title: HCT_mRNA_DOX_r3

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file

growth_protocol: HCT-116 degron cell lines: RAD21- mAID-mClover1 and HCT116-OsTIR1-MED26-AID2 were cultured in McCoy's 5A medium supplemented with L-Glutamine (Gibco), 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), at 37 °C; 5% CO2.  ES (E14) RAD213 and CTCF degron4 cell lines were cultured in knock-out DMEM (Gibco), ES cell qualified FBS (ATCC), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 1:10,000LIF (10,000x) on 0.1% gelatin coated dishes at 37 °C; 5% CO2.  Primary WT and Myc knockout B cells were derived from Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (Sigma) (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice).  The deletion of floxed allele was checked as previously5 with PCR or intracellular staining of Myc protein. B cells were isolated from spleen of WT and KO mice, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies) and activated for 4 hours with 50 mg/ml LPS and 2.5 ng/ml IL4 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco), at 37 °C; 5% CO2 B220 positive primary bone marrow B cells were derived from C57BL/6J wild-type mice, enriched with CD45R (B220) MicroBeads Kit (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec). Splenic B cells were derived from C57BL/6J wild-type mice immunized with a keyhole limpet haemocyanin (KLH; 25 µg/footpad, Sigma-Aldrich) in the presence of 10% CFA adjuvant (Sigma-Aldrich). After 5 days B cells were isolated from spleen, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies), and activated for 72 hours with 50 mg/ml LPS, 2.5 ng/ml IL4 and anti-CD180 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco),  at 37 °C; 5% CO2.  CH12 B lymphoma cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco), at 37 °C; 5% CO2. LNK (NK cell line) cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 10 mM HEPES, 1:100 NEAA (Gibco), 1:100 sodium pyruvate (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 200 IU/ml IL-2 (Sigma-Aldrich). Skin cells for scRNA-Seq: whole epidermis from mouse neonates. Keratinocytes were isolated from Fvb neonate (P0-P2) skin (n = 2) as described in Lichti et al., 20086. Cells were subjected to MACS Dead Cell removal kit (Miltenyi Biotech) using the manufacturer’s protocol. Skin cells for mRNA half-lives estimation: primary keratinocyte. Skins from a pool of Fvb neonatal mice were collected at P0-P2 and incubated overnight in 2.0 U/mL Dispase II (Sigma) in KBM-Gold (Lonza) on an end-over-end rotator. The following day, skins were washed twice in 1x PBS (Sigma), and epidermises were separated from dermises. Epidermises were placed basal side down and floated in pre-warmed 0.25% Trypsin-EDTA (Thermo Scientific) for 20min on an orbital shaker at room temperature. An equal volume of pre-warmed 2.5mg/mL Soybean Trypsin Inhibitor (Thermo Scientific) was added to finish trypsinization, and epidermises were rubbed vigorously against bottom of plate using curved forceps to dislodge keratinocytes. Dislodged cells were pooled into a tube on ice in KBM-Gold. Pooled cells were pipetted ~40 times with a 10ml serological pipette and strained with a 100um filter before pelleting cells at 300xg for 10min at 4°C. Cells were resuspended in 4.5mL KBM-Gold per epidermis and cell count was obtained using Cellometer ViaStain AOPI Solution (Sigma). The cells were subjected to Percoll (GE LifeSciences; ratio of 10X PBS:Percoll:KBM-Gold media was 1:4:5, where the cells were at a concentration of 1 million per mL of final volume) gradient ultracentrifugation using a swinging bucket rotor (11,000 rpm for 42 minutes at 4°C) to separate the basal and suprabasal fractions. The cells at the top band were suprabasal cells and separated from the pellet at the bottom of the tube which were basal cells. The basal cell sample was carefully pipetted out, washed twice with 4°C 1x PBS, seeded onto collagen-coated (Collage Type I; Corning) 6-well plates at 1x106 cells per well, and incubated at 37°C overnight to allow cells to attach to the plate before proceeding with experiments.  Mast cells: Mouse bone marrow-derived mast cells (BMMC) were differentiated from the marrow of tibias and femurs of C57/BL6 mice and cultured for 8 weeks in RPMI 1640 containing 10% FBS, 1M HEPES, 100 U/mL penicillin, 100 μg/mL streptomycin, 4 mM l-glutamine, 1 mM sodium pyruvate, non-essential amino acids, 50 μM 2-mercaptoethanol, IL-3 (20 ng/mL) and stem cell factor (SCF) (20 ng/mL). The purity of mast cells was monitored by assessing the expression of the receptors for SCF (CD117;Kit) and for IgE (FcεRI) by flow cytometry. By the end of 6-8 weeks in culture more than 98% of the cultured population was FcεRI+/CD117+ double-posiHCT-116 cells, obtained from the American Type Culture Collection  (ATCC),  were cultured in McCoy's 5A medium supplemented with L-Glutamine (Gibco), 10% fetal bovine serum (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
HCT-116 cells (0.5 million) were lysed in 100 µl of lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen). RNA was isolated and treated with DNase following the manufacturer’s protocol. scRNA-Seq was performed using 10x Genomics system
RNA-Seq:NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NovaSeq6000 (Illumina). scRNA-Seq:Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeqXplus machine (Illumina).

treatment_protocol: HCT-116 cells were treated with 200 nM doxorubicin (Sigma) for 24 hours. Following the 24-hour treatment, the doxorubicin-containing medium was removed from the cells. To ensure complete removal of any residual doxorubicin, the cells were washed thoroughly 3x with PBS. The cells were then allowed to recover over a period of 6 days in doxorubicin-free conditions, with the medium being replaced with fresh one, three times during this period. After the 6-day recovery period, the cells were subjected to flow cytometry, microscopy, bulk mRNA sequencing, and scRNA-Seq

tag: cell type

value: colorectal carcinoma cell

value: WT

value: 200nM Doxorubicin 24h


title: HCT_mRNA_DOX_r2

status: Public on Oct 09 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: genotype

tag: treatment


title: 2-1-25_8h_DMSO_3_18_22_S21

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

data_processing:
Base calling was performed by bcl2fastq v 2.20
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10a
Gene counts were performed with RSEM v1.3.3
Normalization was performed with DESeq2 v1.31.15
Assembly: Genome Reference Consortium Human Build 38 reference genome version 107
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the STAR alignments

source_name: HCT116 ATF4 deficient

growth_protocol: HCT116 and HCT116 ATF4 deficient cells were grown in McCoys medium, supplmented with Newborn Calf Serum (NBCS) and Fetal Bovine Serum (FBS) is a 3:1 ratio to give 12% serum, and 90 units/ml penicillin, 90µg/ml streptomycin

extract_protocol:
EZ-10 DNAaway RNA Miniprep (Bio Basic)
The Illumina Stranded mRNA prep, Ligation Reference Guide (1000000124518) was used. The Illumina Poly(A) Capture (2004893), cDNA synthesis (2004895) and RNA PRE Ligation (20040897) kits were used to purify polyadenylated mRNA and synthesize first and second strand cDNA. Anchors were ligated using the IDT for Illumina RNA index Anchors (200040899), and samples were indexed using the IDT for Illumina DNA/RNA UD Indexes Set A (20026121).

treatment_protocol: Cells were treated for 2 or 8 hours with 30µM Isoginkgetin, 2µM Thapsigargin, an equivalent volume of DMSO or left untreated.

value: HCT116 ATF4 deficient

tag: duration of_chemical_exposure

value: 8 hours

tag: chemical

value: DMSO

tag: batch

tag: technical control

value: FALSE

tag: reference rna

tag: solvent control

value: TRUE

tag: chemical exposure_date

tag: cell seeding_date

tag: library well


title: H1

city: Beijing

first: Junchao

last: Jiang

address: Dongdan Santiao, Doncheng District

country: China

institute: Peking Union Medical College

data_processing:
CLC Genomics Workbench V11.0.1
Assembly: mm10
Supplementary files format and content: Text files include RPKM values

source_name: lung tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing library.
RNA library for RNA-seq was prepared using SMARTER Mrna-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: lung tissue


title: 2-1-25_2h_Tg_3_18_22_S18

value: 2 hour

value: Thapsigargin


title: HCT_mRNA_UTR_r3


title: HCT_mRNA_DOX_r1


title: HCT_mRNA_UTR_r2


title: 2-1-25_2h_DMSO_3_31_22_S9

value: 2 hours


title: HCT_mRNA_UTR_r1


title: H4


title: 2-1-25_2h_DMSO_3_23_22_S31


title: S16-MAFG-MITF-3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

library_source: genomic

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to human genome GRCh38 using BOWTIE2 (v2.4.1).
Peak Calling was performed using IgG as control to identify regions of open chromatin  using MACS2 (v 2.1.1.20160309).
Only peaks significantly enriched than background with q <0.01 were considered confident and subjected for downstream analysis.
Peaks were annotated by ChIPseeker (v1.32.1) with gene model TxDb.Hsapiens.UCSC.hg38.knownGene (v 3.15.0).
Consensus peak identifiers were obtained by GenomicRanges (v1.48.0).
bigWig files were generated using the deeptool bamCoverage function.
narrowPeak files were generted using MACS2 v2 with default setings.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak(except for Input sample)
Library strategy: Cut&Run

molecule: genomic DNA

source_name: Melanoma

growth_protocol: Cell lines were cultured in DMEM containing 5% FBS and 1% Pen-Strep at 37˚C in a humidified atmosphere containing 5% CO2

extract_protocol:
At approximately 80% confluency, adherent cells were scraped from the plate, washed with PBS, and counted. Isolation of cell nuclei and experimental procedures were performed as described using the CUTANA ChIC/CUT&RUN Kit version 4.0. Approximately 250,000 cells were used for each sample.
All resulting DNA from each sample was used for library preparation using the KAPA HyperPrep Kit

value: Melanoma

value: Cancer

value: overexpress MAFG, treat with anti-MITF


title: S15-MAFG-MITF-2


title: S14-MAFG-MITF-1


title: 2-1-25_8h_DMSO_3_23_22_S10


title: S12-MAFG-MAFG-2

value: overexpress MAFG, treat with anti-MAFG


title: S13-MAFG-MAFG-3


title: S11-MAFG-MAFG-1


title: 2-1-25_2h_Tg_3_25_22_S14


title: 2-1-25_2h_Tg_3_31_22_S16


title: Replicate 4, 5 Days

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: Leptospira interrogans serovar manilae, NZ_CP011931.1
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Leptospira interrogans serovar Manilae

source_name: serovar Manilae strain L495

extract_protocol:
Total RNA was extracted from biofilm or planktonic cells. Cells were collected by centrifugation for 15 min at 3000xg at 4°C and resuspended in 1mL TRIzol
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit following manufacturer's protocol

