title: Sample_166 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 296_Other

status: Public on Apr 15 2022

type: RNA

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

country: USA

institute: University of Michigan

description: Gene Expression data from the tubulointerstitial compartment of human Glomerular Disease (Other)

hyb_protocol: According to manufacturer's protocols.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using RMA method and Human Entrez Gene custom CDF annotation version 19 (Brainarray) on three individual batches. Each of the hybridizations was normalized seperately and expression matrix contains the batch corrected data using Combat.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Other Glomerular Disease

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

extract_protocol: total RNA

tag: tissue

value: Tubulointerstitial compartment from kidney biopsy


title: U87 siCTRL RNAseq IDHmut rep1

type: SRA

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description:
data_norm_DESeq2_1.xlsx
SRT_F31_0009_P01_V11

library_source: transcriptomic

data_processing:
In the RNAseq primary analysis, Illumina-specific adapters, low-quality 5’ and 3’ bases and short reads were removed in the FASTQ files using Trimmomatic tool.
RNA sequencing reads were aligned to a reference human genome sequence (hg38) using the STAR aligner.
Duplicates were identified and marked using Picard Tools and the resulting RNAseq mapped reads were summarized and counted by gene using HTseq, in paired-end mode, reverse-stranded mode and considering only reads with MAPQ values of 3 or higher and primary aligment.
Low-expressed genes were prefiltered and an a analysis of differentially expressed genes was performed using DESeq2.
In the ChIPseq primary analysis, reads with phred values >30 were retained for downstream analysis.
PCR duplicates were marked and removed using Picard Tools and the resulting reads were mapped to the human genome with the BWA-MEM algorithm.
Peaks were called with MACS2 software using default parameters, and secondary peak analysis was performed with the R libraries ChipSeeker and clusterProfiler.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 normalized abundance measurements ouput
Supplementary_files_format_and_content: MACS2 narrow peaks files

molecule: polyA RNA

source_name: U87 siCTRL RNAseq IDHmut

extract_protocol:
RNA libraries were prepared using KAPA Stranded mRNAseq protocol
DNA libraries for ChIPseq were prepared using Qiaseq Ultra Low Input protocol

tag: cell type

value: U87 human glioma cell line

value: brain

tag: genotype

value: IDH1 knockdown

tag: sample type

value: IDH1 mutant-U-87 isogenic cell line

tag: transfection

value: REST-targeting siRNA


title: 75_FSGS

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Focal Segmental Glomerulosclerosis


title: U87 RNAseq IDHwt rep1

description:
data_norm_DESeq2_2.xlsx
RAG_F11_0006_P01_V11

source_name: U87 RNAseq IDHwt

value: wild type

value: U87 MG

value: untreated


title: Sample_194 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

data_processing:
fastQC 0.11.5
fastqScreen 0.11.4
cutadapt 1.14 -m 50 -A CTGTCTCTTATA -a CTGTCTCTTATA
STAR 2.5.2.a --bamRemoveDuplicatesType UniqueIdentical --twopassMode Basic --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
htseq-count --stranded=no --order=pos --mode=union
Genome_build: GRCh 38.86

source_name: Tubulointerstitium from kidney biopsy

extract_protocol:
Qiagen Allprep DNA/RNA Micro Kit (cat# 80284)
Takara SMART-Seq v4 Ultra Low Input RNA Kit (cat# 634891)
oligo(dT)

value: Tubulointerstitium from kidney biopsy

tag: disease

value: Membranous Nephropathy


title: U87 siCTRL RNAseq IDHwt rep2

description:
data_norm_DESeq2_1.xlsx
SRT_F11_0011_P01_V11

source_name: U87 siCTRL RNAseq IDHwt

value: siCTRL


title: 49_FSGS


title: U87 RNAseq IDHmut rep1

description:
data_norm_DESeq2_2.xlsx
RAG_F31_0005_P01_V11

source_name: U87 RNAseq IDHmut


title: Sample_42 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: U87 REST ChIPseq IDH1wt rep2

library_source: genomic

molecule: genomic DNA

source_name: U87 REST ChIPseq IDH1wt

tag: chip antibody

value: REST antibody (Merck-Millipore, 17-641)


title: U87 REST ChIPseq IDH1mut rep2

source_name: U87 REST ChIPseq IDH1mut


title: U87 input ChIPseq IDH1mut rep2

source_name: U87 input ChIPseq IDH1mut


title: 111_MN

source_name: Tubulointerstitial RNA from kidney biopsy of patient with Membranous Nephropathy


title: U87 siCTRL RNAseq IDHwt rep1

description:
data_norm_DESeq2_1.xlsx
SRT_F11_0007_P01_V11


title: U87 siREST RNAseq IDHwt rep1

description:
data_norm_DESeq2_1.xlsx
SRT_F11_0008_P01_V21

source_name: U87 siREST RNAseq IDHwt


title: U87 input ChIPseq IDH1mut rep1


title: U87 REST ChIPseq IDH1mut rep1


title: Sample_25 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 83_FSGS


title: Sample_179 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: U87 input ChIPseq IDH1wt rep1

source_name: U87 input ChIPseq IDH1wt


title: Sample_35 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_74 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: U87 REST ChIPseq IDH1wt rep1


title: Sample_45 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: U87 input ChIPseq IDH1wt rep2


title: 81_FSGS


title: Mouse brain tissue - vDG - DEX7

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX7-AK_S256

data_processing:
Quality Control of sequencing data with FastQC v0.11.4
Adapter trimming with cutadapt
Extraction of unique molecular identifiers (UMIs) with UMI-tools v0.5.4
Alignment of reads to reference genome using STAR v2.6.0a
Deduplication of reads with UMI-tools
Quantification of gene expression with featureCounts v1.6.4
Normalization with DESeq2 v1.30.1 in R v4.0.5
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file with raw counts of all samples
Supplementary_files_format_and_content: Tab-delimited files with normalized (DESeq2 vsd) counts per brain region

organism: Mus musculus

source_name: Mouse brain tissue - vDG

growth_protocol: C57Bl/6 adult male mice were group-housed, a maximum of 4 animals per cage, in a room with a 12-hour light–dark cycle, room temperature (RT) 20–24 °C, and relative humidity 45–65%. Animals were used as approved by the Government of Upper Bavaria.

extract_protocol:
Brains were perfused, extracted and kept in -80oC until further use. The brain regions were extracted by punching of coronal sections following the Paxinos stereotaxic coordinates. RNA was extracted from each brain region of each animal using an automated Chemagic 360 instrument with an integrated dispenser and the chemagic RNA Tissue Kit (CMG-1212) in Paxgene tubes following manufacturer’s instructions.
Messenger RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA Fwd kit (Lexogen) following manufacturer’s instructions with the addition of unique molecular identifiers (UMIs- UMI Second Strand Synthesis Module for QuantSeq FWD) for tagging of individual transcripts. Libraries were single-end sequenced on a whole Flow Cell of an Illumina HiSeq4000 sequencer using 75bp long reads for a total coverage of an average of 10M reads per library.

treatment_protocol: Animals were treated with 10mg/kg dexamethasone or saline 0.9% intraperitoneally for 4 hours.

tag: animal

tag: strain

tag: Sex

value: male

tag: age

value: 3 month

tag: treatment

value: Dexamethasone

tag: mouse_weight (g)

tag: researcher

tag: plate

tag: lane

value: A

tag: row

tag: rin

tag: cryostat


title: Mouse brain tissue - vDG - DEX6

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX6-AK_S290

value: E


title: Sample_1 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: tissue


title: Sample_27 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 102_MN

value: Tubulointerstitial compartment from kidney biopsy


title: Sample_130 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - DEX3

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX3-AK_S276

value: C


title: 82_FSGS


title: 9883

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay.

scan_protocol: iScan Illumina scanning protocol using iScan control software.

data_processing: Background correction using negative control probes and quantile normalization using negative and positive control probes. Batch effects removal.

source_name: Whole blood

label_protocol: In vitro transcription was generated from 100 ng of RNA using Ambion Illumina TotalPrep RNA Amplification Kits (Applied Biosystems/Ambion).

extract_protocol: RNA were purified using Tempus™ Spin RNA Isolation Kit (ThermoFisher Scientific) and quantified using a ND-8000 spectrophotometer (NanoDrop Technologies) before being checked for integrity on the 2100 BioAnalyzer (Agilent Technologies).

tag: participant id

tag: diagnosis

value: Healthy

value: Whole blood

tag: randomisation arm

value: MVA HIV-B / LIPO-5


title: 9944

value: LIPO-5 / MVA HIV-B


title: Sample_100 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

tag: disease


title: Sample_153 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 9884

value: GTU-MultiHIV B / LIPO-5


title: 9764


title: 9788

value: GTU-MultiHIV B / MVA HIV-B


title: Mouse brain tissue - vDG - DEX5

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX5-AK_S248

tag: animal

value: D


title: 9625


title: 94_MN


title: Mouse brain tissue - vDG - CNTRL6

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL6-AK_S296

tag: strain

value: Vehicle


title: 9690


title: 9711


title: Mouse brain tissue - vDG - CNTRL7

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL7-AK_S250

tag: Sex


title: Sample_30 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 9857


title: 9865


title: 210_Other


title: 133_MN


title: 9869


title: Mouse brain tissue - vDG - CNTRL3

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL3-AK_S282

value: male

tag: age


title: 9398


title: 9745


title: Sample_141 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vCA1 - DEX9

