping genes by averaging to the geometric mean of the internal spike-in controls.

source_name: Lung

label_protocol: The spatial transcriptomic panel included >1600 targeted cancer transcriptome atlas panel with 27 additional SARS-CoV-2 targets added (including ORF1ab and S protein)  to encompass a comprehensive detection of host immune and inflammatory response alongside direct SARS-CoV-2 infection genes.

extract_protocol: Unstained sections were freshly cut from FFPE blocks at 4µm-thickness onto positively charged slides, stored at 4ºC.

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV23.MTB.0_RNA_R1_quant.sf

tag: ethnicity

value: Caucasian

tag: Sex

tag: age

tag: sexually transmitted infections

value: Genvoya

tag: active ingredient

value: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir

tag: art start year

tag: recreational drugs

value: cannabis

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3B1_112019

tag: isolate

tag: growth time


title: RNA-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV23.MTB.1_RNA_R1_quant.sf

value: M

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

value: not detected

tag: prescription drugs


title: NLGF460: Hippocampal sample from AppNL-G-F bendro treated mouse

tag: sample id

tag: biological replicate

tag: processing batch

tag: vehicle

tag: genotype

tag: treatment

tag: condition

tag: tissue


title: Patient 1 Lung Scan 26689 A8 ROI 009

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV21.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

tag: sexually transmitted infections

value: Truvada, Tivicay

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

value: yes

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: Patient 1 Lung Scan 26689 A8 ROI 012


title: Patient 1 Lung Scan 26689 A8 ROI 011


title: Patient 1 Lung Scan 26689 A8 ROI 010


title: Patient 1 Lung Scan 26689 A8 ROI 007


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3B1_111919

tag: isolate

tag: growth time


title: Patient 1 Lung Scan 26689 A8 ROI 006

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV20.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

value: Truvada, Tybost, Prezista

value: Emtricitabine, Tenofovir_DF, Cobiscistat, Darunavir


title: NLGF380: Hippocampal sample from AppNL-G-F not-treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Not.treated

tag: sample id

tag: biological replicate

tag: processing batch

tag: vehicle

tag: genotype

value: AppNL-G-F

tag: treatment

value: Not-treated

tag: condition

tag: tissue

value: hippocampus


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h3B1_111819

tag: isolate

tag: growth time


title: AB7705_3xTg_15m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_15m

source_name: Hippocampal sample from 3xTg mouse

extract_protocol:
Total RNA was extracted from mouse hippocampal samples using a RNeasy Mini kit (Qiagen), according to the manufacturer’s protocol and were sent for whole transcriptome sequencing at the Centro Nacional de Análisis Genómico (CNAG-CRG). Total RNA was assayed for quantity and quality using Qubit RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
The RNA-Seq libraries were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina Platforms (Roche-Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The first strand cDNA was synthesized using random priming. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double-stranded cDNA was 3’adenylated and Illumina indexed adapters (Illumina) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.
Each library was paired-end sequenced using TruSeq SBS Kit v4-HS, with a read length of 2x76bp. On average, we generated 80 million reads for each of the 24 samples of 3xTg-AD and C57BL/6x129/Sv mice in a fraction of a sequencing lane on HiSeq2000 (Illumina, Inc) following the manufacturer’s protocol. Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.64) and followed by generation of FASTQ sequence files by CASAVA.

tag: age


title: RNA-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV21.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: sexually transmitted infections

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: Patient 1 Lung Scan 26689 A8 ROI 005

