title: VPR-D4, DOX-treatment, rep2 (Input)

description: Library name: VPR-D4_DOX_rep2, INPUT

data_processing:
Libraries were processed using trim_galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10) to remove sequencing adapters, low-quality base pairs and too short reads with the following parameters: --stringency 1 --length 105 --quality 30.
Filtered reads were mapped to the mm10 genome using bowtie2 ((Langmead & Salzberg, 2012); https://github.com/BenLangmead/bowtie2) (version 2.5.4) with the following parameters: --very-sensitive --end-to-end -X 400 --no-mixed --no-discordant.
After mapping, mitochondrial reads were filtered out using samtools view (Li et al, 2009) (version 1.20) and the grep command (grep -v chrM).
Duplicates were removed using picard tools (MarkDuplicates and REMOVE_DUPLICATES) (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) (version 3.3.0).
To obtain a set of uniquely mapped reads, BAM files were further filtered using the following criteria: minimum MAPQ of 1 and absence of the “XS:i” flag.
BAM files of samples sequenced in multiple runs were merged.
MACS ((Zhang et al, 2008); https://github.com/macs3-project/MACS) (version 2.2.9.1) was used to perform peak calling on the filtered reads of IP samples with the corresponding input libraries as control. Biological replicates were indicated as pooled samples with the following options: -f BAMPE --keep-dup all --call-summits.
Narrow peaks were retained after excluding those overlapping the ENCODE mm10 blacklist. Peaks with a signal value <18 were removed. Peak files are available for conditions in which at least 1 peak was detected.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for input sample)

growth_protocol: Cell lines derived from PGK12.1 mouse embryonic stem cells were maintained on gelatin-coated petri dishes in serum-containing ES cell medium (DMEM) supplemented with 15% ESC-grade foetal bovine serum (FBS), 1000U/ml leukemia inhibitory factor (LIF, Millipore) and 0.1mM B-mercaptoethanol in humidified atmosphere at 37°C with 8% CO2.

extract_protocol:
Cells were harvested using trypsin, washed in 1X PBS and fixed with 1% (v/v) formaldehyde for 10 min at room temperature. Fixation was quenched with 0.125 M glycine for 5 min. Cells were then pelleted, washed three times with cold PBS, aliquoted (~10 x 10^6 cells per Eppendorf tube per IP) and frozen in dry ice. Pellets were lysed in 350 μL buffer LB3 (10 mM Tris-HCl/pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x protease inhibitors) for 10 min at 4 °C on a rotating wheel. Samples were sonicated using a Bioruptor (Diagenode) for 30 min at maximum output (3 cycles of 10 min: 30 sec on/off, with 5 min on ice between cycles) to reach a fragmentation between 200-500 bp. Lysates were then supplemented with 100 μL of buffer LB3, 50 μL of 10% Triton X-100 and centrifuged at full speed for 5 min at 4 °C; the supernatant (sonicated chromatin) was collected, and 10% was saved as input. In parallel, 50 μL Dynabeads Protein G (Invitrogen) per IP were washed and resuspended in 400 μL PBS with 0.5% BSA, then blocked for 1 h at room temperature with antibodies for IP (Cas9, Active Motif AB_2793760: 4 μg/IP; Normal Mouse IgG, Merck 12-371: 4 μg/IP). Antibody-conjugated beads were resuspended in 50 μL of buffer LB3 and incubated with chromatin overnight at 4 °C on a rotating wheel. Beads were washed subsequently twice with TF-WBI (20 mM Tris-HCl/pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), twice with TF-WBIII (250 mM LiCl, 1% Triton X-100, 0.7% Na-DOC, 10 mM Tris-HCl, 1 mM EDTA), and twice with TET (0.2% Tween-20, 10 mM Tris-HCl/pH 8.0, 1 mM EDTA). Chromatin was eluted from beads with 70 μL elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl/pH 8.0) containing 4 μL proteinase K (10 mg/ml) for 1 h at 55 °C, followed by overnight incubation at 65 °C to reverse crosslinking. A second elution was performed with 30 μL of the same buffer for 1 min, and both eluates were pooled.
DNA was purified using Qiagen MinElute columns according to the manufacturer’s instructions. Then, DNA fragments were repaired, A-tailed, ligated with Illumina adapter, and sequenced.

treatment_protocol: For induction of the engineered effectors and for each cell line, cells grown on 10 cm petri dishes were treated without or with 1µg/ml doxycycline (Sigma) for 48h.

value: embryonic stem cells

value: dCas9-VPR effector

tag: treatment

value: doxycycline

tag: chip antibody


title: VPR-D4, DOX-treatment, rep2 (ChIP)

status: Public on Jun 17 2026

type: SRA

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Library name: VPR-D4_DOX_rep2, ChIP

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: time

value: Cas9, Active Motif AB_2793771


title: VPR-D4, DOX-treatment, rep1 (Input)

description: Library name: VPR-D4_DOX_rep1, INPUT


title: VPR-D4, DOX-treatment, rep1 (ChIP)

description: Library name: VPR-D4_DOX_rep1, ChIP

value: Cas9, Active Motif AB_2793770


title: VPR-D4, rep2 (Input)

description: Library name: VPR-D4_rep2, INPUT

value: mock


title: VPR-D4, rep1 (Input)

description: Library name: VPR-D4_rep1, INPUT


title: VPR-D4, rep1 (ChIP)

description: Library name: VPR-D4_rep1, ChIP

value: Cas9, Active Motif AB_2793768


title: VPR-D4, rep2 (ChIP)

description: Library name: VPR-D4_rep2, ChIP

value: Cas9, Active Motif AB_2793769


title: LP11026

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

description:
Library name: Sample12
Column name in raw_counts_All_Samples.tsv: LP11026

library_source: transcriptomic

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N's, and trim bases with a quality of less than 30 from the 3' ends of the reads. On average, 8.7 million reads were left after this procedure. Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted raw reads per gene. Differential gene expression was calculated using DESeq2 version 1.40.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Supplementary files format and content: raw_counts_All_Samples.tsv contains a matrix with raw gene counts, gene symbols, and gene types for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: humanHuman oral squamous cell carcinoma (HSC-2) cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich, St. Louis, MO, USA) containing 1% antibiotic-antimycotic (Sigma-Aldrich, St. Louis, MO), and 10% fetal bovine serum (Bio&Sell GmbH, Nuremberg, Germany).

extract_protocol:
Total RNA was extracted using the GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with rDNase set (Macherer-Nagel, Düren, Germany ).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3' FWD protocol version 2 with unique dual indices (Lexogen GmbH, Vienna, Austria). 15 PCR cycles were used for library preparation, as determined by quantitative PCR (qPCR) according to the library preparation manual.

treatment_protocol: Gingival fibroblasts were exposed to the lysates of platelet-poor plasma (PPP) and heated PPP (Alb-gel/hPPP), buffy coat (C-PRF/BC) in a serum-free medium for 24 h at 37 °C, 5% CO2, and 95% humidity.

value: human oral squamous cell carcinoma

value: treated with hemin


title: LP11025

description:
Library name: Sample11
Column name in raw_counts_All_Samples.tsv: LP11025

value: treated with IL-1β/TNF-α + hemin


title: VPR-B4, DOX-treatment, rep2 (Input)

description: Library name: VPR-B4_DOX_rep2, INPUT


title: LP11024

description:
Library name: Sample10
Column name in raw_counts_All_Samples.tsv: LP11024

value: treated with IL-1β/TNF-α


title: VPR-B4, DOX-treatment, rep2 (ChIP)

description: Library name: VPR-B4_DOX_rep2, ChIP

value: Cas9, Active Motif AB_2793767


title: LP11023

description:
Library name: Sample9
Column name in raw_counts_All_Samples.tsv: LP11023

value: untreated


title: VPR-B4, DOX-treatment, rep1 (Input)

description: Library name: VPR-B4_DOX_rep1, INPUT


title: VPR-B4, DOX-treatment, rep1 (ChIP)

description: Library name: VPR-B4_DOX_rep1, ChIP

value: Cas9, Active Motif AB_2793766


title: LP11015

description:
Library name: Sample8
Column name in raw_counts_All_Samples.tsv: LP11015


title: VPR-B4, rep2 (Input)

description: Library name: VPR-B4_rep2, INPUT


title: LP11014

description:
Library name: Sample7
Column name in raw_counts_All_Samples.tsv: LP11014


title: VPR-B4, rep2 (ChIP)

description: Library name: VPR-B4_rep2, ChIP

value: Cas9, Active Motif AB_2793765


title: LP11013

description:
Library name: Sample6
Column name in raw_counts_All_Samples.tsv: LP11013


title: VPR-B4, rep1 (Input)

description: Library name: VPR-B4_rep1, INPUT


title: LP11012

description:
Library name: Sample5
Column name in raw_counts_All_Samples.tsv: LP11012


title: VPR-B4, rep1 (ChIP)

description: Library name: VPR-B4_rep1, ChIP

value: Cas9, Active Motif AB_2793764


title: ATF1 (fused to YFP, MNase, NLS), rep 3

city: Rehovot

first: Naama

last: Barkai

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Library name: ATF1_3
Human TF ChEC-seq profile in budding yeast

data_processing:
After demultiplexing using bcl2fastq (Illumina), reads were filtered using cutadapt with the following parameters: ‘--pair-filter=any -m 15 --action=trim’.
Alignment to the S. cerevisiae genome R64-1-1 was done using Bowtie2 (‘--very-sensitive --trim-to 30 --dovetail’).
genomeCoverageBed (‘-5 -fs 1 -d’) was used to achieve single bp resolution of MNase cut sites.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content:
*.out file contains genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
*.bam.bw file contains normalized genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria). Normalization: ribosomal locus (chr12: 450,000-490,001), CUP1 and CUP2 sites (chr8: 212,408-215,118), and partial GAL11 promoter (chr15: 234,421 - 234,548) were filtered out contains genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Library strategy: ChEC-seq

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Stationary phase cultures from freshly picked colonies were diluted into 5 mL fresh SD media and grown overnight to OD600 = 4.

extract_protocol:
Samples were treated with Proteinase K (0.5 mg/mL, 55°C, 30 min), extracted with equal volume phenol-chloroform pH 8 (Sigma-Aldrich), vortexed, and centrifuged (17,000g, 15 min). DNA was precipitated with 3 volumes cold 96% EtOH, 45 mg Glycoblue, and 20 mM sodium acetate (–80°C, >1 hr), pelleted (17,000g, 4°C, 10 min), washed with 70% EtOH, dried, and resuspended in 30 µL RNase A solution (0.33 mg/mL in TE: 10 mM Tris, 1 mM EDTA) for 20 min at 37°C. Small fragments were enriched by SPRI cleanup (Ampure XP): 0.8× (24 µL) beads for reverse cleanup (5 min, RT), supernatant retained; then 1× (30 µL) beads plus 5.4× (162 µL) isopropanol (5 min, RT). Beads were washed twice with 85% EtOH and DNA eluted in 30 µL 0.1× TE.
Following RNase treatment and reverse SPRI cleanup, DNA fragments were used for end-repair and A-tailing (ERA). A 5.4 µL ERA mix (1× T4 DNA ligase buffer [NEB], 0.5 mM dNTPs, 0.25 mM ATP, 2.75% PEG 4000, 6 U T4 PNK [NEB], 0.5 U T4 DNA Polymerase [Thermo Scientific], 0.5 U Taq DNA polymerase [Bioline]) was added to 14.6 µL sample and incubated at 12°C for 20 min, 37°C for 15 min, and 58°C for 45 min. ERA products were subjected to reverse SPRI cleanup with 0.5× (10 µL) SPRI beads (Ampure XP, Beckman Coulter); supernatant was retained, and small fragments were purified with 1.3× (26 µL) SPRI beads plus 5.4× (108 µL) isopropanol. After two 85% EtOH washes, DNA was eluted in 17 µL 0.1× TE. For ligation, 16.4 µL eluate was added to a 40 µL reaction (1× Quick ligase buffer [NEB], 4000 U Quick ligase [NEB], 6.4 nM Y-shaped barcode adaptors with T-overhang) and incubated 15 min at 20°C. Ligation products were cleaned by double SPRI: first 1.2× (48 µL) SPRI, eluted in 30 µL 0.1× TE; then without bead separation, 1.3× (39 µL) HXN buffer (2.5 M NaCl, 20% PEG 8000) was added and DNA eluted in 24 µL 0.1× TE. Next, 23 µL eluate was amplified in a 50 µL PCR (1× Kappa HIFI [Roche], 0.32 µM barcoded forward and reverse primers) with 45 s at 98°C; 16 cycles of 15 s at 98°C and 15 s at 60°C; and 1 min at 72°C. Final libraries were cleaned with 1.1× (55 µL) SPRI and eluted in 15 µL 0.1× TE. Concentration and size distribution were assessed by Qbit (Thermo Scientific) and TapeStation (Agilent). Libraries were pooled equimolarly, diluted to 2 nM, and sequenced on NovaSeq 6000/NovaSeq X (Illumina) with the following parameters: Read1, 61 nt; Index1, 8 nt; Index2, 8 nt; Read2, 61 nt.

