title: BG56_SC_ColdDiss_Methanol

extract_protocol:
Cold tissue dissociation  Kidneys were dissociated using a modified version of the published protocol described in (Adam, Potter, & Potter, 2017). Based on the weight, in a pre-cooled Miltenyi C-tube, a protease solution (5mM CaCl2 [Invitrogen; AM9530G], 10mg/mL B. Licheniformis protease [Sigma; P5380], 125U/mL DNase I [Sigma; D5025], 1xDPBS) was prepared for each kidney.  The kidneys were then minced on ice into a smooth paste using a scalpel. The minced kidney was transferred into 4-6mL of the protease solution (dependent on weight) and triturated using a 1mL pipette for 15 seconds every two minutes for a total of eight minutes.  Following trituration, the C-tubes were placed onto a Miltenyi gentleMACS octo dissociator in a cool room (4°C), and the m_brain_03 program was run twice in succession. Once complete, the samples were triturated for 15 seconds every two minutes on ice for an additional 16 minutes using a 1mL pipette. 10µL of each sample was then loaded into a haemocytometer to assess whether tissue dissociation was complete. The dissociated cells were transferred to a 15mL centrifuge tube and 3mL of ice-cold PBS+10%FBS [Gibco; A3160401] was added.   The cell suspension was centrifuged at 1200g for five minutes at 4°C. The supernatant was removed and the pellet was resuspended in 2mL of PBS+10%FBS. The cells were then filtered through a 70µm cell strainer, which was subsequently rinsed with 2mL of PBS+0.01% BSA. The cells were then centrifuged again at 1200g for five minutes at 4°C followed by removal of the supernatant and resuspension of the pellet in 5mL of PBS+0.01%BSA. The cells were then filtered through a 40µm cell strainer, which was subsequently rinsed with 2mL of PBS+0.01% BSA. The cells were again centrifuged at 1200g for five minutes at 4°C followed by removal of the supernatant and resuspension of the cells in 5mL of PBS+0.04%BSA. The cells were counted and checked for viability using the ReadyProbes Blue/Red Kit on the Countess II FL.   Methanol fixation  Fixing  The methanol-fixation protocol was based on (Chen, Cheung, Shi, Zhou, & Lu, 2018). After tissue dissociation, the cells were concentrated to approximately 5x106 cells/mL by centrifuging at 1000g for 10 minutes. 200µL of the cell suspensions were aliquoted into 2mL cryovials resting on ice. 800µL of 100% methanol [Sigma; 494437] (chilled at -20°C) was then added dropwise to each sample while gently stirring the cells to prevent clumping. The cryovials were stored at -20°C for 30 minutes, then directly transferred to -80°C (no gradient cooling).  Rehydrating  Cryovials of methanol fixed cells were removed from -80°C and placed on ice to equilibrate to 4°C (approximately 10 minutes). The cells were then transferred to a 1.5mL centrifuge tube and centrifuged at 1000g for five minutes at 4°C. The supernatant was discarded and the pellet was resuspended in a small volume of SSC cocktail (3xSSC [Sigma; S0902], 0.04% BSA, 40mM DTT [Sigma; 43816], 0.5U/mL RNasin plus [Promega; N2615]) to reach a concentration of approximately 2000cells/µL. The cells were then filtered through a pre-wetted (with 1mL of nuclease-free water) 40µm pluristrainer mini filter [PluriSelect; 43-10040]. The cells were counted using the ReadyProbes Blue/Red Kit on the Countess II, then adjusted to 2000cells/µL based on the count. The cells were loaded onto a 10x chip (A/B depending on version used) at a volume that dilutes the SSC to 0.125x to prevent reverse transcription inhibition. All single cell libraries were constructed in biological triplicate using the 10x Chromium 3’ workflow as per manufacturers’ directions.
Refer to extract protocol for each individual file
Single cell libraries prepared using 10x 3’ v2&v3 kits following the manufacturers protocol. Bulk libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina following the manufacturers protocol. For the bulk libraries, rRNA was removed using either poly(A)+ selection using the NEBNext Poly(A) mRNA magnetic isolation module [E7490], or the NEBNext rRNA depletion kit (human/mouse/rat) kit [E6310].

value: Cold tissue dissociation, methanol-fixed suspension

value: scRNA-seq, 10x v2 chemistry


title: TT-seq_MJ-20-5_HCT-116_MED14-dTAG_1h_DMSO_A

status: Public on May 11 2020

type: SRA

city: Wien

first: Georg

middle: E

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences

description: cross-compare only to MJ-20-5 samples!

library_source: transcriptomic

data_processing:
Library strategy: TT-seq
alignment: STAR v2.3.0 to a fused index of hg38_ERCC; later filtered with 'samtools view -q 7 -f2'
spike-in_counting: reads aligning to ERCC spike-ins were counted with HTSeq
Further data processing was carried out using the R/Bioconductor environment, essentially as described (PMID: 27257258).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig generation: strand-specific signal tracks were computed with 'bedtools genomeCoverageBed -bg -strand' followed by UCSC 'bedGraphToBigWig' and normalized based on signal coverage in 25kb windows at the end of very long (> 175kb) genes, which are too long to be affected by the applied short-term MED14 degradation (limited by Pol II elongation velocity).

molecule: total RNA

organism: Homo sapiens

source_name: HCT-116 colon carcinoma cell line

growth_protocol: KBM7 cells were grown in IMDM medium supplemented with 10% FBS and 1% Pen/Strep. HCT-116 cells were grown in RPMI medium supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
TT-seq libraries were generated as previously described (PMID: 27257258). Cells were harvested by 3000g for 2min and total RNA extracted using Qiazol. RNA spike-ins were added and RNA was sonicated to generate fragments of <1.5 kb. 4sU-labeled RNA was purified using streptavidin beads (Miltenyi Biotec) before size-selection and library preparation.
NuGEN Ovation Universal RNA-Seq System, starting with 100 ng RNA inputs.

treatment_protocol:
150-200mio KBM7 MED14-dTAG cells were treated for 0.5-2h with 500nM dTAG7, 500nM NVP2, or DMSO. 500 µM 4-thio-Uridine (4sU) were added from DMSO stocks for the last 5min to label newly synthesized RNA. 5x20mio HCT-116 MED14-dTAG cells grown in 15cm dishes were treated for 1-2h with 500nM dTAGV-1 or DMSO and labeled with 500µM 4-thio-Uridine (4sU) from DMSO stocks for the last 10min to label newly synthesized RNA.
150-200mio KBM7 MED14-dTAG cells were treated for 0.5-2h with 500nM dTAG7, 500nM NVP2, or DMSO. 500 ÂµM 4-thio-Uridine (4sU) were added from DMSO stocks for the last 5min to label newly synthesized RNA. 5x20mio HCT-116 MED14-dTAG cells grown in 15cm dishes were treated for 1-2h with 500nM dTAGV-1 or DMSO and labeled with 500ÂµM 4-thio-Uridine (4sU) from DMSO stocks for the last 10min to label newly synthesized RNA.

tag: genotype

tag: treatment

value: 1h DMSO

tag: experiment id


title: BG55_SC_WarmDiss_Methanol

city: Perth

first: Alistair

middle: R. R.

last: Forrest

state: WA

address: 6 Verdun Street, Nedlands

country: Australia

institute: Harry Perkins Institute of Medical Research, the University of Western Australia

data_processing:
Bulk RNA-seq data processing  BCL files were demultiplexed and converted into FASTQ using bcl2fastq utility of Illumina BaseSpace Sequence Hub. FastQC was used for read quality control (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapters and low-quality bases were trimmed using Trim Galore with parameters --paired --quality 5 --stringency 5 --length 20 --max_n 10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Reads matching to ribosomal DNA repeat sequence BK000964 (https://www.ncbi.nlm.nih.gov/nuccore/BK000964) and low complexity reads were removed with TagDust2 (Lassmann, 2015). The remaining reads were mapped to GRCm38.84 version of mouse genome using STAR version 2.6.1a with default settings (Dobin et al., 2013). Picard MarkDuplicates tool was employed to identify duplicates (https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). FeatureCounts was then used to derive gene count matrix (Liao, Smyth, & Shi, 2014). Counts were normalised to gene length and then to library sizes using weighted trimmed mean of M-values (TMM) method in edgeR (Robinson, McCarthy, & Smyth, 2010), to derive gene length corrected trimmed mean of M-values (GeTMM) as described in (Smid et al., 2018).  scRNA-seq and snRNA-seq data processing  BCL files were demultiplexed and converted into FASTQ using bcl2fastq utility of Illumina BaseSpace Sequence Hub. scRNA-seq and snRNA-seq libraries were processed using Cell Ranger 2.1.1 with mm10-2.1.0 reference. Reads mapped to exons were used for scRNA-seq samples, whereas both intronic and exonic reads were counted for snRNA-seq. Custom pre-mRNA reference for snRNA-seq was built as described in https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#premrna. Raw gene-barcode matrices from Cell Ranger output were used for downstream processing. Cells were distinguished from background noise using EmptyDrops (Lun et al., 2019). Only genes detected in a minimum of 10 cells were retained; cells with 200-3000 genes and under 50% of mitochondrial reads were retained, as per Park et al. study (Park et al., 2018). Nuclei were additionally filtered to have at least 450 UMIs for v2 chemistry and 900 UMIs for v3 chemistry, and mitochondrial genes were removed. Outlier cells with high ratio of number of detected UMI to genes (>3 median absolute deviations from median) were removed using Scater (McCarthy, Campbell, Lun, & Wills, 2017). Seurat v2 was used for sample integration (canonical correlation analysis), normalisation (dividing by the total counts, multiplying by 10,000 and natural-log transforming), scaling, clustering and differential expression analysis (Wilcoxon test) (Butler, Hoffman, Smibert, Papalexi, & Satija, 2018).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each individual library. For bulk RNA-seq libraries, files include one column with counts for the corresponding sample. For single-cell and single-nuclei libraries, files include multiple columns where each column corresponds to one cell or nuclei.