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV20.MTB.0_RNA_R1_quant.sf

tag: Sex

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs


title: Patient 1 Lung Scan 26689 A8 ROI 004


title: NLGF459: Hippocampal sample from AppNL-G-F dexketo treated mouse

description: Mouse hippocampal sample - AppNL-G-F_Dexketo

tag: sample id

tag: biological replicate

tag: processing batch

tag: vehicle

tag: genotype

tag: treatment

value: Dexketo treated

tag: condition

tag: tissue


title: RNA-Seq Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV19.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: age

tag: sexually transmitted infections

value: Triumeq

tag: active ingredient

value: Abacavir, Dolutegravir, Lamivudine

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G2_112019

tag: isolate

tag: growth time


title: WT294: Hippocampal sample from WT not-treated mouse

description: Mouse hippocampal sample - WT

tag: sample id

tag: biological replicate

tag: processing batch

tag: vehicle

tag: genotype

value: WT

tag: treatment


title: Patient 1 Lung Scan 26689 A8 ROI 003

tag: scan id

tag: roi(lable)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G2_111919


title: RNA-Seq Person living with HIV sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV18.MTB.1_RNA_R1_quant.sf

tag: ethnicity

value: Caucasian

tag: Sex

tag: age

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

value: Viread, Tivicay, 3TC

tag: active ingredient

value: Tenofovir_DF, Dolutegravir, Lamivudine

tag: art start year

tag: recreational drugs

tag: lane


title: Patient 1 Lung Scan 26689 A8 ROI 002


title: AB7704_3xTg_8m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_8m

tag: sample id

tag: processing batch

tag: condition

tag: tissue


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G1_112019

tag: isolate

tag: growth time


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G2_111819


title: RNA-Seq Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV19.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: M

value: cannabis

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run


title: RNA-Seq Person living with HIV sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV18.MTB.0_RNA_R1_quant.sf

tag: age

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

value: not detected

tag: prescription drugs

tag: active ingredient

tag: art start year


title: AB7702_wt_15m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_15m

source_name: Hippocampal sample from WT mouse

tag: sample id

tag: processing batch

tag: genotype

tag: condition

tag: tissue


title: AB7707_3xTg_3m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_3m


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G1_111919

tag: isolate

tag: growth time


title: RNA-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV17.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: Viread, Tivicay, Edurant

value: Tenofovir_DF, Dolutegravir, Rilpivirine

tag: recreational drugs

tag: cigarette smoker

value: yes

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: Patient 1 Lung Scan 26689 A8 ROI 001

tag: scan id

tag: roi(lable)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2G1_111819


title: AB7701_wt_8m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_8m

tag: sample id

tag: processing batch

tag: age


title: Patient 1 Kidney Scan 26689 A5 ROI 012

source_name: Kidney


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_112019


title: RNA-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV17.MTB.0_RNA_R1_quant.sf

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: sequencing run


title: AB7700_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

tag: genotype

tag: condition

tag: tissue


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_111919

tag: isolate

tag: growth time


title: AB7699_3xTg_15m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_15m


title: Patient 1 Kidney Scan 26689 A5 ROI 011

tag: scan id

tag: roi(lable)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B3_111819


title: Patient 1 Kidney Scan 26689 A5 ROI 010


title: RNA-Seq Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV16.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: Genvoya

value: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: AB7698_3xTg_8m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_8m

tag: sample id

tag: processing batch

tag: age

value: hippocampus


title: Patient 1 Kidney Scan 26689 A5 ROI 009


title: RNA-Seq Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV16.MTB.1_RNA_R1_quant.sf

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

tag: sequencing run


title: AB7697_3xTg_3m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_3m

tag: genotype

tag: condition

tag: tissue


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B2a_111919

tag: isolate

tag: growth time


title: Patient 1 Kidney Scan 26689 A5 ROI 008

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV15.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: HIV x 2003

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: AB7696_wt_15m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_15m

tag: sample id

tag: processing batch

tag: age


title: AB7695_wt_8m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_8m

tag: genotype

tag: condition

tag: tissue


title: Patient 1 Kidney Scan 26689 A5 ROI 006

tag: scan id


title: RNA-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV15.MTB.0_RNA_R1_quant.sf