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX9-AK_S235

source_name: Mouse brain tissue - vCA1

value: 3 month

tag: treatment


title: Mouse brain tissue - vDG - CNTRL5

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL5-AK_S242

tag: mouse_weight (g)


title: 9430


title: 9400


title: 9395


title: Sample_32 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 9366


title: 9369


title: 9389


title: 9598


title: Sample_66 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 9393


title: Mouse brain tissue - vCA1 - DEX4

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX4-AK_S267

value: Dexamethasone

tag: researcher

value: F


title: Sample_182 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: Mouse brain tissue - vCA1 - DEX13

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX13-AK_S257

tag: plate

value: B


title: Sample_126 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 9358


title: 9314


title: Mouse brain tissue - vCA1 - DEX12

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX12-AK_S243

tag: lane

value: E


title: 9319

value: Healthy


title: Sample_191 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_155 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 9266

value: Whole blood


title: Sample_80 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Mouse brain tissue - vCA1 - CNTRL9

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL9-AK_S230

value: C

tag: row


title: 9214

value: LIPO-5 / MVA HIV-B


title: 9225

value: MVA HIV-B / LIPO-5


title: Sample_44 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: Mouse brain tissue - vCA1 - CNTRL12

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL12-AK_S249

tag: rin


title: Sample_124 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vCA1 - CNTRL4

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL4-AK_S273

tag: cryostat


title: 9339

tag: tissue

value: GTU-MultiHIV B / MVA HIV-B


title: 9255

tag: participant id


title: Mouse brain tissue - PVN - DEX6

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX6-AK_S262

source_name: Mouse brain tissue - PVN

value: A


title: 9207

tag: diagnosis


title: 9117

tag: randomisation arm

value: GTU-MultiHIV B / LIPO-5


title: Mouse brain tissue - PVN - DEX2

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX2-AK_S244

value: male


title: Sample_112 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease

value: Minimal Change Disease


title: 9132


title: Sample_24 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 9159


title: 9178


title: 9063


title: Mouse brain tissue - vCA1 - CNTRL13

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL13-AK_S251

tag: animal

value: 3 month

value: Vehicle


title: Sample_165 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - CNTRL6

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL6-AK_S268

tag: strain


title: Sample_64 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - CNTRL13

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL13-AK_S259

tag: Sex

value: D


title: 9012


title: Mouse brain tissue - PVN - DEX13

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX13-AK_S253

tag: age

value: Dexamethasone


title: 9091

value: Healthy


title: Sample_131 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 9089

value: Whole blood


title: 8950


title: Sample_129 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 8975


title: Mouse brain tissue - PFC - DEX12

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX12-AK_S239

source_name: Mouse brain tissue - PFC

tag: treatment


title: Mouse brain tissue - PFC - DEX11

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX11-AK_S231

tag: mouse_weight (g)


title: Sample_114 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Mouse brain tissue - PFC - CNTRL8

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL8-AK_S291

tag: researcher

value: F


title: Mouse brain tissue - PFC - DEX8

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX8-AK_S297

tag: plate


title: Sample_63 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PFC - CNTRL12

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL12-AK_S245

tag: lane


title: 9001

value: MVA HIV-B / LIPO-5


title: 8714


title: Mouse brain tissue - PFC - CNTRL11

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL11-AK_S236

tag: row


title: 8875


title: 8667


title: 8707


title: Sample_96 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: 8660


title: 8585


title: Sample_83 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 8476


title: 8582


title: Sample_81 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 8497


title: 8808


title: 8630


title: Mouse brain tissue - dDG - DEX9

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX9-AK_S293

source_name: Mouse brain tissue - dDG

value: B

tag: rin


title: 8540


title: 8703


title: Sample_102 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 8467

value: LIPO-5 / MVA HIV-B


title: 8455

value: GTU-MultiHIV B / MVA HIV-B


title: 8452


title: 8447


title: 8446


title: 8406


title: Mouse brain tissue - dDG - DEX5

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX5-AK_S264

value: male

value: C

tag: cryostat


title: Sample_108 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: tissue

value: Minimal Change Disease


title: Sample_106 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 8324

tag: participant id


title: Sample_161 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 8308

tag: diagnosis

value: GTU-MultiHIV B / LIPO-5


title: Sample_116 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: Sample_136 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dDG - CNTRL5

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL5-AK_S270

value: 3 month

value: Vehicle


title: Mouse brain tissue - dDG - CNTRL9

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL9-AK_S287


title: 8342

value: Healthy

tag: randomisation arm


title: 8265

value: Whole blood


title: 8252


title: Mouse brain tissue - dDG - DEX12

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX12-AK_S278

value: Dexamethasone

value: E


title: Sample_119 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease


title: Mouse brain tissue - dDG - DEX10

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX10-AK_S233

tag: animal

value: F


title: 8284


title: Mouse brain tissue - dDG - CNTRL12

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL12-AK_S284

tag: strain


title: 8243


title: 8240


title: Mouse brain tissue - dDG - CNTRL10

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL10-AK_S238

tag: Sex


title: Sample_33 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: Mouse brain tissue - dCA1 - DEX7

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX7-AK_S292

source_name: Mouse brain tissue - dCA1

tag: age

value: A


title: Sample_149 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

value: Membranous Nephropathy


title: Sample_76 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dCA1 - DEX6

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX6-AK_S247

tag: treatment


title: bk98 Stri (ID 4516)

city: San Francisco

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

data_processing:
Sequencing reads were first trimmed for adaptor sequences using trim_galore (https://github.com/FelixKrueger/TrimGalore, --quality 20, --paired, --overlap 10, adaptors AAAAAAAAAA and GTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGATCT). We first generated an initial alignment to the Bengalese finch genome (lonStrDom2, GCF_005870125.1) using STAR v2.7.8a (STARsolo mode, default parameters, --outFilterIntronMotifs RemoveNoncanonical) (Dobin et al., 2013). To better annotate the 3’ UTRs of Bengalese finch gene models, we identified transcript 3’ ends by assembling transcripts using these initial alignments and the RNA-seq assembler Stringtie (Kovaka et al., 2019) (--fr -m 100). These Stringtie models were then intersected with the NCBI Bengalese finch transcriptome (lonStrDom2, GCF_005870125.1). New Stringtie exons were filtered by same-strandedness to the intersected references gene, minimal expression level (at least 10% of expression max for a given gene), and at least within 10 kilobases from the 3’ end of the gene. 3’UTRs of the reference transcriptome were extended out to these new exons. Reads were then re-aligned to this extended transcriptome using the ‘bus’ subcommand from kallisto v0.46.1 (Bray et al., 2016; Melsted et al., 2021) followed by barcode error correction using bustools v0.39.3 ‘correct’, sorting using ‘sort’, and read counting using ‘count’.
Gene filtering: genes were kept if they were expressed in at least 1/8 of the total number of samples (8 brain regions were assayed)
Sample filtering: samples were removed if the number of detected genes in the sample was less than 30% of the total number of genes
Assembly: lonStrDom2, GCF_005870125.1
Supplementary files format and content: dat_filtered.csv - Gene (rows) by samples (columns) matrix of unique molecular identifier counts. Column names correspond to ‘id’ column in ‘metadata.csv’
Supplementary files format and content: metadata.csv – Sample-, animal-level metadata for dat_filtered.csv