organism: Mus musculus

source_name: adult whole kidney

extract_protocol:
Warm tissue dissociation  Kidneys were dissociated using the Multi-tissue dissociation kit 2 from Miltenyi Biotec [130-110-203] as per manufacturers’ instruction, with minor variations. Once the weight of the kidney was determined, the kidney was quartered and placed into a gentleMACS C-tube [Miltenyi Biotech; 130-096-334] containing the enzyme mix described in the kit’s protocol. The tube was centrifuged briefly, then placed onto the gentleMACS octo dissociator (Miltenyi Biotech), and the 37C_Multi_E program was run after attaching the heating elements. Following completion of the program, the tube was briefly centrifuged.   The homogenate was filtered through a 70µm cell strainer [Greiner; 54207] into a 50mL centrifuge tube [Greiner; 227270], the strainer was then rinsed with 15mL of PBS. The cell suspension was centrifuged at 400g for 10 minutes; once complete, the supernatant was removed and the pellet was resuspended in 5mL of PBS+0.04% BSA [Sigma; A7638]. The cell suspension was then filtered through a 40µm strainer [Greiner; 542040], which was subsequently rinsed with 2mL of PBS+0.04% BSA. The cells were again centrifuged at 400g for 10 minutes. The supernatant was then removed and the pellet was resuspended in 5mL of PBS+0.04% BSA. Cell count and viability was estimated using the Countess II FL (ThermoFisher) and the ReadyProbes Blue/Red kit [Invitrogen; R37610].   Methanol fixation  Fixing  The methanol-fixation protocol was based on (Chen, Cheung, Shi, Zhou, & Lu, 2018). After tissue dissociation, the cells were concentrated to approximately 5x106 cells/mL by centrifuging at 1000g for 10 minutes. 200µL of the cell suspensions were aliquoted into 2mL cryovials resting on ice. 800µL of 100% methanol [Sigma; 494437] (chilled at -20°C) was then added dropwise to each sample while gently stirring the cells to prevent clumping. The cryovials were stored at -20°C for 30 minutes, then directly transferred to -80°C (no gradient cooling).  Rehydrating  Cryovials of methanol fixed cells were removed from -80°C and placed on ice to equilibrate to 4°C (approximately 10 minutes). The cells were then transferred to a 1.5mL centrifuge tube and centrifuged at 1000g for five minutes at 4°C. The supernatant was discarded and the pellet was resuspended in a small volume of SSC cocktail (3xSSC [Sigma; S0902], 0.04% BSA, 40mM DTT [Sigma; 43816], 0.5U/mL RNasin plus [Promega; N2615]) to reach a concentration of approximately 2000cells/µL. The cells were then filtered through a pre-wetted (with 1mL of nuclease-free water) 40µm pluristrainer mini filter [PluriSelect; 43-10040]. The cells were counted using the ReadyProbes Blue/Red Kit on the Countess II, then adjusted to 2000cells/µL based on the count. The cells were loaded onto a 10x chip (A/B depending on version used) at a volume that dilutes the SSC to 0.125x to prevent reverse transcription inhibition. All single cell libraries were constructed in biological triplicate using the 10x Chromium 3’ workflow as per manufacturers’ directions.
Refer to extract protocol for each individual file
Single cell libraries prepared using 10x 3’ v2&v3 kits following the manufacturers protocol. Bulk libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina following the manufacturers protocol. For the bulk libraries, rRNA was removed using either poly(A)+ selection using the NEBNext Poly(A) mRNA magnetic isolation module [E7490], or the NEBNext rRNA depletion kit (human/mouse/rat) kit [E6310].

tag: strain

tag: Sex

value: Male

tag: workflow

value: Warm tissue dissociation, methanol-fixed suspension

tag: sequencing protocol


title: TT-seq_MJ-19-29_MED14-dTAG_30min_NVP2_B

description: cross-compare only to MJ-19-29 samples

data_processing:
library strategy: TT-seq
alignment: STAR v2.3.0 to a fused index of hg38_ERCC; later filtered with 'samtools view -q 7 -f2'
spike-in_counting: reads aligning to ERCC spike-ins were counted with HTSeq
Further data processing was carried out using the R/Bioconductor environment, essentially as described (PMID: 27257258).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig generation: unnormalized, strand-specific signal tracks were computed with 'bedtools genomeCoverageBed -bg -strand' followed by UCSC 'bedGraphToBigWig'

source_name: KBM7_MED14-dTAG_30min 500nM NVP2

treatment_protocol:
150-200mio KBM7 MED14-dTAG cells were treated for 0.5-2h with 500nM dTAG7, 500nM NVP2, or DMSO. 500 µM 4-thio-Uridine (4sU) were added from DMSO stocks for the last 5min to label newly synthesized RNA. 5x20mio HCT-116 MED14-dTAG cells grown in 15cm dishes were treated for 1-2h with 500nM dTAGV-1 or DMSO and labeled with 500µM 4-thio-Uridine (4sU) from DMSO stocks for the last 10min to label newly synthesized RNA.
150-200mio cells were treated for 0.5-2h with 500nM dTAG7, 500nM NVP2, or DMSO. 500 ÂµM 4-thio-Uridine (4sU) were added from DMSO stocks for the last 5min to label newly synthesized RNA.

tag: cell line

tag: cell type

value: chronic myeloid leukemia cell line

tag: genotype/variation

value: 30min 500nM NVP2


title: TT-seq_MJ-19-29_MED14-dTAG_30min_NVP2_A

description: cross-compare only to MJ-19-29 samples


title: siGLI1_RNA-seq  rep1

city: Rochester

first: Stephanie

middle: Lynn

last: Safgren

state: Minnesota

address: 200 1st Street SW, Gonda 19 366C

department: Oncology Research

country: USA

institute: Mayo Clinic

description:
15-060-4
Gli1 knockdown

data_processing:
Base calling was performed with the Illumina bcl2fastq
Sequences were trimmed with TrimGalore (v0.4.5), aligned to hg19 (NCBI build 37) using bowtie2 (v2.3.3.1) with maximum fragment length 2000.  FeatureCounts (Subread v1.6.4) was used to count reads and summarize then Deseq2 (v2.11.40.6 in Galaxy) was used to determine differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each gene per sample

source_name: skeletal muscle

growth_protocol: RMS13 cells grown in RPMI media with 10% fetal bovine supplemented.  Cells were replated before reaching comfluency and media was replaced as needed typically every 2-3 days.

extract_protocol:
mRNA was isolated from cultured cells following the protocol in the Qiagen RNeasy kit including the DNase I step.
mRNA version 2 library prep kit (Illumina)

treatment_protocol: siRNA knockdowns of Gli1 were incubated for 72 hours in standard cell culture conditions.

tag: sirna


title: 233-1-3

type: RNA

city: Lund

first: Jan

last: Marsal

address: BMC D14

country: Sweden

institute: Lund University

hyb_protocol: Processing of samples for microarray hybridization was carried out at KFB as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual.

data_processing: Samples were subjected to the Affymetrix Human Gene 2.1 ST Array and raw data was analyzed using R (version 3.3.0) with Bioconductor pachage xps. Probe level expression values were normalized and summated using Robust Multiarray Analysis (RMA) algorithm based on the gene model for probesets supported by RefSeq and full-length GenBank transcripts, and with a background correction using Epanechnikov Kernel and only the perfect match probes. Finally, expression data were summarized on the level of human gene symbols and finally normalized by quantile normalization with the help of R-package limma.

label: biotin

extract_protocol: Gut biopsies were collected in RNAlater Stabilization Solution (Ambion, Applied Biosystems) and then frozen on dry ice. Samples were sent on dry ice to KFB Center of Excellence for Fluorescent Bioanalytics (Regensburg, Germany) for extracting materials.

tag: status

value: Uninflamed-before


title: 233-1-2

scan_protocol: Processing of samples for microarray hybridization was carried out at KFB as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual.

source_name: Ileum

value: Inflamed-before


title: FOS8

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
RNA-Seq was carried out at Sistemas Genómicos S.L., Parque Tecnológico de Valencia, with Illumina HiSeq 2500 sequencing technology using a 50 bp single-end format.
Reads per kilobase per million mapped read (RPKM) values were obtained using Rockhopper  from the FastQ files obtained from the sequencing. A minimum of 15 RPKM in at least one of the analyzed strains was used as threshold to include the corresponding genes in the analysis.
Genome_build: NC_017671.1
Supplementary_files_format_and_content: RPKM for each sample, as calculated by Rockhopper package

organism: Stenotrophomonas maltophilia

source_name: bacterial culture

growth_protocol: The different bacterial strains were grown overnight in LB broth at 37 ºC and 250 rpm. These cultures were used to inoculate new flasks to reach an 0.01 OD600 and the cultures were grown at 37 ºC until an OD600 of 0.6 was reached.

extract_protocol:
Twenty ml of each bacterial culture were spun down at 6,000 xg for 3 min at 4 ºC and immediately frozen on dry ice and stored at −80 ºC. RNA was isolated from cell pellets using the RNAeasy minikit (QIAGEN) following manufacturer's instructions. To remove remaining genomic DNA, total RNA samples were treated with DNAase I [RNase-Free DNAse Set (QIAGEN)], and a second digestion was then performed following the Turbo DNA-free (AMBION) protocol. The RNA was purified and concentrated using RNAeasy minikit columns. Only RNAs containing no DNA contamination were used for further studies. To analyze the transcriptome of S. maltophilia D457 and mutant strains, RNA was obtained from three independent cultures of each strain, which were then pooled to reduce biological variability.
RNA libraries were prepared using 5 μg of RNA, rRNA was depleted using RiboZero kit and cDNA was synthesized.

tag: mutation

tag: gene

value: pgk

tag: locus

tag: phenotype

value: fosfomycin-resistant


title: TT-seq_MJ-19-29_MED14-dTAG_2h_dTAG7_30min_NVP2_A

description: cross-compare only to MJ-19-29 samples

source_name: KBM7_MED14-dTAG_2h 500nM dTAG7 and last 30min 500nM NVP2


title: 231-2-3

source_name: Rectum

label_protocol: Processing of samples for microarray hybridization was carried out at KFB as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual.