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

value: Triumeq

tag: active ingredient

tag: art start year

tag: sequencing run


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B2a_111819

tag: isolate

tag: growth time


title: RNA-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV14.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: Kivexa, Reyataz, Norvir

value: Abacavir, Lamivudine, Atazanavir, Ritonavir

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: lane


title: RNA-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV14.MTB.1_RNA_R1_quant.sf

value: Caucasian

tag: age

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count


title: Patient 1 Kidney Scan 26689 A5 ROI 005

tag: scan id

tag: roi(lable)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B2a_112019

tag: isolate


title: Patient 1 Kidney Scan 26689 A5 ROI 007


title: AB7694_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

tag: sample id

tag: processing batch

tag: genotype

value: WT

tag: condition

tag: tissue


title: AB7693_3xTg_15m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_15m


title: AB7692_3xTg_8m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_8m


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_112019

tag: growth time


title: RNA-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV13.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: F

tag: viral load

tag: prescription drugs

value: Complera, Reyataz, Isentress

tag: active ingredient

value: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: sequencing run


title: Patient 1 Bladder Scan 26689 A5 ROI 002

source_name: Bladder

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV11.MTB.1_RNA_R1_quant.sf

value: M

tag: age

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

value: Complera

tag: rin

tag: average library size

tag: lane


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_111919

tag: isolate

tag: growth time


title: Patient 1 Kidney Scan 26689 A5 ROI 004


title: Patient 1 Kidney Scan 26689 A5 ROI 003


title: RNA-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV13.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: viral load

value: not detected

tag: prescription drugs

tag: active ingredient

tag: art start year

value: cannabis


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h2B1_111819


title: AB7708_3xTg_3m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_3m

tag: sample id

tag: processing batch

tag: genotype

tag: condition

tag: tissue


title: AB7690_wt_15m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_15m

tag: age


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G2_111919


title: Patient 1 Pancreas Scan 26689 A4 ROI 012

source_name: Pancreas

tag: scan id

tag: roi(lable)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G2_111819


title: RNA-Seq Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV10.MTB.1_RNA_R1_quant.sf

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

value: Intelence, Prezista, Tivicay, Norvir

value: Etravirine, Darunavir, Dolutegravir, Ritonavir

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

value: yes

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: AB7689_wt_8m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_8m

tag: sample id

tag: processing batch

tag: genotype

value: hippocampus


title: RNA-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV11.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: age

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year


title: Patient 1 Pancreas Scan 26689 A4 ROI 011

tag: scan id

tag: roi(lable)


title: RNA-Seq Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV10.MTB.0_RNA_R1_quant.sf

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G2_112019

tag: isolate

tag: growth time


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G1_111919


title: AB7687_3xTg_15m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_15m

tag: sample id

tag: processing batch

tag: genotype

tag: condition

tag: tissue


title: AB7688_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

tag: age


title: exosomes_OSCA-8_2

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
50bp paired-end sequencing RNAseq was performed on the Illumina HiSeq 2500.
Initial quality control analysis of RNA sequencing FASTQ data was performed using FastQC software (v0.11.5).
FASTQ data were trimmed with Trimmomatic (v0.33.0).
Kallisto (v0.43.0) was used for pseudoalignment and quantifying transcript abundance.
For alignment of sequencing reads to canine and murine genes, a kallisto index was built from a multi-sequence FASTA file containing both the canine (CanFam3.1) and murine (GRCm38.p5) genomes
Genome_build: CanFam3.1 and GRCm38.p5

organism: Canis lupus familiaris

source_name: RNA from exosomes

extract_protocol:
Exosome enrichment was performed with ExoQuick reagent.
RNA was extracted with SeraMir ExoRNA Amp kit.
Library prep was performed with Clontech SMARTer Stranded Total RNA-seq Kit v2 - Pico Input Mammalian Kit.

tag: source

value: Exosomes - cell line supernatants

tag: cell line


title: Patient 1 Pancreas Scan 26689 A4 ROI 010

tag: scan id

tag: roi(lable)