organism: Lonchura striata

source_name: Brain

extract_protocol:
A fast Nissl staining procedure was developed to quickly stain cryosections before laser capture microdissection. Anhydrous 100% ethanol solution was prepared by adding 15 g of molecular sieve beads (Sigma 208582, 3 Å, 8-12 mesh) to 500 mL 100% molecular grade ethanol (Sigma E7023). Cresyl violet staining solution was prepared as by dissolving cresyl violet powder (Sigma) to 4% wt/vol in 75% ethanol (75% molecular grade ethanol, 25% nuclease-free water), stirring for two days, then filtering through a 0.22 μm filter. Before staining, a series of 95%, 75%, 50% ethanol solutions were prepared. To stain, each slide was thawed at room temperature on a bench for 20 seconds then transferred to 95% ethanol for 30 seconds, 75% ethanol for 30 seconds, and 50% ethanol for 30 seconds. 400 μL of cresyl violet staining solution was then applied to the slide for 30 seconds. Slides were destained and dehydrated by transferring to 50% ethanol for 30 seconds, 75% ethanol for 30 seconds, 95% ethanol for 30 seconds, then two rounds of 100% ethanol for 30 seconds each. Slides were then allowed to air dry. Time series experiments indicated that RNA quality was maintained for up to 45 minutes following staining.  After staining, slides were loaded onto a Leica LMD7000. Song nuclei were identified by anatomical landmarks (such as lamina and position relative to brain surfaces) and their higher intensity Nissl staining relative to surrounding regions. Sections cut from the surrounding tissue (power 45, aperture 50,  speed 10, specimen balance 0, head 90%, pulse 92, offset 15) into 8-well strip caps containing 31.5 μL of RNA Lysis Buffer/PK (see SPRI RNA purification). After filling each cap with a section, the strip was placed onto a 96-well plate pre-chilled on ice and covered with an ice pack. Once a plate was filled, it was vortexed, spun down at 3,250 x g for 5 minutes at 4 °C, then transferred to dry ice. For long-term storage, plates were stored at -80 °C. The following solutions were prepared before LCM section collection: 50% guanidinium thiocyanate (Sigma) in nuclease-free water, 5X CN buffer (250 mM sodium citrate pH 7.0 (Sigma), 5% NP-40 (Sigma)), and RNA Lysis Buffer (20% guanidine thiocyanate, 1X CN buffer). The following solutions were prepared before RNA purification: RNA Wash Buffer (25 mM sodium citrate pH 7.0, 15% guanidinium thiocyanate, 40% isopropanol) and solid phase reversible immobilization (SPRI) bead solution. SPRI bead solution was prepared by first vortexing Sera-Mag SpeedBeads™ Carboxyl Magnetic Beads, hydrophobic (Fisher) until fully suspended transferring 1 mL beads to a 1.5 mL tube. Beads were washed  by placing the tube on a tube magnet, waiting until solution cleared, removing the solution, adding 1 mL of TE Buffer (10 mM UltraPure Tris HCl, pH 8.0 (ThermoFisher), 1 mM EDTA pH 8 (ThermoFisher)), and pipetting to mix. This wash was repeated once more, then the beads were resuspended in 1 mL TE Buffer. Separately, 9 g polyethylene glycol 8000 (Amresco), 10 mL 5 M NaCl, 500 μL 1 M UltraPure Tris HCl pH 8.0 (ThermoFisher), 100 μL 0.5 M EDTA pH 8.0 (ThermoFisher), and 500 μL 2% sodium azide (Sigma) were combined and brought to ~49 mL using nuclease-free water. Solution was mixed by inversion until PEG 8000 went into solution. Then, 137.5 μL of 20% Tween-20 and 1 mL of beads/TE were added and mixed by inversion. This SPRI bead solution was then stored at 4 °C.   Just before LCM collection, 31.5 μL of RNA Lysis Buffer/PK (1.5 μL of Proteinase K (Ambion), 30 μL of RNA Lysis Buffer) was prepared for each well. To purify RNA following LCM section collection, samples were first allowed to thaw on ice if stored at -80 °C. SPRI bead solution was allowed to come to room temperature, then 40 uL SPRI bead solution was mixed with 47.5 uL isopropanol for each sample. Samples were then lysed by incubating at 42 °C for 30 minutes in a thermocycler then placed at room temperature. 87.5 uL of SPRI/isopropanol solution was added to each sample then mixed 10x by pipetting. Samples were incubated for 5 minutes at room temperature then transferred to a magnetic plate stand. After 3 minutes, the solution was removed, the plate was removed from the magnetic stand, 100 uL of RNA Wash Buffer was added, and beads were resuspended by pipetting. The plate was immediately transferred back to the magnetic plate stand and held there for 2 minutes until the solution cleared. The solution was removed, and the plate was removed from the stand. 100 uL of 70% ethanol was added, beads were resuspended by pipetting 10 times, the plate was returned to the magnetic stand, the solution was allowed to clear for 2 minutes, the solution was removed. This step was repeated for two total ethanol washes. Following the final wash, the beads were allowed to dry for 10 minutes while the plate remained on the stand. Residual ethanol was removed by pipetting. The elute RNA, the plate was removed from the magnet, 15 uL of nuclease-free water was added to each sample, and beads were resuspended by pipetting 10 times. Samples were incubated at room temperature for 5 minutes, then the plate was transferred to a low-elution volume magnetic stand. After 2 minutes or until the solution cleared, 10-12 μL eluted RNA was transferred to new 96-well plates on ice. Plates were sealed using foil adhesive, frozen on dry ice, then transferred to -80 °C for long-term storage.
The SLCR-seq library preparation was adapted from several low input and single-cell RNA-sequencing library protocols (Islam et al., 2014, 2012; Kivioja et al., 2012; Macosko et al., 2015; Picelli et al., 2014, 2013). Barcoded unique molecular identifier (UMI) reverse transcription (RT) primers were prepared in advance in a 96-well plate (RT/TSO/dNTP mix). Each well contained 10 μM barcoded reverse transcription primer (RT_primer, IDT), 10 μM template-switching oligonucleotide with lock nucleic acids (TSO_LNA, Exiqon), and 10 mM dNTPs. Plates were sealed with foil adhesive and stored at -80 °C. Two RT primers were used in this study: one for the initial 18 bird deafening dataset (RT_primer_v1, 25 base UMI, 6 base barcode), and another for the 10 bird unilateral LMAN dataset (RT_primer_v2, 14 base UMI, 12 base barcode). RT_primer_v1 and RT_primer_v2 sets consisted of 24 and 48 barcodes, respectively (Supplemental Table 1). Barcodes were at least one edit distance away from all other barcodes in the set. For library preparation, total RNA prepared from SPRI RNA purification was thawed on ice, then 4 μL total RNA was placed into a well of a 96-well plate chilled on ice. 1 μL RT/TSO/dNTP mix was added and mixed 10 times by pipetting. Plates were sealed with foil adhesive, incubated at 72 °C for 3 minutes, then snap-cooled in ice for at least 2 minutes. An RT Master Mix was prepared containing 1x Enzscript RT buffer (Enzymatics), 5 mM dithiothreitol, 1 mM betaine, 12 mM MgCl2, 0.25 μL Recombinant Ribonuclease Inhibitor (Takara), and 10 U/μL Enzscript Moloney-Murine Leukemia Virus Reverse Transcriptase (Enzymatics). 5 μL of RT Master Mix was added to each sample and mixed by pipetting 10x times. Plates were sealed with foil adhesive and incubated in a thermocycler: 42 °C for 90 minutes, 70 °C for 15 minutes, 4 °C hold. Reactions were then pooled within a barcode set (e.g. barcodes 1-48 from RT_primer_v2 were combined into one tube). To purify cDNA, 0.6x volume of Ampure XP bead solution was added to each pooled sample and mixed by pipetting 10 times. Samples were incubated for 5 minutes and transferred to a tube magnet. After the beads cleared from the solution, the solution was removed, and the beads were washed in 400 μL freshly prepared 80% ethanol for 30 seconds. This step was repeated for a total of two washes. After the second wash, the ethanol solution was removed, and the beads were allowed to dry for 5-10 minutes. Beads were then resuspended in 22 μL of nuclease-free water and incubated for 2 minutes. 20 μL eluted cDNA was transferred to new 1.5 mL LoBind tubes or 96-well plates and either stored at -20 °C or amplified immediately. During the purification a 40 μL cDNA Amplification Master Mix was prepared containing 10 μL KAPA HiFi 5x Buffer, 1 μL 10 mM dNTPs, 4 μL 10 mM TSO_PCR primer, 0.5 μL 1 U/μL KAPA HiFi Hotstart DNA polymerase, and 24.5 μL nuclease-free water. 10 μL of purified cDNA was added to this master mix, pipetted 10x to mix, then amplified under the following cycling parameters: 95 °C for  minutes, then 4 cycles of 98 °C for 30 seconds, 65 °C for 45 seconds, and 72 °C for 3 minutes. Reactions were then placed on ice. During this initial amplification, a second master mix was prepared to determine the target number of amplification cycles by quantitative PCR. This mix contained 3 μL KAPA HiFi 5x Buffer, 0.3 μL 10 mM dNTPs, 1.2 μL 10 mM TSO_PCR primer, 0.15 μL 1 U/μL KAPA HiFi Hotstart DNA polymerase, 0.75 μL 20x EvaGreen (Biotium), and 4.6 μL nuclease-free water. 5 μL of preamplified cDNA was added to this mix and amplified in a real-time PCR machine: 98 °C for 3 minutes, followed by 24 cycles of 98 °C for 20 seconds, 67 °C  for 20 seconds, and 72 °C  for 3 minutes, followed by 72 °C  for 5 minutes. The target number of additional cycles was determined by identifying the Ct at 20% of the max fluorescence then subtracting 5 cycles from this number. This number was generally between 5-7 additional cycles. The remaining 45 μL was placed back into the thermocycler and cycled for 98 °C for 30 seconds, the number of additional cycles at 98 °C for 20 seconds, 67 °C  for 20 seconds, and 72 °C  for 3 minutes, followed by 72 °C for 5 minutes. To purify the amplified cDNA, 0.6x volume of Ampure XP bead solution was added to each reaction and mixed by pipetting 10 times. Samples were incubated for 5 minutes and transferred to a tube magnet. After the beads cleared from the solution, the solution was removed, and the beads were washed in 200 μL freshly prepared 80% ethanol for 30 seconds. This step was repeated for a total of two washes. After the second wash, the ethanol solution was removed, and the beads were allowed to dry for 5 minutes. Beads were then resuspended in 22 μL of nuclease-free water and incubated for 2 minutes. 20 μL eluted cDNA was transferred to new 1.5 mL LoBind tubes or 96-well plates and stored at -20 °C. Sample concentration was quantified using Qubit dSDNA High Sensitivity kit (ThermoFisher), then sample concentrations were standardized to 100 pg/μL. To prepare tagmented DNA, 4 μL (400 pg) of amplified cDNA was added to 10  μL Tagmentation Buffer (Buffer TD from the Nextera XT DNA Sample Prep Kit, Illumina), 1 μL nuclease-free water, and 5 μL ATM (Nextera XT). Reactions were mixed by pipetting 10 times the incubated at 55 °C for 5 minutes. 5 μL of Buffer NT was then added, then the reactions were incubated for 5 minutes at room temperature. Final libraries were constructed by first preparing a PCR master mix containing 20 μL KAPA HiFi 5x Buffer, 2 μL 10 mM dNTPs, 5 μL 10 mM P5-TSO_Hybrid primer, 5 μL 10 mM PCR2 primer, 1 μL 1 U/μL KAPA HiFi Hotstart DNA polymerase, and 42 μL nuclease-free water. PCR2 contains an i7 index (Supplemental Table 1). The 25 μL tagmentation reaction was then added directly to the mix, and mixed by pipetting 10 times. Samples were amplified using 72 °C for 3 minutes; 95 °C for 3 minutes; followed by 16 cycles of 98 °C for 10 seconds, 55 °C for 30 seconds, and 72 °C for 30 seconds; followed by 72 °C for 5 minutes. Samples were then purified by adding 1.2x volumes of Ampure XP, incubating for 5 minutes, then transferring to a tube magnet. After the beads cleared from the solution, the solution was removed, and the beads were washed in 200 μL freshly prepared 80% ethanol for 30 seconds. This step was repeated for a total of two washes. After the second wash, the ethanol solution was removed, and the beads were allowed to dry for 5 minutes. Beads were then resuspended in 22 μL of Low Elution Buffer (10 mM Tris HCl pH 8.0, 0.1 mM EDTA, 0.05% Tween-20) and incubated for 2 minutes. 20 μL eluted cD`NA was transferred to new 1.5 mL LoBind tubes and stored at -20 °C. Library size distributions were assessed using a Bioanalyzer High Sensitivity DNA Chip (Agilent), and library concentrations were determined using the KAPA Library Quantification Kit (Illumina Complete Kit, Roche). Samples were pooled at equal concentrations then size selected using a BluePippin and 2% BluePippin gels. DNA from 180 to 500 bp was selected then purified using the MinElute kit (Qiagen) with two rounds of 10 μL elution in Low Elution Buffer. Samples were stored at -20 °C.