value: Inflamed-after


title: BG52_SC_ColdDiss_Methanol


title: BG54_SC_ColdDiss_Methanol


title: BG53_SC_WarmDiss_Methanol


title: 231-2-2


title: TT-seq_MJ-19-29_MED14-dTAG_2h_dTAG7_B

description: cross-compare only to MJ-19-29 samples

source_name: KBM7_MED14-dTAG_2h 500nM dTAG7

value: 2h 500nM dTAG7


title: 231-2-1

value: Uninflamed-after


title: 231-1-3


title: BG35_SC_WarmDiss_Cryopreserved

extract_protocol:
Warm tissue dissociation  Kidneys were dissociated using the Multi-tissue dissociation kit 2 from Miltenyi Biotec [130-110-203] as per manufacturers’ instruction, with minor variations. Once the weight of the kidney was determined, the kidney was quartered and placed into a gentleMACS C-tube [Miltenyi Biotech; 130-096-334] containing the enzyme mix described in the kit’s protocol. The tube was centrifuged briefly, then placed onto the gentleMACS octo dissociator (Miltenyi Biotech), and the 37C_Multi_E program was run after attaching the heating elements. Following completion of the program, the tube was briefly centrifuged.   The homogenate was filtered through a 70µm cell strainer [Greiner; 54207] into a 50mL centrifuge tube [Greiner; 227270], the strainer was then rinsed with 15mL of PBS. The cell suspension was centrifuged at 400g for 10 minutes; once complete, the supernatant was removed and the pellet was resuspended in 5mL of PBS+0.04% BSA [Sigma; A7638]. The cell suspension was then filtered through a 40µm strainer [Greiner; 542040], which was subsequently rinsed with 2mL of PBS+0.04% BSA. The cells were again centrifuged at 400g for 10 minutes. The supernatant was then removed and the pellet was resuspended in 5mL of PBS+0.04% BSA. Cell count and viability was estimated using the Countess II FL (ThermoFisher) and the ReadyProbes Blue/Red kit [Invitrogen; R37610].   Cryopreservation  Freezing  After tissue dissociation, the cells were centrifuged at 400g for 10 minutes (1200g for five minutes at 4°C for the repeated experiment), then resuspended in freezing media (50% FBS, 40% RPMI-1640 [Gibco; 11875093], 10% DMSO [Sigma; D4540]) to achieve a concentration of 1x106cells/mL. 1mL of the cell suspension was aliquoted into 2mL cryovials, then placed into an isopropanol freezing container (Mr. Frosty) and stored at -80°C overnight. The following day, the cells were transferred to liquid nitrogen storage.  Thawing  The samples were removed from -80°C and immediately placed into a 37°C waterbath for 2-3 minutes to rapidly thaw. The cells were then mixed using a 1mL pipette with a wide-bore tip and the entire volume transferred to a 15mL centrifuge tube [Greiner; 188261]. The cryovial was then rinsed twice with RMPI+10%FBS (rinse media); each time the 1mL of media was added to the 15mL centrifuge in a dropwise manner while gently shaking the tube. 7mL of rinse media was added to the centrifuge tube using a serological pipette – the first 4mL was added dropwise while gently shaking the tube, and the following 3mL added down the side of the tube over two seconds. The tube was then inverted to mix.   The cells were centrifuged at 300g for five minutes. Once completed, the supernatant was removed (leaving 1mL), placed into another 15mL centrifuge tube and centrifuged at 400g for five minutes. The supernatant was discarded (leaving 1mL). The pellet from the supernatant was then resuspended, combined with the pellet in the initial centrifuge tube and mixed. 2mL of PBS+0.04% BSA was added to the centrifuge tube and shaken gently to mix. The cells were then centrifuged again at 400g for five minutes. The supernatant was discarded leaving 0.5mL behind. 0.5mL of PBS+0.04% BSA was added to the cells and gently pipette-mixed 10-15 times to fully resuspend. The cells were then filtered through a pre-wetted (with 1mL of PBS+0.04% BSA) 40µm pluristrainer mini filter. A 20µL aliquot of the cells was used to obtain an estimate of cell count and viability using the ReadyProbes Blue/Red Kit on the Countess II FL. Based on the count, the cells were diluted to a concentration of 700cells/µL. The cells were then loaded onto a 10x chip (A/B depending on version) and immediately processed on the 10x Chromium controller. All single cell libraries were constructed in biological triplicate using the 10x Chromium 3’ workflow as per manufacturers’ directions.
Refer to extract protocol for each individual file
Single cell libraries prepared using 10x 3’ v2&v3 kits following the manufacturers protocol. Bulk libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina following the manufacturers protocol. For the bulk libraries, rRNA was removed using either poly(A)+ selection using the NEBNext Poly(A) mRNA magnetic isolation module [E7490], or the NEBNext rRNA depletion kit (human/mouse/rat) kit [E6310].

value: Warm tissue dissociation, cryopreserved suspension


title: 231-1-2


title: FOS7

value: gapA


title: 8_GrH, liver

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Hepatic gene expression of Ltg/NZO.5.3N/B mice fed a HFD

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: liver

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from murine tissue using TRIzol™ reagent (Invitrogen, Germany). From congenic mice (5 weeks of age), samples of liver were aliquoted for RNA extraction. The procedure was carried out according to manufacturer’s instructions. RNA quality was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) and the manufacturer’s instructions were followed to measure RNA integrity (RIN). Samples with RIN values >8 were subsequently selected for microarray analysis.

treatment_protocol: Mice were fed a high fat diet (45%, fat, Research Diets)

tag: gender

value: male

value: HFD

tag: tissue

value: liver


title: 7_GrN, liver

description: Hepatic gene expression of Ltg/NZO.5.3N/N mice fed a HFD

tag: treatment


title: 6_GrN, liver


title: TT-seq_MJ-19-29_MED14-dTAG_2h_dTAG7_A

description: cross-compare only to MJ-19-29 samples

tag: experiment id


title: BG34_SC_ColdDiss_Cryopreserved

extract_protocol:
Cold tissue dissociation  Kidneys were dissociated using a modified version of the published protocol described in (Adam, Potter, & Potter, 2017). Based on the weight, in a pre-cooled Miltenyi C-tube, a protease solution (5mM CaCl2 [Invitrogen; AM9530G], 10mg/mL B. Licheniformis protease [Sigma; P5380], 125U/mL DNase I [Sigma; D5025], 1xDPBS) was prepared for each kidney.  The kidneys were then minced on ice into a smooth paste using a scalpel. The minced kidney was transferred into 4-6mL of the protease solution (dependent on weight) and triturated using a 1mL pipette for 15 seconds every two minutes for a total of eight minutes.  Following trituration, the C-tubes were placed onto a Miltenyi gentleMACS octo dissociator in a cool room (4°C), and the m_brain_03 program was run twice in succession. Once complete, the samples were triturated for 15 seconds every two minutes on ice for an additional 16 minutes using a 1mL pipette. 10µL of each sample was then loaded into a haemocytometer to assess whether tissue dissociation was complete. The dissociated cells were transferred to a 15mL centrifuge tube and 3mL of ice-cold PBS+10%FBS [Gibco; A3160401] was added.   The cell suspension was centrifuged at 1200g for five minutes at 4°C. The supernatant was removed and the pellet was resuspended in 2mL of PBS+10%FBS. The cells were then filtered through a 70µm cell strainer, which was subsequently rinsed with 2mL of PBS+0.01% BSA. The cells were then centrifuged again at 1200g for five minutes at 4°C followed by removal of the supernatant and resuspension of the pellet in 5mL of PBS+0.01%BSA. The cells were then filtered through a 40µm cell strainer, which was subsequently rinsed with 2mL of PBS+0.01% BSA. The cells were again centrifuged at 1200g for five minutes at 4°C followed by removal of the supernatant and resuspension of the cells in 5mL of PBS+0.04%BSA. The cells were counted and checked for viability using the ReadyProbes Blue/Red Kit on the Countess II FL.  Cryopreservation  Freezing  After tissue dissociation, the cells were centrifuged at 400g for 10 minutes (1200g for five minutes at 4°C for the repeated experiment), then resuspended in freezing media (50% FBS, 40% RPMI-1640 [Gibco; 11875093], 10% DMSO [Sigma; D4540]) to achieve a concentration of 1x106cells/mL. 1mL of the cell suspension was aliquoted into 2mL cryovials, then placed into an isopropanol freezing container (Mr. Frosty) and stored at -80°C overnight. The following day, the cells were transferred to liquid nitrogen storage.  Thawing  The samples were removed from -80°C and immediately placed into a 37°C waterbath for 2-3 minutes to rapidly thaw. The cells were then mixed using a 1mL pipette with a wide-bore tip and the entire volume transferred to a 15mL centrifuge tube [Greiner; 188261]. The cryovial was then rinsed twice with RMPI+10%FBS (rinse media); each time the 1mL of media was added to the 15mL centrifuge in a dropwise manner while gently shaking the tube. 7mL of rinse media was added to the centrifuge tube using a serological pipette – the first 4mL was added dropwise while gently shaking the tube, and the following 3mL added down the side of the tube over two seconds. The tube was then inverted to mix.   The cells were centrifuged at 300g for five minutes. Once completed, the supernatant was removed (leaving 1mL), placed into another 15mL centrifuge tube and centrifuged at 400g for five minutes. The supernatant was discarded (leaving 1mL). The pellet from the supernatant was then resuspended, combined with the pellet in the initial centrifuge tube and mixed. 2mL of PBS+0.04% BSA was added to the centrifuge tube and shaken gently to mix. The cells were then centrifuged again at 400g for five minutes. The supernatant was discarded leaving 0.5mL behind. 0.5mL of PBS+0.04% BSA was added to the cells and gently pipette-mixed 10-15 times to fully resuspend. The cells were then filtered through a pre-wetted (with 1mL of PBS+0.04% BSA) 40µm pluristrainer mini filter. A 20µL aliquot of the cells was used to obtain an estimate of cell count and viability using the ReadyProbes Blue/Red Kit on the Countess II FL. Based on the count, the cells were diluted to a concentration of 700cells/µL. The cells were then loaded onto a 10x chip (A/B depending on version) and immediately processed on the 10x Chromium controller. All single cell libraries were constructed in biological triplicate using the 10x Chromium 3’ workflow as per manufacturers’ directions.
Refer to extract protocol for each individual file
Single cell libraries prepared using 10x 3’ v2&v3 kits following the manufacturers protocol. Bulk libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina following the manufacturers protocol. For the bulk libraries, rRNA was removed using either poly(A)+ selection using the NEBNext Poly(A) mRNA magnetic isolation module [E7490], or the NEBNext rRNA depletion kit (human/mouse/rat) kit [E6310].

tag: strain

value: Cold tissue dissociation, cryopreserved suspension

value: scRNA-seq, 10x v2 chemistry


title: 231-1-1


title: 4_GrN, liver


title: TT-seq_MJ-19-29_MED14-dTAG_2h_DMSO_B

description: cross-compare only to MJ-19-29 samples

source_name: KBM7_MED14-dTAG_2h DMSO

value: 2h DMSO


title: DASH_10_10

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

data_processing:
FastQ reads trimmed for the adapter sequences using Cutadapt version 2.5 with the –nextseq-trim=20
Mapping with segemehl via READemption with the argument –a 80 (NEB samples) or –a 80 –R (Takara samples)
Gene quantification via READemption subcommand gene_quanti with arguments –a –o 10
wig files for coverage plots were generated via READemption subcommand coverage
Genome_build: Salmonella (NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1); Bacteroides (NC_004663.1, NC_004703.1)
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample
Supplementary_files_format_and_content: wig files

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: whole cells

growth_protocol: Salmonella was grown until OD 2.0; Bacteroides until OD 0.5.

extract_protocol:
Cultures were pelleted by centrifugation and RNA was extracted with Trizol. To remove contaminating genomic DNA, samples were further treated with 0.25 U of DNase I (Fermentas) per 1 µg of RNA for 45 min at 37°C, followed by phenol-chloroform extraction and ethanol precipitation of RNA.
Libraries were generated with NEBNext Magnesium RNA Fragmentation Module (# E6150S) in combination with NEB NEBNext Multiplex Small RNA Library Prep Kit for Illumina (#E7560S) or Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (#634411). Where indicated, ribosomal cDNA was depleted by the DASH procedure: Depletion of Abundant Sequences by Hybridization using target specific sgRNAs and Cas9 to remove unwanted high-abundance species in sequencing libraries.

tag: growth phase

value: Exponential

tag: agent

value: DASH

tag: library prep kit

value: NEB NEBNext  Multiplex Small RNA Library Prep Kit for Illumina  #E7560S

tag: rna template in rt (ng)

tag: sgrna pool size

tag: pre-incubation

value: no

tag: cdna

tag: cdna removal

value: Column purification


title: 5_GrH, liver


title: BG33_SC_WarmDiss_Cryopreserved

tag: Sex

value: Male

tag: workflow

tag: sequencing protocol


title: WT

description: SampleWT

tag: mutation

value: wild type

tag: gene

tag: locus

tag: phenotype

value: control


title: FOS4

value: gpmA

value: fosfomycin-resistant


title: FOS1

value: eno


title: TT-seq_MJ-19-1_MED14-dTAG_2h_dTAG7_A

description: cross-compare only to MJ-19-1 samples

data_processing:
library strategy: TT-seq
alignment: STAR v2.3.0 to a fused index of hg38_ERCC; later filtered with 'samtools view -q 7 -f2'
spike-in_counting: reads aligning to ERCC spike-ins were counted with HTSeq
Further data processing was carried out using the R/Bioconductor environment, essentially as described (PMID: 27257258).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig generation: strand-specific signal tracks were computed with 'bedtools genomeCoverageBed -bg -strand' followed by UCSC 'bedGraphToBigWig' and normalized based on signal coverage in 25kb windows at the end of very long (> 175kb) genes, which are too long to be affected by the applied short-term MED14 degradation (limited by Pol II elongation velocity).