value: planktonic culture

tag: strain


title: Replicate 2, 3 Weeks

value: biofilm


title: Replicate 3, 3 Weeks


title: Replicate 1, 3 Weeks


title: Replicate 4, 3 Weeks


title: 2-1-25_2h_Tg_3_23_22_S38


title: S09-MAFG-IgG

value: overexpress MAFG, treat with anti-rabbit IgG


title: Replicate 3, 5 Days


title: S10-MAFG-H3k4me3

value: overexpress MAFG, treat with anti-histone H3K4me3


title: Replicate 2, 5 Days


title: ChIP_ES_SRF_KO_Rad21

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

country: Germany

institute: MPI Molecular Genetics

data_processing:
The ChIP-seq reads were aligned to the reference genome using bowtie2 (version 2.2.4) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig (bw) format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
Assembly: mm10
Supplementary files format and content: Hi-C: Contact matrices in h5 (at 20kb resolution, corrected using Knight and Ruiz (KR) balancing algorithm) and hic formats. For normalization, merging or other processing steps, HiCExplorer (h5) or Juicer tools (hic) can be used.
Supplementary files format and content: ChIP-seq: bigWig files representing read density

organism: Mus musculus

extract_protocol:
ChIP experiments were carried out as previously described [Koch, 2017]. SRF ChIP-seq was performed in WT ESCs and in CM cells on differentiation day 4. Control SRF ChIP-seq was performed in SRF KO ES cells after 48 of treatment with 250 nM dTAG13. SRF ChIP-qPCR was performed in CTCF KO ES cells after 24 hours of treatment with 250 nM dTAG13. CTCF ChIP-qPCR was performed in SRF KO ES cells after 24 hours of treatment with 250 nM dTAG13. Crosslinking was performed directly on cells in the medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 50 mM Hepes pH 7.8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10minutes at room temperature, while shaking. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5 M glycine and 5minutes incubation. Cells were washed twice with cold PBS, scraped in cold PBS containing 0.05% Triton X-100, and pelleted in aliquots of 5x107. For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10minutes. The solubilized chromatin was then pooled and mixed thoroughly. The chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at-80°C until use. 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 5 washing steps with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.

value: embryonic stem cells

value: SRF KO

value: untreated


title: 2-1-25_2h_DMSO_3_18_22_S11

value: HCT116 ATF4 deficient

value: DMSO

value: FALSE


title: 2-1-25_2h_DMSO_3_25_22_S46

value: TRUE


title: DPH15_L3

city: Eilat

first: Eran

last: Yanowski

address: North beach

country: Israel

institute: National Center for Mariculture

data_processing:
cDNA libraries for NGS were prepared using the TruSeq RNA Library Preparation Kit (Illumina) and  prepared libraries were sequenced on an Illumina NextSeq 500.
The processed reads were subjected to a Blast search against the Blastnr (non-redundant) database
Deseq2 analysis from Count-matrix was performed using UTAP (Kohen, R. et al., 2019)
Assembly: Blastnr
Supplementary files format and content: Tab-delimited text file includes raw counts and normalized counts for each sample.

organism: Thunnus thynnus

source_name: Whole larvae

growth_protocol: The experimental system consisted of nine 1500 l polypropylene V-tanks that tested three rotifer (Brachionus rotundiformis) DHA levels (2.0, 3.6 and 10.9 mg DHA g-1 DW rotifer) on BFT larvae from 2-15 dph in replicates of 3 tanks per treatment

extract_protocol:
tissues were homogenized in Tri-reagent using a tissue homogenizer. Chloroform was added, and the mixture was centrifuged to separate the phases. The aqueous phase containing RNA was collected, and RNA was precipitated with isopropanol. After washing with ethanol, the RNA pellet was air-dried and dissolved in RNase-free water. RNA quality, quantity and integrity of the isolated RNA were assessed using a NanoDrop spectrophotometer and an Agilent Bioanalyzer.
cDNA libraries for NGS were prepared using the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: Prior to being fed to the larvae, the rotifers were enriched on one of three enrichment preparations containing 5.5, 15 or 32% DHA of total fatty acids (TFA). These were produced by different dilutions of a 32% DHA of TFA of a custom  preparation

value: Whole larvae

value: Thunnus thynnus

value: WT

value: 15 days post-hatch, Low DHA level, sample #3


title: DPH15_M3

value: 15 days post-hatch, Medium DHA level, sample #3


title: ChIP_ES_WT_Rad21


title: DPH15_H3

value: 15 days post-hatch, High DHA level, sample #3


title: S06-GFP-MITF-1

value: Melanoma

value: Cancer

value: overexpress GFP, treat with anti-MITF


title: Replicate 1, 5 Days

value: planktonic culture


title: S05-GFP-MAFG-3

value: overexpress GFP, treat with anti-MAFG


title: DPH15_H2

value: 15 days post-hatch, High DHA level, sample #2


title: DPH15_L2

value: 15 days post-hatch, Low DHA level, sample #2


title: ChIP_ES_SRF_KO_SRF_control_rep2

value: embryonic stem cells

value: SRF KO

value: untreated


title: S04-GFP-MAFG-2


title: HiC_ES_SRF_KO_12hours_dTAG13

data_processing:
The Hi-C reads were mapped using HiC-Pro (3.1.0) with the following bowtie2 arguments: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder (global); --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder (local). Genome fragment file for the HiC-Pro was generated for the following ligation sites: GATCGATC, GAATGATC, GATTGATC, GACTGATC, GAGTGATC, GATCAATC, GATCATTC, GATCACTC, GATCAGTC, GAATAATC, GAATATTC, GAATACTC, GAATAGTC, GATTAATC, GATTATTC, GATTACTC, GATTAGTC, GACTAATC, GACTATTC, GACTACTC, GACTAGTC, GAGTAATC, GAGTATTC, GAGTACTC, GAGTAGTC and using MIN_INSERT_SIZE = 100, MAX_INSERT_SIZE = 900. Independent replicates were mapped individually and valid pairs (allValidPairs file generated by HiC-Pro) were concatenated to generate contact matrices. Hi-C contact matrices in h5 format at 10 kb resolution were generated using hicBuildMartix tool from HiCExplorer (3.7.2) [Ramirez, 2018] with the following arguments: --minMappingQuality 10 --skipDuplicationCheck -rs ResSites_combined.bed -seq GATC GAATC GATTC GACTC GAGTC --danglingSequence GATC AAT ATT ACT AGT -bs 10000. hicBuildMatrix input sam files containing the mapped reads were generated by converting the allValidPairs into the sam format using custom scripts. The file containing all restriction cut sites (ResSites_combined.bed) was created using hicFindRestSite tool with the argument --searchPattern GATC, followed by the argument --searchPattern GA.TC and concatenation of the output bed files. For independent replicates, the h5 format matrices were merged using hicSumMatrices tool from HiCExplorer. The merged matrices were corrected using hicCorrectMatrix tool with the Knight-Ruiz (KR) matrix balancing algorithm (--correctionMethod KR). Hi-C contact matrices in hic format for Juicebox and Juicer tools analyses were created from a list of all valid pairs (allValidPairs file generated by HiC-Pro; for independent replicates, allValidPairs files were concatenated) using hicpro2juicebox.sh script from the HiC-Pro Utilities with the following argument: -j juicer_tools.2.20.00.jar.
Assembly: mm10
Supplementary files format and content: Hi-C: Contact matrices in h5 (at 20kb resolution, corrected using Knight and Ruiz (KR) balancing algorithm) and hic formats. For normalization, merging or other processing steps, HiCExplorer (h5) or Juicer tools (hic) can be used.
Supplementary files format and content: ChIP-seq: bigWig files representing read density

extract_protocol:
HiC was performed using a total of 5x105 cells per sample. Cells were treated and collected as follows. For non-differentiated ESCs, 2x106 Srf-flox1 cells encoding endogenous CTCF-FKBP were deprived of feeder cells and transfected with 25 μg GFP (Addgene, #11150) or 25 μg GFP-Cre plasmid (Addgene, #13776) using Lipofectamine 2000. 24 hours after the transfection, the medium was refreshed and supplemented with 250 nM dTAG13 or the matching volume of DMSO. After 24 hours of incubation with dTAG13 or DMSO, 5x105 of GFP-positive WT (GFP + DMSO), SRF KO (GFP-Cre + DMSO), CTCF KO (GFP + dTAG13), or SRF/CTCF dKO (GFP-Cre + dTAG13) cells were sorted using FACS Aria II. For dTAG13-induced SRF KO ESCs, 1x106 F1G4 cells encoding endogenous SRF-FKBP were treated with 250 nM dTAG13 for 24 hours, and 5x105 cells were collected using FACS Aria II. For CM cells, Srf-flex1 cells carrying H2B-mCherry (WT) or H2B-Venus-T2A-Cre (KO) were trypsinized at day 4 of cardiac mesoderm differentiation, and 5x105 cells expressing mCherry or Venus were sorted on a FACS Aria II. Sorted cells were crosslinked using Low Input crosslinking protocol provided by the Arima-HiC Kit user guide (A 160134 v01) and frozen in liquid nitrogen.
Proximally-ligated DNA was generated using Arima-HiC Kit (A510008) following the manufacturer’s protocol. HiC library was generated using KAPA Hyper Prep Kit (Roche, 07962312001) and KAPA single-indexed adapters (Roche, 08005702001) according to Arima’s Library preparation user guide. Covaris S220 was used for DNA shearing. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips. Paired-end sequencing was performed on the HiSeq 4000 with 2x 75 bp read length or on the NovaSeq 6000 with 2x 100 bp read length.


title: DPH15_H1

value: 15 days post-hatch, High DHA level, sample #1


title: DPH10_M3

value: Whole larvae

value: 10 days post-hatch_Medium DHA level_sample#3


title: S08-GFP-MITF-3


title: DPH15_M1

value: Thunnus thynnus

value: WT

value: 15 days post-hatch, Medium DHA level, sample #1


title: DPH15_L1

value: 15 days post-hatch, Low DHA level, sample #1


title: DPH15_M2

value: 15 days post-hatch, Medium DHA level, sample #2


title: S02-GFP-H3k4me3

value: Melanoma

value: Cancer

value: overexpress GFP, treat with anti-histone H3K4me3


title: DPH10_L2

value: 10 days post-hatch_Low DHA level_sample#2


title: S03-GFP-MAFG-1

value: overexpress GFP, treat with anti-MAFG


title: S07-GFP-MITF-2

value: overexpress GFP, treat with anti-MITF


title: 293T, Delta_M, fraction 13 to 14, 48 hpi

city: New York

first: Chuan-Tien

last: Hung

state: New York

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Trimming, alignment, and quantification were all performed in Partek Flow v10.0. The reference genome was generated by concatenating the hg38 (release 110) using STAR (v2.7.11a). Counts were generated with Homo sapiens annotation (Partek E/M). Normalization was performed by transcripts per kilobase million. Unaligned reads were then aligned to rHPIV3-JS-G.luc-EGFP (Genbank: KY295925) using BWA-MEM (BWA v0.7.17). Transcriptional gradient analyses was performed using IGVtools on samples with >100 aligned reads.
Assembly: hg38 and rHPIV3-JS-G.luc-EGFP (KY295925)
Supplementary files format and content: The processed data file includes normalized gene counts (shown by TPM values) for each sample.