value: Brain

tag: region

value: Stri

tag: ID

tag: nest

value: magnolia

tag: reference

value: anterior

value: intact

tag: library


title: Sample_159 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

source_name: Tubulointerstitium from kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: 8075

value: MVA HIV-B / LIPO-5


title: 8099

value: GTU-MultiHIV B / MVA HIV-B


title: Mouse brain tissue - dCA1 - DEX12

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX12-AK_S283

value: male

value: 3 month

tag: mouse_weight (g)

tag: researcher

tag: plate

tag: lane

value: D

tag: row

tag: rin


title: 7990

tag: participant id

tag: diagnosis

value: Healthy

tag: tissue

value: Whole blood

tag: randomisation arm

value: GTU-MultiHIV B / LIPO-5


title: Sample_135 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease


title: 8036


title: Mouse brain tissue - dCA1 - CNTRL6

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL6-AK_S241

tag: animal

tag: strain

tag: Sex

tag: age

tag: treatment

value: Vehicle

value: C

tag: cryostat


title: Mouse brain tissue - dCA1 - CNTRL7

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL7-AK_S286

tag: mouse_weight (g)

value: A


title: Sample_8 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

value: Membranous Nephropathy


title: 8058

value: LIPO-5 / MVA HIV-B


title: 7976


title: 8102


title: 8223


title: 8017


title: 8152


title: 7921


title: 8123


title: Mouse brain tissue - dCA1 - CNTRL12

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL12-AK_S277

tag: researcher


title: Sample_109 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 7952


title: Sample_14 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - DEX6

description:
CER_deseq2_expression_vsd.txt
CER-DEX6-AK_S246

source_name: Mouse brain tissue - CER

value: Dexamethasone

tag: plate

value: B


title: Sample_176 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 7755

value: MVA HIV-B / LIPO-5


title: 7705


title: 7829


title: 7818


title: 7844


title: 7702


title: 7694

value: GTU-MultiHIV B / MVA HIV-B


title: Mouse brain tissue - CER - DEX5

description:
CER_deseq2_expression_vsd.txt
CER-DEX5-AK_S237

value: male

value: 3 month

tag: lane

value: E


title: 7680

value: Healthy

value: Whole blood


title: Sample_16 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - DEX2

description:
CER_deseq2_expression_vsd.txt
CER-DEX2-AK_S288

tag: row


title: Sample_89 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - CNTRL6

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL6-AK_S240

value: Vehicle

tag: rin


title: Sample_104 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - CNTRL5

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL5-AK_S232


title: Sample_5 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_29 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - CNTRL2

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL2-AK_S294

value: C


title: Mouse brain tissue - AMY - DEX8

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX8-AK_S261

source_name: Mouse brain tissue - AMY

value: F


title: 7650

tag: participant id


title: Mouse brain tissue - AMY - DEX2

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX2-AK_S280

value: A


title: 7647

tag: diagnosis


title: 7645

tag: tissue


title: 7511

tag: randomisation arm


title: 7597


title: Sample_60 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

tag: disease

value: Membranous Nephropathy


title: 7452


title: Sample_162 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 7403


title: 7441

value: LIPO-5 / MVA HIV-B


title: 7608


title: 7641


title: 7506


title: Mouse brain tissue - AMY - DEX11

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX11-AK_S265

tag: animal

value: Dexamethasone

value: D


title: Sample_91 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - AMY - CNTRL8

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL8-AK_S255

tag: strain


title: Sample_26 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 7361

value: GTU-MultiHIV B / LIPO-5


title: 7285

value: GTU-MultiHIV B / MVA HIV-B


title: 7343


title: Mouse brain tissue - AMY - CNTRL2

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL2-AK_S274

tag: Sex

value: male


title: Sample_122 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 7267

value: MVA HIV-B / LIPO-5


title: 7250

value: Healthy


title: 7245

value: Whole blood


title: Mouse brain tissue - AMY - CNTRL11

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL11-AK_S271

tag: age

value: 3 month

value: Vehicle


title: 7253


title: Mouse brain tissue - vDG - DEX9

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX9-AK_S227

tag: treatment

value: F


title: Sample_84 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_50 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: Mouse brain tissue - vDG - DEX2

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX2-AK_S192

value: A

tag: cryostat


title: Sample_121 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: Sample_59 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - DEX1

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX1-AK_S177

tag: mouse_weight (g)

value: B


title: Mouse brain tissue - vDG - CNTRL9

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL9-AK_S221

tag: researcher


title: Mouse brain tissue - vDG - CNTRL2

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL2-AK_S198

tag: plate


title: Sample_198 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Sample_70 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - CNTRL1

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL1-AK_S171

tag: lane


title: Sample_65 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 7183


title: 7210

value: LIPO-5 / MVA HIV-B


title: 7229


title: 7172


title: 7106


title: 7117


title: Mouse brain tissue - vCA1 - DEX5

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX5-AK_S191

value: Dexamethasone

tag: row


title: Sample_68 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: Sample_183 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 6881

value: GTU-MultiHIV B / LIPO-5


title: 6969


title: 7247

value: GTU-MultiHIV B / MVA HIV-B


title: 6879


title: Mouse brain tissue - vCA1 - DEX1

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX1-AK_S217

value: male

tag: rin


title: 7093

tag: participant id

value: MVA HIV-B / LIPO-5


title: 6845

tag: diagnosis

value: Healthy


title: 6974

tag: tissue

value: Whole blood


title: 7147

tag: randomisation arm


title: 6834


title: 6970


title: Sample_178 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease

value: Other Nephrotic Syndrome


title: Mouse brain tissue - vCA1 - DEX15

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX15-AK_S160

tag: animal

value: 3 month

value: C


title: Mouse brain tissue - vCA1 - DEX10

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX10-AK_S170

tag: strain


title: 7237


title: 6788


title: 6797


title: 6796


title: 6937


title: 6800


title: Sample_34 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vCA1 - CNTRL5

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL5-AK_S186

tag: Sex

value: Vehicle

value: F


title: Sample_94 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: 6668


title: Sample_168 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_197 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vCA1 - CNTRL1

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL1-AK_S223

tag: age

value: B


title: Mouse brain tissue - vCA1 - CNTRL15

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL15-AK_S166

tag: treatment


title: Mouse brain tissue - vCA1 - CNTRL10

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL10-AK_S176

value: A

tag: cryostat


title: 6734


title: Sample_190 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_142 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: Mouse brain tissue - PVN - DEX5

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX5-AK_S174

value: Dexamethasone

tag: mouse_weight (g)

value: E


title: Mouse brain tissue - PVN - DEX15

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX15-AK_S209

tag: researcher


title: Sample_173 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - DEX14

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX14-AK_S201

tag: plate

value: D


title: 6543

value: GTU-MultiHIV B / LIPO-5


title: Mouse brain tissue - PVN - DEX12

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX12-AK_S222

value: male

tag: lane


title: 6382

value: GTU-MultiHIV B / MVA HIV-B


title: 6422

value: Healthy

value: MVA HIV-B / LIPO-5


title: 6561

value: Whole blood

value: LIPO-5 / MVA HIV-B


title: 6387


title: 6457


title: 6327


title: Sample_163 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Nephrotic Syndrome, unspecified


title: 6259


title: 6429


title: 6400


title: Sample_133 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: Sample_164 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - CNTRL5

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL5-AK_S180

value: 3 month

value: Vehicle

tag: row


title: 6376


title: Mouse brain tissue - PVN - CNTRL15

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL15-AK_S215

value: F

tag: rin


title: 6183

tag: participant id


title: 6201

tag: diagnosis


title: 6210

tag: tissue


title: 6212

tag: randomisation arm


title: 6190


title: Sample_113 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

tag: disease


title: Mouse brain tissue - PVN - CNTRL14

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL14-AK_S195

tag: animal


title: Sample_193 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_156 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - CNTRL12

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL12-AK_S216

tag: strain

value: A


title: Mouse brain tissue - PFC - DEX3

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX3-AK_S188

tag: Sex

value: Dexamethasone

value: C


title: Sample_120 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 6168


title: Sample_138 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 6114


title: Sample_88 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_147 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PFC - DEX13

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX13-AK_S213

tag: age

value: D


title: Mouse brain tissue - PFC - CNTRL2

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL2-AK_S168

tag: treatment

value: E


title: 6035


title: Sample_175 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Mouse brain tissue - PFC - DEX2