tag: cell line

tag: cell type

value: chronic myeloid leukemia cell line

tag: genotype/variation

tag: treatment

value: 2h 500nM dTAG7

tag: experiment id


title: BG32_SC_ColdDiss_Cryopreserved

tag: strain


title: H3K9me3 40%-30-3

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

library_source: genomic

data_processing:
bowtie2 (version 2.3.4.1) was used to map raw reads
macs2 (version 2.2.5) was used to call broad peaks
DiffBind (version 2.10.0) was used for the differential analysis of consensus peaks
genome build; GRCh38
processed data files format and content; H3K9me3_ChIP.all_peaks.tsv containing location, foldchanges and p-values for consensus peaks

molecule: genomic DNA

source_name: normal human epidermal keratinocyte

growth_protocol: Human epidermal stem/progenitor cells (EPCs) isolated from pooled neonatal human foreskin biopsies were purchased from CellnTec (HPEKp) and grown in suppliers cell culture medium (CnT-Prime; CellnTec). Cells were used in passages 2.

extract_protocol:
For ChIP-Seq cells were fixed in 1% methanol-free paraformaldehyde after which cells were scraped in PBS, lysed, and sonicated using a Covaris M20 sonicator to generate 300-600 bp fragments. 3 µg of antibody (H3K9me3 Abcam ab8898 or IgG control Cell Signaling #5415) and protein G Dynabeads were added to precipitate solubilized chromatin. Samples were subsequently eluted and crosslinks were reversed. DNA treated with proteinase K and RNAse was purified by phenol:chloroform extraction, followed by ethanol precipitation, after which DNA content was quantified using Qubit.
For ChIP sequencing with TruSeq ChIP library preparation kit according to the manufacturers protocol.

treatment_protocol: 400,000 cells were plated on fibronectin-coated (20 µg/ml) elastic silicone chambers 16 hours prior to initiating 40% cyclic uniaxial stretch at 0.1Hz in a custom-build uniaxial stretcher. 3 h before initiation of cyclic stretch, culture medium was replaced by medium containing 1.8 mM Ca2+.Cells were stretched for indicated amount of time.

tag: tissue

value: skin

value: normal human epidermal keratinocyte

tag: passage

value: Passage 2

tag: chip ab

value: H3K9me3 Abcam ab8898


title: BG31_SC_WarmDiss_Cryopreserved

value: Warm tissue dissociation, cryopreserved suspension

value: scRNA-seq, 10x v2 chemistry


title: TT-seq_MJ-19-1_MED14-dTAG_2h_dTAG7_B

description: cross-compare only to MJ-19-1 samples


title: DASH_3500_35000_Takara_Bacteroides

organism: Bacteroides thetaiotaomicron VPI-5482

tag: growth phase

value: Exponential

tag: agent

value: DASH

tag: library prep kit

value: Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian #634411

tag: rna template in rt (ng)

tag: sgrna pool size

tag: pre-incubation

value: yes

tag: cdna

tag: cdna removal

value: Proteinase K


title: BG30_SC_ColdDiss_Cryopreserved

tag: Sex

value: Male

tag: workflow

value: Cold tissue dissociation, cryopreserved suspension

tag: sequencing protocol


title: TT-seq_MJ-19-1_MED14-dTAG_2h_DMSO_B

description: cross-compare only to MJ-19-1 samples

tag: cell line

tag: cell type

tag: genotype/variation

tag: treatment

value: 2h DMSO


title: H3K9me3 40%-30-1

tag: tissue

tag: passage


title: 233-1-1

tag: status

value: Uninflamed-before


title: H3K9me3 40%-30-2

tag: chip ab


title: DASH_100_1000_Takara_Bacteroides

tag: strain

tag: growth phase

tag: agent

tag: library prep kit


title: TT-seq_MJ-19-1_MED14-dTAG_2h_DMSO_A

description: cross-compare only to MJ-19-1 samples

value: chronic myeloid leukemia cell line

tag: experiment id


title: BG6_SC_WarmDiss_Fresh

extract_protocol:
Warm tissue dissociation  Kidneys were dissociated using the Multi-tissue dissociation kit 2 from Miltenyi Biotec [130-110-203] as per manufacturers’ instruction, with minor variations. Once the weight of the kidney was determined, the kidney was quartered and placed into a gentleMACS C-tube [Miltenyi Biotech; 130-096-334] containing the enzyme mix described in the kit’s protocol. The tube was centrifuged briefly, then placed onto the gentleMACS octo dissociator (Miltenyi Biotech), and the 37C_Multi_E program was run after attaching the heating elements. Following completion of the program, the tube was briefly centrifuged.   The homogenate was filtered through a 70µm cell strainer [Greiner; 54207] into a 50mL centrifuge tube [Greiner; 227270], the strainer was then rinsed with 15mL of PBS. The cell suspension was centrifuged at 400g for 10 minutes; once complete, the supernatant was removed and the pellet was resuspended in 5mL of PBS+0.04% BSA [Sigma; A7638]. The cell suspension was then filtered through a 40µm strainer [Greiner; 542040], which was subsequently rinsed with 2mL of PBS+0.04% BSA. The cells were again centrifuged at 400g for 10 minutes. The supernatant was then removed and the pellet was resuspended in 5mL of PBS+0.04% BSA. Cell count and viability was estimated using the Countess II FL (ThermoFisher) and the ReadyProbes Blue/Red kit [Invitrogen; R37610]. The cells were then diluted to 700cells/µL and were immediately loaded onto a 10x chip A and processed on the 10x Chromium controller. All single cell libraries were constructed in biological triplicate using the 10x Chromium 3’ workflow as per manufacturers’ directions.
Refer to extract protocol for each individual file
Single cell libraries prepared using 10x 3’ v2&v3 kits following the manufacturers protocol. Bulk libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina following the manufacturers protocol. For the bulk libraries, rRNA was removed using either poly(A)+ selection using the NEBNext Poly(A) mRNA magnetic isolation module [E7490], or the NEBNext rRNA depletion kit (human/mouse/rat) kit [E6310].

value: Warm tissue dissociation, fresh suspension


title: 3_GrH, liver

tag: gender

value: male

value: HFD

value: liver


title: TT-seq_MJ-19-1_MED14-dTAG_1h_dTAG7_B

description: cross-compare only to MJ-19-1 samples

source_name: KBM7_MED14-dTAG_1h 500nM dTAG7

value: 1h 500nM dTAG7


title: 1_GrN, liver


title: BG5_SC_ColdDiss_Fresh

extract_protocol:
Cold tissue dissociation  Kidneys were dissociated using a modified version of the published protocol described in (Adam, Potter, & Potter, 2017). Based on the weight, in a pre-cooled Miltenyi C-tube, a protease solution (5mM CaCl2 [Invitrogen; AM9530G], 10mg/mL B. Licheniformis protease [Sigma; P5380], 125U/mL DNase I [Sigma; D5025], 1xDPBS) was prepared for each kidney.  The kidneys were then minced on ice into a smooth paste using a scalpel. The minced kidney was transferred into 4-6mL of the protease solution (dependent on weight) and triturated using a 1mL pipette for 15 seconds every two minutes for a total of eight minutes.  Following trituration, the C-tubes were placed onto a Miltenyi gentleMACS octo dissociator in a cool room (4°C), and the m_brain_03 program was run twice in succession. Once complete, the samples were triturated for 15 seconds every two minutes on ice for an additional 16 minutes using a 1mL pipette. 10µL of each sample was then loaded into a haemocytometer to assess whether tissue dissociation was complete. The dissociated cells were transferred to a 15mL centrifuge tube and 3mL of ice-cold PBS+10%FBS [Gibco; A3160401] was added.   The cell suspension was centrifuged at 1200g for five minutes at 4°C. The supernatant was removed and the pellet was resuspended in 2mL of PBS+10%FBS. The cells were then filtered through a 70µm cell strainer, which was subsequently rinsed with 2mL of PBS+0.01% BSA. The cells were then centrifuged again at 1200g for five minutes at 4°C followed by removal of the supernatant and resuspension of the pellet in 5mL of PBS+0.01%BSA. The cells were then filtered through a 40µm cell strainer, which was subsequently rinsed with 2mL of PBS+0.01% BSA. The cells were again centrifuged at 1200g for five minutes at 4°C followed by removal of the supernatant and resuspension of the cells in 5mL of PBS+0.04%BSA. The cells were counted and checked for viability using the ReadyProbes Blue/Red Kit on the Countess II FL. The cells were further diluted to a concentration of 700cells/µL with PBS/0.04%BSA and loaded directly onto a 10x chip (A/B depending on experiment) and isolated using the 10x Chromium controller. All single cell libraries were constructed in biological triplicate using the 10x Chromium 3’ workflow as per manufacturers’ directions.
Refer to extract protocol for each individual file
Single cell libraries prepared using 10x 3’ v2&v3 kits following the manufacturers protocol. Bulk libraries were prepared using the NEBNext ultra II directional RNA library prep kit for Illumina following the manufacturers protocol. For the bulk libraries, rRNA was removed using either poly(A)+ selection using the NEBNext Poly(A) mRNA magnetic isolation module [E7490], or the NEBNext rRNA depletion kit (human/mouse/rat) kit [E6310].

tag: Sex

value: Cold tissue dissociation, fresh suspension


title: BG4_SC_WarmDiss_Fresh

tag: workflow

value: scRNA-seq, 10x v2 chemistry


title: H3K9me3  0%-2

value: skin

value: normal human epidermal keratinocyte

value: Passage 2

value: H3K9me3 Abcam ab8898


title: noDASH_Takara_Bacteroides

value: Exponential

value: Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian #634411

tag: rna template in rt (ng)

tag: sgrna pool size

tag: pre-incubation

tag: cdna

tag: cdna removal

value: Proteinase K


title: H3K9me3  0%-1

tag: tissue

tag: cell type


title: DASH_1000_10000_NEB_Bacteroides

value: DASH

value: NEB NEBNext  Multiplex Small RNA Library Prep Kit for Illumina  #E7560S

value: yes


title: BG2_SC_WarmDiss_Fresh

value: Male

value: Warm tissue dissociation, fresh suspension

tag: sequencing protocol


title: BG3_SC_ColdDiss_Fresh


title: DASH_1000_10000_Takara_Bacteroides


title: DASH_100_1000_NEB_Bacteroides


title: 2_GrH, liver

value: male

tag: treatment

value: HFD


title: TT-seq_MJ-19-1_MED14-dTAG_1h_DMSO_B

description: cross-compare only to MJ-19-1 samples

source_name: KBM7_MED14-dTAG_1h DMSO

tag: cell line

value: chronic myeloid leukemia cell line

tag: genotype/variation

value: 1h DMSO


title: TT-seq_MJ-19-1_MED14-dTAG_1h_DMSO_A

description: cross-compare only to MJ-19-1 samples


title: noDASH_NEB_Bacteroides

tag: strain

tag: growth phase

tag: agent


title: BG1_SC_ColdDiss_Fresh

value: Cold tissue dissociation, fresh suspension

value: scRNA-seq, 10x v2 chemistry


title: H3K9me3 input-1

value: skin

value: normal human epidermal keratinocyte

tag: passage

tag: chip ab


title: DASH_3500_35000_NEB_Bacteroides

tag: library prep kit


title: H3K9me3 input-2

value: Passage 2

value: H3K9me3 Abcam ab8898


title: TT-seq_MJ-19-1_MED14-dTAG_1h_dTAG7_A

description: cross-compare only to MJ-19-1 samples

value: 1h 500nM dTAG7

tag: experiment id


title: OT-I central memory T cells via MVA i.d. [2197AA]

status: Public on May 10 2020

city: Boston

first: Thomas

last: Kupper

state: MA

address: 77 Avenue Louis Pasteur - HIM671

department: Dermatology

institute: Brigham and Women's Hospital

description: Gene expression data

hyb_protocol: Following fragmentation, 4.1 ug of cDNA were hybridized for 16 hr at 45 C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

organism: Mus

source_name: OT-I central memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova i.d.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 33.5 ng total RNA using amplification kit Nugen Ovation Pico WTA, Lot # 1408175A, followed by labeling 5 ug cDNA using kit Encore Biotin Module, Lot # 1409115-A.