treatment_protocol: Cells were pelleted (1,500g, 2 min), resuspended in 0.5 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1× cOmplete EDTA-free protease inhibitors [Roche; one tablet per 50 mL], 1 mM PMSF), transferred to 2 mL 96-well plates (Thermo Scientific), and washed twice with 1 mL Buffer A. Cells were resuspended in 150 µL Buffer A + 0.1% digitonin, transferred to an Eppendorf 96-well plate, and permeabilized at 30°C for 5 min. CaCl₂ was added to 2 mM and incubated for 30 s to activate MNase, then stopped with an equal volume of stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA, 1% SDS).

tag: strain genotype

value: Saccharomyces cerevisiae cells

tag: human tf

tag: locus

value: HO

tag: promoter


title: LP11004

description:
Library name: Sample4
Column name in raw_counts_All_Samples.tsv: LP11004


title: VPR-B7, DOX-treatment, rep2 (Input)

description: Library name: VPR-B7_DOX_rep2, INPUT

value: embryonic stem cells

value: dCas9-VPR effector

value: doxycycline


title: VPR-B7, DOX-treatment, rep2 (ChIP)

description: Library name: VPR-B7_DOX_rep2, ChIP

value: Cas9, Active Motif AB_2793763


title: LP11003

description:
Library name: Sample3
Column name in raw_counts_All_Samples.tsv: LP11003


title: LP11002

description:
Library name: Sample2
Column name in raw_counts_All_Samples.tsv: LP11002


title: VPR-B7, DOX-treatment, rep1 (Input)

description: Library name: VPR-B7_DOX_rep1, INPUT


title: LP11001

description:
Library name: Sample1
Column name in raw_counts_All_Samples.tsv: LP11001


title: VPR-B7, DOX-treatment, rep1 (ChIP)

description: Library name: VPR-B7_DOX_rep1, ChIP

value: Cas9, Active Motif AB_2793762


title: Panc10.05 Harr-2-3 RNA

city: Bronx

first: Kamini

last: Singh

state: NY

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

country: USA

institute: Albert Einstein College of Medicine

description: Library name: Sample 48

data_processing:
Sequence Alignment: Total RNA-sequencing (RNA-seq) and ribosome sequencing (Ribo-seq) reads were first adapter trimmed using TrimGalore. Trimmed reads that aligned to a house rRNA panel from 45S rRNA and rRNA from different Mycoplasma species were filtered out. Unfiltered reads were aligned to the GRCh38 (ENSEMBL build 105) human reference genome and transcriptome using STAR aligner. Sequencing RNA-seq and Ribo-seq reads that mapped to CDS regions were extracted using a shell script with SAMtools. Unique Ribo-seq reads between 15-30nt (MiaPaca-2) or 25-35nt (Panc10.05) were defined as ribosome footprints (RF) and were used for further analysis.
Footprint Analysis: RiboDiff was used to analyze translation efficiency based on ribosome footprinting and mRNA sequencing data. Genes with significantly changed translation efficiency were defined by a q-value cut-off of 0.0001 for MiaPaca2 cells treated with Sotorasib and 0.1 for Panc10.05 cells treated with MRTX1133.
RF and RNA coverages reported as BIGWIG files were converted from STAR-generated .bam alignment files as reads per million (RPM) values for positive (pos) or negative (neg) strands. Negative strand coverage is reported as -1 * (RPM) for visualization purposes.
Start sites for the p-site metagene plots were identified by the ORF-RATER pipeline using harringtonine-treated samples as input
Assembly: GRCh38.105
Supplementary files format and content: MiaPaca2_Sotorasib.RiboDiff.outputs.gene.csv.gz: gzipped comma-separated RiboDiff output file
Supplementary files format and content: Panc10.05_MRTX1133.RiboDiff.outputs.gene.csv.gz: gzipped comma-separated RiboDiff output file
Supplementary files format and content: bw

source_name: Human pancreatic duct

growth_protocol: Pancreatic cancer cell lines were cultured in DMEM media supplemented with 10% fetal bovine serum and penicillin-streptomycin-glutamine

extract_protocol:
Total RNA and ribosome-protected fragments were isolated following published protocol (Ingolia, N.T.; Brar, G.A.; Rouskin, S.; McGeachy, A.M.; Weissman, J.S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 2012, 7, 1534–1550. https://doi.org/10.1038/nprot.2012.086)
Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was conducted with the human genome sequence GRCh38 downloaded from the Ensembl public database (http://www.ensembl.org)

treatment_protocol: Cells were treated with DMSO, Harringtonine (Harr), Sotorasib (Soto), MRTX1133, or Sotorasib & Harringtonine (Soto-Harr)

tag: tissue

value: Human pancreatic duct

value: KRAS G12D

value: Harringtonine treated


title: RNA-seq prefrontal cortex, SAL-SAL, male, replicate 5-1

city: la jolla

first: Yanmiao

last: Du

state: CA

address: 4254 Urey Hall, 9500 Gilman Drive

department: Department of Chemistry and Biochemistry/Cellular and Molecular Medicine

institute: UCSD

description: Library name: RNA_PFC_SAL-SAL_M_5-1

data_processing:
Sequencing reads were trimmed for adapters and quality using Trim Galore (v0.6.7, --paired).
Trimmed reads were aligned to the Mus musculus mm10 reference genome using STAR (v2.7.10a) with --quantMode GeneCounts.
Gene-level counts were validated with HTSeq-count (v0.12.4) using GENCODE vM25 annotation. Genes with total counts <= 10 across all samples were excluded prior to analysis.
Differential expression was performed with DESeq2 (v1.40.2) using median-of-ratios normalization and Wald tests; pairwise contrasts: MOR-SAL vs SAL-SAL and MOR-LPS vs SAL-LPS per brain region. Significance: FDR < 0.05 (Benjamini-Hochberg).
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts per gene for each sample

molecule: polyA RNA

source_name: prefrontal cortex

growth_protocol: Male and female C57BL/6NTac mice (Taconic, Hudson, NY) were bred at the University of Pennsylvania and group-housed (3-5/cage) under a 12-h light/dark cycle (lights on at 0700) with ad libitum access to food and water. All procedures were approved by the University of Pennsylvania Animal Care and Use Committee.

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). Nuclear RNA was extracted from ~5,000 NeuN+ nuclei per sample using RNeasy Mini Kit (74104, Qiagen) with on-column DNase digestion (RNase-Free DNase Set 79254, Qiagen).
RNA-seq libraries were prepared from ~5,000 NeuN+ sorted nuclei using a modified Smart-seq3 protocol with tagmentation-based library construction. Reverse transcription was performed on nuclear RNA, followed by tagmentation with custom P5/P7-adapter-loaded Tn5 transposase (Diagenode) and PCR amplification with KAPA HiFi ReadyMix and barcoded primers. Libraries were size-checked on a TapeStation (G2992AA, Agilent) using the High Sensitivity DNA Analysis Kit (5067-4626), primer-dimers removed with SPRIselect beads, quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp, ~15 million reads per library).

treatment_protocol: Perinatal morphine exposure: 8-12-week-old female mice were implanted with osmotic minipumps (Alzet model 1004) delivering morphine sulfate (10 mg/kg/day, NIDA Drug Supply) or saline, then co-housed with drug-naive males. Pups were transferred to drug-naive surrogates within 4-8 hours of birth. Postnatal morphine (10 mg/kg SC, 10 mL/kg) or saline was administered twice daily (09:00 and 17:00) from PND1 through the morning of PND14, after which mice underwent spontaneous opioid withdrawal. In adulthood, mice were assigned to four groups: SAL-SAL (saline/saline), SAL-LPS (saline/LPS challenge), MOR-SAL (morphine/saline), or MOR-LPS (morphine/LPS challenge). Brain tissues were collected 2 hours after adult LPS or saline injection.

value: prefrontal cortex

value: wild type

value: SAL-SAL


title: RNA-seq prefrontal cortex, SAL-SAL, male, replicate 3-0

description: Library name: RNA_PFC_SAL-SAL_M_3-0


title: Panc10.05 Harr-2-1 RNA

description: Library name: Sample 46


title: Panc10.05 Harr-2-2 RNA

description: Library name: Sample 47


title: RNA-seq prefrontal cortex, SAL-SAL, male, replicate 1-3

description: Library name: RNA_PFC_SAL-SAL_M_1-3


title: Panc10.05 DMSO-2-3 RNA

description: Library name: Sample 45

value: Control


title: RNA-seq prefrontal cortex, SAL-SAL, female, replicate 9-4

description: Library name: RNA_PFC_SAL-SAL_F_9-4


title: RNA-seq prefrontal cortex, SAL-SAL, male, replicate 1-1

description: Library name: RNA_PFC_SAL-SAL_M_1-1


title: Panc10.05 DMSO-2-2 RNA

description: Library name: Sample 44


title: RNA-seq prefrontal cortex, SAL-SAL, female, replicate 9-0

description: Library name: RNA_PFC_SAL-SAL_F_9-0


title: Panc10.05 DMSO-2-1 RNA

description: Library name: Sample 43


title: RNA-seq prefrontal cortex, SAL-SAL, female, replicate 4-3

description: Library name: RNA_PFC_SAL-SAL_F_4-3


title: Panc10.05 MRTX-1-3 RNA

description: Library name: Sample 42

value: MRTX1133 treated


title: Panc10.05 MRTX-1-2 RNA

description: Library name: Sample 41


title: RNA-seq prefrontal cortex, SAL-SAL, female, replicate 4-1

description: Library name: RNA_PFC_SAL-SAL_F_4-1


title: Panc10.05 MRTX-1-1 RNA

description: Library name: Sample 40


title: RNA-seq prefrontal cortex, SAL-SAL, female, replicate 10-3

description: Library name: RNA_PFC_SAL-SAL_F_10-3


title: Panc10.05 DMSO-1-3 RNA

description: Library name: Sample 39


title: RNA-seq prefrontal cortex, SAL-SAL, female, replicate 10-1

description: Library name: RNA_PFC_SAL-SAL_F_10-1


title: Panc10.05 DMSO-1-2 RNA

description: Library name: Sample 38


title: RNA-seq prefrontal cortex, SAL-LPS, male, replicate 3-3

description: Library name: RNA_PFC_SAL-LPS_M_3-3

value: SAL-LPS


title: RNA-seq prefrontal cortex, SAL-LPS, male, replicate 11-0

description: Library name: RNA_PFC_SAL-LPS_M_11-0


title: Panc10.05 DMSO-1-1 RNA

description: Library name: Sample 37


title: MiaPaca2 Soto-Harr-3 RNA

description: Library name: Sample 36

value: KRAS G12C

value: Sotorasib and Harringtonine treated


title: RNA-seq prefrontal cortex, SAL-LPS, male, replicate 1-4

description: Library name: RNA_PFC_SAL-LPS_M_1-4


title: RNA-seq prefrontal cortex, SAL-LPS, male, replicate 1-0

description: Library name: RNA_PFC_SAL-LPS_M_1-0


title: MiaPaca2 Soto-Harr-2 RNA

description: Library name: Sample 35


title: MiaPaca2 Soto-Harr-1 RNA

description: Library name: Sample 34


title: RNA-seq prefrontal cortex, SAL-LPS, female, replicate 9-1

description: Library name: RNA_PFC_SAL-LPS_F_9-1


title: RNA-seq prefrontal cortex, SAL-LPS, female, replicate 9-3

description: Library name: RNA_PFC_SAL-LPS_F_9-3


title: MiaPaca2 Harr-3 RNA

description: Library name: Sample 33


title: RNA-seq prefrontal cortex, SAL-LPS, female, replicate 4-4

description: Library name: RNA_PFC_SAL-LPS_F_4-4


title: MiaPaca2 Soto-3 RNA

description: Library name: Sample 30

value: Sotorasib treated


title: MiaPaca2 Harr-1 RNA

description: Library name: Sample 31


title: MiaPaca2 Harr-2 RNA

description: Library name: Sample 32


title: RNA-seq prefrontal cortex, SAL-LPS, female, replicate 4-0

description: Library name: RNA_PFC_SAL-LPS_F_4-0


title: RNA-seq prefrontal cortex, SAL-LPS, female, replicate 10-2

description: Library name: RNA_PFC_SAL-LPS_F_10-2


title: MiaPaca2 Soto-2 RNA

description: Library name: Sample 29


title: RNA-seq prefrontal cortex, SAL-LPS, female, replicate 10-0

description: Library name: RNA_PFC_SAL-LPS_F_10-0


title: MiaPaca2 Soto-1 RNA

description: Library name: Sample 28


title: RNA-seq prefrontal cortex, MOR-SAL, male, replicate 6-3

description: Library name: RNA_PFC_MOR-SAL_M_6-3

value: MOR-SAL


title: MiaPaca2 DMSO-3 RNA

description: Library name: Sample 27


title: RNA-seq prefrontal cortex, MOR-SAL, male, replicate 6-1

description: Library name: RNA_PFC_MOR-SAL_M_6-1


title: MiaPaca2 DMSO-2 RNA

description: Library name: Sample 26


title: MiaPaca2 DMSO-1 RNA

description: Library name: Sample 25


title: RNA-seq prefrontal cortex, MOR-SAL, male, replicate 17-2

description: Library name: RNA_PFC_MOR-SAL_M_17-2


title: Panc10.05 Harr-2-3 RF

description: Library name: Sample 24

data_processing:
Sequence Alignment: Total RNA-sequencing (RNA-seq) and ribosome sequencing (Ribo-seq) reads were first adapter trimmed using TrimGalore. Trimmed reads that aligned to a house rRNA panel from 45S rRNA and rRNA from different Mycoplasma species were filtered out. Unfiltered reads were aligned to the GRCh38 (ENSEMBL build 105) human reference genome and transcriptome using STAR aligner. Sequencing RNA-seq and Ribo-seq reads that mapped to CDS regions were extracted using a shell script with SAMtools. Unique Ribo-seq reads between 15-30nt (MiaPaca-2) or 25-35nt (Panc10.05) were defined as ribosome footprints (RF) and were used for further analysis.
Footprint Analysis: RiboDiff was used to analyze translation efficiency based on ribosome footprinting and mRNA sequencing data. Genes with significantly changed translation efficiency were defined by a q-value cut-off of 0.0001 for MiaPaca2 cells treated with Sotorasib and 0.1 for Panc10.05 cells treated with MRTX1133.
RF and RNA coverages reported as BIGWIG files were converted from STAR-generated .bam alignment files as reads per million (RPM) values for positive (pos) or negative (neg) strands. Negative strand coverage is reported as -1 * (RPM) for visualization purposes.
Start sites for the p-site metagene plots were identified by the ORF-RATER pipeline using harringtonine-treated samples as input
Assembly: GRCh38.105
Supplementary files format and content: MiaPaca2_Sotorasib.RiboDiff.outputs.gene.csv.gz: gzipped comma-separated RiboDiff output file
Supplementary files format and content: Panc10.05_MRTX1133.RiboDiff.outputs.gene.csv.gz: gzipped comma-separated RiboDiff output file
Supplementary files format and content: bw
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA