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX2-AK_S162

value: male

tag: cryostat


title: Mouse brain tissue - PFC - CNTRL13

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL13-AK_S207

tag: mouse_weight (g)


title: Mouse brain tissue - PFC - CNTRL3

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL3-AK_S183

tag: researcher


title: Mouse brain tissue - dDG - DEX6

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX6-AK_S194

tag: plate


title: 6039

value: Healthy

value: GTU-MultiHIV B / MVA HIV-B


title: 6001

value: Whole blood


title: 5987

value: MVA HIV-B / LIPO-5


title: Sample_71 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 5928

value: GTU-MultiHIV B / LIPO-5


title: 5717


title: Mouse brain tissue - dDG - DEX3

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX3-AK_S173

tag: lane


title: 5691


title: 5647


title: 5860


title: Mouse brain tissue - dDG - DEX13

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX13-AK_S220

tag: row


title: Sample_28 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 6008


title: 5589


title: 5631


title: 6064

value: LIPO-5 / MVA HIV-B


title: Mouse brain tissue - dDG - CNTRL6

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL6-AK_S200

value: 3 month

value: Vehicle

tag: rin


title: 5983

tag: participant id


title: 5554

tag: diagnosis


title: Sample_49 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: tissue

value: Tubulointerstitium from kidney biopsy


title: 5545

tag: randomisation arm


title: 5723


title: 5617


title: 5524


title: 5486


title: 5552


title: Sample_160 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease


title: Sample_54 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: Mouse brain tissue - dDG - CNTRL3

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL3-AK_S179

tag: animal


title: Sample_186 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dDG - CNTRL13

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL13-AK_S226

tag: strain


title: Sample_157 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_17 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dCA1 - DEX8

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX8-AK_S184

tag: Sex

value: Dexamethasone


title: 5654


title: Mouse brain tissue - dCA1 - DEX3

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX3-AK_S203

tag: age

value: F


title: 5280


title: 5507


title: 5421


title: Mouse brain tissue - dCA1 - DEX1

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX1-AK_S218

tag: treatment

value: C


title: Mouse brain tissue - dCA1 - DEX13

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX13-AK_S165

value: B

tag: cryostat


title: 5310


title: 5419


title: 5245


title: 5478


title: 5456


title: 5199


title: 5528


title: 5226


title: Sample_196 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Sample_195 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dCA1 - CNTRL8

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL8-AK_S189

value: male

tag: mouse_weight (g)

value: D


title: Sample_174 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_192 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: Sample_53 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 5108

value: Healthy

value: Whole blood

value: GTU-MultiHIV B / MVA HIV-B


title: 5127


title: Mouse brain tissue - dCA1 - CNTRL1

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL1-AK_S224

tag: researcher


title: 5172


title: 5076

value: MVA HIV-B / LIPO-5


title: 5087

value: LIPO-5 / MVA HIV-B


title: 5080


title: Sample_19 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 5072


title: Mouse brain tissue - CER - DEX13

description:
CER_deseq2_expression_vsd.txt
CER-DEX13-AK_S182

value: 3 month

tag: plate

value: A


title: Mouse brain tissue - CER - DEX8

description:
CER_deseq2_expression_vsd.txt
CER-DEX8-AK_S169

tag: lane


title: Mouse brain tissue - dCA1 - CNTRL13

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL13-AK_S159

value: Vehicle

tag: row


title: 4979


title: Mouse brain tissue - dCA1 - CNTRL3

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL3-AK_S197

tag: rin


title: 5055

tag: participant id

value: GTU-MultiHIV B / LIPO-5


title: 5074

tag: diagnosis


title: Sample_87 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: tissue

value: Tubulointerstitium from kidney biopsy

value: Other Nephrotic Syndrome


title: Mouse brain tissue - CER - DEX12

description:
CER_deseq2_expression_vsd.txt
CER-DEX12-AK_S211

value: Dexamethasone


title: Sample_69 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 4923

tag: randomisation arm


title: Sample_82 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease

value: Membranous Nephropathy


title: 4811


title: 4968


title: 4837


title: Sample_180 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 4831


title: 4722


title: Mouse brain tissue - CER - CNTRL8

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL8-AK_S163

tag: animal

value: male

value: F


title: 4864


title: 4719


title: Sample_36 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - CNTRL13

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL13-AK_S187

tag: strain


title: Sample_77 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 4904


title: Mouse brain tissue - CER - CNTRL12

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL12-AK_S205

tag: Sex

value: B


title: Mouse brain tissue - AMY - DEX4

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX4-AK_S178

tag: age

value: C


title: Mouse brain tissue - AMY - DEX14

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX14-AK_S185

tag: treatment

value: E


title: 4625

value: Healthy

value: Whole blood


title: 4694

value: GTU-MultiHIV B / MVA HIV-B


title: 4672


title: Sample_150 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_12 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 4614

value: MVA HIV-B / LIPO-5


title: Mouse brain tissue - AMY - DEX12

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX12-AK_S225

value: 3 month

value: D

tag: cryostat


title: Sample_75 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 4617

value: GTU-MultiHIV B / LIPO-5


title: 4510


title: 4618

value: LIPO-5 / MVA HIV-B


title: 4567


title: Mouse brain tissue - AMY - DEX10

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX10-AK_S204

tag: mouse_weight (g)

value: A


title: Sample_57 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

value: Other Nephrotic Syndrome


title: Mouse brain tissue - AMY - CNTRL4

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL4-AK_S172

value: Vehicle

tag: researcher


title: Sample_171 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Sample_118 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: Sample_185 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - AMY - CNTRL14

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL14-AK_S190

value: male

tag: plate


title: Mouse brain tissue - AMY - CNTRL12

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL12-AK_S219

tag: lane


title: 4568


title: 4420


title: 4481


title: 4566


title: 4610


title: 4509


title: 4506


title: 4475


title: 4290


title: 4308


title: Sample_51 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 4282


title: Mouse brain tissue - AMY - CNTRL10

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL10-AK_S210

tag: row


title: Sample_47 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - DEX11

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX11-AK_S109

value: Dexamethasone

value: F

tag: rin


title: Sample_22 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 4275

tag: participant id

value: Healthy

value: Whole blood


title: Mouse brain tissue - vDG - DEX10

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX10-AK_S148

value: E


title: Mouse brain tissue - vDG - DEX12

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX12-AK_S101

value: 3 month

value: B


title: Sample_52 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_151 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - CNTRL12

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL12-AK_S94


title: Sample_39 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_127 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - CNTRL10

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL10-AK_S155


title: 4288

tag: diagnosis

value: GTU-MultiHIV B / LIPO-5


title: 4262

tag: tissue

value: LIPO-5 / MVA HIV-B


title: 4237

tag: randomisation arm

value: GTU-MultiHIV B / MVA HIV-B


title: 4209


title: 4156


title: 4236


title: 4146


title: 4093


title: Mouse brain tissue - vCA1 - DEX6

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX6-AK_S126

value: D


title: 4114


title: 4266

value: MVA HIV-B / LIPO-5


title: 4171


title: Sample_125 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

tag: disease


title: Mouse brain tissue - vCA1 - DEX3

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX3-AK_S81

tag: animal

value: A


title: 4248


title: Mouse brain tissue - vDG - CNTRL11

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL11-AK_S116

tag: strain

value: Vehicle


title: Mouse brain tissue - vCA1 - DEX2

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX2-AK_S136

tag: Sex

value: male

value: G


title: Sample_167 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: Sample_62 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: 4076

value: Healthy


title: Sample_9 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 4045

value: Whole blood


title: 3980


title: Mouse brain tissue - vCA1 - DEX14

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX14-AK_S95

tag: age

value: Dexamethasone

value: C


title: 3898


title: 3936


title: 3891


title: 3938


title: 3954


title: Sample_56 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_144 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_152 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: Mouse brain tissue - vCA1 - CNTRL3

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL3-AK_S87

value: 3 month

tag: treatment


title: Sample_2 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_154 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vCA1 - CNTRL2

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL2-AK_S143

tag: cryostat


title: Mouse brain tissue - PVN - DEX7

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX7-AK_S113

tag: mouse_weight (g)


title: Sample_43 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - DEX8

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX8-AK_S84

tag: researcher

value: E


title: Mouse brain tissue - vCA1 - CNTRL6

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL6-AK_S120

tag: plate


title: Sample_99 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: Mouse brain tissue - PVN - DEX4

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX4-AK_S138

tag: lane

value: B


title: Sample_98 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - PVN - DEX10

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX10-AK_S122

value: F

tag: row


title: 4060

value: GTU-MultiHIV B / MVA HIV-B


title: 3717

value: MVA HIV-B / LIPO-5


title: 3650


title: 3658

value: LIPO-5 / MVA HIV-B


title: 3873

value: GTU-MultiHIV B / LIPO-5


title: 3753


title: 3713


title: Mouse brain tissue - PVN - CNTRL8

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL8-AK_S90

value: male

value: Vehicle

tag: rin


title: 3816

tag: participant id


title: 3790

tag: diagnosis


title: 3751

tag: tissue


title: 3619

tag: randomisation arm


title: 3659


title: 3602


title: 3599


title: Mouse brain tissue - PVN - CNTRL4

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL4-AK_S131


title: 3622


title: 3596


title: 3579


title: Sample_199 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

tag: disease

value: Minimal Change Disease


title: Sample_73 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3564

value: Healthy

value: Whole blood


title: Mouse brain tissue - PVN - CNTRL10

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL10-AK_S128

tag: animal


title: Mouse brain tissue - PVN - CNTRL7

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL7-AK_S106

tag: strain

value: C


title: 3549


title: Sample_4 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: Mouse brain tissue - PFC - DEX7

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX7-AK_S141

tag: Sex

value: 3 month

value: Dexamethasone


title: Mouse brain tissue - PFC - DEX1

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX1-AK_S146

tag: age


title: Sample_117 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 3507


title: Sample_18 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Mouse brain tissue - PFC - DEX10