growth_protocol: OT-I naïve cells were sorted from naïve OT-I Thy1.1+ Rag1-/- mice and adoptively transferred into cognate receipt mice one day before infection

extract_protocol: RNA was extracted with an RNeasy Micro kit (74004; Qiagen). RNA quality and quantity was assessed with a Bioanalyzer 2100 (Agilent).

treatment_protocol: Mice was infected with 1.8 × 106 p.f.u. of MVA-Ova via indicated infection routes

tag: gender

value: Female


title: P3 of OT-I cells activated via MVA intra-tperitoneal injection [2140F]

description: Gene expression data

source_name: P3 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tperitoneal injection


title: OT-I effector memory T cells via MVA s.s. [2197Z]

description: Gene expression data

source_name: OT-I effector memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova s.s.


title: P1 of OT-I cells activated via MVA intra-tperitoneal injection [2140D]

description: Gene expression data

source_name: P1 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tperitoneal injection


title: OT-I central memory T cells via MVA i.m. [2197EE]

description: Gene expression data

source_name: OT-I central memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova i.m.


title: OT-I central memory T cells via MVA s.s. [2197Y]

description: Gene expression data

source_name: OT-I central memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova s.s.


title: OT-I activated T cells via MVA i.m. [2174J]

description: Gene expression data

source_name: OT-I activated T cells were sorted from lymph nodes of mice 5 days post infected with MVA-Ova i.m.


title: OT-I activated T cells via MVA i.d. [2174H]

description: Gene expression data

source_name: OT-I activated T cells were sorted from lymph nodes of mice 5 days post infected with MVA-Ova i.d.


title: OT-I central memory T cells via MVA s.c. [2197CC]

description: Gene expression data

source_name: OT-I central memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova s.c.


title: OT-I Naïve T cells [2174K]

description: Gene expression data

source_name: OT-I T cells were sorted from spleen of naïve OT-I mice


title: P3 of OT-I cells activated via MVA intra-tracheal administration [2174D]

description: Gene expression data

source_name: P3 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tracheal administration


title: P2 of OT-I cells activated via MVA intra-tracheal administration [2174C]

description: Gene expression data

source_name: P2 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tracheal administration


title: OT-I activated T cells via MVA s.s. [2174G]

description: Gene expression data

source_name: OT-I activated T cells were sorted from lymph nodes of mice 5 days post infected with MVA-Ova s.s.


title: OT-I activated T cells via MVA s.c. [2174I]

description: Gene expression data

source_name: OT-I activated T cells were sorted from lymph nodes of mice 5 days post infected with MVA-Ova s.c.


title: P5 of OT-I cells activated via MVA intra-tracheal administration [2174F]

description: Gene expression data

source_name: P5 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tracheal administration


title: P4 of OT-I cells activated via MVA intra-tracheal administration [2174E]

description: Gene expression data

source_name: P4 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tracheal administration


title: P4 of OT-I cells activated via MVA intra-tperitoneal injection [2140G]

description: Gene expression data

source_name: P4 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tperitoneal injection


title: OT-I effector memory T cells via MVA i.d. [2197BB]

description: Gene expression data

source_name: OT-I effector memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova i.d.


title: P4 of OT-I cells activated via MVA s.s. [2125E]

description: Gene expression data

source_name: P4 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova s.s.


title: OT-I effector memory T cells via MVA s.c. [2197DD]

description: Gene expression data

source_name: OT-I effector memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova s.c.


title: P2 of OT-I cells activated via MVA intra-tperitoneal injection [2140E]

description: Gene expression data

source_name: P2 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tperitoneal injection


title: OT-I effector memory T cells via MVA i.m. [2197FF]

description: Gene expression data

source_name: OT-I effector memory T cells were sorted from spleen of mice 45 days post infected with MVA-Ova i.m.


title: OT-I Naïve T cells [2197A]

description: Gene expression data


title: P1 of OT-I cells activated via MVA intra-tracheal administration [2174B]

description: Gene expression data

source_name: P1 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tracheal administration


title: P5 of OT-I cells activated via MVA s.s. [2125F]

description: Gene expression data

source_name: P5 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova s.s.


title: P0 of OT-I cells activated via MVA intra-tracheal administration [2174A]

description: Gene expression data

source_name: P0 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tracheal administration


title: P5 of OT-I cells activated via MVA intra-tperitoneal injection [2140H]

description: Gene expression data

source_name: P5 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tperitoneal injection


title: Healthy Control uninfected 72 hours subject 14

first: Niamh

last: Troy

address: Northern Entrance, 15 Hospital Ave, Nedlands

institute: Telethon Kids Institute

description:
V223
processed data file: genecounts.csv

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer.
The Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT2 (v2.0.4).
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (filtered and normalised data).

source_name: Bronchial epithelium

growth_protocol: Primary BEC were grown in air liquid interface (ALI) cultures.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: ALI cultures were infected apically with RV1a MOI of 0.001. At each timepoint, cells were lysed in RLT (Qiagen) buffer for RNA extraction and RNAseq sample preparation.

tag: diagnosis

value: Healthy

tag: age (yrs)

value: Bronchial epithelial cells

value: Uninfected

tag: time point

value: 72 hours


title: P3 of OT-I cells activated via MVA s.s. [2125D]

description: Gene expression data

source_name: P3 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova s.s.


title: OT-I Naïve T cells [2140A]

description: Gene expression data

source_name: OT-I T cells were sorted from spleen of naïve OT-I mice


title: Healthy Control virus 72 hours subject 13

description:
V218
processed data file: genecounts.csv

value: Rhinovirus 1A infected


title: Healthy Control uninfected 24 hours subject 14

description:
V221
processed data file: genecounts.csv

value: 24 hours


title: Healthy Control virus 96 hours subject 13

description:
V219
processed data file: genecounts.csv

value: 96 hours


title: Healthy Control virus 96 hours subject 14

description:
V229
processed data file: genecounts.csv


title: Healthy Control uninfected 96 hours subject 14

description:
V224
processed data file: genecounts.csv


title: Asthma virus 48 hours subject 10

description:
V237
processed data file: genecounts.csv

value: Asthma

value: 48 hours


title: Asthma uninfected 48 hours subject 10

description:
V232
processed data file: genecounts.csv


title: Healthy Control virus 72 hours subject 14

description:
V228
processed data file: genecounts.csv


title: Healthy Control virus 24 hours subject 14

description:
V226
processed data file: genecounts.csv


title: Asthma uninfected 24 hours subject 10

description:
V231
processed data file: genecounts.csv


title: P2 of OT-I cells activated via MVA s.s. [2125C]

description: Gene expression data

source_name: P2 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova s.s.


title: Asthma virus 24 hours subject 10

description:
V236
processed data file: genecounts.csv


title: P0 of OT-I cells activated via MVA s.s. [2125A]

description: Gene expression data

source_name: P0 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova s.s.


title: Healthy Control uninfected 48 hours subject 14

description:
V222
processed data file: genecounts.csv


title: Asthma virus 72 hours subject 10

description:
V238
processed data file: genecounts.csv


title: Asthma uninfected 72 hours subject 10

description:
V233
processed data file: genecounts.csv


title: P1 of OT-I cells activated via MVA s.s. [2125B]

description: Gene expression data

source_name: P1 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova s.s.


title: Healthy Control virus 48 hours subject 13

description:
V217
processed data file: genecounts.csv


title: Asthma virus 96 hours subject 10

description:
V239
processed data file: genecounts.csv


title: TT-seq_MJ-19-29_MED14-dTAG_2h_DMSO_A

description: cross-compare only to MJ-19-29 samples

source_name: KBM7_MED14-dTAG_2h DMSO

value: chronic myeloid leukemia cell line

value: 2h DMSO


title: Healthy Control virus 24 hours subject 13

description:
V216
processed data file: genecounts.csv


title: Healthy Control uninfected 72 hours subject 13

description:
V213
processed data file: genecounts.csv


title: Healthy Control uninfected 96 hours subject 13

description:
V214
processed data file: genecounts.csv


title: Asthma uninfected 96 hours subject 10

description:
V234
processed data file: genecounts.csv


title: Healthy Control virus 48 hours subject 14

description:
V227
processed data file: genecounts.csv


title: Healthy Control uninfected 48 hours subject 13

description:
V212
processed data file: genecounts.csv


title: Healthy Control virus 72 hours subject 12

description:
V208
processed data file: genecounts.csv


title: Healthy Control virus 48 hours subject 12

description:
V207
processed data file: genecounts.csv


title: Healthy Control uninfected 24 hours subject 13

description:
V211
processed data file: genecounts.csv


title: Healthy Control uninfected 72 hours subject 12

description:
V203
processed data file: genecounts.csv


title: COPD Virus 96 hours subject 5

description:
V199
processed data file: genecounts.csv

value: COPD


title: Healthy Control uninfected 24 hours subject 12

description:
V201
processed data file: genecounts.csv


title: Healthy Control uninfected 48 hours subject 12

description:
V202
processed data file: genecounts.csv


title: Healthy Control virus 96 hours subject 12

description:
V209
processed data file: genecounts.csv


title: Healthy Control uninfected 96 hours subject 12

description:
V204
processed data file: genecounts.csv


title: Asthma virus 96 hours subject 9

description:
V189
processed data file: genecounts.csv


title: Asthma virus 48 hours subject 9

description:
V187
processed data file: genecounts.csv


title: COPD uninfected 24 hours subject 5

description:
V191
processed data file: genecounts.csv


title: Asthma virus 24 hours subject 9

description:
V186
processed data file: genecounts.csv


title: COPD Virus 24 hours subject 5

description:
V196
processed data file: genecounts.csv


title: Asthma uninfected 24 hours subject 9

description:
V181
processed data file: genecounts.csv


title: COPD Virus 96 hours subject 4

description:
V179
processed data file: genecounts.csv


title: COPD uninfected 72 hours subject 5

description:
V193
processed data file: genecounts.csv


title: Asthma uninfected 96 hours subject 9

description:
V184
processed data file: genecounts.csv


title: COPD uninfected 96 hours subject 5

description:
V194
processed data file: genecounts.csv


title: Asthma uninfected 72 hours subject 9

description:
V183
processed data file: genecounts.csv


title: COPD Virus 72 hours subject 5

description:
V198
processed data file: genecounts.csv


title: Asthma uninfected 48 hours subject 9

description:
V182
processed data file: genecounts.csv


title: Healthy Control virus 24 hours subject 12

description:
V206
processed data file: genecounts.csv


title: Asthma virus 72 hours subject 9

description:
V188
processed data file: genecounts.csv


title: COPD uninfected 48 hours subject 5

description:
V192
processed data file: genecounts.csv


title: COPD Virus 48 hours subject 5

description:
V197
processed data file: genecounts.csv


title: COPD Virus 72 hours subject 4

description:
V178
processed data file: genecounts.csv


title: COPD uninfected 96 hours subject 4

description:
V174
processed data file: genecounts.csv


title: COPD Virus 48 hours subject 4

description:
V177
processed data file: genecounts.csv


title: COPD uninfected 72 hours subject 4

description:
V173
processed data file: genecounts.csv


title: COPD uninfected 48 hours subject 4

description:
V172
processed data file: genecounts.csv


title: Asthma virus 72 hours subject 8

description:
V168
processed data file: genecounts.csv


title: COPD Virus 24 hours subject 4

description:
V176
processed data file: genecounts.csv


title: Asthma virus 96 hours subject 8

description:
V169
processed data file: genecounts.csv


title: P0 of OT-I cells activated via MVA intra-tperitoneal injection [2140C]