title: RNA-seq prefrontal cortex, MOR-SAL, male, replicate 17-4

description: Library name: RNA_PFC_MOR-SAL_M_17-4


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 7-3

description: Library name: RNA_PFC_MOR-SAL_F_7-3


title: Panc10.05 Harr-2-1 RF

description: Library name: Sample 22


title: Panc10.05 Harr-2-2 RF

description: Library name: Sample 23


title: RNA-seq prefrontal cortex, MOR-SAL, male, replicate 14-1

description: Library name: RNA_PFC_MOR-SAL_M_14-1


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 16-3

description: Library name: RNA_PFC_MOR-SAL_F_16-3


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 7-2

description: Library name: RNA_PFC_MOR-SAL_F_7-2


title: Panc10.05 DMSO-2-2 RF

description: Library name: Sample 20


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 16-1

description: Library name: RNA_PFC_MOR-SAL_F_16-1


title: Panc10.05 DMSO-2-3 RF

description: Library name: Sample 21


title: Panc10.05 DMSO-2-1 RF

description: Library name: Sample 19


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 15-4

description: Library name: RNA_PFC_MOR-SAL_F_15-4


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 15-2

description: Library name: RNA_PFC_MOR-SAL_F_15-2


title: RNA-seq prefrontal cortex, MOR-SAL, female, replicate 15-0

description: Library name: RNA_PFC_MOR-SAL_F_15-0


title: Panc10.05 MRTX1133-1-3 RF

description: Library name: Sample 18


title: Panc10.05 MRTX1133-1-1 RF

description: Library name: Sample 16


title: Panc10.05 MRTX1133-1-2 RF

description: Library name: Sample 17


title: Panc10.05 DMSO-1-3 RF

description: Library name: Sample 15


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 6-4

description: Library name: RNA_PFC_MOR-LPS_M_6-4

value: MOR-LPS


title: Panc10.05 DMSO-1-2 RF

description: Library name: Sample 14


title: Panc10.05 DMSO-1-1 RF

description: Library name: Sample 13


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 8-1

description: Library name: RNA_PFC_MOR-LPS_M_8-1


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 17-3

description: Library name: RNA_PFC_MOR-LPS_M_17-3


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 17-1

description: Library name: RNA_PFC_MOR-LPS_M_17-1


title: MiaPaca2 Soto-Harr-3 RF

description: Library name: Sample 12


title: MiaPaca2 Soto-Harr-2 RF

description: Library name: Sample 11


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 14-0

description: Library name: RNA_PFC_MOR-LPS_M_14-0


title: MiaPaca2 Harr-3 RF

description: Library name: Sample 9


title: MiaPaca2 Soto-Harr-1 RF

description: Library name: Sample 10


title: MiaPaca2 Harr-2 RF

description: Library name: Sample 8


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 13-0

description: Library name: RNA_PFC_MOR-LPS_M_13-0


title: MiaPaca2 Harr-1 RF

description: Library name: Sample 7


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 7-1

description: Library name: RNA_PFC_MOR-LPS_F_7-1


title: MiaPaca2 Soto-3 RF

description: Library name: Sample 6


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 14-4

description: Library name: RNA_PFC_MOR-LPS_M_14-4


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 18-1

description: Library name: RNA_PFC_MOR-LPS_F_18-1


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 6-0

description: Library name: RNA_PFC_MOR-LPS_M_6-0


title: MiaPaca2 Soto-2 RF

description: Library name: Sample 5


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 16-4

description: Library name: RNA_PFC_MOR-LPS_F_16-4


title: MiaPaca2 Soto-1 RF

description: Library name: Sample 4


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 15-3

description: Library name: RNA_PFC_MOR-LPS_F_15-3


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 15-1

description: Library name: RNA_PFC_MOR-LPS_F_15-1


title: MiaPaca2 DMSO-3 RF

description: Library name: Sample 3


title: MiaPaca2 DMSO-2 RF

description: Library name: Sample 2


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 12-0

description: Library name: RNA_PFC_MOR-LPS_F_12-0


title: MiaPaca2 DMSO-1 RF

description: Library name: Sample 1


title: RNA-seq prefrontal cortex, MOR-LPS, female, replicate 12-2

description: Library name: RNA_PFC_MOR-LPS_F_12-2


title: RNA-seq striatum, SAL-SAL, male, replicate 3-4

description: Library name: RNA_Striatum_SAL-SAL_M_3-4

source_name: striatum

value: striatum


title: p27k-mVenus High from hCD19 positive tumor_sample 1

city: Austin

first: Bryan

last: McClellan

state: TX

address: 1601B Trinity St, Hdb 6.302

institute: University of Texas at Austin

description:
Library name: 130_Pos
Column_Name_in_rawcountsandDeseq2_130-Pos

data_processing:
raw datafiles were generated by GeneWiz
Assembly: mm10
Supplementary files format and content: CSV raw count file contains raw transcipt counts for each sample

source_name: tumor

growth_protocol: Prior to subcutanoues implantation in NSG mice, mT4-2D cells were grown in DMEM + 10%FBS + 1% penicillin/streptomcycin at 37 ºC at 5% CO2

extract_protocol:
Cancer cells were sorted directly into Trizol for RNA extraction.
RNA extraction and library construction for ultra-low input RNA-sequenicng was performed by GeneWiz.

treatment_protocol: Tumors were treated with five million anti-human CD19 CAR T-cells through intraperitineal injectio

value: tumor

value: mT4-2D (KPC mouse)

value: Cancer cell

value: human CD19 Positive

value: Five million anti-human CD19 CAR T-cells

tag: batch


title: p27k-mVenus High from hCD19 positive tumor_sample 3

description:
Library name: 133_Pos
Column_Name_in_rawcountsandDeseq2_133-Pos


title: p27k-mVenus High from hCD19 positive tumor_sample 2

description:
Library name: 131_Pos
Column_Name_in_rawcountsandDeseq2_131-Pos


title: RNA-seq striatum, SAL-SAL, male, replicate 5-3

description: Library name: RNA_Striatum_SAL-SAL_M_5-3


title: p27k-mVenus Negative from hCD19 negative tumor_sample 3

description:
Library name: 133_Neg
Column_Name_in_rawcountsandDeseq2_133-Neg

value: human CD19 Negative


title: RNA-seq striatum, SAL-SAL, male, replicate 3-2

description: Library name: RNA_Striatum_SAL-SAL_M_3-2

value: wild type


title: RNA-seq prefrontal cortex, MOR-LPS, male, replicate 13-2

description: Library name: RNA_PFC_MOR-LPS_M_13-2

value: prefrontal cortex


title: RNA-seq striatum, SAL-SAL, male, replicate 3-0

description: Library name: RNA_Striatum_SAL-SAL_M_3-0

value: SAL-SAL


title: p27k-mVenus Negative from hCD19 negative tumor_sample 2

description:
Library name: 131_Neg
Column_Name_in_rawcountsandDeseq2_131-Neg


title: RNA-seq striatum, SAL-SAL, male, replicate 11-1

description: Library name: RNA_Striatum_SAL-SAL_M_11-1


title: RNA-seq striatum, SAL-SAL, male, replicate 1-3

description: Library name: RNA_Striatum_SAL-SAL_M_1-3


title: p27k-mVenus Negative from hCD19 negative tumor_sample 1

description:
Library name: 130_Neg
Column_Name_in_rawcountsandDeseq2_130-Neg


title: RNA-seq striatum, SAL-SAL, male, replicate 1-1

description: Library name: RNA_Striatum_SAL-SAL_M_1-1


title: PANC1PSB_PS04ULAPANC1PSBS382_TCCATGGAT_L003_R1_001, PANC1, Ravoxertinib-VSP34I

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
The PLATE-Seq FASTQ files were pseudoaligned to the GRCh38 human transcriptome (mRNA & ncRNA) and gene expression was quantified using kallisto (version 0.44.0), tximport package (Soneson et al., 2015), and biomaRt package (Durinck et al., 2009).
The gene expression was quantified as both raw counts (i.e. sequencing fragments per genomic locus) and transcripts per million (i.e. sequencing fragments per genomic locus normalized for transcript/gene length and sample sequencing depth).
Assembly: GRCh38
Supplementary files format and content: Table containing reads count of each gene (row) in each sample (column)
Library strategy: PLATE-Seq

source_name: Human PDA cell line

growth_protocol: Panc1 and Aspc1 pancreatic cancer cells were cultured in 96-well tissue culture-treated plates at optimized density, in 100 μl of Dulbecco's Modified Eagle Medium (DMEM) media supplemented with 10% fetal bovine serum (FBS) and 1X pen/strep

extract_protocol:
After 24 h of incubation, the plates were treated with following drugs: RAF inhibitors – Sorafenib, Dabrafenib, RAF709, PLX8394, GDC-0879; MEK inhibitors – Trametinib, Cobimetinib, Binimetinib, Selumetinib, Rafametinib; and ERK inhibitors – SCH772984, Ulixertinib, AZD0364, Ravoxertinib; in combination with Autophagy inhibitors: Hydroxychloroquine or Compound 19 (Vps34 inhibitor). Each drug was dosed at the concentration at which the cells were 80% viable after 48 h of treatment with monotherapy. After 24 h of treatment, the medium was replaced with 100 ml of FBS supplemented with 10% DMSO and the plates were frozen at −80 °C prior to PLATE-Seq.
Detailed protocol for preparation of the automated PLATE-SEQ experiment was described by Bush et al. (Bush et al., 2017).
Samples were sequenced using PlateSeq approach

value: PDA tumor


title: PANC1PSB_PS04ULAPANC1PSBS381_GCCAAAGTT_L003_R1_001, PANC1, Cobimetinib-VSP34I


title: RNA-seq striatum, SAL-SAL, female, replicate 9-4

description: Library name: RNA_Striatum_SAL-SAL_F_9-4


title: PANC1PSB_PS04ULAPANC1PSBS380_AGCATAGAG_L003_R1_001, PANC1, Trametinib-Hydroxychloroquine

value: Trametinib-Hydroxychloroquine


title: RNA-seq striatum, SAL-SAL, female, replicate 9-2

description: Library name: RNA_Striatum_SAL-SAL_F_9-2


title: PANC1PSB_PS04ULAPANC1PSBS379_GGGTTCTGA_L003_R1_001, PANC1, GDC-0879-Hydroxychloroquine


title: RNA-seq striatum, SAL-SAL, female, replicate 9-0

description: Library name: RNA_Striatum_SAL-SAL_F_9-0


title: PANC1PSB_PS04ULAPANC1PSBS370_ACGTCCTCT_L003_R1_001, PANC1, RAF709-VSP34I


title: RNA-seq striatum, SAL-SAL, female, replicate 10-3

description: Library name: RNA_Striatum_SAL-SAL_F_10-3


title: PANC1PSB_PS04ULAPANC1PSBS368_GTGTTCGAC_L003_R1_001, PANC1, Selumetinib-Hydroxychloroquine

value: Selumetinib-Hydroxychloroquine


title: RNA-seq striatum, SAL-SAL, female, replicate 4-3

description: Library name: RNA_Striatum_SAL-SAL_F_4-3


title: PANC1PSB_PS04ULAPANC1PSBS366_GACTAACAG_L003_R1_001, PANC1, Sorafenib-Hydroxychloroquine

value: Sorafenib-Hydroxychloroquine


title: RNA-seq striatum, SAL-SAL, female, replicate 10-1

description: Library name: RNA_Striatum_SAL-SAL_F_10-1


title: RNA-seq striatum, SAL-LPS, male, replicate 5-2

description: Library name: RNA_Striatum_SAL-LPS_M_5-2

value: SAL-LPS


title: RNA-seq striatum, SAL-LPS, male, replicate 5-0

description: Library name: RNA_Striatum_SAL-LPS_M_5-0


title: PANC1PSB_PS04ULAPANC1PSBS357_TCTTGCCAG_L003_R1_001, PANC1, Binimetinib-VSP34I