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX10-AK_S96

tag: treatment

value: D


title: Sample_181 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3538


title: Sample_78 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_13 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3505


title: 3525


title: Sample_92 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3466


title: 3446


title: 3351


title: 3398


title: 3421


title: 3317


title: 3314


title: Sample_189 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3498


title: 3414


title: 3396


title: 3291

value: GTU-MultiHIV B / MVA HIV-B


title: Sample_177 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3310


title: Mouse brain tissue - dDG - DEX8

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX8-AK_S125

tag: cryostat


title: Sample_188 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dDG - DEX15

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX15-AK_S117

tag: mouse_weight (g)

value: G


title: Mouse brain tissue - PFC - CNTRL10

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL10-AK_S102

tag: researcher


title: Mouse brain tissue - PFC - CNTRL1

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL1-AK_S153

tag: plate


title: Mouse brain tissue - PFC - CNTRL4

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL4-AK_S112

tag: lane

value: B


title: 3196

value: GTU-MultiHIV B / LIPO-5


title: Sample_23 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3270

value: LIPO-5 / MVA HIV-B


title: 3128


title: 3181


title: 3127


title: Mouse brain tissue - dDG - DEX14

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX14-AK_S130

value: male

value: A

tag: row


title: Sample_46 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: Mouse brain tissue - dDG - DEX11

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX11-AK_S83

tag: rin


title: Mouse brain tissue - dDG - CNTRL8

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL8-AK_S119

value: Vehicle


title: 3124

tag: participant id

value: Healthy

value: Whole blood


title: Sample_148 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_15 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 3018

tag: diagnosis


title: Mouse brain tissue - dDG - CNTRL15

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL15-AK_S110

value: 3 month


title: 3054

tag: tissue


title: Sample_187 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 3038

tag: randomisation arm


title: 2876


title: Sample_38 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease


title: Mouse brain tissue - dDG - CNTRL11

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL11-AK_S89

tag: animal


title: 2856

value: MVA HIV-B / LIPO-5


title: Sample_31 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 2918


title: Mouse brain tissue - dCA1 - DEX5

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX5-AK_S132

tag: strain

value: Dexamethasone

value: C


title: Sample_6 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Mouse brain tissue - dDG - CNTRL14

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL14-AK_S137

tag: Sex


title: Mouse brain tissue - dCA1 - DEX2

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX2-AK_S107

tag: age

value: D


title: Mouse brain tissue - dCA1 - DEX11

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX11-AK_S144

tag: treatment


title: 2809


title: 2848


title: 2950


title: Mouse brain tissue - dCA1 - CNTRL9

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL9-AK_S99

value: G

tag: cryostat


title: Sample_110 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 2778


title: 2712

value: GTU-MultiHIV B / LIPO-5


title: Sample_134 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 2728

value: GTU-MultiHIV B / MVA HIV-B


title: 2763


title: 2781


title: 2749


title: 2783


title: 2745


title: Sample_103 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - dCA1 - CNTRL5

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL5-AK_S139

value: male

tag: mouse_weight (g)


title: 2649

value: LIPO-5 / MVA HIV-B


title: 2698


title: 2730


title: Sample_41 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: Mouse brain tissue - dCA1 - CNTRL2

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL2-AK_S114

value: Vehicle

tag: researcher


title: Mouse brain tissue - dCA1 - CNTRL11

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL11-AK_S151

tag: plate

value: A


title: Sample_48 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: 2593

value: Healthy

value: Whole blood


title: 2542


title: 2559

value: MVA HIV-B / LIPO-5


title: Mouse brain tissue - CER - DEX9

description:
CER_deseq2_expression_vsd.txt
CER-DEX9-AK_S154

value: 3 month

tag: lane


title: Sample_107 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 2631


title: Sample_101 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - DEX7

description:
CER_deseq2_expression_vsd.txt
CER-DEX7-AK_S93

value: Dexamethasone

tag: row


title: Sample_169 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: 2622


title: 2501


title: Sample_158 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: Sample_85 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 2532


title: Mouse brain tissue - CER - DEX10

description:
CER_deseq2_expression_vsd.txt
CER-DEX10-AK_S85

value: F

tag: rin


title: Mouse brain tissue - CER - CNTRL9

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL9-AK_S147

value: D


title: 2374

tag: participant id

value: GTU-MultiHIV B / MVA HIV-B


title: 2293

tag: diagnosis


title: Sample_86 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: tissue


title: 2309

tag: randomisation arm

value: GTU-MultiHIV B / LIPO-5


title: 2264


title: Sample_115 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease


title: Mouse brain tissue - CER - CNTRL7

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL7-AK_S100

tag: animal

value: male


title: 2417

value: LIPO-5 / MVA HIV-B


title: Mouse brain tissue - CER - CNTRL3

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL3-AK_S129

tag: strain

value: Vehicle

value: G


title: Mouse brain tissue - CER - DEX3

description:
CER_deseq2_expression_vsd.txt
CER-DEX3-AK_S123

tag: Sex


title: Sample_90 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

value: Minimal Change Disease


title: 2430

value: Healthy

value: Whole blood


title: Sample_67 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - CER - CNTRL10

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL10-AK_S91

tag: age

value: 3 month


title: 2169


title: 2202


title: 2193


title: Mouse brain tissue - AMY - DEX5

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX5-AK_S121

tag: treatment

value: E


title: Mouse brain tissue - AMY - DEX1

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX1-AK_S157

value: Dexamethasone

tag: cryostat


title: Sample_123 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: Sample_170 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: 2086


title: 2233


title: 1951


title: Mouse brain tissue - AMY - DEX15

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX15-AK_S88

tag: mouse_weight (g)

value: B


title: 1918


title: Sample_3 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 2113


title: 2052

value: MVA HIV-B / LIPO-5


title: 1930


title: Sample_11 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - AMY - DEX13

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX13-AK_S98

tag: researcher

value: F


title: Mouse brain tissue - PFC - CNTRL7

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL7-AK_S134

tag: plate


title: Mouse brain tissue - AMY - CNTRL5

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL5-AK_S127

tag: lane


title: 1995

value: GTU-MultiHIV B / LIPO-5


title: Mouse brain tissue - AMY - CNTRL1

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL1-AK_S150

value: male

tag: row


title: Sample_7 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 1834

value: GTU-MultiHIV B / MVA HIV-B


title: Sample_79 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Sample_95 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 1816


title: 1707


title: Mouse brain tissue - AMY - CNTRL13

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL13-AK_S104

value: Vehicle

tag: rin


title: 1812

tag: participant id


title: Sample_146 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: 1638

tag: diagnosis

value: LIPO-5 / MVA HIV-B


title: 1783

value: Healthy

tag: tissue


title: Sample_58 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - DEX8

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX8-AK_S39

value: D


title: 1623

value: Whole blood

tag: randomisation arm


title: Mouse brain tissue - vDG - DEX4

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX4-AK_S53

value: 3 month

value: E


title: 1817


title: 1628


title: 1561


title: 1545


title: Mouse brain tissue - AMY - CNTRL15

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL15-AK_S82


title: Mouse brain tissue - vDG - DEX15

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX15-AK_S68

value: Dexamethasone


title: Sample_184 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease

value: Membranous Nephropathy


title: Sample_132 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - DEX14

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX14-AK_S9

tag: animal

value: A


title: 1492


title: 1592


title: 1467

value: MVA HIV-B / LIPO-5


title: 1579


title: Sample_21 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - DEX13

description:
vDG_deseq2_expression_vsd.txt
vDG-DEX13-AK_S30

tag: strain

value: C


title: Sample_128 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Other Nephrotic Syndrome


title: Sample_97 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vDG - CNTRL4

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL4-AK_S54

tag: Sex

value: male


title: 1512


title: 1477


title: Sample_140 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 1454


title: Mouse brain tissue - vDG - CNTRL15

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL15-AK_S59

tag: age

value: F


title: Sample_105 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Minimal Change Disease


title: 1408


title: Mouse brain tissue - vDG - CNTRL14

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL14-AK_S8

tag: treatment

value: Vehicle


title: Mouse brain tissue - vDG - CNTRL8

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL8-AK_S38

tag: cryostat


title: Sample_10 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy


title: 1406

value: GTU-MultiHIV B / MVA HIV-B


title: Mouse brain tissue - vDG - CNTRL13

description:
vDG_deseq2_expression_vsd.txt
vDG-CNTRL13-AK_S29

tag: mouse_weight (g)


title: 1373

value: Healthy


title: 1327


title: 1340

value: GTU-MultiHIV B / LIPO-5


title: 1892

value: Whole blood


title: Sample_137 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Focal Segmental Glomerulosclerosis


title: 1230


title: 1295


title: 1143


title: 1076


title: 1372


title: 1296


title: 1399


title: 1424


title: Mouse brain tissue - vCA1 - DEX7

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX7-AK_S55

value: 3 month

tag: researcher

value: E


title: 863


title: Sample_172 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Membranous Nephropathy


title: 834


title: 1022


title: Sample_61 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: Mouse brain tissue - vCA1 - DEX11

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX11-AK_S80

value: Dexamethasone

tag: plate

value: G


title: Mouse brain tissue - vCA1 - CNTRL8

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL8-AK_S21

tag: lane

value: B


title: Mouse brain tissue - vCA1 - DEX8

description:
vCA1_deseq2_expression_vsd.txt
vCA1-DEX8-AK_S20

tag: row


title: Mouse brain tissue - vCA1 - CNTRL7

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL7-AK_S56

tag: rin


title: Sample_40 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.