description: Gene expression data

source_name: P0 of OT-I cells were sorted from lymph nodes of mice 60 hour post infected with MVA-Ova intra-tperitoneal injection


title: COPD uninfected 24 hours subject 4

description:
V171
processed data file: genecounts.csv


title: Asthma virus 48 hours subject 8

description:
V167
processed data file: genecounts.csv


title: H3K9me3  0%-3

source_name: normal human epidermal keratinocyte

tag: tissue

value: skin

value: normal human epidermal keratinocyte


title: Asthma virus 24 hours subject 8

description:
V166
processed data file: genecounts.csv

tag: cell type


title: COPD Virus 96 hours subject 3

description:
V159
processed data file: genecounts.csv

value: Male


title: Asthma uninfected 96 hours subject 8

description:
V164
processed data file: genecounts.csv


title: Asthma uninfected 48 hours subject 8

description:
V162
processed data file: genecounts.csv


title: COPD Virus 72 hours subject 3

description:
V158
processed data file: genecounts.csv


title: Asthma uninfected 24 hours subject 8

description:
V161
processed data file: genecounts.csv


title: COPD uninfected 48 hours subject 3

description:
V152
processed data file: genecounts.csv


title: COPD Virus 48 hours subject 3

description:
V157
processed data file: genecounts.csv


title: COPD uninfected 72 hours subject 3

description:
V153
processed data file: genecounts.csv


title: COPD uninfected 96 hours subject 3

description:
V154
processed data file: genecounts.csv


title: COPD Virus 24 hours subject 3

description:
V156
processed data file: genecounts.csv


title: Healthy Control virus 72 hours subject 11

description:
V148
processed data file: genecounts.csv


title: Healthy Control virus 48 hours subject 11

description:
V147
processed data file: genecounts.csv


title: Healthy Control uninfected 72 hours subject 11

description:
V143
processed data file: genecounts.csv


title: Healthy Control uninfected 96 hours subject 11

description:
V144
processed data file: genecounts.csv


title: Healthy Control virus 96 hours subject 11

description:
V149
processed data file: genecounts.csv


title: Healthy Control virus 24 hours subject 11

description:
V146
processed data file: genecounts.csv


title: Healthy Control uninfected 24 hours subject 11

description:
V141
processed data file: genecounts.csv


title: Healthy Control uninfected 48 hours subject 11

description:
V142
processed data file: genecounts.csv


title: Asthma uninfected 72 hours subject 8

description:
V163
processed data file: genecounts.csv


title: Asthma virus 96 hours subject 7

description:
V139
processed data file: genecounts.csv


title: Asthma virus 72 hours subject 7

description:
V138
processed data file: genecounts.csv


title: Asthma virus 24 hours subject 7

description:
V136
processed data file: genecounts.csv


title: Asthma virus 48 hours subject 7

description:
V137
processed data file: genecounts.csv


title: Asthma uninfected 96 hours subject 7

description:
V134
processed data file: genecounts.csv


title: COPD uninfected 24 hours subject 3

description:
V151
processed data file: genecounts.csv


title: Asthma uninfected 72 hours subject 7

description:
V133
processed data file: genecounts.csv


title: Asthma virus 96 hours subject 6

description:
V130
processed data file: genecounts.csv


title: Asthma virus 72 hours subject 6

description:
V129
processed data file: genecounts.csv


title: Asthma uninfected 48 hours subject 7

description:
V132
processed data file: genecounts.csv


title: Asthma virus 48 hours subject 6

description:
V128
processed data file: genecounts.csv


title: Asthma uninfected 72 hours subject 6

description:
V124
processed data file: genecounts.csv


title: Healthy Control virus 96 hours subject 15

description:
V100
processed data file: genecounts.csv


title: Asthma uninfected 96 hours subject 6

description:
V125
processed data file: genecounts.csv


title: Asthma uninfected 24 hours subject 6

description:
V122
processed data file: genecounts.csv


title: Healthy Control virus 72 hours subject 15

description:
V099
processed data file: genecounts.csv


title: Healthy Control virus 48 hours subject 15

description:
V098
processed data file: genecounts.csv


title: Healthy Control uninfected 48 hours subject 15

description:
V093
processed data file: genecounts.csv


title: Healthy Control virus 24 hours subject 15

description:
V097
processed data file: genecounts.csv


title: Asthma virus 24 hours subject 6

description:
V127
processed data file: genecounts.csv


title: COPD Virus 96 hours subject 2

description:
V090
processed data file: genecounts.csv


title: Healthy Control uninfected 96 hours subject 15

description:
V095
processed data file: genecounts.csv


title: Healthy Control uninfected 24 hours subject 15

description:
V092
processed data file: genecounts.csv


title: Healthy Control uninfected 72 hours subject 15

description:
V094
processed data file: genecounts.csv


title: COPD Virus 72 hours subject 2

description:
V089
processed data file: genecounts.csv


title: Asthma uninfected 24 hours subject 7

description:
V131
processed data file: genecounts.csv


title: COPD Virus 24 hours subject 2

description:
V087
processed data file: genecounts.csv


title: COPD uninfected 48 hours subject 2

description:
V083
processed data file: genecounts.csv


title: COPD uninfected 72 hours subject 2

description:
V084
processed data file: genecounts.csv


title: COPD uninfected 96 hours subject 2

description:
V085
processed data file: genecounts.csv


title: COPD Virus 48 hours subject 2

description:
V088
processed data file: genecounts.csv


title: COPD uninfected 24 hours subject 2

description:
V082
processed data file: genecounts.csv


title: COPD Virus 48 hours subject 1

description:
V078
processed data file: genecounts.csv


title: COPD Virus 72 hours subject 1

description:
V079
processed data file: genecounts.csv


title: COPD Virus 96 hours subject 1

description:
V080
processed data file: genecounts.csv


title: COPD Virus 24 hours subject 1

description:
V077
processed data file: genecounts.csv


title: Asthma uninfected 48 hours subject 6

description:
V123
processed data file: genecounts.csv


title: COPD uninfected 48 hours subject 1

description:
V073
processed data file: genecounts.csv


title: COPD uninfected 96 hours subject 1

description:
V075
processed data file: genecounts.csv


title: RNA_BloodLy6CHi-Mono_NASH_grp0_rep2

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

description:
processed data file: rna_raw_counts.txt
processed data file: rna_tpm_counts.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of raw read counts, the parameters -count exons -condenseGenes - noadj were used. To generate a table of TPM values, the parameters -count exons -tpm were used. Differentially expressed genes were identified using raw sequencing read counts by DESeq2 (Love et al., 2014) analysis through the “getDifferentialExpression” HOMER command. Gene ontology analysis was performed using Metascape (Tripathi et al., 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rna_raw_counts.txt: Tab-delimited text file includes table of unnormalized read counts.
Supplementary_files_format_and_content: rna_tpm_counts.txt: Tab-delimited text file includes table of  TPM values.

molecule: polyA RNA

source_name: Sorted peripheral monocytes

extract_protocol:
Hepatic macrophages: Mice were humanely euthanized by exposure to CO2 and liver non-parenchymal cells processed for fluorescence activated cell sorting of Kupffer cells, with modifications from published methodology (Mederacke et al., 2015; Muse et al., 2018; Seki et al., 2007). In brief, livers were retrograde perfused for 3 min at a rate of 5-7 ml/min through the inferior vena cava with HBSS without Ca++ or Mg++ supplemented with 0.5 mM EGTA, 0.5 mM EDTA, and 20 mM HEPES. Perfusions were then switched to 40 ml of a digestion buffer, held at 37C, comprised of HBSS with Ca++ and Mg++ supplemented with 0.033 mg/ml of Liberase TM (Roche), 20 μg/ml DNaseI (Worthington), and 20 mM HEPES. Livers were then excised, minced, and digested for an additional 20 minutes in vitro at 37C with gentle rotation in 20 ml of fresh digestion buffer. The perfusion and digestion steps were performed in the presence of 1 μM flavopiridol to offset transcriptional changes associated with digestion. After tissue digestion, cells were passed through a 70-micron cell strainer and hepatocytes removed by 2 low-speed centrifugation steps at 50 X G for 2 min. Nonparenchymal cells in the supernatant were further separated from debris by pelleting for 15 min at 600 X G in 50 ml of 20% isotonic Percoll (Sigma Aldrich) at room temperature. Cells were then washed from Percoll containing buffer and suspended in 10 ml 28% OptiPrep (Sigma Aldrich) and carefully underlaid beneath 3 ml of wash buffer. The resulting gradient was centrifuged at 1,400 X G for 25 minutes at 4C with no break and cells enriched at the interface were saved and subjected to isotonic erythrocyte lysis. Enriched non-parenchymal cells were then washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Cells were then immunolabeled with specific antibodies of interest, washed, and sorted using a Beckman Coulter MoFlo Astrios EQ configured with spatially separated 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers.
Peripheral monocytes: Mice were humanely euthanized by exposure to CO2. Blood was collected from mice via cardiac puncture into K3EDTA tubes and subjected to RBC lysis (eBioscience). Cells were pelleted by centrifugation at 350 X G for 10 minutes at 4°C and washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Next, cells were stained in wash buffer for an additional 20 minutes with the antibodies listed in the Key Resource Table. Stained cells were washed twice and strained through a 30 μm strainer, then subjected to cell sorting using a Beckman Coulter MoFlo Astrios EQ configured with 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers. Each cell population was hierarchically gated using Beckman Coulter Summit software. Ly6CHi monocytes were defined as CD45PosCD11bHiCD115PosCD19NegCD90.2NegLy6GNegLy6CHi. Ly6CHi monocytes were further restricted to single particles by comparing height and area side scatter pulses, and dead cells were excluded by detecting the integration of the live/dead dye (Zombie NIR).
Whole liver tissue: Mice were humanely euthanized by exposure to CO2 and liver pieces were snap frozen for RNA-seq.
Performed as published previously (Gosselin et al., 2017; Oishi et al., 2016). Isolated cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer and stored at -80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94°C for 9 min. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 μL of fragmented mRNA, 0.5 μL of Random primer (Invitrogen), 0.5 μL of Oligo dT primer (Invitrogen), 0.5 μL of SUPERase-In (Ambion), 1 μL of dNTPs (10 mM) and 1 μL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 μL of water, 1 μL of DTT (100 mM), 0.1 μL Actinomycin D (2 μg/μL), 0.2 μL of 1% Tween-20 (Sigma) and 0.2 μL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer's instruction and eluted with 10 μL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 μL of Blue Buffer (Enzymatics), 1.1 μL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μL of RNAse H (5 U/μL), 1.05 μL of water, 1 μL of DNA polymerase I (Enzymatics) and 0.15 μL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 μL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 μL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 μL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-seq 4000 or a NextSeq 500 (Illumina, San Diego, CA) according to the manufacturer's instructions.