organism:
Homo sapiens
Human respirovirus 3

source_name: HEK 293T

growth_protocol: HEK 293T cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted and on-column DNase I treated using Direct-zol RNA Miniprep kit.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: HEK 293T

value: human embryonic kidney cell

value: HPIV3 delta M infected


title: 293T, Delta_M, fraction 11 to 12, 48 hpi


title: S01-GFP-IgG

value: overexpress GFP, treat with anti-rabbit IgG


title: 293T, Delta_M, fraction 15 to 16, 48 hpi


title: DPH10_L3

value: Whole larvae

value: 10 days post-hatch_Low DHA level_sample#3


title: 293T, Delta_M, fraction 9 to 10, 48 hpi


title: RNA_BM_CD34_UNKNOWN_NT_S26

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

data_processing:
Short read quality control was performed using FastQC v0.11.5
The sequencing adapters and low-quality end reads were trimmed using Trim Galore v0.6.6
STAR v.2.7.9a was used to align the raw reads to GENCODE human reference genome v38. After removing low quality alignments, (mapq < 15)
featureCounts v2.0.1 was used for gene expression quantification
DESeq2 v1.40.1  was used to identify differentially expressed genes between treatment and control groups
Gene set enrichment analysis (GSEA) was performed using fgsea v1.26.0 and Bader lab gene sets, updated August 2022 (http://baderlab.org/GeneSets)
Assembly: GENCODE human reference genome v38
Supplementary files format and content: .CSV
Supplementary files format and content: Differentially expressed genes and GSEA analysis across treated and non-treated groups

source_name: Peripheral Blood

growth_protocol: Cells were cultured in X-Vivo media supplemented with cytokines and BIT

extract_protocol:
RNA was extracted using Qiagen’s RNeasy micro kit 3ng of RNA was used for construction of sequencing libraries
Library preparation completed using TakaraStranded Total RNA pico input mammalian V3 kit
RNA sequencing was performed using Illumina Novaseq 6000 in pair end 2x150 pb resulting in ~77-96M reads/sample

treatment_protocol: Cells were enriched for LSCs and HSPCs by cell sorting for ROS levels or CD34 expression, prior to treatment with DENSpm

value: Peripheral Blood

value: Normal BM

value: CD34 Hematopoietic stem cells

value: 0uM DENSpm


title: 293T, Delta_M, fraction 7 to 8, 48 hpi


title: DPH10_M1

value: Thunnus thynnus

value: WT

value: 10 days post-hatch, Medium DHA level, sample #1


title: DPH10_H3

value: 10 days post-hatch, High DHA level, sample #3


title: DPH10_L1

value: 10 days post-hatch_Low DHA level_sample#1


title: RNA_BM_CD34_UNKNOWN_DENSPM_10uM_24h_S25

value: 10uM DENSpm


title: DPH10_H1

value: 10 days post-hatch, High DHA level, sample #1


title: 293T, Delta_M, fraction 5 to 6, 48 hpi

value: HEK 293T


title: RNA_BM_CD34_44396_NT_S24


title: DPH5_L3

value: 5 days post-hatch_Low DHA level_sample#3


title: 293T, Delta_M, fraction 3 to 4, 48 hpi

value: human embryonic kidney cell

value: HPIV3 delta M infected


title: DPH10_M2

value: Whole larvae

value: 10 days post-hatch_Medium DHA level_sample#2


title: DPH5_M3

value: 5 days post-hatch_Medium DHA level_sample#3


title: DPH5_L1

value: 5 days post-hatch_Low DHA level_sample#1


title: 293T, WT, fraction 15 to 16, 48 hpi

value: HPIV3-WT infected


title: RNA_BM_CD34_44396_DENSPM_10uM_24h_S23

value: Peripheral Blood

value: Normal BM

value: CD34 Hematopoietic stem cells


title: RNA_BM_CD34_44313_NT_S22

value: 0uM DENSpm


title: DPH5_L2

value: Thunnus thynnus

value: WT

value: 5 days post-hatch_Low DHA level_sample#2


title: DPH5_M2

value: 5 days post-hatch_Medium DHA level_sample#2


title: 293T, WT, fraction 13 to 14, 48 hpi

value: HEK 293T


title: 282476_ROSlow_NT_RNA_S20

value: primary AML

value: ROS low Leukemic stem cells


title: Control4


title: DPH5_H3

value: 5 days post-hatch, High DHA level, sample #1


title: 293T, WT, fraction 11 to 12, 48 hpi

value: human embryonic kidney cell


title: RNA_BM_CD34_44313_DENSPM_10uM_24h_S21

value: 10uM DENSpm


title: 293T, WT, fraction 9 to 10, 48 hpi


title: DPH5_M1

value: Whole larvae

value: 5 days post-hatch_Medium DHA level_sample#1


title: DPH5_H2

value: 5 days post-hatch, High DHA level, sample #2


title: 282476_ROSlow_DENSPM_24h_RNA_S19

value: Peripheral Blood


title: Control2


title: DPH10_H2

value: 10 days post-hatch, High DHA level, sample #2


title: 293T, WT, fraction 7 to 8, 48 hpi

value: HPIV3-WT infected


title: Control3


title: Control1


title: 100394_LOW_NT_24h_S16

value: 0uM DENSpm


title: scRNA_HCT_DOXr2

value: colorectal carcinoma cell

value: 200nM Doxorubicin 24h


title: 293T, WT, fraction 5 to 6, 48 hpi


title: 100394_LOW_DENSPM_24h_S15


title: scRNA_HCT_DOXr1

value: WT


title: scRNA_HCT_UTRr2


title: 293T, WT, fraction 3 to 4, 48 hpi


title: scRNA_HCT_UTRr1


title: 8889_ROSlow_NT_RNA_S12


title: 8889_ROSlow_DENSPM_24h_RNA_S11


title: sample17_Nur77-LCA50-2

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

data_processing:
Sequenced reads were mapped to GrCM38/mm10 using STAR
Read count extraction was performed using Homer’s analyzeRepeats.pl
Read normalization and differential expression were performed with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: T cells

extract_protocol:
RNA was isolated using Qiagen RNA mini  kit.
ultra-low input RNA-Seq cDNA library preparation

treatment_protocol: Naïve CD8+ T cells were first isolated followed by knocking down Nur77 using CRISPR RNP method using synthego gRNA kit followed by activation of T cells using anti-CD3/CD28. Activated wild type T cells (scrambled control) and Nurr77 Knockout (KO) T cells were cultured with different doses of LCA (10uM and 50uM) overnight followed by RNA isolation, library preparation and sequencing.

value: T cells


title: sample16_Nur77-LCA50-1


title: sample14_WT-LCA50-2


title: sample15_WT-LCA50-3


title: sample12_Nur77-LCA10-3


title: 8588_LOW_NT_24h_RNA_S8


title: 8588_LOW_DENSPM_10uM_24h_RNA_S7


title: sample11_Nur77-LCA10-2


title: 543_LOW_DENSPM_10uM_24_RNA_S3


title: sample10_Nur77-LCA10-1


title: sample9_WT-LCA10-3


title: 543_LOW_NT_24h_RNA_S4


title: sample7_WT-LCA10-1


title: sample8_WT-LCA10-2


title: sample5_Nur77-2

value: control


title: sample6_Nur77-3


title: sample18_Nur77-LCA50-3


title: TD5 2

city: brussels

first: MARIA

last: ROJO PARDILLO

address: Rte de Lennik 808, 1070 Anderlecht

country: Belgium

institute: IRIBHM J.E. DUMONT

data_processing:
The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) and sequences were produced using a 200 cycles reagent kit
Paired-end reads were mapped against the human reference genome GRCH38 using STAR_2.5.3a software to generate read alignements for each sample.
After transcripts assembling, gene level counts were obtained using HTSeq-0.9.1 and normalized to 20 million of aligned reads
Assembly: GRCh38.90
Supplementary files format and content: Tab-delimited text files contain normalized counts for each sample

source_name: Thyroid

growth_protocol: TPC1 or TPC1 Dicer1 (+/-) (D11) cell lines were maintained in RPMI medium (52400025, ThermoFisher Scientific) supplemented with 10% fetal bovine serum, 2% penicillin/streptomycin and 1% amphotericin B and cultured at a constant temperature of 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA  was extracted using miRNeasy mini kit (2170004, Qiagen) according to the manufacturer’s instructions.
Indexed cDNA libraries were obtained using the TruSeq Stranded mRNA Sample Prep kit (20020595, Illumina) following manufacturer recommendations.

treatment_protocol: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid (99154, Addgene) transiently transfected into TPC1 with Lipofectamine 3000 (L3000001, ThermoFisher Scientific) according to the manufacturer’s instructions. Target single guided RNA (sgRNA) sequences were identified with an online CRISPR design software (CHOPCHOP). The guide RNA (gRNA) sequence chosen was 5’GCCGTGTTGATTGTGACTCGTGG3’ located in exon 11 of Dicer1.

value: Thyroid

value: TPC1 DICER1 (+/-)

value: PTC papillary thyroid carcinoma

value: DICER (+/-)

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC8


title: sample4_Nur77-1


title: sample3_WT-3


title: TD5 1

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC7


title: sample2_WT-2


title: sample13_WT-LCA50-1


title: sample1_WT-1


title: UDCA, replicate 3

treatment_protocol: 1 million in vitro activated CD8+ T cells were exososed to different bile acids 50uM for unconjugated bile acids and 100uM for conjugated bile acids overnight.

value: UDCA


title: WB1 3

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC6


title: TD5 3

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC9


title: WB1 2

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC5


title: TCDCA, replicate 3

value: TCDCA


title: TCDCA, replicate 2


title: WB1 1

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC4


title: UDCA, replicate 1


title: D11 3

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC3


title: TCA, replicate 3

value: TCA


title: TCA, replicate 2


title: D11 2

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC2


title: TCA, replicate 1

value: T cells


title: DehydroLCA, replicate 3

value: DehydroLCA


title: UDCA, replicate 2


title: DehydroLCA, replicate 2


title: DehydroLCA, replicate 1


title: D11 1

value: Thyroid

value: Heterozygous Dicer1 (+/-) cell lines were established by use of a CRISPR/Cas9 plasmid  transiently transfected into TPC1


title: TCDCA, replicate 1


title: IsoLCA, replicate 3

value: IsoLCA


title: IsoLCA, replicate 2


title: TPC1 3

value: PTC papillary thyroid carcinoma

value: wt


title: scRNA_seq-sepsis

city: Augusta

first: Sergei

last: Bombin

institute: Augusta University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
files were processed with cellranger count tool v7.1.0
Assembly: mm10
Supplementary files format and content: cellranger filtered matrix

source_name: liver

extract_protocol:
Cell suspension obtained from liver was resuspended in PBS (without Ca or Mg) with 0.04% BSA.
libraries were generated according to the manufacturer’s instructions using Chromium Next GEM Single Cell 3ʹReagent Kit v3.1

treatment_protocol: Surgical procedure - cecal ligation and puncture (CLP)

value: liver

value: CLP surgery


title: TPC1 2


title: IsoLCA, replicate 1


title: scRNA_seq-sham

description: 10x Genomics

value: Sham surgery (laparotomy)


title: IsoAlloLCA, replicate 3

value: IsoAlloLCA


title: IsoAlloLCA, replicate 1


title: LCA, replicate 3

value: LCA


title: TPC1 1


title: D11 Dicer1 siRNA TRANSFECTED REPLICATA 2

treatment_protocol: Cells were transiently transfected with 5nM of silencer select Dicer1 siRNA (s23754, ThermoFisher Scientific) or negative control (4390846, ThermoFisher Scientific). siRNA transfection was performed using Lipofectamine RNAiMAX reagent (#13778150, ThermoFisher Scientific) according to the manufacturer’s protocol. total RNA was colelcted four days after transfection.