title: 2470

tag: participant id


title: 746

tag: diagnosis

value: LIPO-5 / MVA HIV-B


title: Mouse brain tissue - vCA1 - CNTRL11

description:
vCA1_deseq2_expression_vsd.txt
vCA1-CNTRL11-AK_S70

value: male


title: 685

tag: tissue


title: 784

tag: randomisation arm


title: 1203


title: Sample_139 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

tag: disease


title: 712

value: MVA HIV-B / LIPO-5


title: Mouse brain tissue - PVN - DEX9

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX9-AK_S69

tag: animal


title: 661


title: W6: WSU-DLCL-2 Drugs (2+3): Olaparib + 177Lu-NNV003

city: Oslo

first: Ada

last: Repetto-Llamazares

state: Oslo

address: Kjelsåsveien 168B

department: R&D

country: Norway

institute: Nordic Nanovector ASA

data_processing:
base calling: bcl2fastq v2
Alignment: Star2 aligner
filtering: highly abundant sequences
Differential Gene Expression: Cufflinks and Cuffdiff v2.2.1
Mutations: Isaac Variant Caller version 2.3.13-31 c98c29-dirty and hg19 reference. Variant calls passing all quality requirements were annotated using VEP Ensembl GRCh37 release 98.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Processed data files are differential gene expression analysis files for each treated sample. Ola=olaparib, Hum or HLT=177Lu-NNV003, combo=olaparib+177Lu-NNV003 vs baseline control (untreated samples). D=DOHH2, G=Granta-519, O=Oci-Ly-10, R=Rec-1, S=SUDHL-4, U=U2932, W=WSU-DLCL-2.

source_name: GCB-DLBCL cell line

growth_protocol: REC-1, DOHH-2, SU-DHL-4, WSU-DLCL-2 and U-2932 were cultured in RPMI medium, GRANTA-519 was cultured in DMEM medium and OCI-LY-10 was cultured in IMDM medium. The media were supplemented with 15% (OCI-LY-10) or 10% (all others) heat inactivated foetal bovine serum and 1% penicillin/streptomycin (media and supplement from Thermo Fisher Scientific, USA).

extract_protocol:
The cells including untreated controls were washed and total RNA isolated using RNeasy mini kit (Qiagen©, Germany) following the manufacturers’ protocol. RNA integrity was verified using 2100 Bioanalyzer (Agilent Technologies Inc., CA, USA) and adjusted to an acceptable concentration.
Libraries were generated from the RNA using Illumina stranded mRNA kit (Illumina Inc., CA, USA) and sequenced on an Illumina NextSeq500 system (Illumina Inc., CA, USA) using 75 bp single reads. Obtained reads were aligned against the reference human genome (UCSC hg19) using STARalign v2.5.0.

treatment_protocol: Cells were treated during 24h at 37C with either the individual drugs alone at their corresponding IC50s or with the combination. Control cells for baseline estimations were not given any treatment but were handled in the same way as the treated cells.

value: Combo

tag: cell type

tag: disease classification

value: GCB-DLBCL


title: 666


title: 588


title: 611


title: Mouse brain tissue - PVN - DEX3

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX3-AK_S42

tag: strain

tag: Sex

tag: age

value: D


title: Sample_93 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

value: Other Nephrotic Syndrome


title: Mouse brain tissue - PVN - DEX1

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX1-AK_S15

tag: treatment

tag: mouse_weight (g)

tag: cryostat


title: W4: WSU-DLCL-2 Drug 3: 177Lu-NNV003


title: W3: WSU-DLCL-2 Drug 2: Olaparib

value: Olaparib


title: Mouse brain tissue - PVN - DEX11

description:
PVN_deseq2_expression_vsd.txt
PVN-DEX11-AK_S34

tag: researcher

tag: plate

tag: lane

value: C


title: 495

tag: participant id

value: Healthy

value: Whole blood

value: GTU-MultiHIV B / MVA HIV-B


title: Mouse brain tissue - PVN - CNTRL9

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL9-AK_S73

value: 3 month

value: Vehicle

tag: row

tag: rin


title: 507

tag: diagnosis

tag: tissue

tag: randomisation arm


title: U6: U2932 Drugs (2+3): Olaparib + 177Lu-NNV003

source_name: ABC-DLBCL cell line

tag: cell type

value: ABC-DLBCL


title: 492

value: GTU-MultiHIV B / LIPO-5


title: 489

value: LIPO-5 / MVA HIV-B


title: 497


title: 491


title: W1: WSU-DLCL-2 Baseline control

value: Baseline Control

tag: disease classification


title: Mouse brain tissue - PVN - CNTRL3

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL3-AK_S41

tag: animal

tag: strain

value: male


title: U4: U2932 Drug 3: 177Lu-NNV003


title: Mouse brain tissue - PVN - CNTRL1

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL1-AK_S16

tag: Sex

tag: age

value: B


title: Mouse brain tissue - PVN - CNTRL11

description:
PVN_deseq2_expression_vsd.txt
PVN-CNTRL11-AK_S33

tag: treatment

tag: mouse_weight (g)


title: U3: U2932 Drug 2: Olaparib


title: 448


title: 348


title: 449

value: MVA HIV-B / LIPO-5


title: 330


title: U1: U2932 Baseline control


title: 394


title: 292


title: 207


title: 803


title: Mouse brain tissue - PFC - DEX9

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX9-AK_S45

value: Dexamethasone

tag: researcher

value: D

tag: cryostat


title: S6: SUDHL-4 Drugs (2+3): Olaparib + 177Lu-NNV003

value: Combo

value: GCB-DLBCL


title: Mouse brain tissue - PFC - DEX6

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX6-AK_S3

tag: plate

tag: lane

value: A


title: S4: SUDHL-4 Drug 3: 177Lu-NNV003


title: 259

tag: participant id

value: Healthy


title: Mouse brain tissue - PFC - DEX5

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX5-AK_S60

value: F

tag: row

tag: rin


title: 189

tag: diagnosis

tag: tissue

value: Whole blood


title: 177

tag: randomisation arm


title: S3: SUDHL-4 Drug 2: Olaparib

value: Olaparib

tag: cell type

tag: disease classification


title: S1: SUDHL-4 Baseline control


title: Mouse brain tissue - PFC - DEX14

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX14-AK_S32

tag: animal

tag: strain

value: 3 month

value: C


title: PBS_side_48h_1

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: PBS injected uninfected leg 48h after Lm injection.

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts for features in samples, obtained with featureCounts.

source_name: Poplitial adipose tissue

extract_protocol:
RNA was extracted using RNeasy Kit (QIAGEN) following the manufacturer’s instructions with an additional on-column DNase treatment using the RNase-Free DNase set (Qiagen). RNA was quantified using Qubit 2.0 (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina).

treatment_protocol: A wild type strain of Listeria monocytogenes (Lm) was used for infections. Mice were infected subcutaneously on the footpad with a sublethal dose of 1 × 10^6 colony-forming units (CFU). Mice were left for indicated times before being sacrificed. Control cells were from either PBS injected mouse or from the uninjected leg of infected animal.

value: Adipocyte

value: PBS injection

tag: time point


title: PBS_side_48h_2

tag: treatment


title: Mouse brain tissue - PFC - CNTRL9

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL9-AK_S37

tag: Sex

tag: age

value: Vehicle

tag: mouse_weight (g)


title: PBS_side_24h_1

description: PBS injected uninfected leg 24h after Lm injection.


title: PBS_side_24h_2


title: 197


title: 174

value: GTU-MultiHIV B / MVA HIV-B


title: R4: Rec-1 Drug 3: 177Lu-NNV003

source_name: MCL cell line

value: MCL


title: PBS_2

description: PBS injection control.


title: 163

value: MVA HIV-B / LIPO-5


title: 80


title: 149

value: GTU-MultiHIV B / LIPO-5


title: Mouse brain tissue - PFC - CNTRL6

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL6-AK_S2

value: male

tag: researcher

tag: plate

tag: cryostat


title: 110

tag: participant id


title: 31


title: 16


title: R3: Rec-1 Drug 2: Olaparib


title: Mouse brain tissue - PFC - DEX15

description:
PFC_deseq2_expression_vsd.txt
PFC-DEX15-AK_S51

value: Dexamethasone

tag: lane

value: E

tag: row

tag: rin


title: PBS_1

description: PBS injection control.


title: R1: Rec-1 Baseline control

value: Baseline Control


title: Mouse brain tissue - PFC - CNTRL15

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL15-AK_S52


title: Lm_side_48h_1

description: 48h after L. monocytogenes injection.

value: L. monocytogenes infection


title: Mouse brain tissue - PFC - CNTRL5

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL5-AK_S61

value: F


title: R6: Rec-1 Drugs (2+3): Olaparib + 177Lu-NNV003

value: Combo


title: 30

tag: diagnosis

value: Healthy

tag: tissue

value: Whole blood

tag: randomisation arm

value: LIPO-5 / MVA HIV-B


title: Lm_side_24h_1

description: 24h after L. monocytogenes injection.

tag: cell type

value: Adipocyte


title: Mouse brain tissue - PFC - CNTRL14

description:
PFC_deseq2_expression_vsd.txt
PFC-CNTRL14-AK_S31

tag: animal

tag: strain

value: 3 month

value: C


title: LEAN

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 2.2 (10X genomics)
Samples were processed and analyzed in R (3.6.0) using Seurat (v3)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.

source_name: Large intestine Lamina propria

extract_protocol:
Single cell RNA sequencing was performed using a 10X Genomics Chromium Controller.
Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol. An estimated 5,000 cells were added to each channel with an average of 3,000 cells recovered.  Libraries were sequenced on HiSeq 3000 (Illumina)

treatment_protocol: Obesity was induced by ad libitum feeding of C57/BL6 mice for 12 week with irradiated high fat diet (Rodent Diet 60% kcal from fat, Research Diets, Inc., Cat #D12492). Control diet (chow) containing 24% protein, 47.5% carbohydrate, and 4.9% fat, was given to age and sex matched animals as a control group.