value: Sorted peripheral monocytes

tag: cell subtype

value: Ly6CHi blood monocytes

value: NASH diet


title: RNA_BloodLy6CHi-Mono_NASH_grp0_rep1

tag: treatment


title: C2C12 cells, conditioned media

city: Omaha

first: Pankaj

last: Singh

state: Nebraska

address: 505 S 45th St

department: Eppley

institute: University of Nebraska Medical Center

data_processing:
Groomer 1.0.4 was run to ensure Sanger & Illumina 1.8+ format and run with basic options
FastQC v0.69 was run
Trim_galore v0.4.3.1 was run to remove 4 bases from the 3' end with the remainder set to default settings
FastQC v0.69 was run
Tophat2 v2.1.0 was run using the reference genome and GTF for mm10.  Estimated Mean Inner Distance between Mate Pairs:330 Std. Dev for Distance between Mate Pairs: 181 Max realign edit distance:1000 Max edit distance:2 Library Type:FR Unstranded Final read mismatches:2 Bowtie -n mode:No Anchor length:8 Maximum number of mismatches that can appear in the anchor region of spliced alignment:0 The minimum intron length:70 The maximum intron length:500000 Allow indel search:Yes Max insertion length:3 Max deletion length:3 Maximum number of alignments to be allowed:20 Minimum intron length that may be found during split-segment (default) search:50 Maximum intron length that may be found during split-segment (default) search:500000 Number of mismatches allowed in each segment alignment for reads mapped independently:2 Minimum length of read segments:25 Do you want to supply your own junction data:Yes Use Raw Junctions:No Only look for supplied junctions:No Use coverage-based search for junctions:auto
Cufflinks v2.2.1.0 was run on generated BAM files with illumina's mm10 GTF reference as an annotation guide and for bias correction. Max Intron Length:300000 Min Isoform Fraction:0.1 Pre MRNA Fraction:0.15 3prime overhang tolerance:600 Intronic overhang tolerance:50 Disable tiling of reference transcripts:No Use multi-read correct:Yes Apply length correction:Cufflinks Effective Length Correction
Cuffmerge v 2.2.1.0 was run on cufflinks transcripts using mm10 reference. Minimum isoform fraction was 0.05
Cuffdiff v2.2.1.3 was run with mm10 using the BAMs from tophat2. Each of the replicates were pooled together and utilized the cuffmerge transcript assembly as a reference. Library normalization method:geometric Dispersion estimation method:pooled False Discovery Rate:0.05 Min Alignment Count:10 Use multi-read correct:True Perform Bias Correction:Yes Using reference genome:mm10 Include Read Group Datasets:No apply length correction:cufflinks effective length correction
Genome_build: mm10
Supplementary_files_format_and_content: FPKM of each gene for each sample from cuffdiff

growth_protocol: C2C12 S2-013 was grown in Dulbecco's Modified Eagle Medium containing 10% fetal bovine serum with 100 I.U./ml penicillin, 100 μg/ml streptomycin, and incubated at 37°C in a humidified incubator with 5% CO2. C2C12 was grown to confluency and differentiated in DMEM with 2% horse serum and 1µg/ml insulin for 72 hours.

extract_protocol:
Cells were lysed with TRIzol reagent and total RNA was isolated by using RNAeasy columns as per manufacturer’s protocol
Illumina TrueSeq version 2 library kit following manufacturer's protocol

treatment_protocol: Differentiated C2C12 were given DMEM as control media , 24 hour S2-013 conditioned media, or 24 hour S2-013 conditioned media with 50 µM of resveratrol for 24 hours

tag: cell line

value: myoblast

value: conditioned media


title: C2C12 cells, conditioned media + resveratrol

value: conditioned media + resveratrol


title: CSF miRNA PH0003-3841

city: Medford

first: Eric

middle: R

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

description: miRNA

data_processing:
Initial checks for sample quality, as well as adapter sequence identification, was performed using FastQC (version 0.11.3, bioinformatics.babraham.ac.uk/projects/fastqc/). For each sample, low-quality reads were removed using FastX (version 0.0.14, hannonlab.cshl.edu/fastx_toolkit/) FASTQ Quality Filter, using a quality score of 80%.
TruSeq Adapter Index 2 adapter sequence 9 (5′-GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG-3′) was removed from each read using Cutadapt (version 1.7.1), removing reads with fewer than 15 remaining nucleotides.
Reads with the same sequence were combined using FastX (version 0.0.14) Collapser, reporting the number of duplicated reads per sequence.
Reads were aligned to human genome version hg19 using Bowtie (version 1.1.1), allowing for 0 mismatches.
Bam files were converted to bed files using bedtools (version 2.25.0) bamToBed.24 miRNAs were defined as reads aligning within ±4 bases from the start coordinate of annotated miRNAs from mirBase (version 20), filtered for the 2,083 probes.
miRNA reads were counted using GenomicRanges (version 1.22.4) R package, removing reads greater than 27 bases.
Counts were normalized using the DESeq2/variance stabilization transformation in DESeq2 (version 1.10.1). These values were then adjusted for batch effects from their sequencing run, using ComBat (version 3.18.0). These values can be found in NormalizedCounts_DESeq2_VarianceStabilizedTransformation.csv.
Genome_build: hg19
Supplementary_files_format_and_content: Text file of miRNA counts

source_name: Cerebrospinal Fluid

extract_protocol:
CSF acquisition was added to the PREDICT-HD protocol at the end of the study at 6 sites. All participants underwent screening for the lumbar puncture (LP) the day prior to sample acquisition so that biospecimens would be collected after fasting and that screening blood sample laboratories could be conducted. Exclusion criteria for LP were (1) use of anticoagulant medication (i.e., warfarin, heparin) or antiplatelets (aspirin) within 14 days; (2) unable to fast for 8 hours; (3) any acute or chronic infection; (4) history of any chronic inflammatory disorder; (5) unstable medical or psychiatric disorder, disease, or illness; and (6) abnormalities in blood-based screening (e.g., abnormalities in prothrombin time, partial thromboplastin time, or low platelets). In a sterile environment, a Sprotte 24-G atraumatic spinal needle was used after adequate local anesthesia was administered. The site coordinator recorded the time for each component of the protocol. The first 1–2 mL of CSF from the first syringe was immediately sent at room temperature for basic CSF analyses conducted locally within 4 hours (i.e., for cell count, erythrocytes, total protein, and glucose). Remaining CSF was transferred to 15 mL conical polypropylene tubes at room temperature, mixed gently by inverting 3–4 times, and then centrifuged at 2,000 g for 10 minutes. Aliquots of 1.5 mL of supernatant were transferred to precooled 2-mL microcentrifuge tubes, and stored at −80°C until shipment on dry ice to the National Institute of Neurological Disorders and Stroke biorepository.
Fifteen microliters of CSF was processed for miRNA levels using the HTG Molecular Diagnostics miRNA whole transcriptome protocol HTG EdgeSeq system (htgmolecular.com/products/htg-edg-system-edgeseq). This process includes specific probes for 2,083 miRNAs, producing both raw small-RNA sequencing files and prequantified data. A maximum of 24 samples can be processed in a single run and samples were randomly assigned to each of 3 batches.

treatment_protocol: CSF samples for 60 participants were chosen by the PREDICT-HD Data Management Team. All samples were blinded by a unique code specific for this substudy. The samples included 15 participants clinically diagnosed with HD according to traditional criteria with diagnostic confidence level of 4 on the Unified Huntington’s Disease Rating Scale, 30 participants determined to be prodromal gene expansion carriers for HD, and 15 healthy controls. Disease burden in the prodromal participants was determined by calculation of the CAG–Age Product (CAP = age × [CAG − 33.66]), developed to reflect age-adjusted cumulative exposure to the effects of mutant huntingtin.

value: CSF

tag: prodromal status

value: HD

tag: cag repeats

tag: Sex

value: m

tag: age


title: CSF miRNA PH0004-7384

description: miRNA


title: CSF miRNA PH0003-8205

description: miRNA

value: Control

value: f


title: CSF miRNA PH0003-8257

description: miRNA

value: Pre-Med


title: CSF miRNA PH0003-9291

description: miRNA


title: CSF miRNA PH0003-8189

description: miRNA

value: Pre-Low


title: CSF miRNA PH0004-2429

description: miRNA


title: CSF miRNA PH0003-8263

description: miRNA

value: Pre-High


title: CSF miRNA PH0003-3858

description: miRNA


title: CSF miRNA PH0004-3973

description: miRNA


title: CSF miRNA PH0003-8830

description: miRNA


title: CSF miRNA PH0004-7453

description: miRNA


title: CSF miRNA PH0004-9362

description: miRNA


title: CSF miRNA PH0005-4067

description: miRNA


title: COPD uninfected 72 hours subject 1

description:
V074
processed data file: genecounts.csv

value: COPD

value: Bronchial epithelial cells

value: Uninfected

value: 72 hours


title: COPD uninfected 24 hours subject 1

description:
V072
processed data file: genecounts.csv

value: Male

value: 24 hours


title: CSF miRNA PH0004-3989

description: miRNA


title: CSF miRNA PH0004-7694

description: miRNA


title: CSF miRNA PH0004-7376

description: miRNA


title: CSF miRNA PH0003-8929

description: miRNA


title: CSF miRNA PH0003-8782

description: miRNA


title: CSF miRNA PH0003-9386

description: miRNA


title: C2C12 cells, control

value: myoblast

value: control


title: CSF miRNA PH0003-8383

description: miRNA


title: CSF miRNA PH0004-0282

description: miRNA


title: CSF miRNA PH0003-8376

description: miRNA


title: CSF miRNA PH0003-8356

description: miRNA


title: CSF miRNA PH0004-0317

description: miRNA


title: CSF miRNA PH0003-8248

description: miRNA


title: CSF miRNA PH0003-8213

description: miRNA


title: CSF miRNA PH0003-8183

description: miRNA


title: CSF miRNA PH0003-8327

description: miRNA


title: Ls174tOxR1

city: Chapel Hill

first: Courtney

middle: Michelle

last: Vaughn

state: NC

address: 120 Mason Farm Rd CB#7260

institute: The University of North Carolina at Chapel Hill

description: replicate 1

data_processing:
Library strategy: XR-Seq
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: hg38
Supplementary_files_format_and_content: no

source_name: Ls174t cell line

extract_protocol: 10 colorectal cancer cell lines obtained from the ATCC (Rko, Ls1034, Dld1, Ls180, Colo205) and from the UNC Tissue Culture Facility (Colo320, Hct116, Ht29, Sw480, Ls174t) and grown according to ATCC specifications. For oxaliplatin treatments, cells were plated into R-150 plates and grown to about 90 percent confluence.  200μM oxaliplatin was added to each plate and cells were incubated at 32 degrees celcius for 2 hours.  Plates were then placed on ice and cooled cells were harvested by scraping and rinsing with ice-cold PBS. Cells were pelleted, transferred to Eppendorf tubes, and resuspended in 2mL of lysis buffer. Cells were lysed by homoginization and the soluble fraction was processed with RNase A and proteinase K.  Samples were immunoprecipitated with anti-XPG antibody, and then ligated to adapters and processed for sequencing (XR-seq).   Approximately 10 plates were used for each XR-seq assay.  After PCR amplification, libraries wrere sequencing on HS4000.