value: TPC1 DICER1 (+/-)

value: knock down

value: 4 days after transfection


title: iWAT SVF, PBS treated, biol rep 1

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

data_processing:
All libraries were sequenced on the Illumina Novaseq 6000 instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the mouse genome (version: mm10) by TopHat 2 software.
Read count extraction was performed using GFOLD software.
The expression matrix of all samples was subjected to the Bayesian workflow for differential gene modeling based on the “edgeR” and “limma” R packages.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: iWAT SVF

extract_protocol:
Total RNA was isolated from the iWAT SVF using Trizol reagent (Invitrogen; ThermoFisher) according to the manufacturer’s instructions.
RNA-Seq libraries (with each treatment in triplicate) were constructed according to standard Illumina protocols.

value: iWAT SVF

value: PBS


title: iWAT SVF, MHE treated, biol rep 2

value: MHE


title: Control, replicate 3

value: T cells

value: control


title: IsoAlloLCA, replicate 2


title: LCA, replicate 2


title: LCA, replicate 1


title: D11 Dicer1 siRNA TRANSFECTED REPLICATA 1

value: Thyroid

value: DICER (+/-) knock down


title: iWAT SVF, MHE treated, biol rep 1


title: Control, replicate 1


title: iWAT SVF, PBS treated, biol rep 2


title: D11 NEGATIVE CONTROL REPLICATA 3

value: PTC papillary thyroid carcinoma

value: DICER (+/-)


title: D11 NEGATIVE CONTROL REPLICATA 2


title: BAAT-1, HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
barcode5
sample5_barcodes.tsv.gz
sample5_features.tsv.gz
sample5_matrix.mtx.gz

library_source: other

data_processing:
*library strategy: CITE-seq
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the mm10 mouse reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: CellRanger output files:  sample*_barcodes.tsv.gz, sample*_features.tsv.gz, sample*_matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: whole liver

extract_protocol:
Livers were enzymatically digested using 0.5% type IV collagenase and DNase, followed by filtration with 70 µm cell strainers. Immune cells were further purified using 40% isotonic percoll and later incubated with ACK lysis buffer to lyse red blood cells. Immune cells.T cells (CD45hiCD3+) and all remaining immune cells (CD45hi) were sorted from each group, stained with CITE-seq antibodies and then subjected to scRNA-seq. Sorted cells were partitioned into an emulsion of nanoliter-sized droplets using a 10x Genomics Chromium Single Cell Controller and RNA sequencing libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics, Cat# PN-120237). gene expression libraries were generated using 10X Genomics Chromium Single Cell 3’ Library Construction Kits according to manufacturer protocols.
10x Chromium Single cell 3’  Kit cDNA, Illumina Novaseq 6000

value: whole liver

value: AAV-sgBaat

tag: library type

value: HTO

tag: hto

value: TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody


title: control, HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
barcode2
sample2_barcodes.tsv.gz
sample2_features.tsv.gz
sample2_matrix.mtx.gz

value: AAV-sgSCR

value: TotalSeq™-B0075 anti-mouse CD90.2 (Thy1.2) Antibody


title: Ba/F3_focused_screen_raw_file_1

city: Amsterdam

first: Connor

middle: Antonio

last: Richterich

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequence reads were aligned to a reference library (suplementary file), reads containing mismatches removed, and sgRNA distributions quantified and scored using MAGeCK RRA (version 0.5.6)
Reads were demultiplexed based on sample barcodes (see processed datafile for indices) and aligned against reference library (Suplementary file [reference_library.csv])  and reads with missmatches removed (see processed data file. A single file [Raw_Reads.txt] was generated for simplicity)
Processed datafile was used as input file for mageck analysis. Null distribution was generated for calculating p-values based on control sgRNAs within library.
Outputs for mageck sgRNA summaries supplied as supplementary file (MAGeck_sgRNA_summary.tabular)
Supplementary files format and content: Tabular data containing read counts for each sample (demultiplexed based on sample barcode) and sgRNA (aligned against reference library).
Library strategy: CRISPR Screen

growth_protocol: All cells were cultured at 37C and 5% CO2 in RPMI (ThermoFisher #11875093) supplemented with 10% (v/v)  FCS (ThermoFisher #26140079), penicillin-streptomycin (ThermoFisher #15140148) and 0.2ng/mL recombinant murine IL-3 (Immunotools #12340032)

extract_protocol:
DirectPCR Lysis reagent (Viagen Biotech #301-C)
SgRNA sequences were  amplified using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs #M0541S), following the manufacturer’s instructions, using primers containing sample barcodes


title: D11 NON TRANSFECTED REPLICATA 3

value: TPC1 DICER1 (+/-)

tag: cell type


title: D2_CS_8

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

data_processing:
Raw reads from single-end sequencing with a 75 bp read length were processed by trimming the adapter sequences using Cutadapt.
Trimmed reads were mapped to the reference mm10 genome using HISAT.
Duplicate fragments were discarded, retaining only unique reads.
Reads were sorted by chromosomal coordinates using samtools.
We utilized MACS2 (Model-based Analysis of ChIP-Seq) to identify sites of chromatin openness (i.e., peaks) in our ATAC-seq samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing peaks

source_name: Brain

extract_protocol:
Nuclei pellets were resuspended gently in transposition reaction mix (25 µL 2X TD Buffer [Illumina Cat #FC-121-1030], 2.5 µL transposase [Illumina Cat #FC-121-1030] and 22.5 µL nuclease-free water) and incubated at 37℃ for 30 min followed immediately with purification using Qiagen MinElute kit whereby transposed DNA were eluted in 10 µl Elution Buffer. Transposed DNA fragments were amplified initially using 1X NEBnext PCR master mix (New England Labs Cat #M0541), 25 µM customized Nextera PCR primers 1 and 2 and 0.6% final concentration of 100X SYBR Green I (Invitrogen Cat #S-7563) in a thermocycler with the following parameters: 72℃ for 5 min; 98℃ for 30 sec; 5 cycles of 98℃ for 10 sec, 63℃ for 30 sec; and 72℃ for 1 min. A side qPCR amplification using a small aliquot of the amplified DNA was used to determine the necessary additional number of cycles to stop amplification prior to saturation (1/4 of max fluorescent intensity) to reduce GC and size bias. The remaining DNA samples were amplified to the correct number of cycles and then purified and eluted using Qiagen PCR Cleanup kit in 20 µl of Elution buffer.
Library quality control (QC) was performed using Agilent Bioanalyzer High Sensitivity DNA chip with the samples diluted 1:5.

value: Brain

value: D2 MSN

value: CS


title: Control, replicate 2


title: native liver, HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
barcode1
sample1_barcodes.tsv.gz
sample1_features.tsv.gz
sample1_matrix.mtx.gz

value: mock

value: TotalSeq™-B0380 anti-rat CD90/mouse CD90.1 (Thy-1.1) Antibody


title: D2_CS_5


title: D2_CS_6


title: D11 Dicer1 siRNA TRANSFECTED REPLICATA 3

tag: cell line

value: knock down

value: 4 days after transfection


title: BAAT-1, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
gene5

molecule: polyA RNA

value: mRNA


title: D2_CS_4


title: D2_CS_2


title: D11 NON TRANSFECTED REPLICATA 1

value: Thyroid

value: PTC papillary thyroid carcinoma

tag: genotype


title: control, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
gene2

value: whole liver

tag: treatment


title: native liver, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
gene1


title: D11 NON TRANSFECTED REPLICATA 2

value: DICER (+/-)


title: OC014_IL4I1

type: RNA

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: IL4I1 macs

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data was processed with the minfi package in R

label: Cy3, Cy5

source_name: tumor associated macrophage

label_protocol: Standard Illumina Protocol

growth_protocol: Peripheral blood monocytes were purified using CD14 magnetic-activated cell sorting (MACS © MicroBeads, Miltenyi Biotec) and cultured in RPMI 1640 in the presence of 15ng/mL macrophage colony-stimulating factor (M-CSF) for 5 days in normoxia (21% O2) or hypoxia (1% O2). Cells were further stimulated with 10 ng/mL of lypopolysaccharide (LPS) or with PBS for 48h additional hours.

extract_protocol: Genomic DNA was extracted and purified from monocytes or macrophages using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

tag: donor

tag: age

tag: Sex

value: F

tag: condition

value: IL4I1 macs


title: D2_CS_1


title: D2_CS_3


title: D11 NEGATIVE CONTROL REPLICATA 1


title: TPC1 Dicer1 siRNA TRANSFECTED REPLICATA 2


title: D1_CC_4

value: D1 MSN

value: CC


title: OC005_FOLR2

description: FOLR2 macs

value: FOLR2 macs


title: Pol II AID wash-off 3 hours, second-round, new RNA, 100G, scFLUENT-seq

first: Xiaohua

last: Shen

state: Beijing

address: China, Tsinghua university, school of medicine

department: Medical School

institute: Tsinghua University

data_processing:
the SeekSoul Tools (http://seeksoul.seekgene.com/zh/v1.2.2/index.html) was used to to process the cleaned reads. Number of cells detected using the SeekSoul Tools pipeline was used as the input for UMI-tools v1.1.2. whitelist command with options: --bc-pattern=CCCCCCCCCCCCCCCCCNNNNNNNNNNNN --set-cell-number. Reads with matched cell barcodes in the whitelist file were retained for subsequent analysis using UMI-tools extract command. Each RNA read was tagged with the cell barcode (base 1-17 of Read1) and UMI (base 18-29 of Read1). Cell barcodes were extracted using UMI-tools extract command. Reads were trimmed of TSO sequences and adapters using Cutadapt v0.6.6 and aligned to the mouse (mm10, GENCODE release vM22), human (GRCh38, GENCODE release v32) or a concatenated mouse and human (for the species-mixing experiment) reference genome assembly using STAR v2.7.3a.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: single-cell nascent RNA sequencing

molecule: nuclear RNA

source_name: mouse ESC

extract_protocol:
Nuclei of mouse ESCs were extracted using cytolysis buffer (0.1% BSA, 200 U RNase inhibitor, 0.2% NP-40, 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2) and fixed using 1% formaldehyde. Fixed nuclei were used for biotin-tagging reaction using in-situ click working solution (50 mM Hepes pH 7.5, 2.5 mM THPTA, 2.5 mM CuSO4, 4 mM Biotin-PEG3-azide, 10 mM Sodium ascorbate) and incubated at 25°C,350 rpm with 10 s on and 10s off on a ThermoMixer for 0.5 h. The nuclei were sent to single-cell sequencing.
cDNA products were amplified by PCR following 98℃ 3 min, (98℃ 10 sec, 63℃ 15 sec, 72℃ 1min) for 10 cyles, 72℃ 5 min, 4℃ Hold. The products were purified, checked for cDNA amount, and served as the template of the second PCR. Finally, after purification, one-fourth volume of cDNA was amplified by index PCR. The reaction was set on a thermal cycler with the following program: 98℃ 3 min, (98℃ 10 sec, 54℃ 15 sec, 72℃ 1min) for 7cyles, 72℃ 5 min, 4℃ Hold. The indexed sequencing libraries were purified using 0.8 DNA clean beads. Specifically, for supernatant fraction, rRNA/mtRNA blocking probes were added to the first round of PCR to remove cDNA from rRNA and mtRNA.