value: CD45 postive

tag: treatment

value: Cotnrol diet


title: O3: Oci-Ly-10 Drug 2: Olaparib

value: Olaparib

tag: disease classification

value: ABC-DLBCL


title: PBS

description: Footpad PBS injection

source_name: Popliteal adipose tissue

extract_protocol:
Mice were euthanized and adipose tissue was separated from lymph nodes and surrounding muscle. Isolated tissue was then minced and digested in DMEM (Gibco) containing 2.5% bovine serum albumin, 2 mM L-glutamine, 100 U/mL Penicillin/Streptomycin, 2 mg/mL Collagenase I (Thermo) and 2 mg/mL Collagenase II (Thermo) for 45 min at 37°C with gentle rotation. During the last 15 minutes of incubation 2 mM EDTA was added to the media. Finally, the cell suspension was filtered through a 100 µm strainer. Cells in stromal vascular fraction (SVF) were separated from the adipocyte layer by centrifugation. Single live cells were further purified via fluorescent activated cell sorting, excluding dead cells labelled with LIVE/DEAD Fixable Aqua Dead Cell Stain Kit and doublets based on side and forward light scatter.
scRNA-seq of SVF cells was performed using a 10X Genomics Chromium Controller. Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol. Libraries were sequenced on HiSeq 3000 (Illumina).

treatment_protocol: A wild type strain of Listeria monocytogenes (L. mono) was used for infections. Mice were infected subcutaneously on the footpad with a sublethal dose of 1 × 106 colony-forming units (CFU). Mice were left for 2 days before being sacrificed. Matching PBS injected control or from uninfected footpad were used

value: Stromal vascular fraction

value: PBS injection


title: O6: Oci-Ly-10 Drugs (2+3): Olaparib + 177Lu-NNV003


title: Mouse brain tissue - dDG - DEX4

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX4-AK_S6

tag: Sex

value: male

tag: age

value: Dexamethasone

value: A


title: Lm_side_24h_2

description: 24h after L. monocytogenes injection.

value: L. monocytogenes infection

tag: time point


title: HFD

value: High fat diet


title: Lm_side_48h_2

description: 48h after L. monocytogenes injection.


title: Mouse brain tissue - dDG - DEX7

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX7-AK_S35

tag: mouse_weight (g)

tag: researcher

tag: plate


title: LM

description: Footpad L. monocytogenes injection


title: Primary infection with H. polygyrus

description: Single infection with H. polygyrus

source_name: Stromal vascular fraction from mesenteric adipose tissue

growth_protocol: For isolation of cells from mFAT mice were euthanised and transcardially perfused with 10ml of ice-cold PBS. mFAT was separated from mLN, intestine and omentum, minced and digested in 3ml of low glucose DMEM containing 25mM HEPES, 1% low fatty acid BSA, 2mM L-glutamine (L-glut), 100U/ml Penicillin/Streptomycin (P/S), with the addition of Liberase TL (0.2mg/ml, Roche) and DNase I (0.25mg/ml, Roche) for 30-40min in 37°C rotating. After digestion 2ml DMEM containing 2mM EDTA was added and the suspension filtered through 70um strainer. Cells in SVF were then separated from the adipocyte layer by centrifugation.

extract_protocol:
Single cell RNA sequencing was performed using a 10X Genomics Chromium Controller.
Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol.  Libraries were sequenced on HiSeq 3000 (Illumina)

treatment_protocol: All mice were maintained in specific-pathogen-free conditions in the animal facility of the Max Planck Institute for Immunobiology and Epigenetics (Freiburg, Germany), and all corresponding animal protocols were approved by the animal care committee of the Regierungspraesidium Freiburg. To induce H. polygyrus infection mice were gavage with 200 L3 infectious stage larvae in PBS. For primary infection mice were left for 11-13 days before being sacrificed. For recovery mice were orally treated with anti-helminth pyrantel pamoate (1mg/mouse) and left for 4-5 weeks. For secondary infection mice were gavaged with 200 L3 H. polygyrus at the end of recovery stage and sacrificed at 11-13 days post-secondary infection. In all the experiments mice were age and sex matched, in particular in the experiments with primary and secondary infections mice were aged matched, such that at the point of sacrifice all experimental groups of mice were at the same age.

tag: infection status

value: Single infection

value: Mesenteric adipose


title: Mouse brain tissue - dDG - DEX2

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX2-AK_S43

tag: lane

value: D

tag: row

tag: cryostat


title: Secondary infection with H. polygyrus

description: Secondary infection with H. polygyrus after primary infection is cleared

value: Secondary infection

tag: tissue


title: Mouse brain tissue - dDG - DEX1

description:
dDG_deseq2_expression_vsd.txt
dDG-DEX1-AK_S62

value: 3 month

value: F

tag: rin


title: G6: Granta Drugs (2+3): Olaparib + 177Lu-NNV003

value: Combo

tag: cell type

value: MCL


title: O1: Oci-Ly-10 Baseline control

value: Baseline Control


title: Control mouse

description: Control mice

value: Naive


title: Mouse brain tissue - dDG - CNTRL7

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL7-AK_S25

tag: animal

value: Vehicle

value: C


title: G4: Granta Drug 3: 177Lu-NNV003


title: G3: Granta Drug 2: Olaparib

value: Olaparib


title: O4: Oci-Ly-10 Drug 3: 177Lu-NNV003

value: ABC-DLBCL


title: Mouse brain tissue - dDG - CNTRL4

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL4-AK_S7

tag: strain

value: male

value: A


title: Control

description: Naive

value: Stromal vascular fraction

tag: treatment

value: Control


title: Tumoral 5

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

description: Tumoral tissue from from 55 weeks old C57BL/6J mice overexpressing ChREBP

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MouseGene2.0ST (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V21 was used for annotation.

source_name: ChREBP overexpressing HCC tumors 5

label_protocol: 250 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

extract_protocol: Extraction of total RNA was performed with SV total RNA isolation system from Promega.

tag: gender

value: Male

value: 55 weeks

value: Liver


title: Tumoral 6

source_name: ChREBP overexpressing HCC tumors 6


title: Mouse brain tissue - dDG - CNTRL2

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL2-AK_S44

tag: Sex

value: 3 month

value: D


title: Tumoral 4

source_name: ChREBP overexpressing HCC tumors 4

tag: age


title: Tumoral 3

source_name: ChREBP overexpressing HCC tumors 3


title: D4: DOHH2 Drug 3: 177Lu-NNV003

tag: disease classification

value: GCB-DLBCL


title: Sample_143 RNAseq counts from the tubulointerstitial compartment from kidney biopsies.

value: Tubulointerstitium from kidney biopsy

tag: disease

value: Focal Segmental Glomerulosclerosis


title: Mouse brain tissue - dCA1 - DEX14

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX14-AK_S12

value: Dexamethasone

tag: mouse_weight (g)

tag: researcher


title: D6: DOHH2 Drugs (2+3): Olaparib + 177Lu-NNV003

value: Combo


title: Mouse brain tissue - dCA1 - DEX15

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX15-AK_S79

tag: plate

value: G


title: Mouse brain tissue - dDG - CNTRL1

description:
dDG_deseq2_expression_vsd.txt
dDG-CNTRL1-AK_S58

source_name: Mouse brain tissue - dDG

value: Vehicle

tag: lane

value: F


title: Tumoral 2

source_name: ChREBP overexpressing HCC tumors 2


title: Non tumoral adjacent 5

description: Non tumoral adjacent liver tissue from 55 weeks old C57BL/6J mice overexpressing ChREBP

source_name: Non tumoral adjacent liver tissue5


title: D3: DOHH2 Drug 2: Olaparib

value: Olaparib


title: Tumoral 1

source_name: ChREBP overexpressing HCC tumors 1


title: G1: Granta Baseline control

value: Baseline Control

value: MCL


title: Non tumoral adjacent 2

source_name: Non tumoral adjacent liver tissue2


title: D1: DOHH2 Baseline control


title: Non tumoral adjacent 4

source_name: Non tumoral adjacent liver tissue4


title: Normal 4

description: Normal liver tissue from 55 weeks old C57BL/6J mice

source_name: Normal  liver tissue 4


title: Non tumoral adjacent 3

source_name: Non tumoral adjacent liver tissue3


title: Normal 5

source_name: Normal  liver tissue 5


title: Mouse brain tissue - dCA1 - CNTRL4

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL4-AK_S63

source_name: Mouse brain tissue - dCA1

value: male

tag: row


title: Sample 11: IM-0223 ILF2-OV

type: protein

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description: test

data_processing:
RPPA slides were assayed with 306 antibodies, analyzed by Array-Pro Analyzer 6.3 then by SuperCurve_1.5.0 via SuperCurveGUI_2.1.1
RPPA Core Facility at the University of Texas MD Anderson Cancer Center
Ratio was calculated as follow: (expression of gene X in OV-  expression of gene X in contorl EV)/expression of gene X in control EV
Fold Change worksheet reports test/control (i.e., EV/OV) ratios.

molecule: protein

source_name: Melanoma cells (cultured(

growth_protocol: Cell lines were grown until 80% confluency and dettached using cell stripper non-enzimatic solution. Cells were washed with PBS and pelleted. Protein extraction were as described in extract protocol.

extract_protocol: Protein extractions, quantification, and downstream RPPA analysis were performed by CCSG-supported RPPA Core Facility at the University of Texas MD Anderson Cancer Center.

tag: cell line

tag: passages after establishing stable clones

tag: transfected vector


title: Sample 9: IM-0223 EV

description: control

value: Control empty vector


title: Non tumoral adjacent 1

source_name: Non tumoral adjacent liver tissue1

value: Male

value: 55 weeks

tag: tissue


title: Normal 1

source_name: Normal  liver tissue 1

value: Liver


title: Normal 2

source_name: Normal  liver tissue 2