title: PANC1PSB_PS04ULAPANC1PSBS358_CTTAACAGC_L003_R1_001, PANC1, PLX8394-VSP34I


title: PANC1PSB_PS04ULAPANC1PSBS347_ATACGCAGC_L003_R1_001, PANC1, Ulixertinib-VSP34I


title: PANC1PSB_PS04ULAPANC1PSBS345_TACCACGCT_L003_R1_001, PANC1, AZD0364-VSP34I


title: RNA-seq striatum, SAL-LPS, male, replicate 3-3

description: Library name: RNA_Striatum_SAL-LPS_M_3-3


title: RNA-seq striatum, SAL-LPS, male, replicate 1-4

description: Library name: RNA_Striatum_SAL-LPS_M_1-4


title: PANC1PSB_PS04ULAPANC1PSBS356_AGGCTTCCT_L003_R1_001, PANC1, SCH772984-Hydroxychloroquine


title: RNA-seq striatum, SAL-LPS, male, replicate 11-0

description: Library name: RNA_Striatum_SAL-LPS_M_11-0


title: PANC1PSB_PS04ULAPANC1PSBS344_TACGAGTCG_L003_R1_001, PANC1, Refametinib-Hydroxychloroquine

value: Refametinib-Hydroxychloroquine


title: RNA-seq striatum, SAL-LPS, male, replicate 1-2

description: Library name: RNA_Striatum_SAL-LPS_M_1-2


title: RNA-seq striatum, SAL-LPS, female, replicate 9-3

description: Library name: RNA_Striatum_SAL-LPS_F_9-3


title: PANC1PSB_PS04ULAPANC1PSBS343_CTTGGACGT_L003_R1_001, PANC1, Dabrafenib-Hydroxychloroquine

value: Dabrafenib-Hydroxychloroquine


title: PANC1PSB_PS04ULAPANC1PSBS335_CACGACTTT_L003_R1_001, PANC1, Trametinib-VSP34I


title: RNA-seq striatum, SAL-LPS, female, replicate 4-4

description: Library name: RNA_Striatum_SAL-LPS_F_4-4

value: striatum


title: PANC1PSB_PS04ULAPANC1PSBS332_GTCCCTTTG_L003_R1_001, PANC1, Ravoxertinib-Hydroxychloroquine

value: Ravoxertinib-Hydroxychloroquine


title: PANC1PSB_PS04ULAPANC1PSBS334_AAGGTTCCA_L003_R1_001, PANC1, GDC-0879-VSP34I


title: RNA-seq striatum, SAL-LPS, female, replicate 9-1

description: Library name: RNA_Striatum_SAL-LPS_F_9-1


title: PANC1PSB_PS04ULAPANC1PSBS323_ATGACAAGC_L003_R1_001, PANC1, Selumetinib-VSP34I


title: RNA-seq striatum, SAL-LPS, female, replicate 4-0

description: Library name: RNA_Striatum_SAL-LPS_F_4-0


title: RNA-seq striatum, SAL-LPS, female, replicate 10-4

description: Library name: RNA_Striatum_SAL-LPS_F_10-4


title: PANC1PSB_PS04ULAPANC1PSBS320_GGGAGACAT_L003_R1_001, PANC1, RAF709-Hydroxychloroquine


title: RNA-seq striatum, SAL-LPS, female, replicate 2-2

description: Library name: RNA_Striatum_SAL-LPS_F_2-2


title: RNA-seq striatum, SAL-LPS, female, replicate 10-2

description: Library name: RNA_Striatum_SAL-LPS_F_10-2


title: PANC1PSB_PS04ULAPANC1PSBS311_ACATTCCAC_L003_R1_001, PANC1, SCH772984-VSP34I


title: RNA-seq striatum, SAL-LPS, female, replicate 10-0

description: Library name: RNA_Striatum_SAL-LPS_F_10-0


title: PANC1PSB_PS04ULAPANC1PSBS308_AGTGTTACC_L003_R1_001, PANC1, PLX8394-Hydroxychloroquine


title: RNA-seq striatum, MOR-SAL, male, replicate 8-0

description: Library name: RNA_Striatum_MOR-SAL_M_8-0

value: MOR-SAL


title: PANC1PSB_PS04ULAPANC1PSBS299_TCGATGCCT_L003_R1_001, PANC1, Refametinib-VSP34I


title: PANC1PSB_PS04ULAPANC1PSBS307_ATTCGGCGA_L003_R1_001, PANC1, Binimetinib-Hydroxychloroquine

value: Binimetinib-Hydroxychloroquine


title: MED4 uninfected Control Standard Light 24h Replicate 3

city: Richland

first: Lindsey

last: Anderson

state: WA

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

description:
Library name: Ctr-24h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 24h Replicate 3

data_processing:
Read trimming / QC (TrimGalore v0.6.10; CutAdapt v5.0)
Read mapping & quantification (Rsubread v2.20)
Assembly: GCF_000011465.1 (26-JAN-2024), GCF_000858745.1 (11-JAN-2023)
Supplementary files format and content: rna_seq_counts.csv, comma-separated values table with raw RNA-seq counts

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: prokaryotic cell

growth_protocol: MED4 cells grown on Pro99 substituting Salish Seawater for Sargasso Seawater. For optimal growth, the medium was supplemented with 2× Pro99 nitrogen and phosphorus while maintaining 1× trace metals. Cultures were maintained at 21°C and 45 µmol photons m⁻² s⁻¹ (standard light conditions) in a 12 h light: 12 h dark photocycle.

extract_protocol:
RNA was extracted from exponentially growing cells using the Qiagen RNeasy Plus Mini Kit according to the manufacturer’s instructions. Samples underwent DNase treatment and rRNA depletion
Paired-end sequencing (2 × 150 bp) with single-indexing on an Illumina NovaSeq X

treatment_protocol: P-SSP7 infection experiments were conducted under three light regimes: standard light (45 µmol photons m⁻² s⁻¹), high light (200-250 µmol photons m⁻² s⁻¹), and darkness. MED4 cultures were infected with P-SSP7 (MOI = 10).  Samples were collected in biological triplicate. Sampling was performed at eight time points (0, 0.5, 1, 2, 4, 8, and 24 h post-infection), with additional time points at 26 and 32 h for the dark treatment to capture transcriptional responses upon return to standard light. For standard and high-light conditions, an uninfected control was processed in parallel with the infection experiment.

value: prokaryotic cell

value: WT

tag: agent

value: Control

tag: light regime

value: Standard Light

tag: time point


title: MED4 uninfected Control Standard Light 24h Replicate 2

description:
Library name: Ctr-24h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 24h Replicate 2


title: PANC1PSB_PS04ULAPANC1PSBS297_GAGTGGAAG_L003_R1_001, PANC1, Ulixertinib-Hydroxychloroquine

value: Ulixertinib-Hydroxychloroquine


title: RNA-seq striatum, MOR-SAL, male, replicate 17-4

description: Library name: RNA_Striatum_MOR-SAL_M_17-4

value: wild type


title: MED4 uninfected Control Standard Light 24h Replicate 1

description:
Library name: Ctr-24h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 24h Replicate 1


title: PANC1PSB_PS04ULAPANC1PSBS298_GGCTCTATT_L003_R1_001, PANC1, Dabrafenib-VSP34I

value: PDA tumor


title: RNA-seq striatum, MOR-SAL, male, replicate 17-2

description: Library name: RNA_Striatum_MOR-SAL_M_17-2


title: MED4 uninfected Control Standard Light 8h Replicate 3

description:
Library name: Ctr-8h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 8h Replicate 3


title: PANC1PSB_PS04ULAPANC1PSBS318_TTCTTGGGA_L003_R1_001, PANC1, VSP34I-Alone


title: RNA-seq striatum, MOR-SAL, female, replicate 18-0

description: Library name: RNA_Striatum_MOR-SAL_F_18-0


title: RNA-seq striatum, MOR-SAL, male, replicate 14-1

description: Library name: RNA_Striatum_MOR-SAL_M_14-1


title: PANC1PSB_PS04ULAPANC1PSBS330_TCTGTTGCT_L003_R1_001, PANC1, Hydroxychloroquine-Alone

value: Hydroxychloroquine-Alone


title: MED4 uninfected Control Standard Light 8h Replicate 1

description:
Library name: Ctr-8h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 8h Replicate 1


title: PANC1PSB_PS04ULAPANC1PSBS294_GAAACTGGC_L003_R1_001, PANC1, VSP34I-Alone


title: MED4 uninfected Control Standard Light 8h Replicate 2

description:
Library name: Ctr-8h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 8h Replicate 2


title: PANC1PSB_PS04ULAPANC1PSBS306_GATCCAAGG_L003_R1_001, PANC1, VSP34I-Alone


title: PANC1PSA_PS03ULAPANC1PSAS286_GTCCTATTC_L003_R1_001, PANC1, Ravoxertinib-VSP34I


title: MED4 uninfected Control Standard Light 4h Replicate 3

description:
Library name: Ctr-4h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 4h Replicate 3


title: PANC1PSA_PS03ULAPANC1PSAS285_GTCTCGATC_L003_R1_001, PANC1, Cobimetinib-VSP34I


title: PANC1PSA_PS03ULAPANC1PSAS284_GCTTTCGTC_L003_R1_001, PANC1, Trametinib-Hydroxychloroquine

value: Trametinib-Hydroxychloroquine


title: PANC1PSA_PS03ULAPANC1PSAS283_CGGGTTCTT_L003_R1_001, PANC1, GDC-0879-Hydroxychloroquine


title: PANC1PSA_PS03ULAPANC1PSAS274_GAAACCTCT_L003_R1_001, PANC1, RAF709-VSP34I


title: RNA-seq striatum, MOR-SAL, female, replicate 12-1

description: Library name: RNA_Striatum_MOR-SAL_F_12-1


title: PANC1PSA_PS03ULAPANC1PSAS272_GAATCGTTC_L003_R1_001, PANC1, Selumetinib-Hydroxychloroquine

value: Selumetinib-Hydroxychloroquine


title: RNA-seq striatum, MOR-LPS, male, replicate 8-3

description: Library name: RNA_Striatum_MOR-LPS_M_8-3

value: MOR-LPS


title: MED4 uninfected Control Standard Light 2h Replicate 3

description:
Library name: Ctr-2h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 2h Replicate 3


title: PANC1PSA_PS03ULAPANC1PSAS262_GGAGTAGCT_L003_R1_001, PANC1, PLX8394-VSP34I


title: PANC1PSA_PS03ULAPANC1PSAS261_CAGCATCAT_L003_R1_001, PANC1, Binimetinib-VSP34I


title: MED4 uninfected Control Standard Light 2h Replicate 2

description:
Library name: Ctr-2h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 2h Replicate 2


title: PANC1PSA_PS03ULAPANC1PSAS260_TTCATTCGG_L003_R1_001, PANC1, SCH772984-Hydroxychloroquine


title: RNA-seq striatum, MOR-LPS, male, replicate 6-4

description: Library name: RNA_Striatum_MOR-LPS_M_6-4


title: MED4 uninfected Control Standard Light 2h Replicate 1

description:
Library name: Ctr-2h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 2h Replicate 1


title: PANC1PSB_PS04ULAPANC1PSBS295_TAGAGACAC_L003_R1_001, PANC1, AZD0364-Hydroxychloroquine


title: PANC1PSA_PS03ULAPANC1PSAS249_GGATGGTAC_L003_R1_001, PANC1, AZD0364-VSP34I


title: RNA-seq striatum, MOR-LPS, male, replicate 6-2

description: Library name: RNA_Striatum_MOR-LPS_M_6-2


title: MED4 uninfected Control Standard Light 1h Replicate 3

description:
Library name: Ctr-1h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 1h Replicate 3


title: PANC1PSA_PS03ULAPANC1PSAS247_AGCGACAGA_L003_R1_001, PANC1, Dabrafenib-Hydroxychloroquine


title: PANC1PSA_PS03ULAPANC1PSAS239_TTGGATGCT_L003_R1_001, PANC1, Trametinib-VSP34I


title: MED4 uninfected Control Standard Light 1h Replicate 2

description:
Library name: Ctr-1h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 1h Replicate 2


title: PANC1PSA_PS03ULAPANC1PSAS238_TTCGGCTCT_L003_R1_001, PANC1, GDC-0879-VSP34I


title: RNA-seq striatum, MOR-LPS, male, replicate 17-3

description: Library name: RNA_Striatum_MOR-LPS_M_17-3


title: MED4 uninfected Control Standard Light 1h Replicate 1

description:
Library name: Ctr-1h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 1h Replicate 1


title: PANC1PSA_PS03ULAPANC1PSAS251_GACCTGGTT_L003_R1_001, PANC1, Ulixertinib-VSP34I


title: RNA-seq striatum, MOR-LPS, male, replicate 17-1

description: Library name: RNA_Striatum_MOR-LPS_M_17-1


title: PANC1PSA_PS03ULAPANC1PSAS235_GTTGTCACA_L003_R1_001, PANC1, Cobimetinib-Hydroxychloroquine

value: Cobimetinib-Hydroxychloroquine


title: PANC1PSA_PS03ULAPANC1PSAS248_GAAGCTCAC_L003_R1_001, PANC1, Refametinib-Hydroxychloroquine