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G1_112019


title: RNA-Seq of Bordetella hinzii isolates, sample: 10h1G1_111819


title: RNA-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV9.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

value: Truvada, Isentress

tag: active ingredient

tag: art start year

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV9.MTB.0_RNA_R1_quant.sf

tag: age

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged


title: AB7686_3xTg_8m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_8m

tag: sample id

tag: processing batch

tag: genotype

tag: condition

tag: tissue


title: Patient 1 Pancreas Scan 26689 A4 ROI 009

tag: scan id

tag: roi(lable)


title: AB7685_3xTg_3m: Hippocampal sample from 3xTg mouse

description: Mouse hippocampal sample - 3xTg_3m


title: AB7684_wt_15m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_15m


title: Patient 1 Bladder Scan 26689 A5 ROI 001


title: RNA-Seq Person living with HIV sample 8, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 8, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV8.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year


title: exosomes_OSCA-8_1

tag: source

tag: cell line


title: Patient 1 Spleen Scan 26689 A4 ROI 006

source_name: Spleen


title: Patient 1 Spleen Scan 26689 A4 ROI 008


title: Patient 1 Spleen Scan 26689 A4 ROI 007


title: exosomes_OSCA-78_3


title: exosomes_OSCA-78_2


title: AB7683_wt_8m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_8m

tag: sample id

tag: processing batch

tag: age


title: Patient 1 Pancreas Scan 26689 A4 ROI 005


title: RNA-Seq Person living with HIV sample 8, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 8, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV8.MTB.1_RNA_R1_quant.sf

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: exosomes_OSCA-32_2


title: RNA-Seq Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV5.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

value: Truvada

value: Emtricitabine, Tenofovir_DF


title: PGC1a_dCTD_rep3

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Pair-end sequencing was performed using the HiSeq 2500 (Illumina) and control software version 2.2.68.
Analyzed on the Galaxy platform (https://usegalaxy.eu/). Reads were trimmed with Trim Galore! (Galaxy version 0.4.3.1) and quality was assessed using FastQC (Galaxy version 0.72+galaxy1). Reads were aligned to the mm10 version of the mouse genome using STAR (Galaxy version 2.7.2b), while strand specificity and read counting was performed with Infer Experiment (Galaxy version 2.6.4.1) and featureCounts (Galaxy version 1.6.4+galaxy1), respectively. Next, we used DESeq2 (Galaxy version 2.11.40.6) for differential expression analysis and the resulting data was annotated with Annotate DESeq2/DEXSeq output tables (Galaxy version 1.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: One excel (xlsx) file containing DESeq2 output, including normalized counts. The file contains two sheets, each with different comparison of the experimental groups.

source_name: C2C12 skeletal muscle cells

growth_protocol: C2C12 myoblasts were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (growth medium). To induce differentiation, growth medium of about 90% confluent myoblasts was changed to DMEM supplemented with 2% horse serum (differentiation medium). Experiments using C2C12 myotubes were performed after 4 days of differentiation. Cells were maintained at 37°C, 95% O2 and 5% CO2.

extract_protocol:
Cells were collected in TRI Reagent (Sigma #T9424), following which RNA was purified using Direct-zol™ RNA MiniPrep (Zymo Research, #R2050).
Libraries were prepared with TruSeq Stranded mRNA Library Kit (Illumina, #20020595).

treatment_protocol: Cells were transduced with HA-Flag-PGC-1alpha FL, deltaCTD or LacZ adenovirus at multiplicity of infection 3. Adenoviruses were prepared in the corresponding medium and cells were transduced for 4 h. Next, cells were washed once with phosphate buffered saline (PBS) and, then, incubated in adenovirus-free medium for a total of 48 h.