value: Ls174t cell line

value: Oxaliplatin

value: human colorectal cancer cell line

tag: antibody

value: anti-XPG antibody


title: CSF miRNA PH0004-9419

description: miRNA

value: CSF

value: m


title: CSF miRNA PH0004-7361

description: miRNA


title: CSF miRNA PH0003-8092

description: miRNA

value: Pre-Med

value: f


title: CSF miRNA PH0003-3826

description: miRNA

value: HD


title: CSF miRNA PH0004-9426

description: miRNA


title: CSF miRNA PH0003-8196

description: miRNA

value: Pre-High


title: CSF miRNA PH0003-3886

description: miRNA


title: Colo320OxR1

description: replicate 1

source_name: Colo320hsr cell line

value: Colo320hsr cell line


title: Ls180OxR2

description: replicate 2

source_name: Ls180 cell line

value: Ls180 cell line


title: CSF miRNA PH0003-8947

description: miRNA


title: CSF miRNA PH0003-8909

description: miRNA

value: Control


title: CSF miRNA PH0004-4582

description: miRNA


title: Colo205OxR2

description: replicate 2

source_name: Colo205 cell line

value: Colo205 cell line


title: CSF miRNA PH0003-9309

description: miRNA

value: Pre-Low


title: CSF miRNA PH0003-8965

description: miRNA


title: CSF miRNA PH0004-4027

description: miRNA


title: CSF miRNA PH0003-8287

description: miRNA


title: CSF miRNA PH0003-3902

description: miRNA


title: Ls1034OxR2

description: replicate 2

source_name: Ls1034 cell line

value: Ls1034 cell line


title: CSF miRNA PH0003-9350

description: miRNA


title: Colo205OxR1

description: replicate 1


title: CSF miRNA PH0003-8085

description: miRNA


title: CSF miRNA PH0003-8404

description: miRNA


title: Ls180OxR1

description: replicate 1


title: CSF miRNA PH0003-8388

description: miRNA


title: Ht29OxR2

description: replicate 2

source_name: Ht29 cell line

value: Ht29 cell line


title: Ht29OxR1

description: replicate 1


title: CSF miRNA PH0003-8370

description: miRNA


title: Hct116OxR1

description: replicate 1

source_name: Hct116 cell line

value: Hct116 cell line


title: Sw480OxR2

description: replicate 2

source_name: Sw480 cell line

value: Sw480 cell line

value: Oxaliplatin


title: CSF miRNA PH0003-8345

description: miRNA


title: RkoOxR2

description: replicate 2

source_name: RKO cell line

value: RKO cell line

value: human colorectal cancer cell line

value: anti-XPG antibody


title: CSF miRNA PH0003-8336

description: miRNA

value: CSF


title: Dld1OxR2

description: replicate 2

source_name: DLD1 cell line

value: DLD1 cell line


title: CSF miRNA PH0003-8409

description: miRNA

value: m


title: CSF miRNA PH0003-8294

description: miRNA

value: Pre-High

value: f


title: CSF miRNA PH0003-3894

description: miRNA


title: CSF miRNA PH0003-8234

description: miRNA


title: Sw480OxR1

description: replicate 1


title: CSF miRNA PH0003-3874

description: miRNA


title: CSF miRNA PH0003-3850

description: miRNA

value: Pre-Med


title: TME_CD45+_CD40ICB_4

city: Philadelphia

first: Austin

middle: P

last: Huffman

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
concatenated from two sources; has two processed data files
ICBCD40_1_filtered_feature_bc_matrix.h5
ICBCD40_2_filtered_feature_bc_matrix.h5

data_processing:
cellranger count
cellranger aggr
seurat
Genome_build: mm10
Supplementary_files_format_and_content: matrix.h5

source_name: Tumor microenvironment immune cells

growth_protocol: c57bl/6j mice were subcutaneously injected with 300k 4662.md10 (a KPC-derived cell line) cells; tumors grew for 14 days before treatment; 12 days after start of treatment mice were sacrificed and CD45+ cells were isolated

extract_protocol:
CD45 antibody based FACS isolation and Illumina 10X single-cell sequencing platform
10x genomics chromium single-cell platform

treatment_protocol: CD40 agonist and/or ICB (anti-PD-1 AND anti-CTLA-4)

value: Tumor

value: CD45+ immune

value: anti-PD-1, anti-CTLA-4, and CD40 agonist


title: CSF miRNA PH0003-3821

description: miRNA


title: Dld1OxR1

description: replicate 1


title: Hct116OxR2

description: replicate 2


title: TME_CD45+_CD40ICB_3


title: Ls1034OxR1

description: replicate 1

value: Ls1034 cell line


title: CSF miRNA PH0003-8301

description: miRNA

value: Control


title: TME_CD45+_CD40ICB_1


title: TME_CD45+_CD40ICB_2


title: TME_CD45+_CD40_4

value: CD40 agonist


title: BMDMs, 0h control, r2

city: New York

first: Ruslana

last: Bryk

state: NY

address: 413 East 69 Street

department: Microbiology and Immunology

institute: Weill Cornell Medicine

description:
0h control
combResults.s0hr_vehicle

data_processing:
Single-end sequencing with 40-50 million reads was performed at the Weill Cornell Genomics Core Facility on Illumina Hi-Seq platform.
The RNA-seq data were analyzed by Weill Cornell Genomics Core Facility using DE-seq algorithm.
Supplementary_files_format_and_content: Files include normalized RPKM values for each Sample
2062 regulated genes RNA seq.xls:  test compound 2062 final data
combResults_2062.csv:  test compound 2062 combined 1h, 2h, 6h
Control compounds for 2062 RNAseq data.xls:  control compound final data
combResults.control_compound.csv:  control compound combined 1h, 2h, 6h
combResults.s0hr_vehicle.csv:  0h and vehicle combined 1h, 2h, 6h

source_name: bone marrow derived macrophage

extract_protocol:
Detailed method desribed in publication 'Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB' by Bryk et al (2020) PLOS Pathogens
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMDM

tag: strain

tag: compound

value: control

tag: time


title: BMDMs, 0h control, r3

description:
0h control
combResults.s0hr_vehicle

growth_protocol: Detailed method desribed in publication 'Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB' by Bryk et al (2020) PLOS Pathogens


title: BMDMs, 0h control, r1

description:
0h control
combResults.s0hr_vehicle

treatment_protocol: Detailed method desribed in publication 'Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB' by Bryk et al (2020) PLOS Pathogens


title: BMDMs, vehicle (DMSO), 6h, r3

description:
vehicle treatment 6h
combResults.s0hr_vehicle

value: vehicle


title: BMDMs, vehicle (DMSO), 6h, r2


title: TME_CD45+_CD40_2


title: TME_CD45+_CD40_1


title: TME_CD45+_ICB_4

value: anti-PD-1 & anti-CTLA-4


title: BMDMs, vehicle (DMSO), 6h, r1


title: BMDMs, vehicle (DMSO), 2h, r2

description:
vehicle treatment 2h
combResults.s0hr_vehicle


title: BMDMs, vehicle (DMSO), 2h, r3


title: TME_CD45+_ICB_1


title: TME_CD45+_ICB_3


title: BMDMs, vehicle (DMSO), 1h, r3

description:
vehicle treatment 1h
combResults.s0hr_vehicle


title: TME_CD45+_ICB_2


title: TME_CD45+_Untx_4

value: untreated


title: BMDMs, vehicle (DMSO), 1h, r2


title: TME_CD45+_Untx_3


title: TME_CD45+_Untx_2


title: BMDMs, vehicle (DMSO), 1h, r1


title: BMDMs, control inactive compound, 6h, r2

description:
treatment with inactive compound 6h
combResults.control_compound
Control compounds for 2062 RNAseq data.xls

value: control inactive compound

tag: compound concentration

value: 10 uM


title: TME_CD45+_CD40_3


title: TME_CD45+_Untx_1


title: BMDMs, control inactive compound, 6h, r1


title: RNA_Ly6CLow-RM_grp0_rep2

source_name: Sorted hepatic macrophages

value: Sorted hepatic macrophages

value: CD11b-Hi Ly6C-Lo recruited macrophages

value: NASH diet


title: BMDMs, control inactive compound, 2h, r2

description:
treatment with inactive compound 2h
combResults.control_compound
Control compounds for 2062 RNAseq data.xls


title: BMDMs, vehicle (DMSO), 2h, r1


title: RkoOxR1

description: replicate 1

value: RKO cell line

value: Oxaliplatin

value: human colorectal cancer cell line

value: anti-XPG antibody


title: BMDMs, control inactive compound, 1h, r3

description:
treatment with inactive compound 1h
combResults.control_compound
Control compounds for 2062 RNAseq data.xls


title: RNA_Ly6CLow-RM_grp0_rep1


title: BMDMs, control inactive compound, 2h, r3


title: CSF miRNA PH0003-8244

description: miRNA

value: CSF

value: m


title: BMDMs, control inactive compound, 1h, r2


title: RNA_Ly6CHi-RM_grp0_rep1

value: CD11b-Hi Ly6C-Hi recruited macrophages


title: RNA_Ly6CHi-RM_grp0_rep2


title: BMDMs, control inactive compound, 1h, r1

value: BMDM


title: RNA_KN-RM_grp0_rep1

value: F4/80-Hi Tim4-Neg Kupffer niche recruited macrophages


title: BMDMs, 2062, 6h, r2

description:
treatment with active compound 6h
combResults_2062
2062 regulated genes RNA seq


title: BMDMs, 2062, 6h, r3


title: RNA_KC-N_grp0_rep1

value: F4/80-Hi Tim4-Pos Kupffer cells


title: RNA_KC-N_4wkNASH_rep1


title: BMDMs, 2062, 6h, r1


title: BMDMs, 2062, 2h, r3

description:
treatment with active compound 2h
combResults_2062
2062 regulated genes RNA seq


title: BMDMs, 2062, 2h, r2


title: BMDMs, control inactive compound, 6h, r3


title: BMDMs, 2062, 2h, r1


title: RNA_KC-N_30wkNASH_rep4


title: RNA_KC-N_30wkNASH_rep3


title: BMDMs, 2062, 1h, r3

description:
treatment with active compound 1h
combResults_2062
2062 regulated genes RNA seq


title: BMDMs, control inactive compound, 2h, r1


title: RNA_KC-N_30wkNASH_rep2


title: RNA_KN-RM_grp0_rep2


title: RNA_KC-N_grp0_rep2


title: RNA_KC-N_30wkNASH_rep1


title: RNA_KC-N_20wkNASH_rep3


title: RNA_KC-N_20wkNASH_rep2


title: BMDMs, 2062, 1h, r2


title: BMDMs, 2062, 1h, r1


title: RNA_KC-N_1wkNASH_rep2


title: RNA_KC-N_20wkNASH_rep1


title: RNA_KC-N_4wkNASH_rep2


title: RNA_KC-N_1wkNASH_rep1