value: Refametinib-Hydroxychloroquine


title: RNA-seq striatum, MOR-LPS, male, replicate 6-0

description: Library name: RNA_Striatum_MOR-LPS_M_6-0

value: striatum


title: PANC1PSA_PS03ULAPANC1PSAS227_CAGTCTGAT_L003_R1_001, PANC1, Selumetinib-VSP34I


title: MED4 uninfected Control Standard Light 0.5h Replicate 3

description:
Library name: Ctr-05h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 0.5h Replicate 3


title: PANC1PSA_PS03ULAPANC1PSAS225_GCGCGTTTT_L003_R1_001, PANC1, Sorafenib-VSP34I


title: RNA-seq striatum, MOR-LPS, male, replicate 14-4

description: Library name: RNA_Striatum_MOR-LPS_M_14-4


title: PANC1PSA_PS03ULAPANC1PSAS224_AGCAATGTC_L003_R1_001, PANC1, RAF709-Hydroxychloroquine


title: MED4 uninfected Control Standard Light 0.5h Replicate 2

description:
Library name: Ctr-05h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 0.5h Replicate 2


title: PANC1PSA_PS03ULAPANC1PSAS215_GCTGCTCTA_L003_R1_001, PANC1, SCH772984-VSP34I


title: RNA-seq striatum, MOR-LPS, male, replicate 14-2

description: Library name: RNA_Striatum_MOR-LPS_M_14-2


title: PANC1PSA_PS03ULAPANC1PSAS212_CCGCATATT_L003_R1_001, PANC1, PLX8394-Hydroxychloroquine


title: PANC1PSB_PS04ULAPANC1PSBS331_GATAGGTAG_L003_R1_001, PANC1, Cobimetinib-Hydroxychloroquine


title: MED4 uninfected Control Standard Light 0.5h Replicate 1

description:
Library name: Ctr-05h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 0.5h Replicate 1


title: RNA-seq striatum, SAL-LPS, female, replicate 2-0

description: Library name: RNA_Striatum_SAL-LPS_F_2-0

value: SAL-LPS


title: PANC1PSB_PS04ULAPANC1PSBS321_TGTAGAGGA_L003_R1_001, PANC1, Sorafenib-VSP34I


title: PANC1PSA_PS03ULAPANC1PSAS211_AGGGTGAAG_L003_R1_001, PANC1, Binimetinib-Hydroxychloroquine


title: PANC1PSA_PS03ULAPANC1PSAS236_AATCGGACG_L003_R1_001, PANC1, Ravoxertinib-Hydroxychloroquine

value: Ravoxertinib-Hydroxychloroquine


title: RNA-seq striatum, MOR-LPS, male, replicate 13-2

description: Library name: RNA_Striatum_MOR-LPS_M_13-2


title: MED4 uninfected Control Standard Light 0h Replicate 3

description:
Library name: Ctr-0h-3
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 0h Replicate 3


title: PANC1PSA_PS03ULAPANC1PSAS203_CGACTATGA_L003_R1_001, PANC1, Refametinib-VSP34I


title: PANC1PSA_PS03ULAPANC1PSAS202_CTATTCGGT_L003_R1_001, PANC1, Dabrafenib-VSP34I


title: RNA-seq striatum, MOR-LPS, female, replicate 7-1

description: Library name: RNA_Striatum_MOR-LPS_F_7-1


title: PANC1PSA_PS03ULAPANC1PSAS201_ATGGTGCGA_L003_R1_001, PANC1, Ulixertinib-Hydroxychloroquine


title: PANC1PSB_PS04ULAPANC1PSBS354_TCAGACGGT_L003_R1_001, PANC1, Hydroxychloroquine-Alone


title: MED4 uninfected Control Standard Light 0h Replicate 2

description:
Library name: Ctr-0h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 0h Replicate 2


title: RNA-seq striatum, MOR-LPS, female, replicate 16-4

description: Library name: RNA_Striatum_MOR-LPS_F_16-4


title: PANC1PSA_PS03ULAPANC1PSAS199_TACTATCGG_L003_R1_001, PANC1, AZD0364-Hydroxychloroquine


title: PANC1PSB_PS04ULAPANC1PSBS342_TCTCACATC_L003_R1_001, PANC1, Hydroxychloroquine-Alone


title: MED4 uninfected Control Standard Light 0h Replicate 1

description:
Library name: Ctr-0h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 0h Replicate 1


title: PANC1PSA_PS03ULAPANC1PSAS246_CCGTAAGCT_L003_R1_001, PANC1, Hydroxychloroquine-Alone


title: PANC1PSA_PS03ULAPANC1PSAS234_GCTGTTTCA_L003_R1_001, PANC1, Hydroxychloroquine-Alone


title: RNA-seq striatum, MOR-LPS, female, replicate 16-2

description: Library name: RNA_Striatum_MOR-LPS_F_16-2


title: MED4 uninfected Control High Light 24h Replicate 3

description:
Library name: Ctr-hl-24h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 24h Replicate 3

value: High Light


title: RNA-seq striatum, MOR-SAL, female, replicate 15-2

description: Library name: RNA_Striatum_MOR-SAL_F_15-2

value: MOR-SAL


title: PANC1PSA_PS03ULAPANC1PSAS222_GGAAAGTCC_L003_R1_001, PANC1, VSP34I-Alone


title: PANC1PSA_PS03ULAPANC1PSAS258_GAGAACAAG_L003_R1_001, PANC1, Hydroxychloroquine-Alone


title: RNA-seq striatum, MOR-LPS, female, replicate 16-0

description: Library name: RNA_Striatum_MOR-LPS_F_16-0


title: PANC1PSA_PS03ULAPANC1PSAS210_GTTCACTCT_L003_R1_001, PANC1, VSP34I-Alone


title: MED4 uninfected Control High Light 24h Replicate 2

description:
Library name: Ctr-hl-24h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 24h Replicate 2

value: prokaryotic cell

value: WT


title: PANC1PSA_PS03ULAPANC1PSAS198_ATACAGCAC_L003_R1_001, PANC1, VSP34I-Alone


title: RNA-seq striatum, MOR-SAL, female, replicate 15-0

description: Library name: RNA_Striatum_MOR-SAL_F_15-0


title: RNA-seq striatum, MOR-LPS, female, replicate 15-3

description: Library name: RNA_Striatum_MOR-LPS_F_15-3


title: MED4 uninfected Control High Light 24h Replicate 1

description:
Library name: Ctr-hl-24h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 24h Replicate 1

value: Control


title: ASPC1PSB_PS02ULAASPC1PSBS189_ATTCAGGTC_L003_R1_001, ASPC1, Cobimetinib-VSP34I


title: ASPC1PSB_PS02ULAASPC1PSBS190_TTTCTAGCC_L003_R1_001, ASPC1, Ravoxertinib-VSP34I


title: ASPC1PSB_PS02ULAASPC1PSBS188_ACCAGAAAG_L003_R1_001, ASPC1, Trametinib-Hydroxychloroquine


title: MED4 uninfected Control High Light 8h Replicate 3

description:
Library name: Ctr-hl-8h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 8h Replicate 3


title: MED4 uninfected Control Standard Light 4h Replicate 1

description:
Library name: Ctr-4h-1
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 4h Replicate 1

value: Standard Light


title: ASPC1PSB_PS02ULAASPC1PSBS187_GATCGGAAC_L003_R1_001, ASPC1, GDC0879-Hydroxychloroquine


title: RNA-seq striatum, MOR-LPS, female, replicate 15-1

description: Library name: RNA_Striatum_MOR-LPS_F_15-1

value: wild type


title: RNA-seq striatum, MOR-LPS, female, replicate 12-2

description: Library name: RNA_Striatum_MOR-LPS_F_12-2


title: ASPC1PSB_PS02ULAASPC1PSBS178_CACAGCATG_L003_R1_001, ASPC1, RAF709-VSP34I

value: PDA tumor


title: MED4 uninfected Control High Light 8h Replicate 2

description:
Library name: Ctr-hl-8h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 8h Replicate 2


title: ASPC1PSB_PS02ULAASPC1PSBS176_AGGCCTAAT_L003_R1_001, ASPC1, Selumetinib-Hydroxychloroquine


title: RNA-seq striatum, MOR-LPS, female, replicate 12-0

description: Library name: RNA_Striatum_MOR-LPS_F_12-0


title: ASPC1PSB_PS02ULAASPC1PSBS174_GTTGGATCC_L003_R1_001, ASPC1, Sorafenib-Hydroxychloroquine

value: Sorafenib-Hydroxychloroquine


title: MED4 uninfected Control High Light 8h Replicate 1

description:
Library name: Ctr-hl-8h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 8h Replicate 1


title: RNA-seq striatum, MOR-LPS, male, replicate 8-1

description: Library name: RNA_Striatum_MOR-LPS_M_8-1


title: ASPC1PSB_PS02ULAASPC1PSBS166_CTCATTGAC_L003_R1_001, ASPC1, PLX8394-VSP34I


title: RNA-seq hypothalamus, SAL-SAL, male, replicate 5-3

description: Library name: RNA_Hypothalamus_SAL-SAL_M_5-3

source_name: hypothalamus

value: hypothalamus

value: SAL-SAL


title: ASPC1PSB_PS02ULAASPC1PSBS165_CATCGCAGT_L003_R1_001, ASPC1, Binimetinib-VSP34I


title: MED4 uninfected Control Standard Light 4h Replicate 2

description:
Library name: Ctr-4h-2
MED4 uninfected Control, Standard Light (45 µmol photons m⁻² s⁻¹), 4h Replicate 2


title: ASPC1PSB_PS02ULAASPC1PSBS164_CTAGACCAA_L003_R1_001, ASPC1, SCH772984-Hydroxychloroquine


title: MED4 uninfected Control High Light 4h Replicate 3

description:
Library name: Ctr-hl-4h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 4h Replicate 3


title: RNA-seq hypothalamus, SAL-SAL, male, replicate 5-1

description: Library name: RNA_Hypothalamus_SAL-SAL_M_5-1


title: ASPC1PSB_PS02ULAASPC1PSBS155_AGATTGGCG_L003_R1_001, ASPC1, Ulixertinib-VSP34I


title: MED4 uninfected Control High Light 4h Replicate 2

description:
Library name: Ctr-hl-4h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 4h Replicate 2


title: ASPC1PSB_PS02ULAASPC1PSBS153_GTTTTGCTG_L003_R1_001, ASPC1, AZD0364-VSP34I


title: PANC1PSA_PS03ULAPANC1PSAS270_GCGTTGGTA_L003_R1_001, PANC1, Sorafenib-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-SAL, male, replicate 3-2

description: Library name: RNA_Hypothalamus_SAL-SAL_M_3-2


title: ASPC1PSB_PS02ULAASPC1PSBS152_TACGAGCGT_L003_R1_001, ASPC1, Refamatinib-Hydroxychloroquine

value: Refamatinib-Hydroxychloroquine


title: ASPC1PSB_PS02ULAASPC1PSBS151_GGATGTAGA_L003_R1_001, ASPC1, Dabrafenib-Hydroxychloroquine

value: Dabrafenib-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-SAL, male, replicate 11-1

description: Library name: RNA_Hypothalamus_SAL-SAL_M_11-1


title: MED4 uninfected Control High Light 4h Replicate 1

description:
Library name: Ctr-hl-4h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 4h Replicate 1


title: ASPC1PSB_PS02ULAASPC1PSBS143_CATCCGTAT_L003_R1_001, ASPC1, Trametinib-VSP34I


title: MED4 uninfected Control High Light 2h Replicate 3

description:
Library name: Ctr-hl-2h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 2h Replicate 3


title: ASPC1PSB_PS02ULAASPC1PSBS142_GTAGACGTG_L003_R1_001, ASPC1, GDC0879-VSP34I


title: MED4 uninfected Control High Light 2h Replicate 2

description:
Library name: Ctr-hl-2h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 2h Replicate 2


title: RNA-seq hypothalamus, SAL-SAL, male, replicate 1-3

description: Library name: RNA_Hypothalamus_SAL-SAL_M_1-3


title: ASPC1PSB_PS02ULAASPC1PSBS140_TACTACTCC_L003_R1_001, ASPC1, Ravoxertinib-Hydroxychloroquine


title: ASPC1PSB_PS02ULAASPC1PSBS131_CTGGTTTTC_L003_R1_001, ASPC1, Selumetinib-VSP34I


title: ASPC1PSB_PS02ULAASPC1PSBS139_GCGTACTAG_L003_R1_001, ASPC1, Cobimetinib-Hydroxychloroquine

value: Cobimetinib-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-SAL, male, replicate 1-1

description: Library name: RNA_Hypothalamus_SAL-SAL_M_1-1


title: MED4 uninfected Control High Light 2h Replicate 1

description:
Library name: Ctr-hl-2h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 2h Replicate 1


title: RNA-seq hypothalamus, SAL-SAL, female, replicate 9-4

description: Library name: RNA_Hypothalamus_SAL-SAL_F_9-4


title: MED4 uninfected Control High Light 1h Replicate 3

description:
Library name: Ctr-hl-1h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 1h Replicate 3


title: ASPC1PSB_PS02ULAASPC1PSBS129_CGGACAGAT_L003_R1_001, ASPC1, Sorafenib-VSP34I