tag: cell line

value: C2C12 skeletal muscle cells

tag: differentiation state

value: C2C12 myotubes

tag: genotype

value: PGC1a delta CTD overexpression


title: AB7682_wt_3m: Hippocampal sample from WT mouse

description: Mouse hippocampal sample - WT_3m

tag: sample id

tag: processing batch

value: WT

tag: age

tag: condition

tag: tissue


title: PGC1a_dCTD_rep2


title: RNA-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV4.MTB.0_RNA_R1_quant.sf

value: Caucasian

value: M

tag: prescription drugs

value: Biktarvy

tag: active ingredient

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

tag: rin

tag: average library size


title: PGC1a_dCTD_rep1

tag: cell line


title: RNA-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV4.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

value: no

tag: quantiferon tb reagent

tag: cd4 count

tag: viral load

value: not detected

tag: sequencing run

tag: lane


title: RNA-Seq Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV5.MTB.1_RNA_R1_quant.sf

tag: age

tag: prescription drugs

tag: active ingredient


title: Patient 1 Spleen Scan 26689 A4 ROI 002

description: Unstained 4μm-thick sections were cut from FFPE blocks from two patients and immunoflourescently labeled with PanCK, CD45, CD68 and DAPI. Twelve regions of interest (ROIs) per slide were selected for targeted spatial transcriptomics (GeoMx, Nanostring) with >1,600 cancer atlas transcripts and 10 additional SARS-CoV-2 genes.

tag: scan id

tag: roi(lable)


title: Patient 1 Spleen Scan 26689 A4 ROI 001


title: RNA-Seq Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PLWH.AMV3.MTB.1_RNA_R1_quant.sf

tag: art start year

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged


title: exosomes_OS-2_2

tag: source

tag: cell line


title: Patient 1 Lymph node Scan 26689 A24 ROI 011

source_name: Lymph node


title: RNA-Seq Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PLWH.AMV3.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

tag: quantiferon tb reagent

tag: rin

tag: average library size


title: exosomes_OSCA-32_1


title: PGC1a_FL_rep3

tag: differentiation state

tag: genotype

value: PGC1a full length overexpression


title: exosomes_OS-1_4


title: exosomes_OS-2_1


title: Patient 1 Spleen Scan 26689 A4 ROI 004

tag: scan id


title: PGC1a_FL_rep2


title: Patient 1 Lymph node Scan 26689 A24 ROI 012

tag: roi(lable)


title: RNA-Seq Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP37.MTB.0_RNA_R1_quant.sf

tag: age

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: active ingredient

tag: art start year

value: cannabis

tag: sequencing run

tag: lane


title: exosomes_OS-1_2

tag: source

tag: cell line


title: RNA-Seq Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP36.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

value: gonorrhea PCR+

tag: quantiferon tb reagent

tag: recreational drugs

value: ketamine

tag: cigarette smoker

value: yes

tag: bal sampling date

tag: mtb challenged


title: Patient 1 Lymph node Scan 26689 A24 ROI 010

tag: scan id

tag: roi(lable)


title: RNA-Seq Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP37.MTB.1_RNA_R1_quant.sf

tag: age

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: rin

tag: average library size


title: LacZ_rep3

tag: cell line

tag: differentiation state

tag: genotype

value: Control LacZ overexpression


title: Patient 1 Spleen Scan 26689 A4 ROI 003


title: LacZ_rep2


title: PGC1a_FL_rep1


title: exosomes_OS-1_1

tag: source

value: Exosomes - cell line supernatants


title: LacZ_rep1


title: exosomes_OS-1_3


title: Patient 1 Lymph node Scan 26689 A24 ROI 009


title: RNA-Seq Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP35.MTB.1_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: sexually transmitted infections

value: Chlamydia â€“ 2018

tag: quantiferon tb reagent

value: Truvada

tag: active ingredient

value: Emtricitabine, Tenofovir_DF

tag: art start year

value: cocaine

tag: sequencing run

tag: lane


title: cells_OSCA_8_B

source_name: RNA from cells

value: Cell line OSCA-8


title: cells_OSCA_8_A


title: Patient 1 Lymph node Scan 26689 A24 ROI 007

tag: scan id

tag: roi(lable)


title: Patient 1 Lymph node Scan 26689 A24 ROI 006


title: Patient 1 Lymph node Scan 26689 A24 ROI 008


title: Patient 1 Lymph node Scan 26689 A24 ROI 005


title: RNA-Seq Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP35.MTB.0_RNA_R1_quant.sf

value: Caucasian

tag: age

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged


title: Input_CS

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1. Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles with spike-in were normalized by the total number of fly reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bedgraph.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)

extract_protocol:
For RNAseq: RNA was extracted using RNeasy Lipid Tissue Mini kit (Qiagen).
For ChIPseq: ChIP experiments were carried out following a standard protocol in the lab (Morey et al., Cell Stem Cell 2013).
Libraries were prepared according to Illumina instructions.