value: mouse ESC

value: Pol II AID IAA-wash-off 3 hours, second round


title: D1_CC_3

value: Brain


title: OC005_IL4I1

description: IL4I1 macs


title: TPC1 Dicer1 siRNA TRANSFECTED REPLICATA 3


title: D1_CC_2


title: OC014_FOLR2

description: FOLR2 macs


title: D1_CC_1


title: OC03_TREM2

description: TREM2 macs

value: TREM2 macs


title: OC001_TREM2

description: TREM2 macs


title: D1_CS_4

value: CS


title: OC013_TREM2

description: TREM2 macs


title: D1_CS_3


title: D1_CS_2


title: Pol II AID IAA-treated 24 hours, second-round, new RNA, 100G, scFLUENT-seq

value: Pol II AID IAA-treated 24 hours, second round


title: TPC1 NEGATIVE CONTROL REPLICATA 2

value: wt

value: 4 days after transfection


title: TPC1 NEGATIVE CONTROL REPLICATA 3

value: Thyroid


title: D1_CS_1


title: OC03_IL4I1

description: IL4I1 macs


title: Pol II AID wash-off 48 hours, first-round, new RNA, 100G, scFLUENT-seq

value: Pol II AID IAA-wash-off 48 hours


title: D1_SC_3

value: SC


title: Pol II AID wash-off 3 hours, first-round, new RNA, 100G, scFLUENT-seq

value: Pol II AID IAA-wash-off 3 hours


title: D1_SC_4


title: D1_SC_2


title: D2_CC_1

value: D2 MSN


title: TPC1 NEGATIVE CONTROL REPLICATA 1

value: PTC papillary thyroid carcinoma


title: OC014_TREM2

description: TREM2 macs

value: F


title: Pol II AID IAA-treated 24 hours, first-round, new RNA, 100G, scFLUENT-seq

value: Pol II AID IAA-treated 24 hours


title: TPC1 NON TRANSFECTED REPLICATA 3


title: OC005_TREM2

description: TREM2 macs


title: D2_SS_2

value: SS


title: OC013_IL4I1

description: IL4I1 macs

value: IL4I1 macs


title: D2_SS_1


title: Ba/F3_focused_screen_raw_file_2


title: TPC1 NON TRANSFECTED REPLICATA 2


title: D2_SC_1


title: D1_SS_2

value: D1 MSN


title: TPC1 NON TRANSFECTED REPLICATA 1


title: Pol II AID IAA-treated 1 hour, old RNA, 100G, scFLUENT-seq

value: mouse ESC

value: Pol II AID IAA-treated 1 hour


title: H9S74inflamed3

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description:
single-cell mRNA-seq data
batch3_inflamedVsNaive_counts.txt

data_processing:
FastX-Toolkit v. 0.0.13.2 (Gordon, A., FastX-Toolkit. 2009) quality trimmer was used to further trim reads based on quality score and FASTX-Toolkit quality chart was used to make read per-base quality plots. A trimscore and a trim length of 30 were used.
Tophat2 was used to align reads to the reference genome. Tophat2 was run with defaults except that the number of mismatches allowed was 1.
The htseq-count script in HTSeq v.0.6.151 and Biopython v.2.7.3 were used to generate a counts matrix in “intersection-nonempty” mode, with feature set to “exon” and attribute parameter set to “gene_id”.
R version R-3.4.1 and the package Seurat v. 1.4 was used to cluster cells into subpopulations using the first 4 principal components, a resolution of 0.5, and k.param = 4.
The FindAllMarkers() function within Seurat was used to identify cluster markers using the zero-inflated “bimod” model and a false discovery rate (FDR) of 0.01. FindAllMarkers() was likewise used to identify differentially expressed genes between inflamed and naïve cells, controlling the FDR at 5%.
Assembly: Mus musculus GRCm38.p6 reference genome49
Supplementary files format and content: count matrices are provided as tab delimited text files

source_name: prostate

extract_protocol:
tissue procurement: Prosates from naïve or inflamed POET3 mice
Minced mouse prostate tissues were digested in 1 mg/mL collagenase (Sigma-Aldrich) in RPMI-1640 (Gibco) media containing 10% FBS (Corning) with shaking at 37ºC for 2 hours, followed by trypsinization. Dissociated cells were passed through 20G needles and 40 µm cell strainers to eliminate aggregates, followed by removal of red blood cells by ACK buffer. To enrich basal prostate stem cells (bPSC), isolated cells were stained with Zombie Violet Live/Dead Fixable Viability Dye (Biolegend) in PBS, followed by incubation with 1:100 diluted fluorescence-conjugated specific antibodies (Biolegend): CD45-FITC (#103108), CD31-FITC (#102506), Sca-1-APC (#122512) and CD49f-PE (#313612). Once stained, fluorescence activated cell sorting was performed on the BD FACSAria under sterile conditions.
Data was collected using the C1 Fluidigm instrument with SMARTer chemistry (Clontech) to generate cDNA from captured single cells. Libraries were prepared using a Nextera kit (Illumina).
Single-end 1x50 bp reads were sequenced using the HiSeq2500 on rapid run mode.

value: prostate

value: basal prostate stem cells

value: male

tag: batch

value: inflamed

tag: wellid


title: Pol II AID IAA-treated 1 hour, first-round, new RNA, 100G, scFLUENT-seq


title: Obese HAT-3

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

data_processing:
Sequenced reads were aligned to Homo sapiens reference genome GRCh38 (hg38) with STAR v. 2.7.6a
mRNA expressions were quantified from the aligned reads by using STAR from option -quantMode
Gene symbols were annotated using the biomaRt R package
Principal component analysis (PCA) was performed after normalization. DEGs were identified using DESeq2, with FDR < 0.05 and absolute log2fold-change higher than 1. DEGs for each comparison were plotted using the ComplexHeatmap R package
To define the biological function significantly associated with the DEGs identified from each comparison, we performed gene set enrichment analysis suing the enrichGO function from clusterProfiler R package
Assembly: Genome_build: Homo sapiens reference genome GRCh38 (hg38)
Supplementary files format and content: Supplementary_files_format_and_content: Processed data files are provided as .csv

source_name: Atrial tissue

growth_protocol: HiPSCs were maintained on human recombinant vitronectin coated plates in mTeSR medium. HiPSCs were then differentiated using the cardiomyocyte differentiation kit (Gibco), and guided into atrial subtypes using 1µmol/l all-trans retinoic acid (protocol adapted from Devalla et al., 2015). At day 10, glucose starvation metabolic selection was used to enrich the iPSC-aCM culture. For matured iPSC-aCMs, thyroid hormone, insulin-like growth factor, dexamethasone, palmitic acid, and oleic acid were added to the foundational maintenance media from day 18-32, and the cells were subjected to electrical field stimulation from day 18-25.

extract_protocol:
All total RNA samples were isolated Trizol phenol chloroform method at 1.5 ug of RNA.
Strand-specific RNA-Seq libraries were prepared using a TruSEQ mRNA-SEQ library protocol (illinuma provided). Library quality and quantity was assessed using Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000.

treatment_protocol: HiPSC-aCMs were treated it Palmitic acid (PA) or bovine serum albumin (BSA) for 5 days at 0.5 mM; GSK-2795039, a Nox2 small molecule inhibitor was used with PA at 20 uM to block Nox2 in PA-HiPSC-aCMs

value: Atrial tissue

value: HAT

value: WT


title: H9S182inflamed2

description:
single-cell mRNA-seq data
batch2_inflamedVsNaive_counts.txt


title: OC001_IL4I1

description: IL4I1 macs


title: Ba/F3_Genome_wide_screen

data_processing:
Sequence reads were aligned to a reference library, reads containing mismatches removed, and sgRNA distributions quantified and scored using MAGeCK RRA (version 0.5.6)
Reads were demultiplexed based on sample barcodes and aligned against reference library (Addgene #73632/3)  and reads with missmatches removed (see processed data file)
Processed datafile was used as input file for mageck analysis. Null distribution was generated for calculating p-values based on control sgRNAs within library.
For mageck analysis either all samples, or only select samples were used (Outputs for sgRNA summaries supplied as supplementary files: Select_sgRNA_summary.tabular, All_sgRNA_summary.tabular)
Assembly: N/A
Supplementary files format and content: Tabular data containing read counts for each sample (demultiplexed based on sample barcode) and sgRNA (aligned against reference library).
Library strategy: CRISPR Screen

extract_protocol:
DirectPCR Lysis reagent (Viagen Biotech #301-C)
SgRNA sequences were  amplified using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs #M0541S), following the manufacturer’s instructions, using primers containing sample barcodes. Barcodes denoted in processed data file.


title: Pol II AID IAA-treated 1 hour, new RNA, 100G, scFLUENT-seq


title: H8S68inflamed3


title: OC013_FOLR2

description: FOLR2 macs

value: FOLR2 macs


title: OC001_FOLR2

description: FOLR2 macs


title: Obese HAT-2


title: H8S176inflamed2


title: Obese HAT-1


title: OC03_FOLR2

description: FOLR2 macs


title: H7S94naive3

value: naive


title: H7S61inflamed3


title: D2_CS_7

value: Brain

value: D2 MSN

value: CS


title: Pol II AID non-treated, time-course, new RNA, 100G, scFLUENT-seq

value: Pol II AID non-treated


title: H7S170inflamed2


title: D1_SS_1

value: SS


title: Lean HAT-3


title: Pol II AID non-treated, new RNA, replicate 1, 100G, scFLUENT-seq


title: H6S87naive3


title: mouse ESCs, wild type [PRO-Seq]

data_processing:
PRO-seq raw data were trimmed with Cutadapt, and UMI-tools extract command was used to extract the UMI sequences: umi_tools extract --bc-pattern=NNNX --bc-pattern2=NNNX --extract-method string. Cleaned reads were aligned to mm10 using HISAT2 v2.1.0 with default settings. Reads were deduplicated using umi_tools dedup command. Only uniquely mapped reads were retained for subsequent analysis. Uniquely mapped reads were filtered using samtools view command with options: -h -q 30 -F 0x04 -F 0x100. The filtered bam files were converted to plus- and minus-strand bigwig files using deeptools v3.5.3 bamCoverage command with options: --filter forward -p 5 -bs 10 --normalizeUsing CPM.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: PRO-seq

extract_protocol:
Briefly, 106-107 ESCs were trypsinized and collected by centrifugation at 1,000 g for 5 min at 4°C. The cell pellet was resuspended in ice-cold permeablization buffer (10 mM Tris-HCl (pH 7.4), 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP-40, 0.5 mM DTT, 4 U/mL RNase inhibitor,  proteinase inhibitor cocktail) and incubated on ice for 5 min before centrifugation. The extracted nuclei were washed twice with permeabilization buffer and stored in 100 μL storage buffer (10 mM Tris-HCl (pH 8.0), 25% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 5 mM DTT) at -80°C.
VAHTS Universal V6 RNA-seq Library Prep kit (Vazyme #NR604) was used for RNA library construction. Library construction was conducted according to the manufacturer’s protocol (with UMI barcoded dual index, RK21702) and the libraries were sequenced on the Illumina platform.