title: ASPC1PSB_PS02ULAASPC1PSBS119_GGGTCACAA_L003_R1_001, ASPC1, SCH772984-VSP34I


title: ASPC1PSB_PS02ULAASPC1PSBS128_CGACAGGTT_L003_R1_001, ASPC1, RAF709-Hydroxychloroquine


title: MED4 uninfected Control High Light 1h Replicate 2

description:
Library name: Ctr-hl-1h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 1h Replicate 2


title: ASPC1PSB_PS02ULAASPC1PSBS115_CAGTAGTAC_L003_R1_001, ASPC1, Binimetinib-Hydroxychloroquine

value: Binimetinib-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-SAL, female, replicate 4-3

description: Library name: RNA_Hypothalamus_SAL-SAL_F_4-3


title: RNA-seq hypothalamus, SAL-SAL, female, replicate 4-1

description: Library name: RNA_Hypothalamus_SAL-SAL_F_4-1


title: MED4 uninfected Control High Light 1h Replicate 1

description:
Library name: Ctr-hl-1h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 1h Replicate 1


title: ASPC1PSB_PS02ULAASPC1PSBS105_ATACACGAG_L003_R1_001, ASPC1, Ulixertinib-Hydroxychloroquine

value: Ulixertinib-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-SAL, female, replicate 10-3

description: Library name: RNA_Hypothalamus_SAL-SAL_F_10-3


title: MED4 uninfected Control High Light 0.5h Replicate 3

description:
Library name: Ctr-hl-05h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 0.5h Replicate 3


title: ASPC1PSB_PS02ULAASPC1PSBS103_AGAGTGTTC_L003_R1_001, ASPC1, AZD0364-Hydroxychloroquine


title: ASPC1PSB_PS02ULAASPC1PSBS162_TAGTCCGTA_L003_R1_001, ASPC1, Hydroxychloroquine-Alone

value: Hydroxychloroquine-Alone


title: RNA-seq hypothalamus, SAL-SAL, female, replicate 10-1

description: Library name: RNA_Hypothalamus_SAL-SAL_F_10-1


title: ASPC1PSB_PS02ULAASPC1PSBS150_AAAGCGTCT_L003_R1_001, ASPC1, Hydroxychloroquine-Alone


title: MED4 uninfected Control High Light 0.5h Replicate 2

description:
Library name: Ctr-hl-05h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 0.5h Replicate 2

value: High Light


title: elav[null]_fne[null]_rep1

status: Public on Jun 18 2026

first: David

middle: W. J.

last: McQuarrie

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medicine, Cornell University

description: Library name: Sample7

data_processing:
Sequencing quality was assessed using a standard quality-control pipeline. Adapter sequences were removed with Trim Galore (v0.6.7), and reads were aligned to the D. melanogaster dm6 reference genome using STAR (v2.7.11a). Gene-level counts were generated with FeatureCounts (v2.0.8) and used for differential gene expression analysis with DESeq2 (v1.40.2) under default parameters.
Assembly: dm6
Supplementary files format and content: tab-delimited text file with counts for each sample replicate

organism: Drosophila melanogaster

source_name: Embryo

extract_protocol:
RNA was extracted with Trizol followed by phenol chloroform extraction.
mRNA was enriched from total RNA by poly(A) selection. Sequencing libraries were constructed by Novogene (UK) Company Limited using their standard Illumina-compatible mRNA library preparation protocol (Plant and Animal Eukaryotic mRNA, WOBI) and sequenced on an Illumina NovaSeq X Plus system.

value: Embryo

value: elav[null] fne[null] rep1


title: ASPC1PSB_PS02ULAASPC1PSBS138_TCCAACACG_L003_R1_001, ASPC1, Hydroxychloroquine-Alone


title: MED4 uninfected Control High Light 0.5h Replicate 1

description:
Library name: Ctr-hl-05h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 0.5h Replicate 1

value: prokaryotic cell

value: WT


title: RNA-seq hypothalamus, SAL-LPS, male, replicate 3-3

description: Library name: RNA_Hypothalamus_SAL-LPS_M_3-3

value: SAL-LPS


title: ASPC1PSB_PS02ULAASPC1PSBS126_TCCGGTTGA_L003_R1_001, ASPC1, VSP34I-Alone


title: ASPC1PSB_PS02ULAASPC1PSBS114_CATGAAGTC_L003_R1_001, ASPC1, VSP34I-Alone


title: MED4 uninfected Control High Light 0h Replicate 3

description:
Library name: Ctr-hl-0h-3
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 0h Replicate 3

value: Control


title: RNA-seq hypothalamus, SAL-LPS, male, replicate 11-0

description: Library name: RNA_Hypothalamus_SAL-LPS_M_11-0

value: wild type


title: ASPC1PSA_PS01ULAASPC1PSAS94_TGTTGATGC_L003_R1_001, ASPC1, Ravoxertinib-VSP34I

value: PDA tumor


title: MED4 uninfected Control High Light 0h Replicate 2

description:
Library name: Ctr-hl-0h-2
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 0h Replicate 2


title: RNA-seq hypothalamus, SAL-LPS, male, replicate 1-4

description: Library name: RNA_Hypothalamus_SAL-LPS_M_1-4

value: hypothalamus


title: RNA-seq hypothalamus, SAL-LPS, male, replicate 1-2

description: Library name: RNA_Hypothalamus_SAL-LPS_M_1-2


title: ASPC1PSB_PS02ULAASPC1PSBS102_TCCGCAGAA_L003_R1_001, ASPC1, VSP34I-Alone


title: ASPC1PSA_PS01ULAASPC1PSAS93_TAACCCGTC_L003_R1_001, ASPC1, Cobimetinib-VSP34I


title: ASPC1PSA_PS01ULAASPC1PSAS92_AAGCCTGAC_L003_R1_001, ASPC1, Trametinib-Hydroxychloroquine

value: Trametinib-Hydroxychloroquine


title: MED4 uninfected Control High Light 0h Replicate 1

description:
Library name: Ctr-hl-0h-1
MED4 uninfected Control, High Light (200–250 µmol photons m⁻² s⁻¹), 0h Replicate 1


title: RNA-seq hypothalamus, SAL-LPS, male, replicate 1-0

description: Library name: RNA_Hypothalamus_SAL-LPS_M_1-0


title: ASPC1PSA_PS01ULAASPC1PSAS91_GTCATGTAG_L003_R1_001, ASPC1, GDC0879-Hydroxychloroquine


title: ASPC1PSA_PS01ULAASPC1PSAS82_AAAACGGCG_L003_R1_001, ASPC1, RAF709-VSP34I


title: MED4 P-SSP7 Infected Standard Light 24h Replicate 3

description:
Library name: Inf-24h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 24h Replicate 3

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7

value: Standard Light


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 9-3

description: Library name: RNA_Hypothalamus_SAL-LPS_F_9-3


title: ASPC1PSA_PS01ULAASPC1PSAS80_TGAAGCATC_L003_R1_001, ASPC1, Selumetinib-Hydroxychloroquine

value: Selumetinib-Hydroxychloroquine


title: ASPC1PSA_PS01ULAASPC1PSAS70_ATTGCGACT_L003_R1_001, ASPC1, PLX8394-VSP34I


title: MED4 P-SSP7 Infected Standard Light 24h Replicate 2

description:
Library name: Inf-24h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 24h Replicate 2


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 9-1

description: Library name: RNA_Hypothalamus_SAL-LPS_F_9-1


title: ASPC1PSA_PS01ULAASPC1PSAS78_GGGCTTCAA_L003_R1_001, ASPC1, Sorafenib-Hydroxychloroquine

value: Sorafenib-Hydroxychloroquine


title: ASPC1PSA_PS01ULAASPC1PSAS69_ACTGCATGG_L003_R1_001, ASPC1, Binimetinib-VSP34I


title: MED4 P-SSP7 Infected Standard Light 24h Replicate 1

description:
Library name: Inf-24h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 24h Replicate 1


title: ASPC1PSA_PS01ULAASPC1PSAS68_CTCGTTACC_L003_R1_001, ASPC1, SCH772984-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 4-4

description: Library name: RNA_Hypothalamus_SAL-LPS_F_4-4


title: ASPC1PSA_PS01ULAASPC1PSAS59_CACCTACAA_L003_R1_001, ASPC1, Ulixertinib-VSP34I


title: MED4 P-SSP7 Infected Standard Light 8h Replicate 3

description:
Library name: Inf-8h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 8h Replicate 3


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 3-1

description: Library name: RNA_Hypothalamus_SAL-LPS_F_3-1


title: ASPC1PSA_PS01ULAASPC1PSAS56_GCTTCGACA_L003_R1_001, ASPC1, Refamatinib-Hydroxychloroquine

value: Refamatinib-Hydroxychloroquine


title: MED4 P-SSP7 Infected Standard Light 8h Replicate 2

description:
Library name: Inf-8h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 8h Replicate 2


title: ASPC1PSA_PS01ULAASPC1PSAS55_TTTTCTGCG_L003_R1_001, ASPC1, Dabrafenib-Hydroxychloroquine

value: Dabrafenib-Hydroxychloroquine


title: ASPC1PSA_PS01ULAASPC1PSAS46_TTAACCCCG_L003_R1_001, ASPC1, GDC0879-VSP34I


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 10-2

description: Library name: RNA_Hypothalamus_SAL-LPS_F_10-2


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 10-4

description: Library name: RNA_Hypothalamus_SAL-LPS_F_10-4


title: MED4 P-SSP7 Infected Standard Light 8h Replicate 1

description:
Library name: Inf-8h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 8h Replicate 1


title: ASPC1PSA_PS01ULAASPC1PSAS47_TCCAGACTA_L003_R1_001, ASPC1, Trametinib-VSP34I


title: ASPC1PSA_PS01ULAASPC1PSAS44_GTGGCCAAA_L003_R1_001, ASPC1, Ravoxertinib-Hydroxychloroquine

value: Ravoxertinib-Hydroxychloroquine


title: MED4 P-SSP7 Infected Standard Light 4h Replicate 3

description:
Library name: Inf-4h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 4h Replicate 3


title: ASPC1PSB_PS02ULAASPC1PSBS116_AGCGCATTG_L003_R1_001, ASPC1, PLX8394-Hydroxychloroquine


title: RNA-seq hypothalamus, SAL-LPS, female, replicate 10-0

description: Library name: RNA_Hypothalamus_SAL-LPS_F_10-0


title: ASPC1PSA_PS01ULAASPC1PSAS43_CATTGTTGG_L003_R1_001, ASPC1, Cobimetinib-Hydroxychloroquine

value: Cobimetinib-Hydroxychloroquine


title: E18 n3 Xenium

type: RNA

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

hyb_protocol: Samples were incubated in a probe solution for 16-24 hours at 50°C. For all datasets, the solution contained the same set of 347-gene targeting probes: 247 from the 10x Genomics predesigned mouse brain panel, and 100 from a custom add-on that allowed better resolution of key cell types within the ventricular-subventricular zone. Nonspecific probe binding was next washed off via PBS-T, a 30-minute incubation in post-hybridization buffer at 37°C, and additional PBS-T washes. Ligation of the hybridized probes was performed by incubating the samples in ligation enzymes for 2 hours at 37°C. After a series of PBS-T washes, the ligated probes were amplified via rolling circle amplification; to achieve this, samples were incubated with amplification enzyme for 2 hours at 30°C. These steps were next followed by autoflorescence quenching and nuclear staining.

scan_protocol: Image processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system. Data was acquired on instrument software versions 2.0.1.0 to 3.1.0.0, and onboard analysis versions 2.0.0.10 to 3.1.0.4.

data_processing: Following on-instrument analysis, all datasets were run through 10x Genomics Xenium Ranger v3 software (xeniumranger resegment function) with settings as recommended by the manufacturer to assign transcripts to the closest nucleus within a maximum distance of 2 µm.

label: Xenium probe set

source_name: Brain (embryonic coronal brain sections containing the lateral ventricles)

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Brain tissue was collected from mice at E15, E18, and P2. Samples were fixed in 4% paraformaldehyde (Electron Microscopy Sciences) for 24 hours at 4°C and subsequently cryopreserved in 30% sucrose for 48 hours. Samples were embedded in O.C.T. (Tissue-Tek) and cryosectioned coronally onto Xenium slides (chemistry v1) at a thickness of 10 μm. Afterwards, all samples were processed as per the Xenium worflow for fixed frozen tissue, which involved washes in PBS, water, 100% ethanol, and 70% ethanol, followed by decrosslinking.

treatment_protocol: E15 samples were collected from pregnant mice that were intraperitoneally administered 200 µL of 0.1% BSA in PBS 48 hours prior to collection.

tag: tissue preservation method

value: Other

tag: preservation method

value: Fixed frozen


title: ASPC1PSA_PS01ULAASPC1PSAS35_CTCCCCTTT_L003_R1_001, ASPC1, Selumetinib-VSP34I

tag: treatment


title: ASPC1PSA_PS01ULAASPC1PSAS57_TATGGCGAT_L003_R1_001, ASPC1, AZD0364-VSP34I


title: MED4 P-SSP7 Infected Standard Light 4h Replicate 2

description:
Library name: Inf-4h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 4h Replicate 2

value: prokaryotic cell

value: WT


title: ASPC1PSA_PS01ULAASPC1PSAS33_CTGATGTCT_L003_R1_001, ASPC1, Sorafenib-VSP34I