treatment_protocol: Patients with  tumoral adenocortical Cushing Syndrome and control patients matched by BMI, sex, age and cardiometabolic features.

tag: tissue

value: visceral adipose tissue

tag: chip antibody

tag: status

value: CS

tag: drosophila spike-in

value: YES


title: RNA-Seq Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP36.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: M

tag: sexually transmitted infections

tag: quantiferon tb reagent

value: no

value: not detected

tag: active ingredient

tag: art start year

tag: rin

tag: average library size


title: cells_OSCA_78_B

tag: source

value: Cell line OSCA-78

tag: cell line


title: Patient 1 Lymph node Scan 26689 A24 ROI 004

tag: scan id

tag: roi(lable)


title: cells_OS-2_B

value: Cell line OS-2


title: cells_OS-2_A


title: H3K4me3_CTL_H465

value: CTL


title: cells_OSCA_78_A


title: H3K4me3_CTL_HCTR10


title: RNA-Seq Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP34.MTB.1_RNA_R1_quant.sf

value: Asian

tag: age

value: Chlamydia â€“ 2017

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged

value: yes

tag: sequencing run

tag: lane


title: RNA-Seq Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP33.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: depression

tag: sexually transmitted infections

tag: quantiferon tb reagent

value: Truvada, Remeron

tag: active ingredient

tag: art start year

value: speed


title: RNA-Seq Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP32.MTB.1_RNA_R1_quant.sf

value: Truvada

value: Emtricitabine, Tenofovir_DF

tag: rin

tag: average library size


title: H3K4me3_CTL_H425

tag: tissue

value: visceral adipose tissue

tag: chip antibody

tag: status

tag: drosophila spike-in


title: Input_CTL


title: cells_OS-1_B

tag: source

value: Cell line OS-1

tag: cell line


title: cells_OS-1_A


title: RNA-Seq Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP33.MTB.1_RNA_R1_quant.sf

value: Caucasian

tag: age

tag: cd4 count

tag: viral load

tag: prescription drugs

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged


title: H3K4me3_CS_VC06

value: CS

value: YES


title: Patient 1 Lymph node Scan 26689 A24 ROI 001

tag: scan id

tag: roi(lable)


title: Patient 1 Lymph node Scan 26689 A24 ROI 003


title: Patient 1 Lymph node Scan 26689 A24 ROI 002


title: RNA-Seq Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP34.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

value: M

tag: sexually transmitted infections

tag: quantiferon tb reagent

value: no

value: not detected

tag: active ingredient

tag: art start year

tag: rin

tag: average library size

tag: sequencing run

tag: lane


title: RNA-Seq Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis challenged library

description:
Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis challenged library
mRNA, poly-A selected
PrEP.AMP31.MTB.1_RNA_R1_quant.sf

tag: age

tag: cd4 count

tag: viral load

tag: prescription drugs


title: Patient 1 Lung Scan 26689 A10 ROI 012


title: H3K4me3_CS_VC04

tag: tissue

tag: chip antibody

tag: status

tag: drosophila spike-in


title: H3K4me3_CTL_HCTR13

value: CTL


title: RNA-Seq Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library

description:
Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library
mRNA, poly-A selected
PrEP.AMP32.MTB.0_RNA_R1_quant.sf

tag: ethnicity

tag: Sex

tag: recreational drugs

tag: cigarette smoker

tag: bal sampling date

tag: mtb challenged


title: Patient 1 Lung Scan 26689 A10 ROI 011

tag: scan id

tag: roi(lable)