title: H6S164inflamed2


title: H5S82naive3


title: Lean HAT-2


title: mouse ESCs, wild type

data_processing:
EU-seq raw data were trimmed using fastx_toolkit v0.0.14 (fastx_trimmer -f 18 -Q 33) for R1 reads, followed by barcode matching using fastx_barcode_splitter.pl command (barcode:AAACCCAATGAAACACT). R2 reads were trimmed using trim_galore -q 5 --phred33 --stringency 12 --length 20 -e 0.1 --no_report_file --trim-n -a AGATCGGAAGAGCGTCGTGTAG --dont_gzip --clip_R2 32 --three_prime_clip_R2 17 paired command. fastq-pair was used for pairing R1 reads and R2 reads. Cleaned paired reads were aligned to mm10 using HISAT2 v2.1.0 with default settings. The filtered bam files were converted to plus- and minus-strand bigwig files using deeptools v3.5.3 bamCoverage command with options: --filter forward -p 5 -bs 10 --normalizeUsing CPM.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: EU-seq

extract_protocol:
Nuclei of mouse ESCs were extracted using cytolysis buffer (0.1% BSA, 200 U RNase inhibitor, 0.2% NP-40, 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2) and fixed using 1% formaldehyde. Fixed nuclei were used for biotin-tagging reaction using in-situ click working solution (50 mM Hepes pH 7.5, 2.5 mM THPTA, 2.5 mM CuSO4, 4 mM Biotin-PEG3-azide, 10 mM Sodium ascorbate) and incubated at 25°C,350 rpm with 10 s on and 10s off on a ThermoMixer for 0.5 h. The nuclei were further processed for in-situ reverse transcription and lysed for biotinylated RNA pull-down.
VAHTS Universal V6 RNA-seq Library Prep kit (Vazyme #NR604) was used for RNA library construction. Library construction was conducted according to the manufacturer’s protocol (with UMI barcoded dual index, RK21702) and the libraries were sequenced on the Illumina platform.


title: H5S23naive2


title: Pol II AID non-treated, old RNA, 100G, scFLUENT-seq


title: Lean HAT-1


title: WT BMDM, LPS, 4hr, biol rep 1

city: Nashville

first: Margaret

middle: Ann

last: Mcbride

state: Tennessee

address: 1211 Medical Center Drive

department: Anesthesiology

institute: Vanderbilt University Medical Center

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. STAR-software was used to align reads to the reference genome. Expression levels were quantified using FPKM.
Reads that met the following citeria were removed. 1. reads containing adapters; 2., reads containing N > 10% (N represents base that could not be determined); 3. low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: mm10
Supplementary files format and content: excel file including raw counts for each sample
Supplementary files format and content: excel file including FPKM  for each sample

source_name: bone marrow-derived macrophage

growth_protocol: Murine bone marrow-servied macrophages were cultured from whole bone marrow and maintained in RPMI 1640 supplemented with 10% FBS, 1% antibiotic/anitbmycotic solution, and 10ug/mL murine macrophage colony stimulating factor

extract_protocol:
Total RNA was isolated under an RNase-free environment using the RNeasy Mini Kit (Qiagen, Hilden, Germany) which included a DNAse treatment step. Total RNA quality and concentration were verified with a Thermo Scientific NanoDrop 2000 spectrophotometer.
Sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocol.

treatment_protocol: BMDM were treated with  MPLA (1μg/mL), or DMSO (1uL/mL) in supplemnted RPMI for 4h, 24h, or 3 days (3dp) prior to RNA harvest. The 3dp groups were treated as specifiec for 24 hours, after which the BMDM were washed with PBS and the supplemented RPMI without the treatment was replaced.  The BMDM then rested for 3 additional days prior to RNA harvest.

value: bone marrow-derived macrophage

value: Male

value: 4hrs post 1μg/mL LPS


title: PA-GSK-HiPSC-aCM-3

source_name: Atrial cells

value: Atrial cells

value: HiPSC-aCM

value: Palmitic Acid + GSK


title: D1_SC_1

value: D1 MSN

value: SC


title: H4S148inflamed2

value: prostate

value: basal prostate stem cells

value: male

value: inflamed


title: PA-GSK-HiPSC-aCM-2

value: WT


title: WT BMDM, DMSO control, biol rep 4

value: 3 days post 0.1% DMSO for 24 hrs


title: H5S156inflamed2


title: H4S77naive3

value: naive


title: Pol II AID wash-off 48 hours, second-round, new RNA, 100G, scFLUENT-seq

value: mouse ESC

value: Pol II AID IAA-wash-off 48 hours, second round


title: WT BMDM, DMSO control, biol rep 3

value: bone marrow-derived macrophage


title: WT BMDM,MPLA, 3dp, biol rep 2

value: Male

value: 3 days post 1µg/mL MPLA for 24 hrs


title: H3S16naive2


title: H3S34inflamed3


title: PA-HiPSC-aCM-3

value: Atrial cells

value: Palmitic Acid


title: H3S140inflamed2


title: H2S64naive3


title: WT BMDM,MPLA then LPS, biol rep 1

value: 3 days post 1µg/mL MPLA for 24 hrs. then LPS for 4 hours


title: H6S53inflamed3


title: H2S26inflamed3


title: WT BMDM,MPLA, 3dp, biol rep 1


title: PA-HiPSC-aCM-1

value: HiPSC-aCM


title: PA-HiPSC-aCM-2


title: H12S55naive2


title: WT BMDM,DMSO control, biol rep 2


title: H1S5naive2


title: H12S13inflamed2


title: H3S71naive3


title: PA-GSK-HiPSC-aCM-1

value: Palmitic Acid + GSK


title: BSA-HiPSC-aCM-3

value: BSA


title: H11S49naive2

value: prostate

value: basal prostate stem cells


title: H10S43naive2

value: male


title: BSA-HiPSC-aCM-2

value: WT


title: WT BMDM, MPLA, 4h, biol rep 2

value: 4hrs post 1μg/mL MPLA


title: H11S6inflamed2

value: inflamed


title: G9S38naive2

value: naive


title: BSA-HiPSC-aCM-1


title: WT BMDM,DMSO control, biol rep 1

value: 3 days post 0.1% DMSO for 24 hrs


title: WT BMDM, MPLA, 24h, biol rep 2

value: bone marrow-derived macrophage

value: 24hrs post 1μg/mL MPLA


title: H10S189inflamed2


title: H10S110naive3


title: G9S103naive3


title: WT BMDM, MPLA, 4h, biol rep 1

value: Male


title: G8S98naive3


title: G8S34naive2


title: Collagen_TGFb_bioink_1

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

data_processing:
First 5 steps were carried out by Novogene UK. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Filter the raw reads and obtain the clean reads - (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
HISAT2 is selected to map the filtered sequenced reads to the reference genome.
Gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008)
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Therefore, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ～ NB(μij,σij2) And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Assembly: GO analysis with ShinyGO and StringDB, and GSEA analysis with GSEA Software (Broad Institute)
Supplementary files format and content: ensembl_homo_sapiens_grch38
Supplementary files format and content: Processed data is in text matrix format. It contains rows with all differentially expressed genes (Gene ID) (for later analysis 1.5 FC and adj p-value<0.05 were used), columns with the respective log2FoldChange, padj, and gene_name, as well as  columns with counts and FPKM values for each sample.

source_name: Adipose-derived MSCs/SVF cells

extract_protocol:
Pure Link RNA Mini kit (cat # 12183018A, ThermoFisher Scientific, USA)
Sequencing was outsourced to Novogene UK -  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used for library preparation with AMPure XP beads (Beckman Coulter, Beverly, USA) for size selection and PCR purification steps, both performed as instructed by the manufacturers.

treatment_protocol: No treatment - cells were grown in 4 different conditions - standard 2D (monolayer) cultures, 3D spheroid/micromasses, bioprinted in pure collagen, bioprinted in collagen+TGFb bioink

value: Adipose-derived MSCs/SVF cells

value: hTERT A41hWAT-SVF

value: SVF (stromal vascular fraction)

value: cells bioprinted in collagen+TGFb bioink


title: WT BMDM, MPLA, 24h, biol rep 1


title: H2S10naive2


title: TPC1 Dicer1 siRNA TRANSFECTED REPLICATA 1

value: Thyroid

value: PTC papillary thyroid carcinoma

value: knock down

value: 4 days after transfection


title: G8S175inflamed2

value: prostate

value: basal prostate stem cells

value: male


title: Collagen_bioink_2

value: cells bioprinted in collagen bioink


title: G7S93naive3

value: naive


title: G7S60inflamed3

value: inflamed


title: G6S86naive3


title: Irg1KO BMDM, LPS, 4hr, biol rep 2

value: bone marrow-derived macrophage

value: 4hrs post 1μg/mL LPS


title: Irg1KO BMDM, DMSO control, biol rep 4

value: Male

value: 3 days post 0.1% DMSO for 24 hrs


title: G6S52inflamed3


title: Collagen_TGFb_bioink_2

value: Adipose-derived MSCs/SVF cells

value: hTERT A41hWAT-SVF


title: 3D_spheroids_2

value: SVF (stromal vascular fraction)

value: cells grown in 3D spheroids/micromasses


title: G6S27naive2


title: 3D_spheroids_1


title: Irg1KO BMDM,MPLA then LPS, biol rep 2

value: 3 days post 1µg/mL MPLA for 24 hrs. then LPS for 4 hours


title: G5S46inflamed3


title: Irg1KO BMDM,MPLA, 3dp, biol rep 2

value: 3 days post 1µg/mL MPLA for 24 hrs


title: Irg1KO BMDM, LPS, 4hr, biol rep 1


title: G4S76naive3


title: G6S163inflamed2


title: G4S147inflamed2


title: 2D_ctrl_2

value: control grown in monolayer


title: 2D_ctrl_1


title: G5S155inflamed2

value: prostate


title: Irg1KO BMDM,MPLA then LPS, biol rep 1


title: G3S33inflamed3

value: basal prostate stem cells


title: G3S15naive2

value: male


title: WT,IFNg,sample 13

city: Los Angeles

first: Yiqian

last: Gu

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

data_processing:
Utilizing STAR-2.7.11a, reads were aligned to the reference genome hg38. The "mappedReadsPerGene.out.tab" files from each sample were integrated to "raw_counts.txt" then utilized for quantifying normalized expression values.
Assembly: hg38
Supplementary files format and content: txt files including raw count of genes for each sample