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 8-0

description: Library name: RNA_Hypothalamus_MOR-SAL_M_8-0

value: MOR-SAL


title: ASPC1PSB_PS02ULAASPC1PSBS107_GTGAGAAAG_L003_R1_001, ASPC1, Refamatinib-VSP34I


title: ASPC1PSA_PS01ULAASPC1PSAS32_ACGGTAGAC_L003_R1_001, ASPC1, RAF709-Hydroxychloroquine


title: ASPC1PSB_PS02ULAASPC1PSBS106_CAATTCTCG_L003_R1_001, ASPC1, Dabrafenib-VSP34I


title: MED4 P-SSP7 Infected Standard Light 4h Replicate 1

description:
Library name: Inf-4h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 4h Replicate 1


title: ASPC1PSA_PS01ULAASPC1PSAS23_GCCAAACGA_L003_R1_001, ASPC1, SCH772984-VSP34I


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 6-3

description: Library name: RNA_Hypothalamus_MOR-SAL_M_6-3

value: wild type


title: ASPC1PSA_PS01ULAASPC1PSAS20_TATGTCAGC_L003_R1_001, ASPC1, PLX8394-Hydroxychloroquine

value: PDA tumor


title: MED4 P-SSP7 Infected Standard Light 2h Replicate 3

description:
Library name: Inf-2h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 2h Replicate 3


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 6-1

description: Library name: RNA_Hypothalamus_MOR-SAL_M_6-1

value: hypothalamus


title: ASPC1PSA_PS01ULAASPC1PSAS19_TAGTTCGGG_L003_R1_001, ASPC1, Binimetinib-Hydroxychloroquine

value: Binimetinib-Hydroxychloroquine


title: MED4 P-SSP7 Infected Standard Light 2h Replicate 2

description:
Library name: Inf-2h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 2h Replicate 2

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: ASPC1PSA_PS01ULAASPC1PSAS11_TGGAAGTGT_L003_R1_001, ASPC1, Refamatinib-VSP34I


title: ASPC1PSA_PS01ULAASPC1PSAS10_CTTTCACCT_L003_R1_001, ASPC1, Dabrafenib-VSP34I


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 17-0

description: Library name: RNA_Hypothalamus_MOR-SAL_M_17-0


title: ASPC1PSA_PS01ULAASPC1PSAS9_GTCTTAAGC_L003_R1_001, ASPC1, Ulixertinib-Hydroxychloroquine

value: Ulixertinib-Hydroxychloroquine


title: Cerebellum, Sedentary Wt, 116

city: Albany

first: J

middle: Andrew

last: Berglund

address: 1400 Washington Avenue

department: Biology

institute: University at Albany, State University of New York

description: Library name: 116

data_processing:
After sequencing the quality of the fastq files were checked using the program FastQC (version 0.11.9).
FASTQ files with >20% adapter content were trimmed using fastp (version 0.24.0) and quality re-confirmed using FastQC
STAR (version 2.7.10a) was used to align the fastq files to the GRcm39/mm39 genome with the --quantModeGeneCounts option added to count the reads per gene.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited text files contain the raw read count abundances for each sample.

source_name: Cerebellum

extract_protocol:
Total RNA was extracted from the cerebellum using TRIzol reagent (Invitrogen). The tissues were first homogenized with RNase-free beads and then processed using the RNeasy kit (Qiagen), followed by DNase treatment.
The NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit (New England Biolabs) was used to prepare RNA-seq libraries, with a total of 250 ng input RNA from each sample. The manufacturer’s protocols were followed, with the following exceptions: 40× adaptor dilutions were used, and 13 cycles of library amplification were performed. The resulting libraries were pooled in equimolar amounts, quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs), quality checked via capillary electrophoresis on the 5300 fragment analyzer (Agilent Bioanalzyer) using the DNF-474 HS NGS kit (Agilent). Libraries with sufficient quantity were loaded into P2 flow cell 1000/2000 by Illumina and were sequenced using paired-end, 151 base pair sequencing on the Illumina NextSeq 2000 sequencer at the University at Albany RNA Institute. All datasets had total read depths greater than 90 million paired-end reads.

value: Cerebellum

value: Wt

value: Sedentary


title: ASPC1PSA_PS01ULAASPC1PSAS7_CGAGTAGAG_L003_R1_001, ASPC1, AZD0364-Hydroxychloroquine


title: ASPC1PSA_PS01ULAASPC1PSAS54_ACCCTCTCA_L003_R1_001, ASPC1, Hydroxychloroquine-Alone

value: Hydroxychloroquine-Alone


title: MED4 P-SSP7 Infected Standard Light 1h Replicate 3

description:
Library name: Inf-1h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 1h Replicate 3

value: Standard Light


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 14-1

description: Library name: RNA_Hypothalamus_MOR-SAL_M_14-1


title: ASPC1PSA_PS01ULAASPC1PSAS66_CCAATACAC_L003_R1_001, ASPC1, Hydroxychloroquine-Alone


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 13-3

description: Library name: RNA_Hypothalamus_MOR-SAL_M_13-3


title: ASPC1PSA_PS01ULAASPC1PSAS42_TCTATCTCC_L003_R1_001, ASPC1, Hydroxychloroquine-Alone


title: RNA-seq hypothalamus, MOR-SAL, male, replicate 13-1

description: Library name: RNA_Hypothalamus_MOR-SAL_M_13-1


title: MED4 P-SSP7 Infected Standard Light 1h Replicate 2

description:
Library name: Inf-1h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 1h Replicate 2


title: ASPC1PSA_PS01ULAASPC1PSAS30_AGATTCCTG_L003_R1_001, ASPC1, VSP34I-Alone


title: ASPC1PSA_PS01ULAASPC1PSAS18_CCCAATAGC_L003_R1_001, ASPC1, VSP34I-Alone


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 7-2

description: Library name: RNA_Hypothalamus_MOR-SAL_F_7-2


title: RNA_RHVA_T3_NKcell

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the human genome by Rsubread version 1.32.2
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function
Genes were identified using Gencode annotation v35
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: Peripheral blood

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (QIAGEN, cat. no. 217084) following manufacturer's protocol
Libraries were made following manufactur's protocol for Illumina's TruSeq Total Stranded RNA kitwith Ribo-zero Gold

value: peripheral blood

tag: donor

value: RHVA

tag: progressed to t1d

value: Yes

tag: Sex

value: M

tag: age

tag: data set

value: B

tag: sequencing batch data set a

tag: sequencing batch data set b

value: NK lymphocyte cells


title: ASPC1PSA_PS01ULAASPC1PSAS6_TCCTTTGCC_L003_R1_001, ASPC1, VSP34I-Alone

tag: cell line


title: MED4 P-SSP7 Infected Standard Light 1h Replicate 1

description:
Library name: Inf-1h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 1h Replicate 1

tag: cell type

value: prokaryotic cell

tag: genotype

value: WT


title: MED4 P-SSP7 Infected Standard Light 0.5h Replicate 3

description:
Library name: Inf-05h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 0.5h Replicate 3


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 18-0

description: Library name: RNA_Hypothalamus_MOR-SAL_F_18-0

tag: tissue

value: hypothalamus

value: wild type

value: MOR-SAL


title: RNA_RHVA_T3_nCD8

value: CD8+ T lymphocyte cells


title: RNA_RHVA_T3_Bcell

value: B lymphocyte cells


title: RNA_RHVA_T1_NKcell


title: MED4 P-SSP7 Infected Standard Light 0.5h Replicate 2

description:
Library name: Inf-05h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 0.5h Replicate 2

tag: agent

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 16-3

description: Library name: RNA_Hypothalamus_MOR-SAL_F_16-3


title: RNA_RHVA_T1_nCD8


title: MED4 P-SSP7 Infected Standard Light 0.5h Replicate 1

description:
Library name: Inf-05h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 0.5h Replicate 1

tag: light regime


title: MED4 P-SSP7 Infected Standard Light 2h Replicate 1

description:
Library name: Inf-2h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 2h Replicate 1

tag: time point


title: RNA_NIFA_T3_NKcell

value: NIFA


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 16-1

description: Library name: RNA_Hypothalamus_MOR-SAL_F_16-1


title: RNA_RHVA_T1_Bcell


title: MED4 P-SSP7 Infected Standard Light 0h Replicate 3

description:
Library name: Inf-0h-3
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 0h Replicate 3


title: RNA_NIFA_T3_nCD8


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 15-2

description: Library name: RNA_Hypothalamus_MOR-SAL_F_15-2


title: RNA_NIFA_T3_Bcell


title: MED4 P-SSP7 Infected Standard Light 0h Replicate 2

description:
Library name: Inf-0h-2
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 0h Replicate 2


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 15-0

description: Library name: RNA_Hypothalamus_MOR-SAL_F_15-0


title: RNA_NIFA_T1_nCD8


title: MED4 P-SSP7 Infected Standard Light 0h Replicate 1

description:
Library name: Inf-0h-1
MED4 P-SSP7 Infected MOI=10,  Standard Light (45 µmol photons m⁻² s⁻¹), 0h Replicate 1


title: RNA_NIFA_T1_NKcell


title: RNA_MASA_T3_NKcell

value: MASA


title: MED4 P-SSP7 Infected High Light 24h Replicate 3

description:
Library name: Inf-hl-24h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 24h Replicate 3

value: High Light


title: RNA_MASA_T3_nCD8

value: peripheral blood


title: RNA-seq hypothalamus, MOR-SAL, female, replicate 12-1

description: Library name: RNA_Hypothalamus_MOR-SAL_F_12-1


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 8-3

description: Library name: RNA_Hypothalamus_MOR-LPS_M_8-3

value: MOR-LPS


title: RNA_MASA_T3_Bcell

value: Yes


title: MED4 P-SSP7 Infected High Light 24h Replicate 2

description:
Library name: Inf-hl-24h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 24h Replicate 2


title: RNA_MASA_T1_NKcell

value: M


title: RNA_MASA_T1_Bcell

value: B


title: RNA_MASA_T1_nCD8


title: MED4 P-SSP7 Infected High Light 24h Replicate 1

description:
Library name: Inf-hl-24h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 24h Replicate 1


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 6-2

description: Library name: RNA_Hypothalamus_MOR-LPS_M_6-2


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 6-0

description: Library name: RNA_Hypothalamus_MOR-LPS_M_6-0


title: RNA_KIHY_T3_NKcell

value: KIHY

value: No

value: F

value: NK lymphocyte cells


title: MED4 P-SSP7 Infected High Light 8h Replicate 3

description:
Library name: Inf-hl-8h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 8h Replicate 3

value: prokaryotic cell

value: WT


title: RNA_NIFA_T1_Bcell


title: RNA_KIHY_T3_nCD8

value: CD8+ T lymphocyte cells


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 17-1

description: Library name: RNA_Hypothalamus_MOR-LPS_M_17-1

value: hypothalamus

value: wild type


title: RNA_KIHY_T3_Bcell

value: B lymphocyte cells


title: MED4 P-SSP7 Infected High Light 8h Replicate 2

description:
Library name: Inf-hl-8h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 8h Replicate 2

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 14-4

description: Library name: RNA_Hypothalamus_MOR-LPS_M_14-4


title: RNA_KIHY_T1_nCD8


title: RNA_KIHY_T1_NKcell


title: RNA_KIHY_T1_Bcell


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 14-0

description: Library name: RNA_Hypothalamus_MOR-LPS_M_14-0


title: MED4 P-SSP7 Infected High Light 8h Replicate 1

description:
Library name: Inf-hl-8h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 8h Replicate 1

value: High Light


title: RNA-seq hypothalamus, MOR-LPS, male, replicate 13-2

description: Library name: RNA_Hypothalamus_MOR-LPS_M_13-2


title: RNA_KIBU_T3_nCD8

value: peripheral blood

value: KIBU


title: RNA_KIBU_T3_NKcell


title: MED4 P-SSP7 Infected High Light 4h Replicate 3

description:
Library name: Inf-hl-4h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 4h Replicate 3


title: MED4 P-SSP7 Infected High Light 4h Replicate 2

description:
Library name: Inf-hl-4h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 4h Replicate 2


title: RNA_KIBU_T1_NKcell


title: RNA_KIBU_T1_nCD8


title: RNA_KIBU_T3_Bcell


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 7-1

description: Library name: RNA_Hypothalamus_MOR-LPS_F_7-1

value: MOR-LPS


title: RNA_KIBU_T1_Bcell


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 18-1

description: Library name: RNA_Hypothalamus_MOR-LPS_F_18-1


title: RNA_JAAD_T3_nCD8

value: JAAD

value: M


title: MED4 P-SSP7 Infected High Light 2h Replicate 3

description:
Library name: Inf-hl-2h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 2h Replicate 3


title: RNA_JAAD_T3_NKcell

value: B


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 16-4

description: Library name: RNA_Hypothalamus_MOR-LPS_F_16-4


title: RNA_JAAD_T3_Bcell

value: No


title: MED4 P-SSP7 Infected High Light 2h Replicate 2

description:
Library name: Inf-hl-2h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 2h Replicate 2


title: RNA_JAAD_T1_NKcell


title: RNA_JAAD_T1_Bcell


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 16-0

description: Library name: RNA_Hypothalamus_MOR-LPS_F_16-0


title: RNA_JAAD_T1_nCD8


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 16-2

description: Library name: RNA_Hypothalamus_MOR-LPS_F_16-2


title: MED4 P-SSP7 Infected High Light 2h Replicate 1

description:
Library name: Inf-hl-2h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 2h Replicate 1


title: RNA_EMRA_T3_NKcell

value: EMRA

value: Yes

value: F


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 15-3

description: Library name: RNA_Hypothalamus_MOR-LPS_F_15-3


title: RNA_EMRA_T3_nCD8


title: MED4 P-SSP7 Infected High Light 1h Replicate 3

description:
Library name: Inf-hl-1h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 1h Replicate 3

value: prokaryotic cell

value: WT


title: RNA_EMRA_T3_Bcell


title: MED4 P-SSP7 Infected High Light 1h Replicate 2

description:
Library name: Inf-hl-1h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 1h Replicate 2


title: RNA_EMRA_T1_nCD8

value: CD8+ T lymphocyte cells


title: RNA_EMRA_T1_NKcell

value: NK lymphocyte cells


title: RNA_EMRA_T1_Bcell

value: B lymphocyte cells


title: MED4 P-SSP7 Infected High Light 1h Replicate 1

description:
Library name: Inf-hl-1h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 1h Replicate 1