source_name: tumor

extract_protocol:
trizol RNA extraction
KAPA RNA HyperPrep Kit

value: tumor

value: WT, IFNg


title: G3S139inflamed2

value: inflamed


title: Collagen_bioink_1

value: cells bioprinted in collagen bioink


title: WT,IFNg,sample 12


title: G2S9naive2

value: naive


title: Irg1KO BMDM,MPLA, 3dp, biol rep 1

value: bone marrow-derived macrophage

value: Male


title: G2S132inflamed2


title: G2S25inflamed3


title: WT,IFNg,sample 11


title: Irg1KO BMDM,DMSO control, biol rep 2

value: 3 days post 0.1% DMSO for 24 hrs


title: G1S4naive2


title: WT,UTR,sample 13

value: WT, UTR


title: G1S126inflamed2


title: G12S54naive2


title: WT,UTR,sample 12


title: Irg1KO BMDM, MPLA, 4h, biol rep 2

value: 4hrs post 1μg/mL MPLA


title: G12S119naive3


title: G11S115naive3


title: G10S81inflamed3


title: Irg1KO BMDM, DMSO control, biol rep 3


title: Irg1KO BMDM, MPLA, 24h, biol rep 2

value: 24hrs post 1μg/mL MPLA


title: Irg1KO BMDM, MPLA, 4h, biol rep 1


title: G11S5inflamed2


title: KO,IFNg,sample 13

value: FOXP3 KO, IFNg


title: G10S109naive3


title: WT,UTR,sample 11


title: KO,IFNg,sample 12


title: G10S42naive2


title: Irg1KO BMDM, MPLA, 24h, biol rep 1


title: F9S37naive2


title: KO,IFNg,sample 11


title: Irg1KO BMDM,DMSO control, biol rep 1


title: F9S181inflamed2


title: G10S188inflamed2


title: F8S67inflamed3


title: EXOMEseq_p53koKPC_syngenic

city: Cambridge

first: Dig

middle: B

last: Mahat

email: mahat@mit.edu, dbm222@cornell.edu

state: MA

address: Koch Institute, MIT, 500 Main St, Building 76, #417

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

data_processing:
We processed the raw sequence data using the BWA-MEM algorithm to align it to the mouse reference genome (mm10). We performed subsequent variant calling using the GATK Best Practices pipeline and filtered the variants from BAM files using Mutect2. We annotated the identified variants with ANNOVAR and filtered them based on quality metrics, allele frequency, and predicted functional impact. Finally, we used CNVkit to determine the copy number status of the mutated positions from BAM files.
Assembly: mm10
Supplementary files format and content: tab-delimited bed files, which includes raw counts for each Sample
Library strategy: Exome-seq

growth_protocol: PDAC cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 4.5 g/L D-Glucose, L-Glutamine, 110 mg/L Sodium Pyruvate (Gibco, 11995) plus 10% heat inactivated fetal bovine serum (Tissue Culture Biologics cat.no. # 101HI, lot # 101226) on tissue culture-treated 10 cm plates (Corning, CLS430167). Cells were grown at 37°C and 5% CO2 and passed with 0.25% Trypsin-EDTA (Gibco, 25200) when 70% confluency was reached.

extract_protocol:
We extracted genomic DNA from the samples using a standard phenol-chloroform extraction method.
We used the Agilent SureSelect mouse All Exon V5 kit to capture the exonic regions according to the manufacturer’s protocol. We then subjected the captured libraries to paired-end sequencing on the Illumina NovaSeq 6000 platform.

value: pancreatic ductal adenocarcinoma


title: EXOMEseq_KPC


title: F7S92naive3


title: KO,UTR,sample 13

value: FOXP3 KO, UTR


title: F7S59inflamed3

value: prostate


title: KO,UTR,sample 12


title: F7S30naive2

value: basal prostate stem cells


title: F7S169inflamed2

value: male


title: KO,UTR,sample 11

value: tumor


title: F6S51inflamed3


title: PROseq_p53koKPC_isogenic_AddBack_BR2

description: Nascent RNA

data_processing:
We clipped adapters from PRO-seq reads using Cutadapt. We discarded reads shorter than 15 bp as they map to multiple sites in the genome. We mapped the reads to the mouse genome mm10 using bowtie2, requiring them to uniquely map to the genome allowing up to 2 mismatches.
Assembly: mm10
Supplementary files format and content: tab-delimited bed files, which includes raw counts for each Sample
Library strategy: PRO-seq

molecule: other

extract_protocol:
We extracted total RNA, which includes biotin-labelled nascent RNA, using Trizol following the the manufacturer's protocol. the total RNA is subjected to three biotin-Streptavidin enrichment to select nascent RNA away from other RNA.
We isolated nascent RNAs with magnetic beads coated with streptavidin, followed by 3’ adapter ligation. After another round of biotin-streptavidin affinity purification, we removed the mRNA cap and ligated the 5’ adapter. Following the third biotin-streptavidin affinity purification, we generated cDNA by reverse transcription and prepared PRO-seq libraries for sequencing using Illumina TruSeq small-RNA adaptors with twelve cycles of PCR


title: PROseq_p53koKPC_isogenic_AddBack_BR1

description: Nascent RNA


title: G5S22naive2


title: placenta

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

country: Japan

institute: Kobe University

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) reference sequences using the Strand NGS software program with default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include Gene Symbol, Entrez Gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: tissue

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries were prepared for TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.E).

value: tissue


title: PROseq_p53koKPC_isogenic_BR2

description: Nascent RNA


title: F6S162inflamed2

value: inflamed


title: F5S81naive3


title: F5S154inflamed2


title: EVT-AS

source_name: iPS-derived differentiated cells

value: iPS-derived differentiated cells


title: F4S39inflamed3


title: F4S75naive3

value: naive


title: F5S45inflamed3


title: EVT


title: PROseq_p53koKPC_isogenic_BR1

description: Nascent RNA


title: PROseq_KPC_BR2

description: Nascent RNA


title: PROseq_KPC_BR1

description: Nascent RNA


title: ST-AS


title: F3S70naive3


title: F4S146inflamed2


title: ST


title: F3S138inflamed2


title: F3S32inflamed3


title: CT-AS


title: F2S8naive2


title: RNAseq_p53koKPC_isogenic_EmptyVector_BR1

data_processing:
We processed the raw sequence data for quality control using FastQC and trimmed adapters with Cutadapt. We aligned high-quality reads to the reference genome (mm10) using bowtie2 and performed transcript quantification using rsem.
Assembly: mm10
Supplementary files format and content: tab-delimited bed files, which includes raw counts for each Sample

source_name: Trp53-/- + pEV

extract_protocol:
We extracted total RNA for RNA-seq using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
We prepared libraries from RNA samples with an RNA integrity number (RIN) greater than 7.0 using the TruSeq Stranded mRNA Library Prep Kit (Illumina), according to the recommended protocol. Sequencing was performed on an Illumina NovaSeq 6000 platform, generating paired-end reads of 150 base pairs.

value: Trp53-/- + pEV


title: F1S59naive3


title: RNAseq_p53koKPC_isogenic_AddBack_BR3


title: CT


title: F1S18inflamed3


title: F2S24inflamed3


title: TE


title: F4S19naive2


title: TE-AS


title: F12S53naive2


title: RNAseq_p53koKPC_isogenic_AddBack_BR2


title: F12S12inflamed2


title: F1S125inflamed2


title: RNAseq_p53koKPC_isogenic_AddBack_BR1


title: F12S118naive3


title: F11S4inflamed2


title: VAC35, HC, d28

city: Siena

first: Simone

last: Lucchesi

address: Viale Bracci, 16

country: Italy

institute: University of Siena

data_processing:
Trimming and removal of low-quality reads was performed with Trimmomatic v0.39 using the following parameters: SLIDINGWINDOW 4:5, MINLEN:36.
STAR v2.7.3 was used to align reads to reference Grch38 human genome
htseq v.2.0.2was used to count the reads of annotated genes
DESeq2 package v1.36.0 was used to normalize gene expression and to perfor diferential gene expression analysis
Assembly: Grch38 human genome
Supplementary files format and content: CSV file containing raw counts for each sample
Supplementary files format and content: CSV file containing vst normalized counts (log2-like) using vst function

source_name: PBMCs

extract_protocol:
RNA  was extracted from PBMC using RNeasy mini kit (Qiagen)
Libraries were prepared using “Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus” kit and sequenced on NovaSeq 6000 System (Illumina)

value: PBMCs

tag: group

value: HC

tag: time

value: d28, Post-boost


title: RNAseq_p53koKPC_isogenic_EmptyVector_BR2


title: F11S48naive2


title: F11S114naive3


title: VAC35, HC, d21

value: d21, Pre-boost


title: F10S80inflamed3


title: RNAseq_p53koKPC_isogenic_clone7_BR2


title: VAC35, HC, d7

value: d7, Post-priming


title: F10S187inflamed2


title: F10S108naive3


title: RNAseq_p53koKPC_syngenic_BR1


title: F2S131inflamed2


title: RNAseq_p53koKPC_isogenic_clone7_BR1


title: RNAseq_p53koKPC_isogenic_BR2


title: E9S180inflamed2


title: E9S102naive3


title: RNAseq_p53koKPC_syngenic_BR2


title: VAC34, HC, d28


title: RNAseq_p53koKPC_isogenic_BR1


title: E8S97naive3


title: VAC30, HC, d28


title: E8S174inflamed2


title: E7S29naive2


title: E7S58inflamed3


title: RNAseq_KPC_BR1


title: RSeT

source_name: iPS cells

value: iPS cells


title: E7S168inflamed2


title: VAC30, HC, d0

value: d0, Pre-priming


title: E6S50inflamed3


title: RNAseq_KPC_BR2

value: pancreatic ductal adenocarcinoma


title: Male_Saline rep4

city: Guangzhou

first: Wenjun

last: Yu

address: Nanfang Hospital, Southern Medical University

institute: Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology

data_processing:
Quality control was performed by FastQC (v0.11.8) with passing all criteria.
Sequence reads were aligned to mouse genome MM10 (UCSC) using STAR (v2.7.1a) under the default parameters.
Aligned reads were quantified using HTSeq-counts (v0.11.2)
Low and un-expressed genes with < 3 reads in at least 5 samples in a group were omitted from the analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

source_name: Whole brain

extract_protocol:
Total RNA was isolated using the RNeasy Plus Universal Mini Kit (Qiagen) according to the instruction.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The female mice (16th day of pregnancy) received an intraperitoneal injection with LPS (150ug/kg) or saline (150ug/kg). For each treatment group, 5 whole brain RNA samples of the male offspring (postnatal 56 days) were prepared.

value: Whole brain

value: WT

value: Maternal Saline injection


title: Male_Saline rep3


title: VAC27, HC, d21


title: E5S153inflamed2

value: prostate

value: basal prostate stem cells

value: male


title: VAC27, HC, d28


title: VAC35, HC, d0


title: E6S161inflamed2

value: inflamed


title: E5S44inflamed3


title: Male_Saline rep2


title: E9S73inflamed3


title: E4S74naive3

value: naive


title: E4S38inflamed3


title: E8S66inflamed3


title: VAC27, HC, d0


title: VAC30, HC, d21


title: VAC26, HC, d28


title: Male_LPS rep4

value: Maternal LPS injection


title: Male_Saline rep1


title: E4S18naive2


title: VAC26, HC, d21

value: PBMCs


title: VAC23, HC, d28

value: HC


title: E4S145inflamed2


title: E3S14naive2


title: Male_LPS rep3


title: E6S26naive2


title: E3S31inflamed3


title: E1S3naive2


title: E3S137inflamed2


title: E2S130inflamed2


title: VAC26, HC, d0


title: VAC23, HC, d21


title: E2S7naive2


title: E3S69naive3


title: E1S17inflamed3


title: Male_LPS rep2


title: E1S124inflamed2


title: E12S52naive2


title: VAC21, HC, d21


title: E2S23inflamed3


title: VAC21, HC, d28

value: d28, Post-boost


title: E11S86inflamed3


title: VAC23, HC, d0


title: Ba/F3_invitro_bulkRNA_rep3

data_processing:
transcript counts were obtained using an in-house generated pipeline (GenSum, https://github.com/NKI-GCF/gensum)
Assembly: GRCm38, pre-built HISAT2 index, genome_snp_tran
Supplementary files format and content: Gene_Table_norm.txt; tab-separated file

extract_protocol:
RNeasy Mini Kit (Qiagen #74004)
TruSeq Stranded mRNA Kit (Illumina #20020594) for whole transcriptome sequencing


title: E12S11inflamed2


title: E11S47naive2


title: E2S63naive3


title: Ba/F3_invitro_bulkRNA_rep2


title: VAC21, HC, d0


title: E12S91inflamed3


title: Male_LPS rep1


title: E11S113naive3


title: E10S41naive2


title: Ba/F3_invitro_bulkRNA_rep1


title: E10S75inflamed3


title: E11S3inflamed2


title: D9S101naive3


title: VAC181, HC, d28


title: VAC181, HC, d21

value: d21, Pre-boost


title: VAC21, HC, d7

value: d7, Post-priming


title: E10S186inflamed2


title: E10S107naive3


title: D9S72inflamed3


title: D8S173inflamed2


title: D9S179inflamed2


title: D7S28naive2


title: D8S65inflamed3


title: D6S85naive3


title: VAC177, HC, d0


title: D7S91naive3


title: VAC177, HC, d28


title: VAC177, HC, d7


title: D5S80naive3


title: D6S49inflamed3


title: PAT9, HDP-high, d28

value: HDP-high


title: VAC181, HC, d7


title: PAT9, HDP-high, d21


title: D5S43inflamed3


title: PAT8, HDP-low, d28

value: HDP-low


title: D8S96naive3


title: D3S30inflamed3


title: D5S152inflamed2


title: VAC181, HC, d0

value: d0, Pre-priming


title: D7S167inflamed2


title: D4S73naive3


title: D6S160inflamed2


title: PAT9, HDP-high, d0


title: D4S144inflamed2


title: D3S68naive3


title: VAC177, HC, d21


title: PAT8, HDP-low, d0


title: D3S13naive2


title: D3S136inflamed2


title: D2S62naive3


title: PAT7, HDP-high, d28


title: D2S6naive2


title: D7S57inflamed3


title: D2S22inflamed3


title: D1S123inflamed2


title: D1S2naive2


title: D12S51naive2


title: PAT7, HDP-high, d0


title: PAT7, HDP-high, d21


title: D12S90inflamed3


title: D12S117naive3


title: D1S16inflamed3


title: PAT65, HDP-high, d21


title: D11S85inflamed3


title: PAT65, HDP-high, d28


title: D11S46naive2


title: D11S112naive3


title: PAT65, HDP-high, d7


title: D11S2inflamed2


title: D10S78inflamed3


title: PAT65, HDP-high, d0


title: D10S185inflamed2


title: PAT5, HDP-low, d28


title: D10S106naive3


title: C9S71inflamed3


title: PAT5, HDP-low, d21


title: PAT48, HDP-low, d28


title: C8S33naive2


title: C9S100naive3


title: C8S64inflamed3


title: C7S90naive3


title: D12S10inflamed2


title: C7S56inflamed3


title: PAT48, HDP-low, d21


title: C6S48inflamed3


title: C6S25naive2


title: PAT48, HDP-low, d7


title: C6S159inflamed2


title: PAT48, HDP-low, d0


title: C5S21naive2


title: C5S151inflamed2


title: C4S37inflamed3


title: D10S40naive2


title: C4S143inflamed2


title: PAT45, HDP-low, d28


title: PAT45, HDP-low, d21


title: C3S67naive3


title: C9S36naive2


title: PAT5, HDP-low, d0


title: PAT45, HDP-low, d7


title: C3S29inflamed3


title: C2S61naive3


title: PAT45, HDP-low, d0


title: C2S21inflamed3


title: PAT8, HDP-low, d21


title: PAT40, HDP-low, d28


title: C1S15inflamed3


title: C1S58naive3


title: PAT40, HDP-low, d7


title: C1S122inflamed2


title: C5S42inflamed3


title: PAT40, HDP-low, d0


title: C12S9inflamed2


title: PAT36, HDP-low, d7


title: C11S84inflamed3


title: C12S89inflamed3


title: C3S135inflamed2


title: C11S1inflamed2


title: C12S50naive2


title: B9S99naive3


title: C10S77inflamed3


title: PAT35, HDP-low, d21


title: C11S111naive3


title: B9S70inflamed3


title: B8S95naive3


title: B9S178inflamed2


title: PAT35, HDP-low, d28


title: PAT36, HDP-low, d0


title: B8S63inflamed3


title: C2S129inflamed2


title: PAT35, HDP-low, d7


title: B7S89naive3


title: B7S55inflamed3


title: PAT33, HDP-high, d28


title: PAT35, HDP-low, d0


title: B7S166inflamed2


title: B6S47inflamed3


title: PAT36, HDP-low, d28


title: B6S24naive2


title: B6S84naive3


title: PAT33, HDP-high, d21


title: C11S45naive2


title: PAT33, HDP-high, d7


title: B6S158inflamed2


title: PAT33, HDP-high, d0


title: B5S41inflamed3


title: B4S36inflamed3


title: B5S150inflamed2


title: PAT32, HDP-high, d21


title: B4S142inflamed2


title: PAT32, HDP-high, d7


title: B5S79naive3


title: PAT32, HDP-high, d28


title: B5S20naive2


title: B3S28inflamed3


title: B4S17naive2


title: B3S66naive3


title: PAT32, HDP-high, d0


title: B8S32naive2


title: PAT30, HDP-high, d21


title: B3S134inflamed2


title: B8S172inflamed2


title: B2S20inflamed3


title: PAT30, HDP-high, d7


title: B3S12naive2


title: B1S57naive3


title: PAT30, HDP-high, d0


title: B1S121inflamed2


title: B12S8inflamed2


title: PAT27, HDP-high, d28


title: B12S116naive3


title: B12S88inflamed3


title: PAT27, HDP-high, d21


title: B1S1naive2


title: PAT27, HDP-high, d0


title: B10S105naive3


title: B11S83inflamed3


title: PAT26, HDP-high, d21


title: PAT26, HDP-high, d28


title: B11S191inflamed2


title: B10S184inflamed2


title: B2S128inflamed2


title: A7S88naive3


title: A7S54inflamed3


title: PAT27, HDP-high, d7


title: B10S76inflamed3


title: A9S177inflamed2


title: A9S69inflamed3


title: PAT26, HDP-high, d7


title: A8S171inflamed2


title: A8S31naive2


title: PAT26, HDP-high, d0


title: A8S62inflamed3


title: A7S165inflamed2


title: A9S35naive2


title: A5S78naive3


title: PAT23, HDP-low, d21


title: A6S83naive3


title: A6S157inflamed2


title: PAT23, HDP-low, d28


title: A5S40inflamed3


title: PAT23, HDP-low, d7


title: A4S72naive3


title: A5S149inflamed2


title: A4S35inflamed3


title: A3S65naive3


title: PAT22, HDP-high, d28


title: PAT22, HDP-high, d21


title: rpoC mutant host infected with phage K- 40 min time point (replicate D)

city: Silver Spring

first: Ramchander Rohit

last: Kongari

state: Maryland

address: 10903 New Hampshire Ave

department: Department of Bacterial, Parasitic and Allergenic products

institute: United States Food and Drug Administration

description:
Novaseq S2 100 bp paired end run
MR206_40_D

data_processing:
Initial quality check was done using FastQC and read mapping distribution was analyzed using MultiQC
Reads were mapped using Bowtie2 and visualized using IGV. For quantitative analysis, read counts were obtained using Kallisto and differntial expression analysis was done using EdgeR package on the Rstudio platform
Assembly: Reads were mapped to the full length genome of phage K (NC_005880.2) and NRS384 (CP027476.1) using Bowtie2 to check for transcriptional activity. No genome building/assembly was performed for our analysis purposes.
Supplementary files format and content: Transcripts per million (TPM) data for all the gene and tRNA features annotated in phage K (as calculated by Kallisto) from all the samples are provided as a separate file

organism: Staphylococcus aureus

growth_protocol: 25 ml TSB cultures were innoculated with 100 ul of overnight cultures and  grown at 30 °C

extract_protocol:
1 mL samples were collected at 2, 5, 10, 20, 30, 40 min after addition of phage, and total RNA was extracted from these samples using the QIAGEN RNEasy Mini Kit.
The samples were further treated with Turbo DNAse to degrade phage/bacterial DNA, and the RNA quality was measured using an Agilent 2100 Bioanalyzer. Ribosomal RNA was depleted using the Illumina Ribozero plus kit, and Illumina RNA-seq libraries were prepared without any enrichment.
A strand-specific RNA seq Novaseq S2 100-bp paired end run was performed on the samples using an Illumina Novaseq 6000 instrument

treatment_protocol: Phage K was added at an MOI of ~5 once the O.D. of the cultures reached 0.3

tag: time point

value: 40 min

value: bacterial cells

value: rpoC G17D

value: infected with phage K


title: A4S141inflamed2

tag: tissue

value: prostate

value: basal prostate stem cells


title: A3S27inflamed3

value: male

value: inflamed


title: A3S133inflamed2


title: PAT23, HDP-low, d0


title: rpoC mutant host infected with phage K- 40 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
MR206_40_B


title: PAT22, HDP-high, d7


title: A2S19inflamed3


title: rpoC mutant host infected with phage K- 30 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
MR206_30_D

value: 30 min


title: PAT22, HDP-high, d0

value: PBMCs


title: PAT21, HDP-high, d28


title: A3S11naive2

value: naive


title: PAT21, HDP-high, d21


title: rpoC mutant host infected with phage K - 40 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_40_A


title: rpoC mutant host infected with phage K- 40 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_40_C


title: rpoC mutant host infected with phage K- 30 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_30_C


title: A2S60naive3