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: RNA-seq hippocampus, SAL-SAL, male, replicate 5-3

description: Library name: RNA_Hippo_SAL-SAL_M_5-3

source_name: hippocampus

value: hippocampus

value: wild type

value: SAL-SAL


title: RNA-seq hypothalamus, MOR-LPS, female, replicate 15-1

description: Library name: RNA_Hypothalamus_MOR-LPS_F_15-1

value: hypothalamus

value: MOR-LPS


title: RNA_CHAN_T3_NKcell

value: peripheral blood

value: CHAN


title: RNA_CHAN_T3_nCD8

value: No

value: B


title: MED4 P-SSP7 Infected High Light 0.5h Replicate 3

description:
Library name: Inf-hl-05h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 0.5h Replicate 3

value: High Light


title: RNA-seq hippocampus, SAL-SAL, male, replicate 5-1

description: Library name: RNA_Hippo_SAL-SAL_M_5-1


title: RNA-seq hippocampus, SAL-SAL, male, replicate 3-4

description: Library name: RNA_Hippo_SAL-SAL_M_3-4


title: RNA_CHAN_T1_Bcell

value: F


title: MED4 P-SSP7 Infected High Light 0.5h Replicate 1

description:
Library name: Inf-hl-05h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 0.5h Replicate 1

value: prokaryotic cell


title: RNA-seq hippocampus, SAL-SAL, male, replicate 3-2

description: Library name: RNA_Hippo_SAL-SAL_M_3-2


title: MED4 P-SSP7 Infected High Light 0h Replicate 3

description:
Library name: Inf-hl-0h-3
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 0h Replicate 3

value: WT


title: RNA_COAH_T1_NKcell

value: COAH

value: M


title: MED4 P-SSP7 Infected High Light 0h Replicate 2

description:
Library name: Inf-hl-0h-2
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 0h Replicate 2


title: RNA_COAH_T1_Bcell

value: B lymphocyte cells


title: MED4 P-SSP7 Infected Standard Light Exposure 6h after Dark 24h Replicate 3

description:
Library name: Inf-dk-32h-3
MED4 P-SSP7 Infected MOI=10, Standard Light Exposure (45 µmol photons m⁻² s⁻¹) 6h, after Dark 24h, Replicate 3

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7

value: Dark to Standard Light


title: RNA-seq hippocampus, SAL-SAL, male, replicate 1-1

description: Library name: RNA_Hippo_SAL-SAL_M_1-1

value: hippocampus

value: wild type


title: MED4 P-SSP7 Infected High Light 0h Replicate 1

description:
Library name: Inf-hl-0h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 0h Replicate 1


title: RNA_AYMA_T3_NKcell

value: AYMA

value: Yes

value: NK lymphocyte cells


title: RNA_AYMA_T3_Bcell

value: peripheral blood


title: RNA-seq hippocampus, SAL-SAL, female, replicate 9-4

description: Library name: RNA_Hippo_SAL-SAL_F_9-4

value: SAL-SAL


title: RNA_AYMA_T3_nCD8

value: B

value: CD8+ T lymphocyte cells


title: MED4 P-SSP7 Infected Standard Light Exposure 6h after Dark 24h Replicate 2

description:
Library name: Inf-dk-32h-2
MED4 P-SSP7 Infected MOI=10, Standard Light Exposure (45 µmol photons m⁻² s⁻¹) 6h, after Dark 24h, Replicate 2


title: RNA_AYMA_T1_nCD8


title: MED4 P-SSP7 Infected Standard Light Exposure 6h after Dark 24h Replicate 1

description:
Library name: Inf-dk-32h-1
MED4 P-SSP7 Infected MOI=10, Standard Light Exposure (45 µmol photons m⁻² s⁻¹) 6h, after Dark 24h, Replicate 1


title: RNA-seq hippocampus, SAL-SAL, female, replicate 9-2

description: Library name: RNA_Hippo_SAL-SAL_F_9-2


title: RNA_AYMA_T1_Bcell


title: RNA-seq hippocampus, SAL-SAL, female, replicate 9-0

description: Library name: RNA_Hippo_SAL-SAL_F_9-0


title: RNA_RHVA_T3_nCD4

value: RHVA

value: A

value: CD4+ T lymphocyte cells


title: MED4 P-SSP7 Infected Standard Light Exposure 2h after Dark 24h Replicate 3

description:
Library name: Inf-dk-26h-3
MED4 P-SSP7 Infected MOI=10, Standard Light Exposure (45 µmol photons m⁻² s⁻¹) 2h, after Dark 24h, Replicate 3

value: prokaryotic cell

value: WT


title: RNA_RHVA_T1_nCD4

value: M


title: RNA-seq hippocampus, SAL-SAL, female, replicate 4-3

description: Library name: RNA_Hippo_SAL-SAL_F_4-3


title: RNA_NIFA_T3_nCD4

value: NIFA


title: MED4 P-SSP7 Infected Standard Light Exposure 2h after Dark 24h Replicate 2

description:
Library name: Inf-dk-26h-2
MED4 P-SSP7 Infected MOI=10, Standard Light Exposure (45 µmol photons m⁻² s⁻¹) 2h, after Dark 24h, Replicate 2

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7

value: Dark to Standard Light


title: RNA-seq hippocampus, SAL-SAL, female, replicate 4-1

description: Library name: RNA_Hippo_SAL-SAL_F_4-1

value: hippocampus

value: wild type


title: RNA_NIFA_T1_nCD4

value: Yes


title: RNA_AYMA_T1_NKcell

value: AYMA

value: NK lymphocyte cells


title: MED4 P-SSP7 Infected Standard Light Exposure 2h after Dark 24h Replicate 1

description:
Library name: Inf-dk-26h-1
MED4 P-SSP7 Infected MOI=10, Standard Light Exposure (45 µmol photons m⁻² s⁻¹) 2h, after Dark 24h, Replicate 1


title: RNA_MASA_T3_nCD4

value: peripheral blood

value: MASA


title: RNA-seq hippocampus, SAL-SAL, female, replicate 10-3

description: Library name: RNA_Hippo_SAL-SAL_F_10-3

value: SAL-SAL


title: MED4 P-SSP7 Infected Dark 24h Replicate 3

description:
Library name: Inf-dk-24h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 24h Replicate 3

value: Dark


title: RNA_KIHY_T1_nCD4

value: KIHY

value: No

value: F

value: A


title: MED4 P-SSP7 Infected High Light 4h Replicate 1

description:
Library name: Inf-hl-4h-1
MED4 P-SSP7 Infected MOI=10, High Light (200–250 µmol photons m⁻² s⁻¹), 4h Replicate 1

value: prokaryotic cell

value: WT

value: High Light


title: RNA_KIHY_T3_nCD4

value: CD4+ T lymphocyte cells


title: RNA_MASA_T1_nCD4

value: M


title: RNA_KIBU_T3_nCD4

value: KIBU


title: MED4 P-SSP7 Infected Dark 24h Replicate 2

description:
Library name: Inf-dk-24h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 24h Replicate 2

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: RNA_KIBU_T1_nCD4


title: RNA-seq hippocampus, SAL-LPS, male, replicate 5-2

description: Library name: RNA_Hippo_SAL-LPS_M_5-2

value: hippocampus

value: wild type

value: SAL-LPS


title: CRH neuron_Ctr2

city: Cold Spring Harbor

first: Yue

last: Wu

address: One Bungtown Rd, Demerec RM 120

department: Cancer and Neuroscience

institute: Cold Spring Harbor Laboratory

description: Library name: Sample2

data_processing:
JupyterHub platform
Quality control: FastQC, Trimming: cutadapt wrapper; Alignment: STAR; featureCounts;
Quantification: Differential expression: DESeq2 and visulization in JupyterHub with R kernel
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Brain neuron

growth_protocol: Primay CRH neurons were freshly isolated from mouse brain and FACSed

extract_protocol:
Total RNA was harvested using Trizol. 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NextSeq2000 P1 PE150 mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: Brain neuron

value: CRH neuron

value: FACSed CRH neuron

value: PBS


title: RNA-seq hippocampus, SAL-LPS, male, replicate 3-3

description: Library name: RNA_Hippo_SAL-LPS_M_3-3


title: RNA_JAAD_T3_nCD4

value: peripheral blood

value: JAAD

value: No


title: RNA_JAAD_T1_nCD4

value: A


title: MED4 P-SSP7 Infected Dark 24h Replicate 1

description:
Library name: Inf-dk-24h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 24h Replicate 1

value: prokaryotic cell

value: WT

value: Dark


title: RNA-seq hippocampus, SAL-LPS, male, replicate 11-0

description: Library name: RNA_Hippo_SAL-LPS_M_11-0


title: RNA_COAH_T3_nCD8

value: COAH

value: M

value: B

value: CD8+ T lymphocyte cells


title: RNA_EMRA_T3_nCD4

value: EMRA

value: Yes

value: F

value: CD4+ T lymphocyte cells


title: RNA_EMRA_T1_nCD4


title: RNA-seq hippocampus, SAL-LPS, male, replicate 1-4

description: Library name: RNA_Hippo_SAL-LPS_M_1-4

value: hippocampus

value: wild type

value: SAL-LPS


title: MED4 P-SSP7 Infected Dark 8h Replicate 3

description:
Library name: Inf-dk-8h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 8h Replicate 3

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: RNA_CHAN_T3_nCD4

value: peripheral blood

value: CHAN

value: No


title: RNA_CHAN_T1_nCD4

value: A


title: MED4 P-SSP7 Infected Dark 8h Replicate 2

description:
Library name: Inf-dk-8h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 8h Replicate 2

value: prokaryotic cell

value: WT

value: Dark


title: RNA-seq hippocampus, SAL-LPS, male, replicate 1-2

description: Library name: RNA_Hippo_SAL-LPS_M_1-2


title: RNA_COAH_T3_Bcell

value: COAH

value: M

value: B

value: B lymphocyte cells


title: MED4 P-SSP7 Infected Dark 8h Replicate 1

description:
Library name: Inf-dk-8h-1
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 8h Replicate 1


title: RNA_COAH_T3_nCD4


title: RNA_COAH_T1_nCD4


title: RNA-seq hippocampus, SAL-LPS, male, replicate 1-0

description: Library name: RNA_Hippo_SAL-LPS_M_1-0


title: RNA_AYMA_T3_nCD4

value: AYMA

value: Yes


title: RNA-seq hippocampus, SAL-LPS, female, replicate 9-3

description: Library name: RNA_Hippo_SAL-LPS_F_9-3

value: hippocampus


title: RNA_CHAN_T1_nCD8

value: F

value: CD8+ T lymphocyte cells


title: RNA_CHAN_T3_Bcell


title: RNA_CHAN_T1_NKcell

value: NK lymphocyte cells


title: MED4 P-SSP7 Infected Dark 4h Replicate 3

description:
Library name: Inf-dk-4h-3
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 4h Replicate 3

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986, Prochlorococcus phage P-SSP7


title: RNA_AYMA_T1_nCD4

value: peripheral blood

value: CD4+ T lymphocyte cells


title: MED4 P-SSP7 Infected Dark 4h Replicate 2

description:
Library name: Inf-dk-4h-2
MED4 P-SSP7 Infected MOI=10, Dark (0 µmol photons m⁻² s⁻¹), 4h Replicate 2


title: ATAC-seq_NP_5

data_processing:
FASTQ files were output using standard Illumina protocols and software.
FASTQ files  from technical replicates are first concatenated
ATAC-seq reads were aligned to the human genome assembly (hg38) using Bowti2 v2.2.5
For each sample, mitochondrial reads are removed from the aligned bam using the removeChrom python script developed by Harvard Informatics (https://github.com/harvardinformatics/ATAC-seq), and only properly paired reads were used for downstream analysis
PCR duplicates were then removed using Picard MarkDuplicates
Peak calling was then carried out using MCAS2  and ATAC-seq reads overlapping the peaks were summarized using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files; columns represent genomic location and the number of reads mapping to the peaks

extract_protocol: As previously described   Corces et al.  2017(OMNI ATAC-seq protocol)

value: Peripheral blood

value: Non-progressors


title: ATAC-seq_NP_4